Polynucleotide encoding a novel cysteine protease of the calpain superfamily, CAN-12, and variants thereof

FIELD OF THE INVENTION

[0002] The present invention provides novel polynucleotides encoding CAN-12 polypeptides, fragments and homologues thereof. The present invention also provides polynucleotides encoding variants of CAN-12 polypeptides, CAN-12v1 and CAN-12v2. Also provided are vectors, host cells, antibodies, and recombinant and synthetic methods for producing said polypeptides. The invention further relates to diagnostic and therapeutic methods for applying these novel CAN-12, CAN-12v1, and CAN-12v2 polypeptides to the diagnosis, treatment, and/or prevention of various diseases and/or disorders related to these polypeptides, particularly neuro- and musculo-degenerative conditions. The invention further relates to screening methods for identifying agonists and antagonists of the polynucleotides and polypeptides of the present invention.

BACKGROUND OF THE INVENTION

[0003] Cysteine or thiol proteases contain a reactive sulphydral moiety activated by an adjacent histidine. Hydrolysis of the substrates peptide bond is initiated when the cysteine sulfur attacks the carbon in the peptide bond forming a thiol-enzyme intermediate, liberating the amino portion of the peptide. The thiol-enzyme intermediate is hydrolyzed by water releasing the substrates C-terminus and restoring the enzyme. There are over 20 some families of cysteine proteases. [Rawlings N. D., & Barrett A. J. Families of cysteine peptidases. Methods in Enzymol. 244 461-486 (1994)]. The present invention relates to a thiol protease of the C2 family that includes the calpain superfamily.

[0004] Calpains are calcium-activated intracellular neutral cysteine proteases (EC 3.4.22.17)(for reviews see Sorimachi et al., Structure and physiological function of calpains. Biochem J. 328:721-32, 1997; Carafoli E and Molinari M. Calpain: a protease in search of a function? Biochem Biophys Res Commun 247:193-203, 1998). Some calpains are expressed ubiquitously while others are tissue-specific. μ-Calpain and m-calpains appear in all tissues, p94 is skeletal muscle specific while nCL-2 is stomach specific. (Sorimachi et al., Structure and physiological function of calpains. Biochem J. 328:721-32, 1997). The best characterized are μ-calpain and m-calpains which consist of two subunits. An 80 kDa large subunit contains both Ca2+ binding sites and the catalytic activity and small 30 kDa subunit with a separate set of Ca2+ binding sites. All the proteolytic activity is contained in the larger subunit of both μ- and m-calpain. In the presence of PEG or chaperones the large subunit is catalytically activated in the absence of the smaller subunit. Other calpains, for example nCL-2 and p94, are proteolytically active monomers with homology to the μ-calpain and m-calpains large subunit.

[0005] The large (catalytic) subunit has four domains (I-IV)(Hosfield et al., Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation. EMBO J. 18:6880-9, 1999; Strobl et al., The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Proc Natl Acad Sci U S A. 97:588-92, 2000). The N-terminus (domain I) contains an alpha helical region and a site of autocatalytic cleavage. Domain II contains the catalytically active domain with the active site amino acids (m-calpain residues Cys105, His262, & Asn286). Domain III contains the linker between the Ca2+ binding domain (in domain IV) and links Ca2+ binding to proteolytic activity. Domain IV contains a calmodulin-like Ca2+ binding regions with EF hands. p94 (also called calpain 3) is similarly organized with domains I-IV, but, also contains a proline-rich N-terminus and two unique insertion loops (IS1 and IS2). nCL-2 is also active as a large monomer with domains I-IV; however, a splice variant (nCL-2′) lacks domains III & IV, but maintains proteolytic activity.

[0006] Calpains are responsible for limited intracellular proteolytic cleavage, as opposed to complete proteolytic digestion. The proteolysis modifies protein function both specifically and irreversibly. Numerous proteins have been identified as calpain substrates (Carafoli E and Molinari M Calpain: a protease in search of a function? Biochem Biophys Res Commun 247:193-203, 1998; Hayes et al., Drug News Perspect 11:215-222, 1998). The best-characterized substrates are large cytostructural and/or membrane associated proteins, calmodulin-binding proteins and transcriptional factors. Physiologically significant substrates for calpain include kinases, phosphatases, channel proteins and cytoskeletal proteins that link transmembrane receptors to the membrane skeleton. Proteolytic modification of these proteins may have fundamental roles in development, differentiation, and cellular transformation in response to cell signaling, cell-cell and/or cell-extracellular matrix interactions. In platelets, calpain activation appears to be linked to clustering of the integrin receptor aIIb3 (Fox JE On the role of calpain and Rho proteins in regulating integrin-induced signaling. Thromb Haemost 82:385-91, 1999).

[0007] Calpains have been implicated in cell signaling through activation of protein kinases and phosphatases (cleaving between regulatory and catalytic domains resulting in changes in activity after hydrolysis) and modulation of their intracellular localization. Calpains have been shown to modify specific enzymes and cytoskeletal proteins as part of calcium-mediated signal pathways. They are also involved in remodeling and disassembling the cytoskeleton, especially where the cytoskeleton attaches to membranes or other subcellular structures.

[0008] Several nuclear transcription factors have been suggested as calpain substrates. Calpains are also involved in the progression of cells through the cell cycle (Carafoli E and Molinari M Calpain: a protease in search of a function? Biochem Biophys Res Commun 247:193-203, 1998) in that calpain activity accelerates some cells through the cell cycle by cleavage of p53. Calpain is also thought to play a role in long term potentiation (memory) and rat strains deficient in the endogenous calpain inhibitor, calpastatin, have increased long term potentiation.

[0009] Calpains in Disease:

[0010] Several diseases have been associated with calpain deficiencies. For example, limb-girdle muscular dystrophy (LGMD) is a group of disorders that primarily cause weakness of the shoulder and pelvic regions. A subtype of LGMD called LGMD2A is caused by defects in the gene for p94 (also called calpain 3)(Richard et al., Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A. Cell 81:27-40, 1995).

[0011] Positional cloning has recently identified single-nucleotide polymorphisms (SNPs) in an intron of the gene coding for calpain-10 that appears to confer insulin resistance in diabetics. Presence of this mutation correlates with reduced levels of calpain 10 in patients susceptible to type II diabetes (Horikawa et al., Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet. 26:163-75, 2000). The same calpain-10 SNP also correlates with type II diabetes in a high-risk population of Pima Indians (Baier et al., A calpain-10 gene polymorphism is associated with reduced muscle mRNA levels and insulin resistance. J Clin Invest. 106:R69-73, 2000).

[0012] Over Activation of Calpain—Ischemic and Traumatic Damage

[0013] Intracellular calcium levels and calpain activity are normally tightly regulated. Under stress, such as follows neuronal excitotoxicity, ischemic stroke, hemoragic stroke, hypoxic stress and/or trauma, intracellular calcium levels rise causing inappropriate calpain proteolytic activity. Calpain activity has been implicated in further cell destruction and non-specific calpain inhibitors have been shown to be protective in animal models (Lee et al., Proc. Natl. Acad. Sci. USA, 88:7233-7237, 1991; Wang K K and Yuen P W. Calpain inhibition: an overview of its therapeutic potential. Trends Pharmacol. Sci. 15:412-9, 1994; Lee, KS, et al., Calcium-activated proteolysis as a therapeutic target in cerebrovascular disease. Annal NY Acad Sci. 825, 95-103, 1997).

[0014] Calpains are activated in neurons following ischemia-induced damage in animal models of stroke. (Lee et al., Proc. Natl. Acad. Sci. USA, 88:7233-7237, 1991). Inhibition of calcium-activated proteolysis by means of high doses of (usually non-specific) calpain inhibitors protect against the degeneration of vulnerable hippocampal neurons after ischemia (Rami et al., Brain Research, 609:67-70, 1993; Wang et al., An alpha-mercaptoacrylic acid derivative is a selective nonpeptide cell-permeable calpain inhibitor and is neuroprotective. Proc Natl Acad Sci U S A. 93:6687-92, 1996). After an ischemic insult, neuronal death is delayed for hours to days. This time interval represents a potential therapeutic window in which to apply effective therapies to minimize brain damage after stroke.

[0015] In addition to neuronal damage, calpains are thought to contribute to cardiac ischemic damage (Iwamoto H et al., Calpain inhibitor-I reduces infarct size and DNA fragmentation of myocardium in ischemic/reperfused rat heart.J Cardiovasc Pharmacol 33:580-6, 1999) and hepatocyte necrosis during and following anoxia (Arora A S et al., Hepatocellular carcinoma cells resist necrosis during anoxia by preventing phospholipase-mediated calpain activation. J Cell Physiol 167:434-42, 1996).

[0016] Neurodegenerative Diseases

[0017] Calpains have been implicated in neurodegenerative diseases ncluding, Alzheimer's disease, Multiple sclerosis, Huntington's disease, Parkinson's disease and amyotrophy. Calpain activation is increased during normal aging and a strong case can be made for the involvement of calpain in the abnormal proteolysis underlying the accumulation of plaque and neurofibriles in brain tissue from people who suffered Alzheimer-type dementia (Iwamoto et al., Brain Research, 561:177-180 1991; Nixon et al., Calcium-activated neutral proteinase (calpain) system in aging and Alzheimer's disease. Ann N Y Acad Sci ;747:77-91, 1994; Grynspan et al., Active site-directed antibodies identify calpain II as an early-appearing and pervasive component of neurofibrillary pathology in Alzheimer's disease. Brain Res 763:145-58, 1997). Calpains are significantly activated in human postmortem brain from patients with Alzheimer's disease, and the degree of activation correlated with those regions of the brain showing the greatest amount of degeneration (Saito et al., Proc. Natl. Acad. Sci. USA, 90:2628-2632, 1993). More recently, it has been recognized that in Alzheimer's disease cyclin-dependent kinase 5 (cdk5) and its neuron-specific activator p35 are involved in neurite outgrowth and cortical lamination. Calpain cleavage of p35 produces p25, which accumulates in the brains of patients with Alzheimers disease. Conversion of p35 to p25 causes prolonged activation and mislocalization of cdk5 which hyperphosphorylates tau, disrupts the cytoskeleton and promotes the death (apoptosis) of primary neurons (Lee et al., Neurotoxicity induces cleavage of p35 to p25 by calpain. Nature. 18;405:360-4, 2000). Compounds that inhibit calpain activity could prove useful in reducing or delaying neurodegeneration caused to Alzheimer's disease.

[0018] Damage Following Trauma

[0019] Traumatic injury also causes calpain activation associated with further cell death, atrophy and shrinkage of the brain. A forceful blow trigger cell damage and increased calpain activity that can cleave structural proteins in the brain for up to weeks afterward (Hayes et al., Potential Contribution of Proteases to Neuronal Damage Drug News & Perspectives 11, 1998).

[0020] Calpain activation has also been implicated in spinal cord injury following trauma (for reviews see: Banik et al., Role of calpain and its inhibitors in tissue degeneration and neuroprotection in spinal cord injury. Ann. N.Y. Acad. Sci. 825:120-7 1997; Banik et al., Role of calpain in spinal cord injury: effects of calpain and free radical inhibitors. Ann. N.Y. Acad. Sci. 844:131-7, 1998). Analogous to brain trauma, secondary pathophysiological alterations occur in the traumatized spinal cord well after the initiating insult. These secondary events ultimately cause cell death and tissue damage. Non-specific calpain inhibitors have shown utility in preventing further damage due to spinal chord injury in animal models (Ray et al., Increased calpain expression is associated with apoptosis in rat spinal cord injury: calpain inhibitor provides neuroprotection. Neurochem Res. 25:1191-8, 2000).

[0021] These studies indicate the potential utility of calpain inhibitors (especially those calpains located in the spinal cord) in treating traumatic injury resulting from automobile crashes, gunshot wounds, and sports accidents.

[0022] Degeneration of Cochlear Tissues Following Noise Exposure

[0023] Calpains are activated during acoustic trauma and calpain inhibitors protect against hearing loss caused by noise (Stracher A Calpain inhibitors as therapeutic agents in nerve and muscle degeneration. Ann N Y Acad Sci 884:52-9, 1999).

[0024] Inflammation

[0025] Calpains also regulate integrin-mediated interaction of T-cells with the extracellular matrix (ECM) and calpain inhibitors prevent acute and chronic inflammation in animal models (Cuzzocrea S et al., Calpain inhibitor I reduces the development of acute and chronic inflammation Am J Pathol 157:2065-79, 2000).

[0026] Multiple Sclerosis

[0027] Multiple sclerosis is characterized by the progressive loss of the myelin of the brain and spinal cord. In autoimmune demyelinating diseases such as multiple sclerosis and experimental allergic encephalomyelitis, the degradation of myelin proteins results in the destabilization of the myelin sheath. Calpains have been implicated in that calpain degrades all major myelin proteins and increased calpain activity is observed in multiple sclerosis (Shields D C et al., A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc. Natl. Acad. Sci. USA 96:11486-91, 1999).

[0028] Cataract Formation

[0029] In the lens, crystallins prevent thermal denaturation and aggregation of other proteins. Crystallins are also substrates for calpains and cataract formation in a rat model of selenite-induced cataract formation is thought to result from calpain activation and cleavage of crystallins (Shearer T R, David L L, Anderson R S, Azuma M. Review of selenite cataract. Curr Eye Res 1992; 11:357-369). In this model the crystallin cleavage could be blocked by calpain inhibitors (Azuma M et al., Cysteine protease inhibitor E64 reduces the rate of formation of selenite cataract in the whole animal. Curr Eye Res 10:657-666, 1991). In a genetic model cataract-prone rats also showed enhanced proteolysis of crystallins and lens cytoskeletin proteins thought to be mediated by calpain (Inomata M et al., Evidence for the involvement of calpain in cataractogenesis in Shumiya cataract rat (SCR). Biochim Biophys Acta 1362:11-23 1997). Calpain activation is also thought to play a role in cataracts induced by buthionine sulfoximine, calcium ionophore A23187, hydrogen peroxide, diamide, xylose, galactose and streptozotocin (Kadoya et al., Role of calpain in hydrogen peroxide cataract. Curr Eye Res 1993; 12:341-346; David et al., Buthionine sulfoximine induced cataracts in mice contain insolubilized crystallins with calpain II cleavage sites, Exp Eye Res 1994; 59:501-504.). These models of cataract formation in rats suggest that calpain-induced proteolysis is a common underlying mechanism. Fragments of alpha-crystallin, consistent with calpain cleavage, have been also observed in cataractous human lens.

[0030] Reovirus Induced Myocarditis

[0031] Infection of neonatal mice with reovirus produces histological myocarditis. This is due to a direct viral injury and apoptosis of myocytes. Calpain inhibitors block reovirus-induced apoptosis in vitro and prevented viral-induced induced myocarditis (DeBiasi et al., Calpain inhibition protects against virus-induced apoptotic myocardial injury. Virol 75:351-61, 2001).

[0032] The inventors of the present invention describe herein, the polynucleotides corresponding to the full-length novel CAN-12 calpain gene, its encoded polypeptide, in addition to the variants CAN-12v1 and CAN-12v2. Also provided are polypeptide alignments illustrating the strong conservation of the CAN-12, CAN-12v1, and CAN-12v2 polypeptides to known proteases and a model of the active conformation of CAN-12. Based on this strong conservation, the inventors have ascribed the CAN-12, CAN-12v1, and CAN-12v2 polypeptides as having calpain proteolytic activity. Data is also provided illustrating the unique tissue expression profile of the CAN-12 polypeptide in esophagus, lymph node, and spinal cord tissues.

[0033] In fact, calpains have been the subject of significant research and development programs designed to identify inhibitors of this disease associated protein class. For example, the following, non-limiting examples of drugs, therapies, or regimens directed to inhibiting calpains are currently known: BDA 410 (Mitsubishi Tokyo); AK 295 (Alkermes; CAS® Registry Number: 160399-35-9, 144231-82-3, and 145731-49-3; (1-(((1-ethyl-3-((3-(4-morpholinyl)propyl)amino)-2,3-dioxopropyl)amino)carbonyl)-3-methylbutyl)carbamic acid phenylmethyl ester stereois); AK275 (Alkermes; CAS® Registry Number: 158798-83-5, and 150519-08-7; N-((phenylmethoxy)carbonyl)-L-leucyl-N-ethyl-L-2-aminobutanamide); inhibitor I (University of Indiana; acetyl-leu-leu-norleucinal); calpeptin (University of Indiana; benzyloxycarbonyl-leu-norleucinal); VASOLEX (Cortex); RESTENEX (Cortex); MDL 28170 (Aventis; CBZ-Val-Phe-H); PI (Sankyo; CAS® Registry Number: 128102-74-9, and 128102-75-0; L-phenylalanyl-L-glutaminyl-L-valyl-L-valyl-3-((3-nitro-2-pyridiny l)dithio)-L-alanylglycinamide); MDL 28170 (Hoechst Marion Roussel); BDA-410 (Mitsubishi-Tokyo); SJA-6017 (Senju; CAS® Registry Number: 190274-53-4; Butanamide,2-(((4-fluorophenyl)sulfonyl)amino)-N-((1S)-1-formyl-3-methylbutyl.).-3-methyl-, (2S)-); Pharmaprojects No. 5123 (Pfizer; 2-Chloro-acetic acid(3-oxo-4-phenyl-3,4-dihydro-1H-quinoxalin-2-ylidene)hydrazide; WO96-25403); CEP-4143 (Cephalon; WO96-14067); MDL-104903 (Aventis; CAS® Registry Number: 180799-56-8;Carbamic acid,((1S)-1-(((4S,5R)-5-hydroxy-4-(phenylmethyl)-3-oxazolidinyl)carbonyl)-2-methylpropyl)-,phenylmethyl ester)); MDL-28170 (Aventis; CAS® Registry Number: 19542-51-9; Alanine, N-(N-carboxy-L-valyl)-3-phenyl-N-benzyl ester, L-); CX-275 (Cortex Pharmaceuticals; PhenylmethylN-((1R)-1-((((1S)-1-ethyl-3-(ethylamino)-2,3-dioxopropyl)amino)carbonyl)-3-methylbutyl)carbamate); NS 7 (Nippon Shinyaku; 4-(4-Fluorophenyl)-2-methyl-6-(5-piperidinopentyloxy)pyrimidine hydrochloride); Calpain inhibitor 1 (Suntory; N-Acetyl-L-leucinyl-L-leucinyl-L-norleucinal); E 64 (Taisho Pharmaceutical (; CAS® Registry Number: 66701-25-5); CEP 4143 (Cephalon); SJA 6017 (Senju; N-(4-Fluorophenylsulfonyl)-L-valyl-L-leucinal); The present invention is directed to antagonists specific to the CAN-12, CAN-12v1, and/or CAN-12v2 polypeptides. Modulating the activity of the calpain polypeptides of the present invention may result in fewer toxicities than the drugs, therapies, or regimens presently known to regulate other known calpains.

[0034] The present invention also relates to recombinant vectors, which include the isolated nucleic acid molecules of the present invention, and to host cells containing the recombinant vectors, as well as to methods of making such vectors and host cells, in addition to their use in the production of CAN-12, CAN-12v1, and CAN-12v2 polypeptides or peptides using recombinant techniques. Synthetic methods for producing the polypeptides and polynucleotides of the present invention are provided. Also provided are diagnostic methods for detecting diseases, disorders, and/or conditions related to the CAN-12, CAN-12v1, and CAN-12v2 polypeptides and polynucleotides, and therapeutic methods for treating such diseases, disorders, and/or conditions. The invention further relates to screening methods for identifying binding partners of the polypeptides, particularly activators and inhibitors of the novel CAN-12, CAN-12v1, and CAN-12v2 polypeptides of the present invention.

BRIEF SUMMARY OF THE INVENTION

[0035] The present invention provides isolated nucleic acid molecules, that comprise, or alternatively consist of, a polynucleotide encoding the CAN-12 protein having the amino acid sequence shown in FIGS. 1A-E (SEQ ID NO:24) or the amino acid sequence encoded by the cDNA clone, CAN-12 (also referred to as protease 5, clone 70).

[0036] The present invention provides isolated nucleic acid molecules, that comprise, or alternatively consist of, a polynucleotide encoding the CAN-12+polypeptide sequence having the amino acid sequence shown in FIGS. 1A-E (SEQ ID NO:2) or the amino acid sequence encoded by the cDNA clone, CAN-12+ (also referred to as protease 5, clone 70; +splice amino acids).

[0037] The present invention provides isolated nucleic acid molecules, that comprise, or alternatively consist of, a polynucleotide encoding the CAN-12v1 protein having the amino acid sequence shown in FIGS. 8A-C (SEQ ID NO:54) or the amino acid sequence encoded by the cDNA clone, CAN-12v1 (also referred to as protease 5, clone 1e), deposited as ATCC Deposit Number PTA-3434 on Jun. 7, 2001.

[0038] The present invention provides isolated nucleic acid molecules, that comprise, or alternatively consist of, a polynucleotide encoding the CAN-12v2 protein having the amino acid sequence shown in FIGS. 9A-C (SEQ ID NO:56) or the amino acid sequence encoded by the cDNA clone, CAN-12v2 (also referred to as protease 5, clone 1e1b-1), deposited as ATCC Deposit Number PTA-3434 on Jun. 7, 2001.

[0039] The present invention also relates to recombinant vectors, which include the isolated nucleic acid molecules of the present invention, and to host cells containing the recombinant vectors, as well as to methods of making such vectors and host cells, in addition to their use in the production of CAN-12, CAN-12v1, and CAN-12v1 polypeptides or peptides using recombinant techniques. Synthetic methods for producing the polypeptides and polynucleotides of the present invention are provided. Also provided are diagnostic methods for detecting diseases, disorders, and/or conditions related to the CAN-12, CAN-12v1, and CAN-12v1 polypeptides and polynucleotides, and therapeutic methods for treating such diseases, disorders, and/or conditions. The invention further relates to screening methods for identifying binding partners of the polypeptides.

[0040] The invention further provides an isolated CAN-12 polypeptide having an amino acid sequence encoded by a polynucleotide described herein.

[0041] The invention further provides an isolated CAN-12v1 polypeptide having an amino acid sequence encoded by a polynucleotide described herein.

[0042] The invention further provides an isolated CAN-12v2 polypeptide having an amino acid sequence encoded by a polynucleotide described herein.

[0043] The invention also provides a machine readable storage medium which comprises the structure coordinates of CAN-12, including all or any parts conserved calpain regions. Such storage medium encoded with these data are capable of displaying on a computer screen or similar viewing device, a three-dimensional graphical representation of a molecule or molecular complex which comprises said regions or similarly shaped homologous regions.

[0044] The invention also provides methods for designing, evaluating and identifying compounds which bind to all or parts of the aforementioned regions. The methods include three dimensional model building (homology modeling) and methods of computer assisted-drug design which can be used to identify compounds which bind or modulate the forementioned regions of the CAN-12 polypeptide. Such compounds are potential inhibitors of CAN-12 or its homologues.

[0045] The invention also provides novel classes of compounds, and pharmaceutical compositions thereof, that are useful as inhibitors of CAN-12 or its homologues.

[0046] The invention also provides novel classes of compounds, and pharmaceutical compositions thereof, that are useful as inhibitors of CAN-12v1 or its homologues.

[0047] The invention also provides novel classes of compounds, and pharmaceutical compositions thereof, that are useful as inhibitors of CAN-12v2 or its homologues.

[0048] The invention further relates to a polynucleotide encoding a polypeptide fragment of SEQ ID NO:2, 24, 54, and/or 56, or a polypeptide fragment encoded by the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1, 23, 53, and/or 55.

[0049] The invention further relates to a polynucleotide encoding a polypeptide domain of SEQ ID NO:2, 24, 54, and/or 56 or a polypeptide domain encoded by the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1,23, 53, and/or 55.

[0050] The invention further relates to a polynucleotide encoding a polypeptide epitope of SEQ ID NO:2, 24, 54, and/or 56 or a polypeptide epitope encoded by the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1, 23, 53, and/or 55.

[0051] The invention further relates to a polynucleotide encoding a polypeptide of SEQ ID NO:2, 24, 54, and/or 56 or the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1,23, 53, and/or 55, having biological activity.

[0052] The invention further relates to a polynucleotide which is a variant of SEQ ID NO:1,23, 53, and/or 55.

[0053] The invention further relates to a polynucleotide which is an allelic variant of SEQ ID NO:1,23, 53, and/or 55.

[0054] The invention further relates to a polynucleotide which encodes a species homologue of the SEQ ID NO:2, 24, 54, and/or 56.

[0055] The invention further relates to a polynucleotide which represents the complimentary sequence (antisense) of SEQ ID NO:1, 23, 53, and/or 55.

[0056] The invention further relates to a polynucleotide capable of hybridizing under stringent conditions to any one of the polynucleotides specified herein, wherein said polynucleotide does not hybridize under stringent conditions to a nucleic acid molecule having a nucleotide sequence of only A residues or of only T residues.

[0057] The invention further relates to an isolated nucleic acid molecule of SEQ ID NO:2, 24, 54, and/or 56, wherein the polynucleotide fragment comprises a nucleotide sequence encoding a calpain protein.

[0058] The invention further relates to an isolated nucleic acid molecule of SEQ ID NO:1, 23, 53, and/or 55 wherein the polynucleotide fragment comprises a nucleotide sequence encoding the sequence identified as SEQ ID NO:2, 24, 54, and/or 56 or the polypeptide encoded by the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1,23, 53, and/or 55.

[0059] The invention further relates to an isolated nucleic acid molecule of of SEQ ID NO:1, 23, 53, and/or 55 wherein the polynucleotide fragment comprises the entire nucleotide sequence of SEQ ID NO:1, 23, 53, and/or 55 or the cDNA sequence included in the deposited clone, which is hybridizable to SEQ ID NO:1,23, 53, and/or 55.

[0060] The invention further relates to an isolated nucleic acid molecule of SEQ ID NO:1, 23, 53, and/or 55, wherein the nucleotide sequence comprises sequential nucleotide deletions from either the C-terminus or the N-terminus.

[0061] The invention further relates to an isolated polypeptide comprising an amino acid sequence that comprises a polypeptide fragment of SEQ ID NO:2, 24, 54, and/or 56 or the encoded sequence included in the deposited clone.

[0062] The invention further relates to a polypeptide fragment of SEQ ID NO:2, 24, 54, and/or 56 or the encoded sequence included in the deposited clone, having biological activity.

[0063] The invention further relates to a polypeptide domain of SEQ ID NO:2, 24, 54, and/or 56 or the encoded sequence included in the deposited clone.

[0064] The invention further relates to a polypeptide epitope of SEQ ID NO:2, 24, 54, and/or 56 or the encoded sequence included in the deposited clone.

[0065] The invention further relates to a full length protein of SEQ ID NO:2, 24, 54, and/or 56 or the encoded sequence included in the deposited clone.

[0066] The invention further relates to a variant of SEQ ID NO:2, 24, 54, and/or 56.

[0067] The invention further relates to an allelic variant of SEQ ID NO:2, 24, 54, and/or 56. The invention further relates to a species homologue of SEQ ID NO:2, 24, 54, and/or 56.

[0068] The invention further relates to the isolated polypeptide of of SEQ ID NO:2, 24, 54, and/or 56, wherein the full length protein comprises sequential amino acid deletions from either the C-terminus or the N-terminus.

[0069] The invention further relates to an isolated antibody that binds specifically to the isolated polypeptide of SEQ ID NO:2, 24, 54, and/or 56.

[0070] The invention further relates to a method for preventing, treating, or ameliorating a medical condition, comprising administering to a mammalian subject a therapeutically effective amount of the polypeptide of SEQ ID NO:2, 24, 54, and/or 56 or the polynucleotide of SEQ ID NO:1, 23, 53, and/or 55.

[0071] The invention further relates to a method of diagnosing a pathological condition or a susceptibility to a pathological condition in a subject comprising the steps of (a) determining the presence or absence of a mutation in the polynucleotide of SEQ ID NO:1, 23, 53, and/or 55; and (b) diagnosing a pathological condition or a susceptibility to a pathological condition based on the presence or absence of said mutation.

[0072] The invention further relates to a method of diagnosing a pathological condition or a susceptibility to a pathological condition in a subject comprising the steps of (a) determining the presence or amount of expression of the polypeptide of of SEQ ID NO:2, 24, 54, and/or 56 in a biological sample; and diagnosing a pathological condition or a susceptibility to a pathological condition based on the presence or amount of expression of the polypeptide.

[0073] The invention further relates to a method for identifying a binding partner to the polypeptide of SEQ ID NO:2, 24, 54, and/or 56 comprising the steps of (a) contacting the polypeptide of SEQ ID NO:2, 24, 54, and/or 56 with a binding partner; and (b) determining whether the binding partner effects an activity of the polypeptide.

[0074] The invention further relates to a gene corresponding to the cDNA sequence of SEQ ID NO:1, 23, 53, and/or 55.

[0075] The invention further relates to a method of identifying an activity in a biological assay, wherein the method comprises the steps of expressing SEQ ID NO:1, 23, 53, and/or 55 in a cell, (b) isolating the supernatant; (c) detecting an activity in a biological assay; and (d) identifying the protein in the supernatant having the activity.

[0076] The invention further relates to a process for making polynucleotide sequences encoding gene products having altered activity selected from the group consisting of SEQ ID NO:2, 24, 54, and/or 56 activity comprising the steps of (a) shuffling a nucleotide sequence of SEQ ID NO:1, 23, 53, and/or 55, (b) expressing the resulting shuffled nucleotide sequences and, (c) selecting for altered activity selected from the group consisting of SEQ ID NO:2, 24, 54, and/or 56 activity as compared to the activity selected from the group consisting of SEQ ID NO:2, 24, 54, and/or 56 activity of the gene product of said unmodified nucleotide sequence.

[0077] The invention further relates to a shuffled polynucleotide sequence produced by a shuffling process, wherein said shuffled DNA molecule encodes a gene product having enhanced tolerance to an inhibitor of any one of the activities selected from the group consisting of SEQ ID NO:2, 24, 54, and/or 56 activity.

[0078] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a gastrointenstinal disorder.

[0079] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a neural disorder.

[0080] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is an inflammatory disease.

[0081] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is an inflammatory disease where proteases, either directly or indirectly, are involved in disease progression.

[0082] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a degenerative disease wherein proteases, either directly or indirectly, are involved in disease progression.

[0083] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is multiple sclerosis.

[0084] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a cancer.

[0085] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a blood disorder.

[0086] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is an immune disorder.

[0087] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a hematopoietic disorder.

[0088] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a disorder related to aberrant protease regulation.

[0089] The invention further relates to a method for preventing, treating, or ameliorating a medical condition with the polypeptide provided as SEQ ID NO:2, 24, 54, and/or 56, in addition to, its encoding nucleic acid, wherein the medical condition is a condition associated with tissue damage caused by calpain activation, either directly or indirectly.

[0090] The invention further relates to a method of identifying a compound that modulates the biological activity of CAN-12, comprising the steps of, (a) combining a candidate modulator compound with CAN-12 having the sequence set forth in one or more of SEQ ID NO:2, 24, 54, and/or 56; and measuring an effect of the candidate modulator compound on the activity of CAN-12.

[0091] The invention further relates to a method of identifying a compound that modulates the biological activity of a calpain, comprising the steps of, (a) combining a candidate modulator compound with a host cell expressing CAN-12 having the sequence as set forth in SEQ ID NO:2, 24, 54, and/or 56; and, (b) measuring an effect of the candidate modulator compound on the activity of the expressed CAN-12.

[0092] The invention further relates to a method of identifying a compound that modulates the biological activity of CAN-12, comprising the steps of, (a) combining a candidate modulator compound with a host cell containing a vector described herein, wherein CAN-12 is expressed by the cell; and, (b) measuring an effect of the candidate modulator compound on the activity of the expressed CAN-12.

[0093] The invention further relates to a method of screening for a compound that is capable of modulating the biological activity of CAN-12, comprising the steps of: (a) providing a host cell described herein; (b) determining the biological activity of CAN-12 in the absence of a modulator compound; (c) contacting the cell with the modulator compound; and (d) determining the biological activity of CAN-12 in the presence of the modulator compound; wherein a difference between the activity of CAN-12 in the presence of the modulator compound and in the absence of the modulator compound indicates a modulating effect of the compound.

[0094] The invention further relates to a compound that modulates the biological activity of human CAN-12 as identified by the methods described herein.

[0095] The invention also provides a machine readable storage medium which comprises the structure coordinates of CAN-12, including all or any parts conserved calpain regions. Such storage medium encoded with these data are capable of displaying on a computer screen or similar viewing device, a three-dimensional graphical representation of a molecule or molecular complex which comprises said regions or similarly shaped homologous regions.

[0096] The invention also provides a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12 according to Table IV or a homologue of said model, wherein said homologue comprises any kind of surrogate atoms that have a root mean square deviation from the backbone atoms of the complex of not more than about 5.0 Å.

[0097] The invention also provides a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12 according to Table IV or a homologue of said model, wherein said homologue comprises any kind of surrogate atoms that have a root mean square deviation from the backbone atoms of the complex of not more than about 5.0 Å, preferably not more than about 4.0A, or less.

[0098] The invention also provides a model comprising all or any part of the model defined by structure coordinates of CAN-12 according to Table IV, or a mutant or homologue of said molecule or molecular complex.

[0099] The invention also provides a method for identifying a mutant of CAN-12 with altered biological properties, function, or reactivity, the method comprising one or more of the following steps: (a) use of the model or a homologue of said model according to Table IV, for the design of protein mutants with altered biological function or properties which exhibit any combination of therapeutic effects described herein; and/or (b) use of the model or a homologue of said model, for the design of a protein with mutations in the active site region comprised of the amino acids from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330 of SEQ ID NO:2 according to Table IV with altered biological function or properties which exhibit any combination of therapeutic effects described herein.

[0100] The invention also provides methods for designing, evaluating and identifying compounds which bind to all or parts of the aforementioned regions. The methods include three dimensional model building (homology modeling) and methods of computer assisted-drug design which can be used to identify compounds which bind or modulate the forementioned regions of the CAN-12 polypeptide. Such compounds are potential inhibitors of CAN-12 or its homologues.

[0101] The invention also relates to method for identifying modulators of CAN-12 biological properties, function, or reactivity, the method comprising the step of modeling test compounds that fit spatially into the EF-hand calcium binding region defined by 1449-K471 of SEQ ID NO:2 using a homologue or portion thereof or analogue in which the original C, N, and O atoms have been replaced with other elements.

[0102] The invention also relates to a method of using said structure coordinates as set forth in Table IV to identify structural and chemical features of CAN-12; employing identified structural or chemical features to design or select compounds as potential CAN-12 modulators; employing the three-dimensional structural model to design or select compounds as potential CAN-12 modulators; synthesizing the potential CAN-12 modulators; screening the potential CAN-12 modulators in an assay characterized by binding of a protein to the CAN-12. The invention also relates to said method wherein the potential CAN-12 modulator is selected from a database. The invention further relates to said method wherein the potential CAN-12 modulator is designed de novo. The invention further relates to a method wherein the potential CAN-12 modulator is designed from a known modulator of activity.

[0103] The invention also provides a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12v2v2 according to Table V or a homologue of said model, wherein said homologue comprises any kind of surrogate atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 5.0 Å.

[0104] The invention also provides a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12v2 according to Table V or a homologue of said model, wherein said homologue comprises any kind of surrogate atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 5.0 Å, preferabbly not more than 4.0A, or less The invention also provides a model comprising all or any part of the model defined by structure coordinates of CAN-12v2 according to Table V, or a mutant or homologue of said molecule or molecular complex.

[0105] The invention also provides a method for identifying a mutant of CAN-12v2 with altered biological properties, function, or reactivity, the method comprising one or more of the following steps: (a) use of the model or a homologue of said model according to Table V, for the design of protein mutants with altered biological function or properties which exhibit any combination of therapeutic effects described herein; and/or (b) use of the model or a homologue of said model, for the design of a protein with mutations in the active site region comprised of the amino acids from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:56 according to Table V with altered biological function or properties which exhibit any combination of therapeutic effects described herein.

[0106] The invention also provides methods for designing, evaluating and identifying compounds which bind to all or parts of the aforementioned regions. The methods include three dimensional model building (homology modeling) and methods of computer assisted-drug design which can be used to identify compounds which bind or modulate the forementioned regions of the CAN-12v2 polypeptide. Such compounds are potential inhibitors of CAN-12v2 or its homologues.

[0107] The invention also relates to method for identifying modulators of CAN-12v2 biological properties, function, or reactivity, the method comprising the step of modeling test compounds that fit spatially into the EF-hand calcium binding regions defined by amino acids 1565 to K587 of SEQ ID NO:56, using a homologue or portion thereof or analogue in which the original C, N, and O atoms have been replaced with other elements.

[0108] The invention also relates to a method of using said structure coordinates as set forth in Table V to identify structural and chemical features of CAN-12v2; employing identified structural or chemical features to design or select compounds as potential CAN-12v2 modulators; employing the three-dimensional structural model to design or select compounds as potential CAN-12v2 modulators; synthesizing the potential CAN-12v2 modulators; screening the potential CAN-12v2 modulators in an assay characterized by binding of a protein to the CAN-12v2. The invention also relates to said method wherein the potential CAN-12v2 modulator is selected from a database. The invention further relates to said method wherein the potential CAN-12v2 modulator is designed de novo. The invention further relates to a method wherein the potential CAN-12v2 modulator is designed from a known modulator of activity.

[0109] The present invention also relates to an isolated polynucleotide consisting of a portion of the human CAN-12 gene consisting of at least 8 bases, specifically excluding Genbank Accession Nos. gilAL540944, and/or gilBM554389.

[0110] The present invention also relates to an isolated polynucleotide consisting of a nucleotide sequence encoding a fragment of the human CAN-12 protein, wherein said fragment displays one or more functional activities specifically excluding Genbank Accession Nos. gilAL540944, and/or gilBM554389.

[0111] The present invention also relates to the polynucleotide of SEQ ID NO:1, 23, 53, and/or 55 consisting of at least 10 to 50 bases, wherein said at least 10 to 50 bases specifically exclude the polynucleotide sequence of Genbank Accession Nos. gilAL540944, and/or gilBM554389.

[0112] The present invention also relates to the polynucleotide of SEQ ID NO:1, 23, 53, and/or 55 consisting of at least 15 to 100 bases, wherein said at least 15 to 100 bases specifically exclude the polynucleotide sequence of Genbank Accession Nos. gilAL540944, and/or gilBM554389.

[0113] The present invention also relates to the polynucleotide of SEQ ID NO:1, 23, 53, and/or 55 consisting of at least 100 to 1000 bases, wherein said at least 100 to 1000 bases specifically exclude the polynucleotide sequence of Genbank Accession Nos. gilAL540944, and/or gilBM554389.

[0114] The present invention also relates to an isolated polypeptide fragment of the human CAN-12 protein, wherein said polypeptide fragment does not consist of the polypeptide encoded by the polynucleotide sequence of Genbank Accession Nos. gilAL540944, and/or gilBM554389.

BRIEF DESCRIPTION OF THE FIGURES/DRAWINGS

[0115] The file of this patent contains at least one Figure executed in color. Copies of this patent with color Figure(s) will be provided by the Patent and Trademark Office upon request and payment of the necessary fee.

[0116] FIGS. 1A-E show the polynucleotide sequence (SEQ ID NO:1) and deduced amino acid sequence (SEQ ID NO:24) of the novel human calpain, CAN-12, of the present invention. The standard one-letter abbreviation for amino acids is used to illustrate the deduced amino acid sequence. The polynucleotide sequence contains a sequence of 4584 nucleotides (SEQ ID NO:1), encoding a polypeptide of about 428 amino acids (SEQ ID NO:24). The polynucleotide sequence of CAN-12 is believed to represent a short splice variant form. As a result, the alternative splicing introduces a stop codon truncating the open reading frame to end at amino acid 428. Additional amino acids beyond amino acid 428 of SEQ ID NO:24 are shown and are represented in bold (beginning at nucleotide 1537 to 1995 of SEQ ID NO:1). These additional amino acids likely corresponde to the polypeptide sequence of alternative splice forms of CAN-12 as evidenced by the presence of the EF-hand calcium binding domain. However, these additional amino acids are not considered to be a part of this splice form (SEQ ID NO:24). Additional splice forms of CAN-12 have been identified and are described herein (CAN-12v1 and CAN-12v2). The CAN-12 polypeptide sequence comprising these additional amino acids is provided as SEQ ID NO:2 to serve as a reference for the CAN-12v1 and CAN12-v2 splice variants. An analysis of the CAN-12 polypeptide determined that it comprised the following features: predicted active site domain amino acids located from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, and/or from about amino acid V327 to about amino acid V330 of SEQ ID NO:24 (FIGS. 1A-E) represented by shading; and a predicted eukaryotic thiol (cysteine) protease active site domain located from about amino acid 90 to about amino acid 111 of SEQ ID NO:24 (FIGS. 1A-E) represented by double underlining. The predicted active site domain amino acids are believed to form the active site binding pocket of the CAN-12 polypeptide and facilitate catalysis of appropriate calpain substrates. The predicted catalytic amino acid residues within the CAN-12 active site are located at amino acid C101, H253, and N277 residues of SEQ ID NO:24 (FIGS. 1A-E) and are denoted by an arrow (“T”). The additional amino acids beyond amino acid 428 of SEQ ID NO:24 depicted in the Figure were predicted to comprise an EF-hand calcium-binding domain located from about amino acid 439 to about amino acid 471 of SEQ ID NO:24 (FIGS. 1A-E) represented by dotted underlining; and a predicted cell attachment sequence located from about amino acid 520 to about amino acid 532 of SEQ ID NO:24 (FIGS. 1A-E) represented in italics. The presence of the eukaryotic thiol (cysteine) protease active site domain in the additional translated amino acids supports the notion that additional splice variants of CAN-12 exist, at least two of which are described herein.

[0117] FIGS. 2A-E show the regions of identity and similarity between the encoded CAN-12 (SEQ ID NO:2), CAN-12v1 (SEQ ID NO:54), and CAN-12v2 polypeptides (SEQ ID NO:56) to other calpains, specifically, the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); the large catalytic subunit of the human CALPAIN1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). The alignment was performed using the CLUSTALW algorithm described elsewhere herein. The darkly shaded amino acids represent regions of matching identity. The lightly shaded amino acids represent regions of matching similarity. Lines between residues indicate gapped regions for the aligned polypeptides. The asterisk (“↑”) denotes the characteristic active site cysteine (C101), histidine (H253), and asparagine (N277) residues of calpain proteases. The CAN-12 polypeptide sequence shown (CAN12+; SEQ ID NO:2) includes the additional translated amino acids beyond amino acid 428 of SEQ ID NO:24 (shown in FIGS. 1A-E) to illustrate their identity with the CAN-12v1 and CAN-12v2 splice variants.

[0118]
FIG. 3 shows a phylogenetic tree organization of various calpain family members with respect to the CAN-12 polypeptide of the present invention. The organization was created using the Vector NTI AlignX algorithm, based upon the CLUSTALW alignment described in FIGS. 2A-E above. As shown, CAN-12 is most closely related, phylogenetically, to the human CAN5 and CAN10 proteins.

[0119]
FIG. 4 shows an expression profile of the novel human calpain, CAN-12. The figure illustrates the relative expression level of CAN-12 amongst various mRNA tissue sources. As shown, transcripts corresponding to CAN-12 expressed highly in spinal cord. The CAN-12 polypeptide was also expressed significantly in lymph node, thymus, and to a lesser extent, in spleen. Expression data was obtained by measuring the steady state CAN-12 mRNA levels by quantitative PCR using the PCR primer pair provided as SEQ ID NO:21 and 22 as described herein.

[0120] FIGS. 5A-B show a table illustrating the percent identity and percent similarity values between the CAN-12+ (SEQ ID NO:2), CAN-12v1 (SEQ ID NO:54), CAN-12v2 (SEQ ID NO:56), and CAN-12 (SEQ ID NO:24) polypeptides of the present invention with other calpains, specifically, the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE) (mCALPAIN 1; Genbank Accession No: gilO88666; SEQ ID NO:7); the mouse CALPAIN LP82 (nLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). The alignment was performed using the CLUSTALW algorithm described elsewhere herein. The darkly shaded amino acids represent regions of matching identity. The lightly shaded amino acids represent regions of matching similarity. Lines between residues indicate gapped regions for the aligned polypeptides.

[0121]
FIG. 6 shows a three-dimensional homology model of the CAN-12 polypeptide based upon the homologous structure of a portion of the human m-calpain, also referred to as, CAN2 (hCAN2; Genbank Accession No. gil4502563; SEQ ID NO:11). The predicted catalytic active site amino acids of the human CAN-12 polypeptide are labeled. The predicted regions of alpha helix structure are represented in magenta; the predicted regions of beta sheet structure are represented in yellow; the predicted regions of flexible loop structure are represented in cyan; the catalytic amino acid residues are shown in a CPK/space filled rendering of the side chain atoms wherein carbon atoms are represented in white, the sulfur atoms are represented in yellow, and the nitrogen atoms are represented in blue. The structural coordinates of the CAN-12 polypeptide are provided in Table IV herein. The homology model of CAN-12 was derived from generating a sequence alignment with the human m-calpain, CAN2 protein (hCAN2; Genbank Accession No. gil4502563; SEQ ID NO:11) using the Proceryon suite of software (Proceryon Biosciences, Inc. N.Y., N.Y.), and the overall atomic model including plausible sidechain orientations using the program LOOK (V3.5.2, Molecular Applications Group).

[0122] FIGS. 8A-C show the polynucleotide sequence (SEQ ID NO: 53) and deduced amino acid sequence (SEQ ID NO:54) of the novel human calpain, CAN-12v1, of the present invention. The standard one-letter abbreviation for amino acids is used to illustrate the deduced amino acid sequence. The polynucleotide sequence contains a sequence of 2095 nucleotides (SEQ ID NO:53), encoding a polypeptide of about 694 amino acids (SEQ ID NO:54). The polynucleotide sequence of CAN-12v1 is believed to represent a novel splice variant of the CAN-12 polynucleotide described herein. An analysis of the CAN-12v1 polypeptide determined that it comprised the following features: predicted active site domain amino acids located from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, and/or from about amino acid V328 to about amino acid V331 of SEQ ID NO:54 (FIGS. 8A-C) represented by shading; a predicted eukaryotic thiol (cysteine) protease active site domain located from about amino acid 90 to about amino acid 111 of SEQ ID NO:54 (FIGS. 8A-C) represented by double underlining; a predicted EF-hand calcium-binding domain located from about amino acid 567 to about amino acid 584 of SEQ ID NO:54 (FIGS. 8A-C) represented by dotted underlining; and a predicted cell attachment sequence located from about amino acid 633 to about amino acid 532 of SEQ ID NO:54 (FIGS. 8A-C) represented in italics. The presence of the eukaryotic thiol (cysteine) protease active site domain, in addition to, the EF-hand calcium binding domain is consistent with the CAN-12v1 polypeptide representing a member of the calpain family of proteases. The predicted active site domain amino acids are believed to form the active site binding pocket of the CAN-12v1 polypeptide and facilitate catalysis of appropriate calpain substrates. The predicted catalytic amino acid residues within the CAN-12v1 active site are located at amino acid C101, H254, and N278 residues of SEQ ID NO:54 (FIGS. 8A-C) and are denoted by an arrow (“↑”).

[0123] FIGS. 9A-C show the polynucleotide sequence (SEQ ID NO: 55) and deduced amino acid sequence (SEQ ID NO:56) of the novel human calpain, CAN-12v2, of the present invention. The standard one-letter abbreviation for amino acids is used to illustrate the deduced amino acid sequence. The polynucleotide sequence contains a sequence of 2104 nucleotides (SEQ ID NO:53), encoding a polypeptide of about 694 amino acids (SEQ ID NO:56). The polynucleotide sequence of CAN-12v2 is believed to represent a novel splice variant of the CAN-12 polynucleotide described herein and likely represents the physiologically relevant splice form. An analysis of the CAN-12v2 polypeptide determined that it comprised the following features: predicted active site domain amino acids located from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, and/or from about amino acid V328 to about amino acid V331 of SEQ ID NO:56 (FIGS. 9A-C) represented by shading; a predicted eukaryotic thiol (cysteine) protease active site domain located from about amino acid 90 to about amino acid 111 of SEQ ID NO:56 (FIGS. 9A-C) represented by double underlining; a predicted EF-hand calcium-binding domain located from about amino acid 565 to about amino acid 587 of SEQ ID NO:56 (FIGS. 9A-C) represented by dotted underlining; and a predicted cell attachment sequence located from about amino acid 636 to about amino acid 648 of SEQ ID NO:56 (FIGS. 9A-C) represented by italics. The presence of the eukaryotic thiol (cysteine) protease active site domain, in addition to, the EF-hand calcium binding domain is consistent with the CAN-12v2 polypeptide representing a member of the calpain family of proteases. The predicted active site domain amino acids are believed to form the active site binding pocket of the CAN-12v2 polypeptide and facilitate catalysis of appropriate calpain substrates. The predicted catalytic amino acid residues within the CAN-12v2 active site are located at amino acid C101, H254, and N278 residues of SEQ ID NO:56 (FIGS. 9A-C) and are denoted by an arrow (“↑”).CAN-12v2 is believed to represent the true physioligical form of CAN-12.

[0124] FIGS. 10A-B show the regions of identity and similarity between the encoded CAN-12+(SEQ ID NO:2), CAN-12v1 (SEQ ID NO:54), CAN-12v2 polypeptides (SEQ ID NO:56), and CAN-12 (SEQ ID NO:24) The alignment was performed using the CLUSTALW algorithm described elsewhere herein. The darkly shaded amino acids represent regions of matching identity. The lightly shaded amino acids represent regions of matching similarity. Lines between residues indicate gapped regions for the aligned polypeptides.

[0125]
FIG. 11 shows a three-dimensional homology model of the CAN-12v2 polypeptide based upon the homologous structure of a portion of the human m-calpain, also referred to as, CAN2 (hCAN2; Genbank Accession No. gil4502563; SEQ ID NO:11). The predicted catalytic active site amino acids of the human CAN-12v2 polypeptide are labeled. The predicted regions of alpha helix structure are represented in magenta; the predicted regions of beta sheet structure are represented in yellow; the predicted regions of flexible loop structure are represented in cyan; the catalytic amino acid residues are shown in a CPK/space filled rendering of the side chain atoms wherein carbon atoms are represeted in white, the sulfur atoms are represented in yellow, and the nitrogen atoms are represented in blue. The structural coordinates of the CAN-12v2 polypeptide are provided in Table V herein. The homology model of CAN-12v2 was derived from generating a sequence alignment with the human m-calpain, CAN2 protein (hCAN2; Genbank Accession No. gil4502563; SEQ ID NO:11) using the SYBYL suite of software (Tripos, Inc., St. Louis, Mo.), and the overall atomic model including plausible sidechain orientations using the program COMPOSER (Tripos, Inc., St. Louis, Mo.).

[0126]
FIG. 12 shows an expanded expression profile of the novel human calpain, CAN-12. The figure illustrates the relative expression level of CAN-12 amongst various mRNA tissue sources. As shown, the CAN-12 polypeptide was expressed at relatively low levels, though predominately in eosphagus, lymph node, and to a lesser extent in other tissues as shown. Expression data was obtained by measuring the steady state CAN-12 mRNA levels by quantitative PCR using the PCR primer pair provided as SEQ ID NO:143 and 144, and Taqman probe (SEQ ID NO:145) as described in Example 6 herein.

[0127]
FIG. 13 shows an energy graph for the CAN-12.v2 model (see FIG. 11) of the present invention (solid line) and the human m-calpain template (PDB code 1dkv) (dotted line) from which the model was generated. The energy distribution for each protein fold is displayed on the y-axis, while the amino acid residue position of the protein fold is displayed on the x-axis. As shown, the CAN-12.v2 model and 1dkv template have similar energies over the aligned region, suggesting that the structural model of CAN-12.v2 represents a “native-like” conformation of the CAN-12.v2 polypeptide. This graph supports the motif and sequence alignments in confirming that the three-dimensional structure coordinates of CAN-12.v2 are an accurate and useful representation of the structure of the CAN-12.v2 polypeptide.

[0128] Table I provides a summary of the novel polypeptides and their encoding polynucleotides of the present invention.

[0129] Table II illustrates the preferred hybridization conditions for the polynucleotides of the present invention. Other hybridization conditions may be known in the art or are described elsewhere herein.

[0130] Table III provides a summary of various conservative substitutions encompassed by the present invention.

[0131] Table IV provides the structural coordinates of the homology model of the CAN-12 polypeptide provided in FIG. 6. A description of the headings are as follows: “Atom No” refers to the atom number within the CAN-12 homology model; “Atom Name” refers to the element whose coordinates are measured, the first letter in the column defines the element; “Residue” refers to the amino acid of the CAN-12 polypeptide within which the atom resides, in addition to the amino acid position in which the atom resides; “X Coord”, “Y Coord”, and “Z Coord” structurally define the atomic position of the element measured in three dimensions.

[0132] Table V provides the structural coordinates of the homology model of the CAN-12v2 polypeptide provided in FIG. 11. A description of the headings are as follows: “Atom No” refers to the atom number within the CAN-12v2 homology model; “Atom Name” refers to the element whose coordinates are measured, the first letter in the column defines the element; “Residue” refers to the amino acid of the CAN-12v2 polypeptide within which the atom resides, in addition to the amino acid position in which the atom resides; “X Coord”, “Y Coord”, and “Z Coord” structurally define the atomic position of the element measured in three dimensions.

DETAILED DESCRIPTION OF THE INVENTION

[0133] The present invention may be understood more readily by reference to the following detailed description of the preferred embodiments of the invention and the Examples included herein. All references to “CAN-12” shall be construed to apply to CAN-12+, CAN-12, CAN-12v1, and/or CAN-12v2 unless otherwise specified herein.

[0134] The invention provides a novel human sequence that encodes a calpain with substantial homology to the large subunits of a variety of known calpains. Calpains affect a variety of cellular processes based upon their involvement in modulating signal transduction. Aberrations in the large subunit polypeptides of calpains have been implicated in a number of diseases and disorders which include, for example, incidence of type II diabetes (Horikawa et al., Nat Genet. 26:163-75 (2000)), limb-girdle muscular dystrophy (Richard et al., Cell 81:27-40 (1995)), ischemia-induced damage in neurons and heart tissue, neurodegnerative disorders such as Alzheimer's disease, Multiple sclerosis, Huntington's disease, Parkinson's disease and amyotrophy, inflammatory disorders, susceptibility to infectious diseases, etc. CAN-12 polynucleotides and polypeptides, including agonists and antagonists thereof are expected to be useful in ameliorating at least some of these disorders. In addition, expression analysis indicates the CAN-12 has strong preferential expression in esophagus, lymph node, spinal cord, and to a lesser extent, in thymus, and spleen. Based on this information, we have provisionally named the gene and protein CAN-12.

[0135] In the present invention, “isolated” refers to material removed from its original environment (e.g., the natural environment if it is naturally occurring), and thus is altered “by the hand of man” from its natural state. For example, an isolated polynucleotide could be part of a vector or a composition of matter, or could be contained within a cell, and still be “isolated” because that vector, composition of matter, or particular cell is not the original environment of the polynucleotide. The term “isolated” does not refer to genomic or cDNA libraries, whole cell total or mRNA preparations, genomic DNA preparations (including those separated by electrophoresis and transferred onto blots), sheared whole cell genomic DNA preparations or other compositions where the art demonstrates no distinguishing features of the polynucleotide/sequences of the present invention.

[0136] In specific embodiments, the polynucleotides of the invention are at least 15, at least 30, at least 50, at least 100, at least 125, at least 500, or at least 1000 continuous nucleotides but are less than or equal to 300 kb, 200 kb, 100 kb, 50 kb, 15 kb, 10 kb, 7.5 kb, 5 kb, 2.5 kb, 2.0 kb, or 1 kb, in length. In a further embodiment, polynucleotides of the invention comprise a portion of the coding sequences, as disclosed herein, but do not comprise all or a portion of any intron. In another embodiment, the polynucleotides comprising coding sequences do not contain coding sequences of a genomic flanking gene (i.e., 5′ or 3′ to the gene of interest in the genome). In other embodiments, the polynucleotides of the invention do not contain the coding sequence of more than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5, 4, 3, 2, or 1 genomic flanking gene(s).

[0137] As used herein, a “polynucleotide” refers to a molecule having a nucleic acid sequence contained in SEQ ID NO:1, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:23 or the cDNA contained within the clone(s) deposited with the ATCC. For example, the polynucleotide can contain the nucleotide sequence of the full length cDNA sequence, including the 5′ and 3′ untranslated sequences, the coding region, with or without a signal sequence, the secreted protein coding region, as well as fragments, epitopes, domains, and variants of the nucleic acid sequence. Moreover, as used herein, a “polypeptide” refers to a molecule having the translated amino acid sequence generated from the polynucleotide as broadly defined.

[0138] In the present invention, the full length sequence identified as SEQ ID NO:1, SEQ ID NO:53, SEQ ID NO:55, and SEQ ID NO:23 was often generated by overlapping sequences contained in one or more clones (contig analysis). A representative clone containing all or most of the sequence for SEQ ID NO:1, SEQ ID NO:53, SEQ ID NO:55, and/or, SEQ ID NO:23 was deposited with the American Type Culture Collection (“ATCC”). As shown in Table I, each clone is identified by a cDNA Clone ID (Identifier) and the ATCC Deposit Number. The ATCC is located at 10801 University Boulevard, Manassas, Va. 20110-2209, USA. The ATCC deposit was made pursuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for purposes of patent procedure. The deposited clone is inserted in the pSport1 plasmid (Life Technologies) using the NotI and SalI restriction endonuclease cleavage sites.

[0139] Unless otherwise indicated, all nucleotide sequences determined by sequencing a DNA molecule herein were determined using an automated DNA sequencer (such as the Model 373, preferably a Model 3700, from Applied Biosystems, Inc.), and all amino acid sequences of polypeptides encoded by DNA molecules determined herein were predicted by translation of a DNA sequence determined above. Therefore, as is known in the art for any DNA sequence determined by this automated approach, any nucleotide sequence determined herein may contain some errors. Nucleotide sequences determined by automation are typically at least about 90% identical, more typically at least about 95% to at least about 99.9% identical to the actual nucleotide sequence of the sequenced DNA molecule. The actual sequence can be more precisely determined by other approaches including manual DNA sequencing methods well known in the art. As is also known in the art, a single insertion or deletion in a determined nucleotide sequence compared to the actual sequence will cause a frame shift in translation of the nucleotide sequence such that the predicted amino acid sequence encoded by a determined nucleotide sequence will be completely different from the amino acid sequence actually encoded by the sequenced DNA molecule, beginning at the point of such an insertion or deletion.

[0140] Using the information provided herein, such as the nucleotide sequence in FIGS. 1A-E (SEQ ID NO:1), a nucleic acid molecule of the present invention encoding the CAN-12 polypeptide may be obtained using standard cloning and screening procedures, such as those for cloning cDNAs using mRNA as starting material. Illustrative of the invention, the nucleic acid molecule described in FIGS. 1A-E (SEQ ID NO:1) was discovered in a cDNA library derived from human liver, brain and testis and spleen.

[0141] The determined nucleotide sequence of the CAN-12 cDNA in FIGS. 1A-E (SEQ ID NO:1) contains an open reading frame encoding a protein of about 428 amino acid residues, with a deduced molecular weight of about 49.5 kDa. The amino acid sequence of the predicted CAN-12 polypeptide is shown in FIGS. 1A-E (SEQ ID NO:24).

[0142] Using the information provided herein, such as the nucleotide sequence in FIGS. 8A-C (SEQ ID NO:53), a nucleic acid molecule of the present invention encoding the CAN-12v1 polypeptide may be obtained using standard cloning and screening procedures, such as those for cloning cDNAs using mRNA as starting material. Illustrative of the invention, the nucleic acid molecule described in FIGS. 8A-C (SEQ ID NO:53) was discovered in a cDNA library derived from human liver, brain and testis and spleen.

[0143] The determined nucleotide sequence of the CAN-12v1 cDNA in FIGS. 8A-C (SEQ ID NO:53) contains an open reading frame encoding a protein of about 694 amino acid residues, with a deduced molecular weight of about 80.3 kDa. The amino acid sequence of the predicted CAN-12v1 polypeptide is shown in FIGS. 8A-C (SEQ ID NO:54).

[0144] Using the information provided herein, such as the nucleotide sequence in FIGS. 9A-C (SEQ ID NO:55), a nucleic acid molecule of the present invention encoding the CAN-12v2 polypeptide may be obtained using standard cloning and screening procedures, such as those for cloning cDNAs using mRNA as starting material. Illustrative of the invention, the nucleic acid molecule described in FIGS. 9A-C (SEQ ID NO:55) was discovered in a cDNA library derived from human liver, brain and testis and spleen.

[0145] The determined nucleotide sequence of the CAN-12v2 cDNA in FIGS. 9A-C (SEQ ID NO:55) contains an open reading frame encoding a protein of about 697 amino acid residues, with a deduced molecular weight of about 80.6 kDa. The amino acid sequence of the predicted CAN-12v2 polypeptide is shown in FIGS. 9A-C (SEQ ID NO:56).

[0146] A “polynucleotide” of the present invention also includes those polynucleotides capable of hybridizing, under stringent hybridization conditions, to sequences contained in SEQ ID NO:1, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:23, the complement thereof, or the cDNA within the clone deposited with the ATCC. “Stringent hybridization conditions” refers to an overnight incubation at 42 degree C. in a solution comprising 50% formamide, 5× SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1× SSC at about 65 degree C.

[0147] Also contemplated are nucleic acid molecules that hybridize to the polynucleotides of the present invention at lower stringency hybridization conditions. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature. For example, lower stringency conditions include an overnight incubation at 37 degree C. in a solution comprising 6× SSPE (20× SSPE=3M NaCl; 0.2M NaH2PO4; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 ug/ml salmon sperm blocking DNA; followed by washes at 50 degree C. with 1× SPE, 0.1% SDS. In addition, to achieve even lower stringency, washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5× SSC).

[0148] Note that variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.

[0149] Of course, a polynucleotide which hybridizes only to polyA+ sequences (such as any 3′ terminal polyA+ tract of a cDNA shown in the sequence listing), or to a complementary stretch of T (or U) residues, would not be included in the definition of “polynucleotide,” since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone generated using oligo dT as a primer).

[0150] The polynucleotide of the present invention can be composed of any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. For example, polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. In addition, the polynucleotide can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA. A polynucleotide may also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications can be made to DNA and RNA; thus, “polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.

[0151] The polypeptide of the present invention can be composed of amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain amino acids other than the 20 gene-encoded amino acids. The polypeptides may be modified by either natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Polypeptides may be branched, for example, as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. (See, for instance, Proteins—Structure and Molecular Properties, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York, pgs. 1-12 (1983); Seifter et al., Meth Enzymol 182:626-646 (1990); Rattan et al., Ann NY Acad Sci 663:48-62 (1992).)

[0152] “A polypeptide having biological activity” refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the present invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. In the case where dose dependency does exist, it need not be identical to that of the polypeptide, but rather substantially similar to the dose-dependence in a given activity as compared to the polypeptide of the present invention (i.e., the candidate polypeptide will exhibit greater activity or not more than about 25-fold less and, preferably, not more than about tenfold less activity, and most preferably, not more than about three-fold less activity relative to the polypeptide of the present invention.)

[0153] The term “organism” as referred to herein is meant to encompass any organism referenced herein, though preferably to eukaryotic organisms, more preferably to mammals, and most preferably to humans.

[0154] As used herein the terms “modulate” or “modulates” refer to an increase or decrease in the amount, quality or effect of a particular activity, DNA, RNA, or protein. The definition of “modulate” or “modulates” as used herein is meant to encompass agonists and/or antagonists of a particular activity, DNA, RNA, or protein.

[0155] The present invention encompasses the identification of proteins, nucleic acids, or other molecules, that bind to polypeptides and polynucleotides of the present invention (for example, in a receptor-ligand interaction). The polynucleotides of the present invention can also be used in interaction trap assays (such as, for example, that described by Ozenberger and Young (Mol Endocrinol., 9(10): 1321-9, (1995); and Ann. N.Y. Acad. Sci., 7;766:279-81, (1995)).

[0156] The polynucleotide and polypeptides of the present invention are useful as probes for the identification and isolation of full-length cDNAs and/or genomic DNA which correspond to the polynucleotides of the present invention, as probes to hybridize and discover novel, related DNA sequences, as probes for positional cloning of this or a related sequence, as probe to “subtract-out” known sequences in the process of discovering other novel polynucleotides, as probes to quantify gene expression, and as probes for microarrays.

[0157] In addition, polynucleotides and polypeptides of the present invention may comprise one, two, three, four, five, six, seven, eight, or more membrane domains.

[0158] Also, in preferred embodiments the present invention provides methods for further refining the biological function of the polynucleotides and/or polypeptides of the present invention.

[0159] Specifically, the invention provides methods for using the polynucleotides and polypeptides of the invention to identify orthologs, homologs, paralogs, variants, and/or allelic variants of the invention. Also provided are methods of using the polynucleotides and polypeptides of the invention to identify the entire coding region of the invention, non-coding regions of the invention, regulatory sequences of the invention, and secreted, mature, pro-, prepro-, forms of the invention (as applicable).

[0160] In preferred embodiments, the invention provides methods for identifying the glycosylation sites inherent in the polynucleotides and polypeptides of the invention, and the subsequent alteration, deletion, and/or addition of said sites for a number of desirable characteristics which include, but are not limited to, augmentation of protein folding, inhibition of protein aggregation, regulation of intracellular trafficking to organelles, increasing resistance to proteolysis, modulation of protein antigenicity, and mediation of intercellular adhesion.

[0161] In further preferred embodiments, methods are provided for evolving the polynucleotides and polypeptides of the present invention using molecular evolution techniques in an effort to create and identify novel variants with desired structural, functional, and/or physical characteristics.

[0162] The present invention further provides for other experimental methods and procedures currently available to derive functional assignments. These procedures include but are not limited to spotting of clones on arrays, micro-array technology, PCR based methods (e.g., quantitative PCR), anti-sense methodology, gene knockout experiments, and other procedures that could use sequence information from clones to build a primer or a hybrid partner.

[0163] Polynucleotides and Polypeptides of the Invention

[0164] Features of the Polypeptide Encoded by Gene No:1

[0165] The polypeptide of this gene provided as SEQ ID NO:24 (FIGS. 1A-E), encoded by the polynucleotide sequence according to SEQ ID NO:1 (FIGS. 1A-E), and/or encoded by the polynucleotide contained within the deposited clone, CAN-12, has significant homology at the nucleotide and amino acid level to a number of calpains, which include, for example, the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). An alignment of the CAN-12 polypeptide with these proteins is provided in FIGS. 2A-E. Based upon such strong conservation, the inventors have ascribed the CAN-12 polypeptide as having proteolytic activity, preferably calpain activity.

[0166] The CAN-12+(SEQ ID NO:2) polypeptide was determined to have 30.7% identity and 38.0% similarity with the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); to have 34.2% identity and 45.4% similarity with the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); to have 37.9% identity and 47.4% similarity with the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); to have 36.3% identity and 43.6% similarity with the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); to have 39.0% identity and 47.6% similarity with the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE ) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); to have 37.8% identity and 45.3% similarity with the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); to have 34.2% identity and 45.4% similarity with the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); to have 40.4% identity and 47.3% similarity with the human CAN 11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); to have 36.8% identity and 45.8% similarity with the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and to have 39.4% identity and 47.2% similarity with the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). The polypeptide sequence used for these percent identity and similarity values comprised the additional amino acids that extend beyond amino acid 428 of SEQ ID NO:24—specifically, SEQ ID NO:2.

[0167] The CAN-12 polypeptide was determined to have 34.3% identity and 42.3% similarity with the human CAN10 protein (type II diabetes linked) (hCAN1O; Genbank Accession No: gilNP—075574; SEQ ID NO:3); to have 40.5% identity and 51.9% similarity with the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); to have 44.3% identity and 51.9% similarity with the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); to have 44.9% identity and 51.8% similarity with the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); to have 46.1% identity and 52.7% similarity with the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE ) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); to have 46.2% identity and 53.5% similarity with the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); to have 44.6% identity and 51.4% similarity with the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); to have 45.5% identity and 51.7% similarity with the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); to have 46.2% identity and 53.5% similarity with the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and to have 44.3% identity and 51.9% similarity with the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). The polypeptide sequence used for these percent identity and similarity values was the full-length CAN-12 polypeptide (SEQ ID NO:24).

[0168] The human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3)is a human calpain gene that encodes a large calpain subunit. CAN10 is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. CAN10 is similar in organization to calpains 5 and 6 and is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM) and located within the NIDDM1 chromosomal region (Nat. Genet. 26 (2), 163-175 (2000)).

[0169] The large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6) is a muscle-specific member of the calpain large subunit family. Loss of CAPN3 function has been associated with limb-girdle muscular dystrophies type 2A (Cell 81 (1), 27-40 (1995)).

[0170] The human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is a calpain that is expressed predominantly in stomach and small intestine and is thought to have specialized functions in the digestive tract, and be associated with gastric cancer.(Biol. Chem. 379 (2), 175-183 (1998); and Jpn. J. Cancer Res. 91 (5), 459-463 (2000)).

[0171] As described above, the CAN-12 polypeptide was found to have significant sequence homology with calpains, particularly members of the m-calpain family. A conserved peptide signature of Qx3(G,E)xC(Y,W)x2(S,T,A,G,C)(S,T,A,G,C,V) Qx {3 } (G)xC(W)x {2 } (A)(A) (referred to as a thiol (cysteine) protease active site domain) common to most calpain family members is found in the protein sequence of CAN-12 from amino acid 90 to amino acid 111 of SEQ ID NO:24 (FIGS. 1A-E). Protein threading and molecular modeling of CAN-12 suggests that CAN-12 has a structural fold similar to representative m-calpains. Moreover, the structural and threading alignments of the present invention suggest that amino acids 101 (“C”), 253 (“H”), and 277 (“N”) of SEQ ID NO:24 (FIGS. 1A-E) may represent the catalytic amino acids within the active site domain. Thus, based upon the sequence and structural homology to known calpains, particularly the presence of the thiol cysteine protease active site domain, the novel CAN-12 is believed to represent a novel human calpain.

[0172] In an alternative embodiment, the following polypeptide is encompassed by the present invention: MSLWPPFRCRWKLAPRYSRRASPQQPQQDFEALLAECLRNGCLFEDTSFPAT LSSIGSGSLLQKLPPRLQWKRPPELHSNPQFYFAKAKRLDLCQGIVGDCWFLA ALQALALHQDILSRVVPLNQSFTEKYAGIFRFWFWHYGNWVPVVIDDRLPVN EAGQLVFVSSTYKNLFWGALLEKAYAKLSGSYEDLQSGQVSEALVDFTGGVT MTINLAEAHGNLWDILEATYNRTLIGCQTHSGKILENGLVEGHAYTLTGIRKV TCKHRPEYLVKLRNPWGKVEWKGDWSDSSSKWELLSPKEKILLLRKDNDGE FWMTLQDFKTHFVLLVICKLTPGLLSQEAAQKWTYTMREGRWEKRSTAGGQ RQLLQDTFWKNPQFLLSVWRPEEGRRSLRPCSVLVSLLQKPRHRCRKRKPLL AIGFYLYRMNK (SEQ ID NO:24). Polynucleotides encoding these polypeptides are also provided (SEQ ID NO:23).

[0173] In confirmation of the strong homology to known calpains, the CAN-12 polypeptide was determined to have several conserved catalytic amino acids at amino acid C101, H253, and N277 of SEQ ID NO:24 (FIGS. 1A-E). As discussed more particularly herein, calpains are a group of structurally diverse, high molecular weight (400 to 500 amino acids) proteins that have a catalytic cysteine amino acid and one or more calcium binding domains. Despite the structural heterogeneity, calpains share some well defined structural-functional characteristics, particularly in their active site domains.

[0174] In preferred embodiments, the CAN-12 polypeptide of the present invention is directed to a polypeptide having structural similarity to calpains.

[0175] Based upon the strong homology to members of the calpain family, the CAN-12 polypeptide is expected to share at least some biological activity with calpains, preferably with m-calpain family members, and more preferable to the large subunits of m-calpain family members, in addition to other calpains and calpain subunits referenced herein and/or otherwise known in the art.

[0176] Expression profiling designed to measure the steady state mRNA levels encoding the CAN-12 polypeptide showed predominately high expression levels in spinal cord tissue; significantly high expression in lymph node and thymus, and to a lesser extent, in spleen tissue (See FIG. 4).

[0177] Expanded analysis of CAN-12 expression levels by TaqMan™ quantitative PCR (see FIG. 6) confirmed that the CAN-12 polypeptide is expressed in the lymph gland. However, the TaqMan™ quantitative PCR determined that the CAN-12 polypeptide is primarily expressed in the eosophagus. In fact, with the exception of the lymph gland, the steady state mRNA level of CAN-12 was approximately 2700 times higher in the esophagus than in all other tissues tested. These data suggest modulators of the CAN-12 polynucleotides and polypeptides may be useful for the treatment, detection, and/or amelioration of the following, non-limiting diseases and disorders associated with the eosphagus: dysphagia, cricoharyngeal incoordination, esophageal carcinoma, esophageal webs, achalasia, symptomatic diffuse esophageal spasm, gastroesophageal reflux, and/or corrosive esophagitis.

[0178] The polynucleotides encoding the CAN-12 polypeptide of the present invention were used to determine the chromosomal localization of the calpain12 gene. Polynuclelotides corresponding to CAN-12 (SEQ ID NO:1) were shown to localize to chromosome 2, specifically 2p16-p21. The comparison of the chromosomal location of the calpain12 gene with the location of chromosomal regions which have been shown to be associated with specific diseases or conditions, e.g. by linkage analysis, can be indicative of diseases in which calpain12 may play a role. Interestingly, a whole-genome linkage scan in multiple sclerosis families (Ebers et al. A full genome search in multiple sclerosis. Nature Genet. 13: 472-476, 1996.) identified 5 susceptibility loci on chromosomes 2, 3, 5, 11, and X. In particular, an association was identified with marker D2S119 on chromosome 2 and MS. The localization of the D2S119 marker was further delimeated to 2p 16-p21 based on a radiation hybrid linkage map retrieved from an online query at NCBI web site: http:/www.ncbi.nlm.nih.gov/genome/sts/. Since the map of calpain 12 and the susceptibility marker D2S119 overlaps, it is reasonable to postulate that calpain 12 may contribute to MS. Furthermore, the transcription profile of calpain12 indicated a prominent expression in spinal cord, and implication of calpains in MS has been suggested (Shields D C et al. A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc Natl Acad Sci U S A. 96:11486-91.1999).

[0179] The CAN-12 polynucleotides and polypeptides of the present invention, including agonists, antagonists, and/or fragments thereof, have uses that include modulating cellular adhesion events, cellular proliferation, and inflammation, in various cells, tissues, and organisms, and particularly in mammalian spinal cord tissue, lymph node, thymus, and spleen tissue, preferably human tissue. CAN-12 polynucleotides and polypeptides of the present invention, including agonists and/or fragments thereof, may be useful in diagnosing, treating, prognosing, and/or preventing neural, immune, hematopoietic, and/or proliferative diseases or disorders.

[0180] The strong homology to human calpains, particularly m-calpains, combined with the predominate localized expression in esophagus tissue suggests the CAN-12 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing gastrointestinal diseases, particularly esophageal diseases and/or disorders which include the following non-limiting examples: aberrant transport of food bolus from the mouth to the stomach, aberrant prevention of retrograde flow of gastrointestinal contents, aberrant esophageal peristaltic contractions, pyrosis, painful swallowing, reflux esophagitis, esophageal motility disorders, esophageal spasms, diffuse esophageal spasm, atypical chest pain, regurgitation, oropharyngeal paralysis, nasal regurgitation, dysphagia, cricopharyngeal bar, globus pharyngeus, achalasia, motor disorders of the esophageal smooth muscle, scleroderma esophagus, gastroesophageal reflux disease (GERD), esophagitis, Barrett's esophagus, viral esophagitis, Herpes simplex virus mediated viral esophagitis, Varicella-zoster virus mediated viral esophagitis, Cytomegalovirus mediated viral esophagitis, bacterial esophagitis, Lactobacillus mediated bacterial esophagitis, Candida mediated esophagitis, radiation esophagitis, corrosive esophagitis, pill-induced esophagitis, esophagitis associated with mucocutaneous and systemic diseases, diverticula, lower esophageal mucosal ring, lower esophageal muscular ring, hiatal hernia, paraesophageal hernia, esophageal rupture, and/or Mallory-Weiss Syndrome.

[0181] Although calpains are typically associated primarily with neurogenerative conditions, their association in gastrointenstinal tissues has precedence. For example, the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is predominately expressed in the stomach and small intestine and is thought to be associated with gastric cancers.

[0182] The strong homology to human calpains, particularly m-calpains, combined with the predominate expression in spinal cord tissue suggests the CAN-12 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing neural diseases, neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the “Neurological Diseases”, “Regeneration” and “Hyperproliferative Disorders” sections below, in the Examples, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0183] Alternatively, the strong homology to human calpains, particularly m-calpains, combined with the localized expression in lymph node, thymus, and spleen tissue suggests the CAN-12 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, ameliorating, and/or preventing immune diseases and/or disorders. Representative uses are described in the “Immune Activity” and “Infectious Disease” sections below, and elsewhere herein. Briefly, the strong expression in immune tissue indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. The CAN-12 polypeptide may also be useful as a preventative agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lense tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren's disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product may be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types.

[0184] Moreover, the protein would be useful in the detection, treatment, and/or prevention of a variety of vascular disorders and conditions, which include, but are not limited to miscrovascular disease, vascular leak syndrome, aneurysm, stroke, embolism, thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0185] In addition, antagonists of the CAN-12 polynucleotides and polypeptides may have uses that include diagnosing, treating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include immune and/or proliferative diseases or disorders, particularly thrombosis, embolism, and other blood disorders. Therapeutic and/or pharmaceutical compositions comprising the CAN-12 polypeptides may be formulated to comprise heparin.

[0186] In addition, antagonists of the CAN-12 polynucleotides and polypeptides may have uses that include diagnosing, treating, ameliorating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include neuronal excitotoxicity, ischemic stroke, hemoragic stroke, hypoxic stress, trauma, cell destruction, spinal cord injury following trauma, degeneration of vulnerable hippocampal neurons after ischemia, reovirus-induced apoptosis, viral-induced induced myocarditis, acute and chronic inflammation, cataract formation, multiple sclerosis, demylenating disorders, acoustic trauma, hearing loss caused by noise, neuronal damage, cardiac ischemic damage, and/or hepatocyte necrosis during and following anoxia

[0187] CAN-12 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include modulating development, differentiation, cellular transformation in response to cell signaling, cell-cell and/or cell-extracellular matrix interactions, clustering of the integrin receptor aIIb3, modulating in long term potentiation (memory), modulating neurite outgrowth, modulating cortical lamination activation of protein kinases and phosphatases, remodeling and disassembling the cytoskeleton, cell cycle modulation, in addition, to ameliorating, preventing, and/or treating limb-girdle muscular dystrophy (LGMD), insulin resistance in diabetics, Alzheimer's disease, Multiple sclerosis, Huntington's disease, Parkinson's disease and amyotrophy.

[0188] Moreover, CAN-12 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include treating, diagnosing, prognosing, and/or preventing hyperproliferative disorders, particularly of the neural and immune systems. Such disorders may include, for example, cancers, and metastatic conditions.

[0189] CAN-12 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include identification of modulators of CAN-12 function including antibodies (for detection or neutralization), naturally-occurring modulators and small molecule modulators. Antibodies to domains (including CAN-12 epitopes provided herein) of the CAN-12 protein could be used as diagnostic agents of inflammatory conditions in patients, are useful in monitoring the activation and presence of cognate proteases, and can be used as a biomarker for the protease involvement in disease states and in the evaluation of inhibitors of the cognate protease in vivo.

[0190] CAN-12 polypeptides and polynucleotides are useful for diagnosing diseases related to over or under expression of CAN-12 proteins by identifying mutations in the CAN-12 gene using CAN-12 probes, or determining CAN-12 protein or mRNA expression levels. CAN-12 polypeptides are also useful for screening for compounds, which affect activity of the protein. Diseases that can be treated with CAN-12 include, the following, non-limiting examples: neuro-regeneration, neuropathic pain, obesity, anorexia, HIV infections, cancers, bulimia, asthma, Parkinson's disease, acute heart failure, hypotension, hypertension, osteoporosis, angina pectoris, myocardial infarction, psychotic, immune, metabolic, cardiovascular, and neurological disorders.

[0191] The predominate expression in neural tissues, combined with the significant expression in a number of other tissues, suggests the CAN-12 polynucleotide and polypeptide of the present invention may be involved in modulating nerve invasion, innervation, nerve maintenance, and potentially myeline sheath maintenance and integrity.

[0192] The CAN-12 polynucleotides and polypeptides, including fragments and antagonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing diseases and disorders of the neural system, particularly Alzheimer's disease, either directly or indirectly, in addition to other neural disorders known in the art or provided in the “Neurological Diseases” section herein, such as modulating nerve invasion, innervation, nerve maintenance, potentially myelin sheath maintenance and integrity, encephalomyelitis, autoimmune encephalomyelitis, human T cell leukemia virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP), and neuro-inflammatory diseases.

[0193] Molecular genetic manipulation of the structure of the active site domain, particularly the predicted catalytic amino acids, and of other functional domains in the calpain family (e.g., active site domain binding pocket) enables the production of calpains with tailor-made activities. Thus, the CAN-12 polypeptides, and fragments thereof, as well as any homologous product resulting from genetic manipulation of the structure, are useful for NMR-based design of modulators of CAN-12 biological activity, and calpains, in general.

[0194] CAN-12 polypeptides and polynucleotides have additional uses which include diagnosing diseases related to the over and/or under expression of CAN-12 by identifying mutations in the CAN-12 gene by using CAN-12 sequences as probes or by determining CAN-12 protein or mRNA expression levels. CAN-12 polypeptides may be useful for screening compounds that affect the activity of the protein. CAN-12 peptides can also be used for the generation of specific antibodies and as bait in yeast two hybrid screens to find proteins the specifically interact with CAN-12 (described elsewhere herein).

[0195] The CAN-12 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing metabolic diseases and disorders, such as diabetes. Moreover, expressed human CAN-12 may be useful in the detection of patients susceptible to diabetes. Also paradigms that would simulate intracellular CAN-12 activity would be useful in treating diabetes.

[0196] The CAN-12 polynucleotides and polypeptides, including fragments thereof, may have uses which include identifying inhibitors of intracellular calpain inhibitors (calpastatins) leading to an effective increase in calpain activity.

[0197] Various approaches to detect alterations or allelic variants at the genomic or mRNA level of CAN-12, could be used as a diagnostic for identifying MS patients, or individuals susceptible to have MS. It is likely that the calpain12 gene comprises polymorphic sites (i.e. SNPs), with specific alleles which may be associated with MS or other neurodegenerative disorders, or associated with an increased likelihood of developing these diseases. Therefore, the invention provides the calpain12 sequence that can be used to design specific primers for the identification of polymorphisms or mutations in calpain12 of patients affected with MS. The presence of a specific allele variant, such as a SNP allele or SNPs haplotype that renders the subject carrying it more susceptible to develop MS or other related diseases could be identified (e.g. a variant in the can12 promoter region that increased transcript levels of can12, or mutations in the coding sequence that increased the stability or half-life of the can12 protein). Other methods such as Northern-blot analysis could be performed to measure transcript levels using a can12 cDNA probe derived from the sequence of the invention.

[0198] Although it is believed the encoded polypeptide may share at least some biological activities with human calpains (particularly m-calpains), a number of methods of determining the exact biological function of this clone are either known in the art or are described elsewhere herein. Briefly, the function of this clone may be determined by applying microarray methodology. Nucleic acids corresponding to the CAN-12 polynucleotides, in addition to, other clones of the present invention, may be arrayed on microchips for expression profiling. Depending on which polynucleotide probe is used to hybridize to the slides, a change in expression of a specific gene may provide additional insight into the function of this gene based upon the conditions being studied. For example, an observed increase or decrease in expression levels when the polynucleotide probe used comes from diseased neural tissue, as compared to, normal tissue might indicate a function in modulating neural function, for example. In the case of CAN-12, spinal cord, lymph node, thymus, and/or spleen tissue should be used to extract RNA to prepare the probe.

[0199] In addition, the function of the protein may be assessed by applying quantitative PCR methodology, for example. Real time quantitative PCR would provide the capability of following the expression of the CAN-12 gene throughout development, for example. Quantitative PCR methodology requires only a nominal amount of tissue from each developmentally important step is needed to perform such experiments. Therefore, the application of quantitative PCR methodology to refining the biological function of this polypeptide is encompassed by the present invention. In the case of CAN-12, a disease correlation related to CAN-12 may be made by comparing the mRNA expression level of CAN-12 in normal tissue, as compared to diseased tissue (particularly diseased tissue isolated from the following: esophagus, spinal cord, lymph node, thymus, and/or spleen tissue). Significantly higher or lower levels of CAN-12 expression in the diseased tissue may suggest CAN-12 plays a role in disease progression, and antagonists against CAN-12 polypeptides would be useful therapeutically in treating, preventing, and/or ameliorating the disease. Alternatively, significantly higher or lower levels of CAN-12 expression in the diseased tissue may suggest CAN-12 plays a defensive role against disease progression, and agonists of CAN-12 polypeptides may be useful therapeutically in treating, preventing, and/or ameliorating the disease. Also encompassed by the present invention are quantitative PCR probes corresponding to the polynucleotide sequence provided as SEQ ID NO:1 (FIGS. 1A-E).

[0200] The function of the protein may also be assessed through complementation assays in yeast. For example, in the case of the CAN-12, transforming yeast deficient in calpain activity, particularly m-calpain activity, and assessing their ability to grow would provide convincing evidence the CAN-12 polypeptide has calpain activity, and possibly m-calpain activity. Additional assay conditions and methods that may be used in assessing the function of the polynucleotides and polypeptides of the present invention are known in the art, some of which are disclosed elsewhere herein.

[0201] Alternatively, the biological function of the encoded polypeptide may be determined by disrupting a homologue of this polypeptide in Mice and/or rats and observing the resulting phenotype. Such knock-out experiments are known in the art, some of which are disclosed elsewhere herein.

[0202] Moreover, the biological function of this polypeptide may be determined by the application of antisense and/or sense methodology and the resulting generation of transgenic mice and/or rats. Expressing a particular gene in either sense or antisense orientation in a transgenic mouse or rat could lead to respectively higher or lower expression levels of that particular gene. Altering the endogenous expression levels of a gene can lead to the observation of a particular phenotype that can then be used to derive indications on the function of the gene. The gene can be either over-expressed or under expressed in every cell of the organism at all times using a strong ubiquitous promoter, or it could be expressed in one or more discrete parts of the organism using a well characterized tissue-specific promoter (e.g., an esophagus, spinal cord, lymph node, thymus, or spleen specific promoter), or it can be expressed at a specified time of development using an inducible and/or a developmentally regulated promoter.

[0203] In the case of CAN-12 transgenic mice or rats, if no phenotype is apparent in normal growth conditions, observing the organism under diseased conditions (neural, immune, hematopoietic diseases or disorders, cancers, etc.) may lead to understanding the function of the gene. Therefore, the application of antisense and/or sense methodology to the creation of transgenic mice or rats to refine the biological function of the polypeptide is encompassed by the present invention.

[0204] In preferred embodiments, the following N-terminal CAN-12 deletion polypeptides are encompassed by the present invention: M1-L581, S2-L581, L3-L581, W4-L581, P5-L581, P6-L581, F7-L581, R8-L581, C9-L581, R10-L581, W11-L581, K12-L581, L13-L581, A14-L581, P15-L581, R16-L581, Y17-L581, S18-L581, R19-L581, R20-L581, A21-L581, S22-L581, P23-L581, Q24-L581, Q25-L581, P26-L581, Q27-L581, Q28-L581, D29-L581, F30-L581, E31-L581, A32-L581, L33-L581, L34-L581, A35-L581, E36-L581, C37-L581, L38-L581, R39-L581, N40-L581, G41-L581, C42-L581, L43-L581, F44-L581, E45-L581, D46-L581, T47-L581, S48-L581, F49-L581, P50-L581, A51-L581, T52-L581, L53-L581, S54-L581, S55-L581, 156-L581, G57-L581, S58-L581, G59-L581, S60-L581, L61-L581, L62-L581, Q63-L581, K64-L581, L65-L581, P66-L581, P67-L581, R68-L581, L69-L581, Q70-L581, W71-L581, K72-L581, R73-L581, P74-L581, P75-L581, E76-L581, L77-L581, H78-L581, S79-L581, N80-L581, P81-L581, Q82-L581, F83-L581, Y84-L581, F85-L581, A86-L581, K87-L581, A88-L581, K89-L581, R90-L581, L91-L581, D92-L581, L93-L581, C94-L581, Q95-L581, G96-L581, 197-L581, V98-L581, G99-L581, D10O-L581, C101-L581, W102-L581, F103-L581, L104-L581, A105-L581, A106-L581, L107-L581, Q108-L581, A109-L581, L110-L581, A111-L581, L112-L581, H113-L581, Q114-L581, D115-L581, 1116-L581, L117-L581, S118-L581, R119-L581, V120-L581, V121-L581, P122-L581, L123-L581, N124-L581, Q125-L581, S126-L581, F127-L581, T128-L581, E129-L581, K130-L581, Y131-L581, A132-L581, G133-L581, 1134-L581, F135-L581, R136-L581, F137-L581, W138-L581, F139-L581, W140-L581, H141-L581, Y142-L581, G143-L581, N144-L581, W145-L581, V146-L581, P147-L581, V148-L581, V149-L581, 1150-L581, D151-L581, D152-L581, R153-L581, L154-L581, P155-L581, V156-L581, N157-L581, E158-L581, A159-L581, G160-L581, Q161-L581, L162-L581, V163-L581, F164-L581, V165-L581, S166-L581, S167-L581, T168-L581, Y169-L581, K170-L581, N171-L581, L172-L581, F173-L581, W174-L581, G175-L581, A176-L581, L177-L581, L178-L581, E179-L581, K180-L581, A181-L581, Y182-L581, A183-L581, K184-L581, L185-L581, S186-L581, G187-L581, S188-L581, Y189-L581, E190-L581, D191-L581, L192-L581, Q193-L581, S194-L581, G195-L581, Q196-L581, V197-L581, S198-L581, E199-L581, A200-L581, L201-L581, V202-L581, D203-L581, F204-L581, T205-L581, G206-L581, G207-L581, V208-L581, T209-L581, M210-L581, T211-L581, 1212-L581, N213-L581, L214-L581, A215-L581, E216-L581, A217-L581, H218-L581, G219-L581, N220-L581, L221-L581, W222-L581, D223-L581, 1224-L581, L225-L581, 1226-L581, E227-L581, A228-L581, T229-L581, Y230-L581, N231-L581, R232-L581, T233-L581, L234-L581, 1235-L581, G236-L581, C237-L581, Q238-L581, T239-L581, H240-L581, S241-L581, G242-L581, K243-L581, 1244-L581, L245-L581, E246-L581, N247-L581, G248-L581, L249-L581, V250-L581, E251-L581, G252-L581, H253-L581, A254-L581, Y255-L581, T256-L581, L257-L581, T258-L581, G259-L581, I260-L581, R261-L581, K262-L581, V263-L581, T264-L581, C265-L581, K266-L581, H267-L581, R268-L581, P269-L581, E270-L581, Y271-L581, L272-L581, V273-L581, K274-L581, L275-L581, R276-L581, N277-L581, P278-L581, W279-L581, G280-L581, K281-L581, V282-L581, E283-L581, W284-L581, K285-L581, G286-L581, D287-L581, W288-L581, S289-L581, D290-L581, S291-L581, S292-L581, S293-L581, K294-L581, W295-L581, E296-L581, L297-L581, L298-L581, S299-L581, P300-L581, K301-L581, E302-L581, K303-L581, 1304-L581, L305-L581, L306-L581, L307-L581, R308-L581, K309-L581, D310-L581, N311-L581, D312-L581, G313-L581, E314-L581, F315-L581, W316-L581, M317-L581, T318-L581, L319-L581, Q320-L581, D321-L581, F322-L581, K323-L581, T324-L581, H325-L581, F326-L581, V327-L581, L328-L581, L329-L581, V330-L581, 1331-L581, C332-L581, K333-L581, L334-L581, T335-L581, P336-L581, G337-L581, L338-L581, L339-L581, S340-L581, Q341-L581, E342-L581, A343-L581, A344-L581, Q345-L581, K346-L581, W347-L581, T348-L581, Y349-L581, T350-L581, M351-L581, R352-L581, E353-L581, G354-L581, R355-L581, W356-L581, E357-L581, K358-L581, R359-L581, S360-L581, T361-L581, A362-L581, G363-L581, G364-L581, Q365-L581, R366-L581, Q367-L581, L368-L581, L369-L581, Q370-L581, D371-L581, T372-L581, F373-L581, W374-L581, K375-L581, N376-L581, P377-L581, Q378-L581, F379-L581, L380-L581, L381-L581, S382-L581, V383-L581, W384-L581, R385-L581, P386-L581, E387-L581, E388-L581, G389-L581, R390-L581, R391-L581, S392-L581, L393-L581, R394-L581, P395-L581, C396-L581, S397-L581, V398-L581, L399-L581, V400-L581, S401-L581, I102-L581, L403-L581, Q404-L581, K405-L581, P406-L581, R407-L581, H408-L581, R409-L581, C410-L581, R411-L581, K412-L581, R413-L581, K414-L581, P415-L581, L416-L581, L417-L581, A418-L581, 1419-L581, G420-L581, F421-L581, Y422-L581, L423-L581, Y424-L581, R425-L581, M426-L581, N427-L581, K428-L581, M429-L581, T430-L581, W431-L581, S432-L581, S433-L581, L434-L581, G435-L581, S436-L581, R437-L581, Q438-L581, P439-L581, F440-L581, F441-L581, S442-L581, L443-L581, E444-L581, A445-L581, C446-L581, Q447-L581, G448-L581, 1449-L581, L450-L581, A451-L581, L452-L581, L453-L581, D454-L581, L455-L581, N456-L581, A457-L581, S458-L581, G459-L581, T460-L581, M461-L581, S462-L581, 1463-L581, Q464-L581, E465-L581, F466-L581, R467-L581, D468-L581, L469-L581, W470-L581, K471-L581, Q472-L581, L473-L581, K474-L581, L475-L581, S476-L581, Q477-L581, K478-L581, V479-L581, F480-L581, H481-L581, K482-L581, Q483-L581, D484-L581, R485-L581, G486-L581, S487-L581, G488-L581, Y489-L581, L490-L581, N491-L581, W492-L581, E493-L581, Q494-L581, L495-L581, H496-L581, A497-L581, A498-L581, M499-L581, R500-L581, E501-L581, A502-L581, G503-L581, R504-L581, H505-L581, R506-L581, K507-L581, S508-L581, W509-L581, S510-L581, C511-L581, G512-L581, H513-L581, T514-L581, R515-L581, A516-L581, G517-L581, C518-L581, T519-L581, L520-L581, 1521-L581, R522-L581, Q523-L581, R524-L581, R525-L581, G526-L581, D527-L581, V528-L581, W529-L581, H530-L581, A531-L581, E532-L581, V533-L581, T534-L581, L535-L581, 1536-L581, R537-L581, S538-L581, V539-L581, T540-L581, L541-L581, K542-L581, D543-L581, V544-L581, D545-L581, L546-L581, Q547-L581, S548-L581, T549-L581, P550-L581, T551-L581, F552-L581, F553-L581, M554-L581, 1555-L581, V556-L581, P557-L581, V558-L581, 1559-L581, L560-L581, A561-L581, N562-L581, 1563-L581, D564-L581, G565-L581, G566-L581, V567-L581, A568-L581, H569-L581, S570-L581, T571-L581, S572-L581, Y573-L581, L574-L581, and/or 1575-L581 of SEQ ID NO:2. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN-12 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein. The invention specifically encompasses the N-terminal deletions from amino acid 1 to amino acid 421 of SEQ ID NO:2.

[0205] In preferred embodiments, the following C-terminal CAN-12 deletion polypeptides are encompassed by the present invention: M1-L581, M1-L580, M1-T579, M1-T578, M1-N577, MI-F576, M1-1575, M1-L574, M1-Y573, M1-S572, M1-T571, M1-S570, M1-H569, M1-A568, M1-V567, M1-G566, M1-G565, M1-D564, M1-1563, M1-N562, MI-A561, M1-L560, M1-1559, M1-V558, M1-P557, M1-V556, M1-1555, M1-M554, M1-F553, M1-F552, M1-T551, M1-P550, M1-T549, M1-S548, M1-Q547, M1-L546, MI-D545, M1-V544, M1-D543, M1-K542, M1-L541, M1-T540, M1-V539, M1-S538, M1-R537, M1-1536, M1-L535, M1-T534, M1-V533, M1-E532, M1-A531, M1-H530, M1-W529, M1-V528, M1-D527, M1-G526, M1-R525, M1-R524, M1-Q523, M1-R522, M1-1521, M1-L520, M1-T519, M1-C518, M1-G517, M1-A516, M1-R515, M1-T514, M1-H513, M1-G512, M1-C511, M1-S510, M1-W509, M1-S508, M1-K507, M1-R506, M1-H505, M1-R504, M1-G503, M1-A502, M1-E501, M1-R500, M1-M499, M1-A498, M1-A497, M1-H496, M1-L495, M1-Q494, M1-E493, M1-W492, M1-N491, M1-L490, M1-Y489, M1-G488, M1-S487, M1-G486, M1-R485, M1-D484, M1-Q483, M1-K482, M1-H481, M1-F480, M1-V479, M1-K478, M1-Q477, M1-S476, M1-L475, M1-K474, M1-I473, M1-Q472, M1-K471, M1-W470, M1-L469, M1-D468, M1-R467, M1-F466, M1-E465, M1-Q464, M1-1463, M1-S462, M1-M461, M1-T460, M1-G459, M1-S458, M1-A457, M1-N456, M1-L455, M1-D454, M1-L453, M1-L452, M1-A451, M1-L450, M1-1449, M1-G448, M1-Q447, M1-C446, M1-A445, M1-E444, M1-L443, M1-S442, M1-F441, M1-F440, M1-P439, M1-Q438, M1-R437, M1-S436, M1-G435, M1-L434, M1-S433, M1-S432, M1-W431, M1-T430, M1-M429, M1-K428, M1-N427, M1-M426, M1-R425, M1-Y424, M1-L423, M1-Y422, M1-F421, M1-G420, M1-1419, M1-A418, M1-L417, M1-L416, M1-P415, M1-K414, M1-R413, M1-K412, M1-R411, M1-C410, M1-R409, M1-H408, M1-R407, M1-P406, M1-K405, M1-Q404, M1-L403, M1-L402, M1-S401, M1-V400, M1-L399, M1-V398, M1-S397, M1-C396, M1-P395, M1-R394, M1-L393, M1-S392, M1-R391, M1-R390, M1-G389, M1-E388, M1-E387, M1-P386, M1-R385, M1-W384, M1-V383, M1-S382, M1-L381, M1-L380, M1-F379, M1-Q378, M1-P377, M1-N376, M1-K375, M1-W374, M1-F373, M1-T372, M1-D371, M1-Q370, M1-L369, M1-L368, M1-Q367, M1-R366, M1-Q365, M1-G364, M1-G363, M1-A362, M1-T361, M1-S360, M1-R359, M1-K358, M1-E357, M1-W356, M1-R355, M1-G354, M1-E353, M1-R352, M1-M351, M1-T350, M1-Y349, M1-T348, M1-W347, M1-K346, M1-Q345, M1-A344, M1-A343, M1-E342, M1-Q341, M1-S340, M1-L339, M1-L338, M1-G337, M1-P336, M1-T335, M1-L334, M1-K333, M1-C332, M1-331, M1-V330, M1-L329, M1-L328, M1-V327, M1-F326, M1-H325, M1-T324, M1-K323, M1-F322, M1-D321, M1-Q320, M1L319, M1-T318, M1-M317, M1-W316, M1-F315, M1-E314, M1-G313, M1-D312, M1-N311, M1-D310, M1-K309, M1-R308, M1-L307, M1-L306, M1-L305, M1-304, M1-K303, M1-E302, M1-K301, M1-P300, M1-S299, M1-L298, M1-L297, M1-E296, M1-W295, M1-K294, M1-S293, M1-S292, M1-S291, M1-D290, M1-S289, M1-W288, M1-D287, M1-G286, M1-K285, M1-W284, M1-E283, M1-V282, M1-K281, M1-G280, M1-W279, M1-P278, M1-N277, M1-R276, M1-L275, M1-K274, M1-V273, M1-L272, M1-Y271, M1-E270, M1-P269, M1-R268, M1-H267, M1-K266, M1-C265, M1-T264, M1-V263, M1-K262, M1-R261, M1-I260, M1-G259, M1-T258, M1-L257, M1-T256, M1-Y255, M1-A254, M1-H253, M1-G252, M1-E251, M1-V250, M1-L249, M1-G248, M1-N247, M1-E246, M1-L245, M1-I244, M1-K243, M1-G242, M1-S241, M1-H240, M1-T239, M1-Q238, M1-C237, M1-G236, M1-1235, M1-L234, M1-T233, M1-R232, M1-N231, M1-Y230, M1-T229, M1-A228, M1-E227, M1-1226, M1-L225, M1-1224, M1-D223, M1-W222, M1-L221, M1-N220, M1-G219, M1-H218, M1-A217, M1-E216, M1-A215, M1-L214, M1-N213, M1-I212, M1-T211, M1-M210, M1-T209, M1-V208, M1-G207, M1-G206, M1-T205, M1-F204, M1-D203, M1-V202, M1-L201, M1-A200, M1-E199, M1-S198, M1-V197, M1-Q196, M1-G195, M1-S194, M1-Q193, M1-L192, M1-D191, M1-E190, M1-Y189, M1-S188, M1-G187, M1-S186, M1-L185, M1-K184, M1-A183, M1-Y182, M1-A181, M1-K180, M1-E179, M1-L178, M1-L177, M1-A176, M1-G175, M1-W174, M1-F173, M1-L172, M1-N171, M1-K170, M1-Y169, M1-T168, M1-S167, M1-S166, M1-V165, M1-F164, M1-V163, M1-L162, M1-Q161, M1-G160, M1-A159, M1-E158, M1-N157, M1-V156, M1-P155, M1-L154, M1-R153, M1-D152, M1-D151, M1-I150, M1-V149, M1-V148, M1-P147, M1-V146, M1-W145, M1-N144, M1-G143, M1-Y142, M1-H141, M1-W140, M1-F139, M1-W138, M1-F137, M1-R136, M1-F135, M1-1134, M1-G133, M1-A132, M1-Y131, M1-K130, M1-E129, M1-T128, M1-F127, M1-S126, M1-Q125, M1-N124, M1-L123, M1-P122, M1-V121, M1-V120, M1-R119, M1-S118, M1-L117, M1-I116, M1-D115, M1-Q114, M1-H113, M1-L112, M1-A111, M1-L111, M1-A109, M1-Q108, M1-L107, M1-A106, M1-A105, M1-L104, M1-F103, M1-W102, M1-C101, M1-D100, M1-G99, M1-V98, M1-197, M1-G96, M1-Q95, M1-C94, M1-L93, M1-D92, M1-L91, M1-R90, M1-K89, M1-A88, M1-K87, M1-A86, M1-F85, M1-Y84, M1-F83, M1-Q82, M1-P81, M1-N80, M1-S79, M1-H78, M1-L77, M1-E76, M1-P75, M1-P74, M1-R73, M1-K72, M1-W71, M1-Q70, M1-L69, M1-R68, M1-P67, M1-P66, M1-L65, M1-K64, M1-Q63, M1-L62, M1-L61, M1-S60, M1-G59, M1-S58, M1-G57, M1-156, M1-S55, M1-S54, M1-L53, M1-T52, M1-A51, M1-P50, M1-F49, M1-S48, M1-T47, M1-D46, M1-E45, M1-F44, M1-L43, M1-C42, M1-G41, M1-N40, M1-R39, M1-L38, M1-C37, M1-E36, M1-A35, M1-L34, M1-L33, M1-A32, M1-E31, M1-F30, M1-D29, M1-Q28, M1-Q27, M1-P26, M1-Q25, M1-Q24, M1-P23, M1-S22, M1-A21, M1-R20, M1-R19, M1-S18, M1-Y17, M1-R16, M1-P15, M1-A14, M1-L13, M1-K12, M1-W11, M1-R10, M1-C9, M1-R8, and/or M1-F7 of SEQ ID NO:2. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein. The invention specifically encompasses the C-terminal deletions from amino acid 428 to amino acid 7 of SEQ ID NO:2.

[0206] Alternatively, preferred polypeptides of the present invention may comprise polypeptide sequences corresponding to, for example, internal regions of the CAN-12 polypeptide (e.g., any combination of both N- and C-terminal CAN-12 polypeptide deletions) of SEQ ID NO:2. For example, internal regions could be defined by the equation: amino acid NX to amino acid CX, wherein NX refers to any N-terminal deletion polypeptide amino acid of CAN-12 (SEQ ID NO:2), and where CX refers to any C-terminal deletion polypeptide amino acid of CAN-12 (SEQ ID NO:2). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0207] The present invention also encompasses immunogenic and/or antigenic epitopes of the CAN-12 polypeptide.

[0208] The CAN-12 polypeptides of the present invention were determined to comprise several phosphorylation sites based upon the Motif algorithm (Genetics Computer Group, Inc.). The phosphorylation of such sites may regulate some biological activity of the CAN-12 polypeptide. For example, phosphorylation at specific sites may be involved in regulating the proteins ability to associate or bind to other molecules (e.g., proteins, ligands, substrates, DNA, etc.). In the present case, phosphorylation may modulate the ability of the CAN-12 polypeptide to associate with other polypeptides, particularly the serine protease substrate for CAN-12, or its ability to modulate serine protease function.

[0209] The CAN-12 polypeptide was predicted to comprise eleven PKC phosphorylation sites using the Motif algorithm (Genetics Computer Group, Inc.). In vivo, protein kinase C exhibits a preference for the phosphorylation of serine or threonine residues. The PKC phosphorylation sites have the following consensus pattern: [ST]-x-[RK], where S or T represents the site of phosphorylation and ‘x’ an intervening amino acid residue. Additional information regarding PKC phosphorylation sites can be found in Woodget J. R., Gould K. L., Hunter T., Eur. J. Biochem. 161:177-184(1986), and Kishimoto A., Nishiyama K., Nakanishi H., Uratsuji Y., Nomura H., Takeyama Y., Nishizuka Y., J. Biol. Chem. . . . 260:12492-12499(1985); which are hereby incorporated by reference herein.

[0210] In preferred embodiments, the following PKC phosphorylation site polypeptides are encompassed by the present invention: LAPRYSRRASPQQ (SEQ ID NO:27), LNQSFTEKYAGIF (SEQ ID NO:28), VFVSSTYKNLFWG (SEQ ID NO:29), GCQTHSGKILENG (SEQ ID NO:30), GIRKVTCKHRPEY (SEQ ID NO:31), DWSDSSSKWELLS (SEQ ID NO:32), KWELLSPKEKILL (SEQ ID NO:33), QKWTYTMREGRWE (SEQ ID NO:34), EEGRRSLRPCSVL (SEQ ID NO:35), KQLKLSQKVFHKQ (SEQ ID NO:36), and/or LIRSVTLKDVDLQ (SEQ ID NO:37). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of the CAN-12 PKC phosphorylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0211] The CAN-12 polypeptide has been shown to comprise four glycosylation site according to the Motif algorithm (Genetics Computer Group, Inc.). As discussed more specifically herein, protein glycosylation is thought to serve a variety of functions including: augmentation of protein folding, inhibition of protein aggregation, regulation of intracellular trafficking to organelles, increasing resistance to proteolysis, modulation of protein antigenicity, and mediation of intercellular adhesion.

[0212] In preferred embodiments, the following asparagine glycosylation site polypeptide is encompassed by the present invention: RVVPLNQSFTEKYA (SEQ ID NO:38), IEATYNRTLIGCQT (SEQ ID NO:39), ALLDLNASGTMSIQ (SEQ ID NO:40), and/or SYLIFNTTLL (SEQ ID NO:41). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12 asparagine glycosylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0213] The CAN-12 polypeptide has been shown to comprise one amidation site according to the Motif algorithm (Genetics Computer Group, Inc.). The precursor of hormones and other active peptides which are C-terminally amidated is always directly followed by a glycine residue which provides the amide group, and most often by at least two consecutive basic residues (Arg or Lys) which generally function as an active peptide precursor cleavage site. Although all amino acids can be amidated, neutral hydrophobic residues such as Val or Phe are good substrates, while charged residues such as Asp or Arg are much less reactive. A consensus pattern for amidation sites is the following: x-G-[RK]-[RK], wherein “X” represents the amidation site. Additional information relating to asparagine glycosylation may be found in reference to the following publications, which are hereby incorporated by reference herein: Kreil G., Meth. Enzymol. 106:218-223(1984); and Bradbury A. F., Smyth D. G., Biosci. Rep. 7:907-916(1987).

[0214] In preferred embodiments, the following amidation site polypeptide is encompassed by the present invention: VWRPEEGRRSLRPC (SEQ ID NO:42). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this CAN-12 amidation site polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0215] The CAN-12 polypeptide has been shown to comprise one RGD cell attachment site domain according to the Motif algorithm (Genetics Computer Group, Inc.). The sequence Arg-Gly-Asp, found in fibronectin, is crucial for its interaction with its cell surface receptor, an integrin. What has been called the ‘RGD’ tripeptide is also found in the sequences of a number of other proteins, where it has been shown to play a role in cell adhesion. Non-limiting examples of these proteins are the following: some forms of collagens, fibrinogen, vitronectin, von Willebrand factor (VWF), snake disintegrins, and slime mold discoidins. The ‘RGD’ tripeptide is also found in other proteins where it may serve the same purpose. A consensus pattern for RGD cell attachment sites is the following: R-G-D. Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Ruoslahti E., Pierschbacher M. D., Cell 44:517-518(1986); and d'Souza S. E., Ginsberg M. H., Plow E. F., Trends Biochem. Sci. 16:246-250(1991).

[0216] In preferred embodiments, the following RGD cell attachment site domain polypeptide is encompassed by the present invention: LIRQRRGDVWHAE (SEQ ID NO:43). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this RGD cell attachment site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0217] In confirmation of the CAN-12 polypeptide being a calpain, it has been shown to comprise one EF-hand calcium-binding domain according to the Motif algorithm (Genetics Computer Group, Inc.). Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Several representative proteins containing EF-hand regions are provided below: For each type of protein, the total number of EF-hand regions known or supposed to exist are provided in parenthesis: Aequorin and Renilla luciferin binding protein (LBP) (Ca=3); Alpha actinin (Ca=2); Calbindin (Ca=4); Calcineurin B subunit (protein phosphatase 2B regulatory subunit) (Ca=4); Calcium-binding protein from Streptomyces erythraeus (Ca=3?); Calcium-binding protein from Schistosoma mansoni (Ca=2?); Calcium-binding proteins TCBP-23 and TCBP-25 from Tetrahymena thermophila (Ca=4?); Calcium-dependent protein kinases (CDPK) from plants (Ca=4); Calcium vector protein from amphoxius (Ca=2); Calcyphosin (thyroid protein p24) (Ca=4?); Calmodulin (Ca=4, except in yeast where Ca=3); Calpain small and large chains (Ca=2); Calretinin (Ca=6); Calcyclin (prolactin receptor associated protein) (Ca=2); Caltractin (centrin) (Ca=2 or 4); Cell Division Control protein 31 (gene CDC31) from yeast (Ca=2?); Diacylglycerol kinase (EC 2.7.1.107) (DGK) (Ca=2); FAD-dependent glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) from mammals (Ca=1); Fimbrin (plastin) (Ca=2); Flagellar calcium-binding protein (1f8) from Trypanosoma cruzi (Ca=1 or 2); Guanylate cyclase activating protein (GCAP) (Ca=3); Inositol phospholipid-specific phospholipase C isozymes gamma-1 and delta-1 (Ca=2) [10]; Intestinal calcium-binding protein (ICaBPs) (Ca=2); MIF related proteins 8 (MRP-8 or CFAG) and 14 (MRP-14) (Ca=2); Myosin regulatory light chains (Ca=1); Oncomodulin (Ca=2); Osteonectin (basement membrane protein BM-40) (SPARC) and proteins that contains an ‘osteonectin’ domain (QR1, matrix glycoprotein SC1) (Ca=1); Parvalbumins alpha and beta (Ca=2); Placental calcium-binding protein (18a2) (nerve growth factor induced protein 42a) (p9k) (Ca=2); Recoverins (visinin, hippocalcin, neurocalcin, S-modulin) (Ca=2 to 3); Reticulocalbin (Ca=4); S-100 protein, alpha and beta chains (Ca=2); Sarcoplasmic calcium-binding protein (SCPs) (Ca=2 to 3); Sea urchin proteins Spec 1 (Ca=4), Spec 2 (Ca=4?), Lps-1 (Ca=8); Serine/threonine protein phosphatase rdgc (EC 3.1.3.16) from Drosophila (Ca=2); Sorcin V19 from hamster (Ca=2); Spectrin alpha chain (Ca=2); Squidulin (optic lobe calcium-binding protein) from squid (Ca=4); and Troponins C; from skeletal muscle (Ca=4), from cardiac muscle (Ca=3), from arthropods and molluscs (Ca=2).

[0218] A consensus pattern for EF hand calcium binding domains is the following:

11 2 3 4 5 6 7 8 9 10 12 13X Y Z -Y -X -ZD-x-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]-x(2)-[DE]-[LIVMFYW],

[0219] wherein X, Y, Z, -Y, -X, and -Z are as defined above, and wherein “x” represents any amino acid. Amino acid residues within the consensus at positions 1 (X), 3 (Y) and 12 (-Z) are the most conserved. The 6th residue in an EF-hand loop is in most cases a Gly.

[0220] Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Kawasaki H., Kretsinger R. H., Protein Prof. 2:305-490(1995); Kretsinger R. H., Cold Spring Harbor Symp. Quant. Biol. 52:499-510(1987); Moncrief N. D., Kretsinger R. H., Goodman M., J. Mol. Evol. 30:522-562(1990); Nakayama S., Moncrief N. D., Kretsinger R. H., J. Mol. Evol. 34:416-448(1992); Heizmann C. W., Hunziker W., Trends Biochem. Sci. 16:98-103(1991); Kligman D., Hilt D. C., Trends Biochem. Sci. 13:437-443(1988); Strynadka N. C. J., James M. N. G., Annu. Rev. Biochem. 58:951-98(1989); Haiech J., Sallantin J., Biochimie 67:555-560(1985); Chauvaux S., Beguin P., Aubert J. -P., Bhat K. M., Gow L. A., Wood T. M., Bairoch A., Biochem. J. 265:261-265(1990); Bairoch A., Cox J. A., FEBS Lett. 269:454-456(1990).

[0221] In preferred embodiments, the following EF-hand calcium binding domain polypeptide is encompassed by the present invention: ILALLDLNASGTMSIQEFRDLWK (SEQ ID NO:44). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this EF-hand calcium binding domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0222] In further confirmation of the CAN-12 polypeptide being a calpain, it has been shown to comprise one eukaryotic thiol (cysteine) protease active site domain according to the Motif algorithm (Genetics Computer Group, Inc.). Eukaryotic thiol proteases (EC 3.4.22.-) are a family of proteolytic enzymes which contain an active site cysteine. Catalysis proceeds through a thioester intermediate and is facilitated by a nearby histidine side chain; an asparagine completes the essential catalytic triad. Non-limiting examples of proteases which are known to belong to this family are provided below: Vertebrate lysosomal cathepsins B (EC 3.4.22.1), H (EC 3.4.22.16), L (EC 3.4.22.15), and S (EC 3.4.22.27); Vertebrate lysosomal dipeptidyl peptidase I (EC 3.4.14.1) (also known as cathepsin C); Vertebrate calpains (EC 3.4.22.17) (Calpains are intracellular calcium-activated thiol protease that contain both a N-terminal catalytic domain and a C-terminal calcium-binding domain; Mammalian cathepsin K, which seems involved in osteoclastic bone resorption; Human cathepsin O; Bleomycin hydrolase (An enzyme that catalyzes the inactivation of the antitumor drug BLM (a glycopeptide); Plant enzymes: barley aleurain (EC 3.4.22.16), EP-B1/B4; kidney bean EP-C1, rice bean SH-EP; kiwi fruit actinidin (EC 3.4.22.14); papaya latex papain (EC 3.4.22.2), chymopapain (EC 3.4.22.6), caricain (EC 3.4.22.30), and proteinase IV (EC 3.4.22.25); pea turgor-responsive protein 15A; pineapple stem bromelain (EC 3.4.22.32); rape COT44; rice oryzain alpha, beta, and gamma; tomato low-temperature induced, Arabidopsis thaliana A494, RD19A and RD21A; House-dust mites allergens DerP1 and EurM1; Cathepsin B-like proteinases from the worms Caenorhabditis elegans (genes gcp-1, cpr-3, cpr-4, cpr-5 and cpr-6), Schistosoma mansoni (antigen SM31) and Japonica (antigen SJ31), Haemonchus contortus (genes AC-1 and AC-2), and Ostertagia ostertagi (CP-1 and CP-3); Slime mold cysteine proteinases CP1 and CP2; Cruzipain from Trypanosoma cruzi and brucei; Throphozoite cysteine proteinase (TCP) from various Plasmodium species; Proteases from Leishmania mexicana, Theileria annulata and Theileria parva; Baculoviruses cathepsin-like enzyme (v-cath); Drosophila small optic lobes protein (gene sol), a neuronal protein that contains a calpain-like domain; Yeast thiol protease BLH1I/YCP1I/LAP3; and Caenorhabditis elegans hypothetical protein CO6G4.2, a calpain-like protein; Two bacterial peptidases are also part of this family—Aminopeptidase C from Lactococcus lactis (gene pepC), and Thiol protease tpr from Porphyromonas gingivalis.

[0223] A consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: Q-x(3)-[GE]-x-C-[YW]-x(2)-[STAGC]-[STAGCV], wherein C is the active site residue, and “x” represents any amino acid. The residue in position 4 of the pattern is almost always cysteine; the only exceptions are calpains (Leu), bleomycin hydrolase (Ser) and yeast YCP1 (Ser); while the residue in position 5 of the pattern is always Gly except in papaya protease IV where it is Glu.

[0224] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [LIVMGSTAN]-x-H-[GSACE]-[LIVM]-x-[LIVMAT](2)-G-x-[GSADNH], wherein H is the active site residue, and “x” represents any amino acid.

[0225] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [FYCH]-[WI]-[LIVT]-x-[KRQAG]-N-[ST]-W-x(3)-[FYW]-G-x(2)-G-[LFYW]-[LIVMFYG]-x-[LIVMF], wherein N is the active site residue, and “x” represents any amino acid.

[0226] Additional information relating to for eukaryotic thiol (cysteine) protease active site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Dufour E., Biochimie 70:1335-1342(1988); Kirschke H., Barrett A. J., Rawlings N. D., Protein Prof. 2:1587-1643(1995); Shi G. -P., Chapman H. A., Bhairi S. M., Deleeuw C., Reddy V. Y., Weiss S. J., FEBS Lett. 357:129-134(1995); Velasco G., Ferrando A. A., Puente X. S., Sanchez L. M., Lopez-Otin C., J. Biol. Chem. . . . 269:27136-27142(1994); Chapot-Chartier M. P., Nardi M., Chopin M. C., Chopin A., Gripon J. C., Appl. Environ. Microbiol. 59:330-333(1993); Higgins D. G., McConnell D. J., Sharp P. M., Nature 340:604-604(1989); Rawlings N. D., Barrett A. J., Meth. Enzymol. 244:461-486(1994), and http://www.expasy.ch/cgi-bin/lists?peptidas.txt, which are hereby incorporated by reference in their entirety herein.

[0227] In preferred embodiments, the following for eukaryotic thiol (cysteine) protease active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALA (SEQ ID NO:45). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this for eukaryotic thiol (cysteine) protease active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0228] The present invention also provides a three-dimensional homology model of the CAN-12 polypeptide (see FIG. 6) representing amino acids 12 to 524 of CAN-12 (SEQ ID NO:2). As referenced herein, SEQ ID NO:2 comprises additoinal amino acids that are not part of the CAN-12 polypeptide sequence but have been added to the sequence for reference to the CAN-12 splice variants referenced herein. The inclusion of the additional amino acids also helps for a more complete homology model. A three-dimensional homology model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995). The homology model of the CAN-12 polypeptide, corresponding to amino acid residues 12 to 524 of SEQ ID NO:2, was based upon the homologous structure of CAN2, a m-calpain family member (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) and is defined by the set of structural coordinates set forth in Table IV herein.

[0229] The CAN-12 homology model of the present invention may provide one basis for designing rational stimulators (agonists) and/or inhibitors (antagonists) of one or more of the biological functions of CAN-12, or of CAN-12 mutants having altered specificity (e.g., molecularly evolved CAN-12 polypeptides, engineered site-specific CAN-12 mutants, CAN-12 allelic variants, etc.).

[0230] Homology models are not only useful for designing rational agonists and/or antagonists, but are also useful in predicting the function of a particular polypeptide. The functional predictions from homology models are typically more accurate than the functional attributes derived from traditional polypeptide sequence homology alignments (e.g., CLUSTALW), particularly when the three dimensional structure of a related polypeptide is known (e.g., m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11). The increased prediction accuracy is based upon the fact that homology models approximate the three-dimensional structure of a protein, while homology based alignments only take into account the one dimension polypeptide sequence. Since the function of a particular polypeptide is determined not only by its primary, secondary, and tertiary structure, functional assignments derived solely upon homology alignments using the one dimensional protein sequence may be less reliable. A 3-dimensional model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995).

[0231] Prior to developing a homology model, those of skill in the art would appreciate that a template of a known protein, or model protein, must first be identified which will be used as a basis for constructing the homology model for the protein of unknown structure (query template). In the case of the CAN-12 polypeptide of the present invention, the model protein template used in constructing the CAN-12 homology model was the m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11).

[0232] Identifying a template can be accomplished using pairwise alignment of protein sequences using such programs as FASTA (Pearson, et al 1990) and BLAST (Altschul, et al, 1990). In cases where sequence similarity is high (greater than 30%), such pairwise comparison methods may be adequate for identifying an appropriate template. Likewise, multiple sequence alignments or profile-based methods can be used to align a query sequence to an alignment of multiple (structurally and biochemically) related proteins. When the sequence similarity is low, more advanced techniques may be used. Such techniques, include, for example, protein fold recognition (protein threading; Hendlich, et al, 1990), where the compatibility of a particular polypeptide sequence with the 3-dimensional fold of a potential template protein is gauged on the basis of a knowledge-based potential.

[0233] Following the initial sequence alignment, the second step would be to optimally align the query template to the model template by manual manipulation and/or by the incorporation of features specific to the polypeptides (e.g., motifs, secondary structure predictions, and allowed conservations). Preferably, the incorporated features are found within both the model and query template.

[0234] The third step would be to identify structurally conserved regions that could be used to construct secondary core structure (SalI, et al, 1995). Loops could be added using knowledge-based techniques, and by performing forcefield calculations (SalI, et al, 1995).

[0235] The term “structure coordinates” refers to Cartesian coordinates generated from the building of a homology model. In this invention, the homology model of residues 12 to 524 of CAN-12 (SEQ ID NO:2) was derived from generating a sequence alignment with m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) using the COMPOSER suite of software within SYBYL6.6 (Tripos Associates, St. Louis, Mo.) and then generating the backbone and side chain conformations. In the original crystal structure (pdb code 1dkv) as well as the crystal structure reported elsewhere (Hosfield et al, 1999), the active site of the enzyme comprising a cysteine, a histidine and an asparagine residue was not “formed”. The helix that contains the active site C101 was altered by moving the helix down one pitch so that the active site geometry could match that found in Papain (pdb code 1b4). This modified structure of human m-calpain was used as the template for construction of the homology model (illustrated in FIG. 6 herein).

[0236] The skilled artisan would appreciate that a set of structure coordinates for a protein represents a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates, as emanate from the generation of similar homology models using different alignment templates (i.e., other than the m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11), and/or using different methods in generating the homology model, will likely have minor effects on the overall shape. Variations in coordinates may also be generated because of mathematical manipulations of the structure coordinates. For example, the structure coordinates set forth in Table IV could be manipulated by fractionalization of the structure coordinates; integer additions, or integer subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above.

[0237] Therefore, various computational analyses are necessary to determine whether a template molecule or a portion thereof is sufficiently similar to all or part of a query template (e.g., CAN-12) in order to be considered the same. Such analyses may be carried out in current software applications, such as SYBYL version 6.6 or INSIGHTII (Molecular Simulations Inc., San Diego, Calif.) version 2000 and as described in the accompanying User's Guides.

[0238] Using the superimposition tool in the program SYBYL, comparisons can be made between different structures and different conformations of the same structure. The procedure used in SYBYL to compare structures is divided into four steps: 1) load the structures to be compared; 2) define the atom equivalencies in these structures; 3) perform a fitting operation; and 4) analyze the results. Each structure is identified by a name. One structure is identified as the target (i.e., the fixed structure); the second structure (i.e., moving structure) is identified as the source structure. The atom equivalency within SYBYL is defined by user input. For the purpose of this invention, we will define equivalent atoms as protein backbone atoms (N, Cα, C and O) for all conserved residues between the two structures being compared. We will also consider only rigid fitting operations. When a rigid fitting method is used, the working structure is translated and rotated to obtain an optimum fit with the target structure. The fitting operation uses an algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atoms is an absolute minimum. This number, given in angstroms, is reported by the SYBYL program. For the purpose of the present invention, any homology model of a CAN-12 that has a root mean square deviation of conserved residue backbone atoms (N, Cα, C, O) of less than 3.0 A when superimposed on the relevant backbone atoms described by structure coordinates listed in Table IV are considered identical. More preferably, the root mean square deviation for the CAN-12 polypeptide is less than 2.0 A.

[0239] The homology model of the present invention is useful for the structure-based design of modulators of the CAN-12 biological function, as well as mutants with altered biological function and/or specificity.

[0240] In accordance with the structural coordinates provided in Table IV and the three dimensional homology model of CAN-12, the CAN-12 polypeptide has been shown to comprise a an active site region embodied by the following amino acids: from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330 of SEQ ID NO:2 or SEQ ID NO:24 (FIGS. 1A-E). In this context, the term “about” may be construed to mean 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids more in either the N- or C-terminal direction of the above referenced amino acids.

[0241] Also more preferred are polypeptides comprising all or any part of the CAN-12 active site domain, or a mutant or homologue of said polypeptide or molecular complex. By mutant or homologue of the molecule is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12 amino acids of not more than about 4.5 Angstroms, and preferably not more than about 3.5 Angstroms.

[0242] In preferred embodiments, the following CAN-12 active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALALHQDILSRVVPLNQSFTEKYAGIFRFWFWH YGNWVPVVIDDRLPVNEAGQLVFVSSTYKNLFWGALLEKAYAKLSGSYEDL QSGQVSEALVDFTGGVTMTINLAEAHGNLWDILIEATYNRTLIGCQTHSGKIL ENGLVEGHAYTLTGIRKVTCKHRPEYLVKLRNPWGKVEWKGDWSDSSSKW ELLSPKEKILLLRKDNDGEFWMTLQDFKTHFVLLV (SEQ ID NO:46). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12 active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0243] The present invention also encompasses polypeptides comprising at least a portion of the CAN-12 active site domain (SEQ ID NO: 46). Such polypeptides may correspond, for example, to the N- and/or C-terminal deletions of the active site domain.

[0244] In preferred embodiments, the following N-terminal CAN-12 active site domain deletion polypeptides are encompassed by the present invention: R1-V241, L2-V241, D3-V241, L4-V241, C5-V241, Q6-V241, G7-V241, 18-V241, V9-V241, G10-V241, D11-V241, C12-V241, W13-V241, F14-V241, L15-V241, A16-V241, A17-V241, L18-V241, Q19-V241, A20-V241, L21-V241, A22-V241, L23-V241, H24-V241, Q25-V241, D26-V241, 127-V241, L28-V241, S29-V241, R30-V241, V31-V241, V32-V241, P33-V241, L34-V241, N35-V241, Q36-V241, S37-V241, F38-V241, T39-V241, E40-V241, K41-V241, Y42-V241, A43-V241, G44-V241, 145-V241, F46-V241, R47-V241, F48-V241, W49-V241, F50-V241, W51-V241, H52-V241, Y53-V241, G54-V241, N55-V241, W56-V241, V57-V241, P58-V241, V59-V241, V60-V241, 161-V241, D62-V241, D63-V241, R64-V241, L65-V241, P66-V241, V67-V241, N68-V241, E69-V241, A70-V241, G71-V241, Q72-V241, L73-V241, V74-V241, F75-V241, V76-V241, S77-V241, S78-V241, T79-V241, Y80-V241, K81-V241, N82-V241, L83-V241, F84-V241, W85-V241, G86-V241, A87-V241, L88-V241, L89-V241, E90-V241, K91-V241, A92-V241, Y93-V241, A94-V241, K95-V241, L96-V241, S97-V241, G98-V241, S99-V241, Y100-V241, E101-V241, D102-V241, L103-V241, Q104-V241, S105-V241, G106-V241, Q107-V241, V108-V241, S109-V241, E110-V241, A111-V241, L112-V241, V113-V241, D114-V241, F115-V241, T116-V241, G117-V241, G118-V241, V119-V241, T120-V241, M121-V241, T122-V241, 1123-V241, N124-V241, L125-V241, A126-V241, E127-V241, A128-V241, H129-V241, G130-V241, N131-V241, L132-V241, W133-V241, D134-V241, 1135-V241, L136-V241, 1137-V241, E138-V241, A139-V241, T140-V241, Y141-V241, N142-V241, R143-V241, T144-V241, L145-V241, 1146-V241, G147-V241, C148-V241, Q149-V241, T150-V241, H151-V241, S152-V241, G153-V241, K154-V241, 1155-V241, L156-V241, E157-V241, N158-V241, G159-V241, L160-V241, V161-V241, E162-V241, 6163-V241, H164-V241, A165-V241, Y166-V241, T167-V241, L168-V241, T169-V241, G170-V241, 1171-V241, R172-V241, K173-V241, V174-V241, T175-V241, C176-V241, K177-V241, H178-V241, R179-V241, P180-V241, E181-V241, Y182-V241, L183-V241, V184-V241, K185-V241, L186-V241, R187-V241, N188-V241, P189-V241, W190-V241, G191-V241, K192-V241, V193-V241, E194-V241, W195-V241, K196-V241, G197-V241, D198-V241, W199-V241, S200-V241, D201-V241, S202-V241, S203-V241, S204-V241, K205-V241, W206-V241, E207-V241, L208-V241, L209-V241, S210-V241, P211-V241, K212-V241, E213-V241, K214-V241, 1215-V241, L216-V241, L217-V241, L218-V241, R219-V241, K220-V241, D221-V241, N222-V241, D223-V241, G224-V241, E225-V241, F226-V241, W227-V241, M228-V241, T229-V241, L230-V241, Q231-V241, D232-V241, F233-V241, K234-V241, and/or T235-V241 of SEQ ID NO:46. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN-12 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0245] In preferred embodiments, the following C-terminal CAN-12 active site domain deletion polypeptides are encompassed by the present invention: R1-V241, R1-L240, R1-L239, R1-V238, R1-F237, R1-H236, R1-T235, R1-K234, R1-F233, R1-D232, R1-Q231, R1-L230, R1-T229, R1-M228, R1-W227, R1-F226, R1-E225, R1-G224, R1-D223, R1-N222, R1-D221, R1-K220, R1-R219, R1-L218, R1-L217, R1-L216, R1-1215, R1-K214, R1-E213, R1-K212, R1-P211, R1-S210, R1-L209, R1-L208, R1-E207, R1-W206, R1-K205, R1-S204, R1-S203, R1-S202, R1-D201, R1-S200, R1-W199, R1-D198, R1-G197, R1-K196, R1-W195, R1-E194, R1-V193, R1-K192, R1-G191, R1-W190, R1-P189, R1-N188, R1-R187, R1-L186, R1-K185, R1-V184, R1-L183, R1-Y182, R1-E181, R1-P180, R1-R179, R1-H178, R1-K177, R1-C176, R1-T175, R1-V174, R1-K173, R1-R172, R1-1171, R1-G170, R1-T169, R1-L168, R1-T167, R1-Y166, R1-A165, R1-H164, R1-G163, R1-E162, R1-V161, R1-L160, R1-G159, R1-N158, R1-E157, R1-L156, R1-I155, R1-K154, R1-G153, R1-S152, R1-H151, R1-T150, R1-Q149, R1-C148, R1-G147, R1-1146, R1-L145, R1-T144, R1-R143, R1-N142, R1-Y141, R1-T140, R1-A139, R1-E138, R1-I137, R1-L136, R1-I135, R1-D134, R1-W133, R1-L132, R1-N131, R1-G130, R1-H129, R1-A128, R1-E127, R1-A126, R1-L125, R1-N124, R1-I123, R1-T122, R1-M121, R1-T120, R1-V119, R1-G118, R1-G117, R1-T116, R1-F115, R1-D114, R1-V113, R1-L112, R1-A111, R1-E110, R1-S109, R1-V108, R1-Q107, R1-G106, R1-S105, R1-Q104, R1-L103, R1-D102, R1-E101, R1-Y100, R1-S99, R1-G98, R1-S97, R1-L96, R1-K95, R1-A94, R1-Y93, R1-A92, R1-K91, R1-E90, R1-L89, R1-L88, R1-A87, R1-G86, R1-W85, R1-F84, R1-L83, R1-N82, R1-K81, R1-Y80, R1-T79, R1-S78, R1-S77, R1-V76, R1-F75, R1-V74, R1-L73, R1-Q72, R1-G71, R1-A70, R1-E69, R1-N68, R1-V67, R1-P66, R1-L65, R1-R64, R1-D63, R1-D62, R1-161, R1-V60, R1-V59, R1-P58, R1-V57, R1-W56, R1-N55, R1-G54, R1-Y53, R1-H52, R1-W51, R1-F50, R1-W49, R1-F48, R1-R47, R1-F46, R1-145, R1-G44, R1-A43, R1-Y42, R1-K41, R1-E40, R1-T39, R1-F38, R1-S37, R1-Q36, R1-N35, R1-L34, R1-P33, R1-V32, R1-V31, R1-R30, R1-S29, R1-L28, R1-127, R1-D26, R1-Q25, R1-H24, R1-L23, R1-A22, R1-L21, R1-A20, R1-Q19, R1-L18, R1-A17, R1-A16, R1-L15, R1-F14, R1-W13, R1-C12, R1-D11, R1-G10, R1-V9, R1-18, and/or R1-G7 of SEQ ID NO:46. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0246] Alternatively, such polypeptides may comprise polypeptide sequences corresponding, for example, to internal regions of the CAN-12 active site domain (e.g., any combination of both N- and C-terminal CAN-12 active site domain deletions) of SEQ ID NO:46. For example, internal regions could be defined by the equation NX to CX, where NX refers to any N-terminal amino acid position of the CAN-12 active site domain (SEQ ID NO:46), and where CX refers to any C-terminal amino acid position of the CAN-12 active site domain (SEQ ID NO:46). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0247] In preferred embodiments, the following CAN-12 active site domain amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L91 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein D92 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L93 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein C94 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q95 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein G96 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein 197 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V98 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein G99 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D100 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C101 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W102 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F103 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L104 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A105 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A106 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L107 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q108 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein A109 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L110 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A111 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L112 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein H113 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q114 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D115 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I116 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L117 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S118 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein R119 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein V120 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V121 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P122 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein L123 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein N124 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein Q125 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S126 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein F127 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T128 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein E129 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K130 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y131 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A132 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G133 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I134 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F135 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R136 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein F137 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W138 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F139 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W140 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein H141 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y142 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein G143 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N144 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein W145 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein V146 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P147 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V148 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V149 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein I150 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D151 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D152 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R153 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L154 is substituted with either an A, C, D, E, F, G, H, 1, K, M, N, P, Q, R, S, T, V, W, or Y; wherein P155 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V156 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein N157 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein E158 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A159 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G160 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q161 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein L162 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V163 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein F164 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V165 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S166 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S167 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein T168 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y169 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein K170 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N171 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L172 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein F173 is substituted with either an A, C, D, E, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W174 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G175 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A176 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L177 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L178 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E179 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K180 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A181 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y182 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A183 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K184 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L185 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S186 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G187 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S188 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein Y189 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein E190 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D191 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L192 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q193 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S194 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G195 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q196 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein V197 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S198 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein E199 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A200 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L201 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V202 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein D203 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F204 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T205 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G206 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G207 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V208 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T209 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein M210 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T211 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein I212 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N213 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L214 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A215 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E216 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A217 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H218 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G219 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N220 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L221 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein W222 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein D223 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I224 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L225 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein I226 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E227 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A228 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T229 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y230 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein N231 is substituted with either an A, C, D, E, F, G, H, 1, K, L, M, P, Q, R, S, T, V, W, or Y; wherein R232 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein T233 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L234 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein 1235 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G236 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C237 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q238 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein T239 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H240 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S241 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G242 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K243 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein 1244 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L245 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E246 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N247 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein G248 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L249 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V250 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E251 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G252 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H253 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A254 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y255 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein T256 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L257 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein T258 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G259 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein 1260 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R261 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K262 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V263 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T264 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein C265 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K266 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H267 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R268 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein P269 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein E270 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y271 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein L272 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V273 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein K274 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L275 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R276 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein N277 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein P278 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein W279 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G280 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K281 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V282 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E283 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W284 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein K285 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G286 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D287 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W288 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein S289 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein D290 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S291 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S292 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S293 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein K294 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W295 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein E296 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L297 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L298 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S299 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein P300 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein K301 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E302 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K303 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein 1304 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L305 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L306 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L307 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R308 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K309 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D310 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N311 is substituted with either an A, C, D, E, F, G, H, 1, K, L, M, P, Q, R, S, T, V, W, or Y; wherein D312 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G313 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E314 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F315 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W316 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein M317 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T318 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L319 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q320 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D321 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F322 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K323 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T324 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H325 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F326 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V327 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein L328 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L329 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; and/or wherein V330 is substituted with either an A, C, D, E, F, G, HI, K, L, M, N, P, Q, R, S, T, W, or Y of SEQ ID NO:2 or SEQ ID NO:24, in addition to any combination thereof. The present invention also encompasses the use of these CAN-12 active site domain amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0248] In preferred embodiments, the following CAN-12 active site domain conservative amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either a K, or H; wherein L91 is substituted with either an A, I, or V; wherein D92 is substituted with an E; wherein L93 is substituted with either an A, I, or V; wherein C94 is a C; wherein Q95 is substituted with a N; wherein G96 is substituted with either an A, M, S, or T; wherein 197 is substituted with either an A, V, or L; wherein V98 is substituted with either an A, I, or L; wherein G99 is substituted with either an A, M, S, or T; wherein D10O is substituted with an E; wherein C101 is a C; wherein W102 is either an F, or Y; wherein F103 is substituted with either a W, or Y; wherein L104 is substituted with either an A, I, or V; wherein A105 is substituted with either a G, I, L, M, S, T, or V; wherein A106 is substituted with either a G, I, L, M, S, T, or V; wherein L107 is substituted with either an A, I, or V; wherein Q108 is substituted with a N; wherein A109 is substituted with either a G, I, L, M, S, T, or V; wherein L110 is substituted with either an A, I, or V; wherein A111 is substituted with either a G, I, L, M, S, T, or V; wherein L112 is substituted with either an A, I, or V; wherein H113 is substituted with either a K, or R; wherein Q114 is substituted with a N; wherein D115 is substituted with an E; wherein I116 is substituted with either an A, V, or L; wherein L117 is substituted with either an A, I, or V; wherein S118 is substituted with either an A, G, M, or T; wherein R119 is substituted with either a K, or H; wherein V120 is substituted with either an A, I, or L; wherein V121 is substituted with either an A, I, or L; wherein P122 is a P; wherein L123 is substituted with either an A, I, or V; wherein N124 is substituted with a Q; wherein Q125 is substituted with a N; wherein S126 is substituted with either an A, G, M, or T; wherein F127 is substituted with either a W, or Y; wherein T128 is substituted with either an A, G, M, or S; wherein E129 is substituted with a D; wherein K130 is substituted with either a R, or H; wherein Y131 is either an F, or W; wherein A132 is substituted with either a G, I, L, M, S, T, or V; wherein G133 is substituted with either an A, M, S, or T; wherein I134 is substituted with either an A, V, or L; wherein F135 is substituted with either a W, or Y; wherein R136 is substituted with either a K, or H; wherein F137 is substituted with either a W, or Y; wherein W138 is either an F, or Y; wherein F139 is substituted with either a W, or Y; wherein W140 is either an F, or Y; wherein H141 is substituted with either a K, or R; wherein Y142 is either an F, or W; wherein G143 is substituted with either an A, M, S, or T; wherein N144 is substituted with a Q; wherein W145 is either an F, or Y; wherein V146 is substituted with either an A, I, or L; wherein P147 is a P; wherein V148 is substituted with either an A, I, or L; wherein V149 is substituted with either an A, I, or L; wherein 1150 is substituted with either an A, V, or L; wherein D151 is substituted with an E; wherein D152 is substituted with an E; wherein R153 is substituted with either a K, or H; wherein L154 is substituted with either an A, I, or V; wherein P155 is a P; wherein V156 is substituted with either an A, I, or L; wherein N157 is substituted with a Q; wherein E158 is substituted with a D; wherein A159 is substituted with either a G, I, L, M, S, T, or V; wherein G160 is substituted with either an A, M, S, or T; wherein Q161 is substituted with a N; wherein L162 is substituted with either an A, I, or V; wherein V163 is substituted with either an A, I, or L; wherein F164 is substituted with either a W, or Y; wherein V165 is substituted with either an A, I, or L; wherein S166 is substituted with either an A, G, M, or T; wherein S167 is substituted with either an A, G, M, or T; wherein T168 is substituted with either an A, G, M, or S; wherein Y169 is either an F, or W; wherein K170 is substituted with either a R, or H; wherein N171 is substituted with a Q; wherein L172 is substituted with either an A, I, or V; wherein F173 is substituted with either a W, or Y; wherein W174 is either an F, or Y; wherein G175 is substituted with either an A, M, S, or T; wherein A176 is substituted with either a G, I, L, M, S, T, or V; wherein L177 is substituted with either an A, I, or V; wherein L178 is substituted with either an A, I, or V; wherein E179 is substituted with a D; wherein K180 is substituted with either a R, or H; wherein A181 is substituted with either a G, I, L, M, S, T, or V; wherein Y182 is either an F, or W; wherein A183 is substituted with either a G, I, L, M, S, T, or V; wherein K184 is substituted with either a R, or H; wherein L185 is substituted with either an A, I, or V; wherein S186 is substituted with either an A, G, M, or T; wherein G187 is substituted with either an A, M, S, or T; wherein S188 is substituted with either an A, G, M, or T; wherein Y189 is either an F, or W; wherein E190 is substituted with a D; wherein D191 is substituted with an E; wherein L192 is substituted with either an A, I, or V; wherein Q193 is substituted with a N; wherein S194 is substituted with either an A, G, M, or T; wherein G195 is substituted with either an A, M, S, or T; wherein Q196 is substituted with a N; wherein V197 is substituted with either an A, I, or L; wherein S198 is substituted with either an A, G, M, or T; wherein E199 is substituted with a D; wherein A200 is substituted with either a G, I, L, M, S, T, or V; wherein L201 is substituted with either an A, I, or V; wherein V202 is substituted with either an A, I, or L; wherein D203 is substituted with an E; wherein F204 is substituted with either a W, or Y; wherein T205 is substituted with either an A, G, M, or S; wherein G206 is substituted with either an A, M, S, or T; wherein G207 is substituted with either an A, M, S, or T; wherein V208 is substituted with either an A, I, or L; wherein T209 is substituted with either an A, G, M, or S; wherein M210 is substituted with either an A, G, S, or T; wherein T211 is substituted with either an A, G, M, or S; wherein 1212 is substituted with either an A, V, or L; wherein N213 is substituted with a Q; wherein L214 is substituted with either an A, I, or V; wherein A215 is substituted with either a G, I, L, M, S, T, or V; wherein E216 is substituted with a D; wherein A217 is substituted with either a G, I, L, M, S, T, or V; wherein H218 is substituted with either a K, or R; wherein G219 is substituted with either an A, M, S, or T; wherein N220 is substituted with a Q; wherein L221 is substituted with either an A, I, or V; wherein W222 is either an F, or Y; wherein D223 is substituted with an E; wherein I224 is substituted with either an A, V, or L; wherein L225 is substituted with either an A, I, or V; wherein 1226 is substituted with either an A, V, or L; wherein E227 is substituted with a D; wherein A228 is substituted with either a G, I, L, M, S, T, or V; wherein T229 is substituted with either an A, G, M, or S; wherein Y230 is either an F, or W; wherein N231 is substituted with a Q; wherein R232 is substituted with either a K, or H; wherein T233 is substituted with either an A, G, M, or S; wherein L234 is substituted with either an A, I, or V; wherein I235 is substituted with either an A, V, or L; wherein G236 is substituted with either an A, M, S, or T; wherein C237 is a C; wherein Q238 is substituted with a N; wherein T239 is substituted with either an A, G, M, or S; wherein H240 is substituted with either a K, or R; wherein S241 is substituted with either an A, G, M, or T; wherein G242 is substituted with either an A, M, S, or T; wherein K243 is substituted with either a R, or H; wherein I244 is substituted with either an A, V, or L; wherein L245 is substituted with either an A, I, or V; wherein E246 is substituted with a D; wherein N247 is substituted with a Q; wherein G248 is substituted with either an A, M, S, or T; wherein L249 is substituted with either an A, I, or V; wherein V250 is substituted with either an A, I, or L; wherein E251 is substituted with a D; wherein G252 is substituted with either an A, M, S, or T; wherein H253 is substituted with either a K, or R; wherein A254 is substituted with either a G, I, L, M, S, T, or V; wherein Y255 is either an F, or W; wherein T256 is substituted with either an A, G, M, or S; wherein L257 is substituted with either an A, I, or V; wherein T258 is substituted with either an A, G, M, or S; wherein G259 is substituted with either an A, M, S, or T; wherein I260 is substituted with either an A, V, or L; wherein R261 is substituted with either a K, or H; wherein K262 is substituted with either a R, or H; wherein V263 is substituted with either an A, I, or L; wherein T264 is substituted with either an A, G, M, or S; wherein C265 is a C; wherein K266 is substituted with either a R, or H; wherein H267 is substituted with either a K, or R; wherein R268 is substituted with either a K, or H; wherein P269 is a P; wherein E270 is substituted with a D; wherein Y271 is either an F, or W; wherein L272 is substituted with either an A, I, or V; wherein V273 is substituted with either an A, I, or L; wherein K274 is substituted with either a R, or H; wherein L275 is substituted with either an A, I, or V; wherein R276 is substituted with either a K, or H; wherein N277 is substituted with a Q; wherein P278 is a P; wherein W279 is either an F, or Y; wherein G280 is substituted with either an A, M, S, or T; wherein K281 is substituted with either a R, or H; wherein V282 is substituted with either an A, I, or L; wherein E283 is substituted with a D; wherein W284 is either an F, or Y; wherein K285 is substituted with either a R, or H; wherein G286 is substituted with either an A, M, S, or T; wherein D287 is substituted with an E; wherein W288 is either an F, or Y; wherein S289 is substituted with either an A, G, M, or T; wherein D290 is substituted with an E; wherein S291 is substituted with either an A, G, M, or T; wherein S292 is substituted with either an A, G, M, or T; wherein S293 is substituted with either an A, G, M, or T; wherein K294 is substituted with either a R, or H; wherein W295 is either an F, or Y; wherein E296 is substituted with a D; wherein L297 is substituted with either an A, I, or V; wherein L298 is substituted with either an A, I, or V; wherein S299 is substituted with either an A, G, M, or T; wherein P300 is a P; wherein K301 is substituted with either a R, or H; wherein E302 is substituted with a D; wherein K303 is substituted with either a R, or H; wherein 1304 is substituted with either an A, V, or L; wherein L305 is substituted with either an A, I, or V; wherein L306 is substituted with either an A, I, or V; wherein L307 is substituted with either an A, I, or V; wherein R308 is substituted with either a K, or H; wherein K309 is substituted with either a R, or H; wherein D310 is substituted with an E; wherein N311 is substituted with a Q; wherein D312 is substituted with an E; wherein G313 is substituted with either an A, M, S, or T; wherein E314 is substituted with a D; wherein F315 is substituted with either a W, or Y; wherein W316 is either an F, or Y; wherein M317 is substituted with either an A, G, S, or T; wherein T318 is substituted with either an A, G, M, or S; wherein L319 is substituted with either an A, I, or V; wherein Q320 is substituted with a N; wherein D321 is substituted with an E; wherein F322 is substituted with either a W, or Y; wherein K323 is substituted with either a R, or H; wherein T324 is substituted with either an A, G, M, or S; wherein H325 is substituted with either a K, or R; wherein F326 is substituted with either a W, or Y; wherein V327 is substituted with either an A, I, or L; wherein L328 is substituted with either an A, I, or V; wherein L329 is substituted with either an A, I, or V; and/or wherein V330 is substituted with either an A, I, or L of SEQ ID NO:2 or SEQ ID NO:24 in addition to any combination thereof. Other suitable substitutions within the CAN-12 active site domain are encompassed by the present invention and are referenced elsewhere herein. The present invention also encompasses the use of these CAN-12 active site domain conservative amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0249] For purposes of the present invention, by “at least a portion of” is meant all or any part of the CAN-12 active site domain defined by the structure coordinates according to Table IV (e.g., fragments thereof). More preferred are molecules comprising all or any parts of the CAN-12 active site domain, according to Table IV, or a mutant or homologue of said molecule or molecular complex. By mutant or homologue of the molecule it is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12 amino acids of not more than 4.5 Angstroms, and preferably not more than 3.5 Angstroms.

[0250] The term “root mean square deviation” means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a term that expresses the deviation or variation from a trend or object. For the purposes of the present invention, the “root mean square deviation” defines the variation in the backbone of a protein from the relevant portion of the backbone of the AR portion of the complex as defined by the structure coordinates described herein.

[0251] A preferred embodiment is a machine-readable data storage medium that is capable of displaying a graphical three-dimensional representation of a molecule or molecular complex that is defined by the structure coordinates of all of the amino acids in Table IV +/−a root mean square deviation from the backbone atoms of those amino acids of not more than 4.0 ANG, preferably 3.0 ANG.

[0252] The structure coordinates of a CAN-12 homology model, including portions thereof, is stored in a machine-readable storage medium. Such data may be used for a variety of purposes, such as drug discovery.

[0253] Accordingly, in one embodiment of this invention is provided a machine-readable data storage medium comprising a data storage material encoded with the structure coordinates set forth in Table IV.

[0254] One embodiment utilizes System 10 as disclosed in WO 98/11134, the disclosure of which is incorporated herein by reference in its entirety. Briefly, one version of these embodiments comprises a computer comprising a central processing unit (“CPU”), a working memory which may be, e.g, RAM (random-access memory) or “core” memory, mass storage memory (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals, one or more keyboards, one or more input lines, and one or more output lines, all of which are interconnected by a conventional bidirectional system bus.

[0255] Input hardware, coupled to the computer by input lines, may be implemented in a variety of ways. Machine-readable data of this invention may be inputted via the use of a modem or modems connected by a telephone line or dedicated data line. Alternatively or additionally, the input hardware may comprise CD-ROM drives or disk drives. In conjunction with a display terminal, keyboard may also be used as an input device.

[0256] Output hardware, coupled to the computer by output lines, may similarly be implemented by conventional devices. By way of example, output hardware may include a CRT display terminal for displaying a graphical representation of a region or domain of the present invention using a program such as QUANTA as described herein. Output hardware might also include a printer, so that hard copy output may be produced, or a disk drive, to store system output for later use.

[0257] In operation, the CPU coordinates the use of the various input and output devices, coordinates data accesses from mass storage, and accesses to and from the working memory, and determines the sequence of data processing steps. A number of programs may be used to process the machine-readable data of this invention. Such programs are discussed in reference to the computational methods of drug discovery as described herein. Specific references to components of the hardware system are included as appropriate throughout the following description of the data storage medium.

[0258] For the purpose of the present invention, any magnetic data storage medium which can be encoded with machine-readable data would be sufficient for carrying out the storage requirements of the system. The medium could be a conventional floppy diskette or hard disk, having a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, on one or both sides, containing magnetic domains whose polarity or orientation could be altered magnetically, for example. The medium may also have an opening for receiving the spindle of a disk drive or other data storage device.

[0259] The magnetic domains of the coating of a medium may be polarized or oriented so as to encode in a manner which may be conventional, machine readable data such as that described herein, for execution by a system such as the system described herein.

[0260] Another example of a suitable storage medium which could also be encoded with such machine-readable data, or set of instructions, which could be carried out by a system such as the system described herein, could be an optically-readable data storage medium. The medium could be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk which is optically readable and magneto-optically writable. The medium preferably has a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, usually of one side of substrate.

[0261] In the case of a CD-ROM, as is well known, the coating is reflective and is impressed with a plurality of pits to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of the coating. A protective coating, which preferably is substantially transparent, is provided on top of the reflective coating.

[0262] In the case of a magneto-optical disk, as is well known, the coating has no pits, but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser. The orientation of the domains can be read by measuring the polarization of laser light reflected from the coating. The arrangement of the domains encodes the data as described above.

[0263] Thus, in accordance with the present invention, data capable of displaying the three dimensional structure of the CAN-12 homology model, or portions thereof and their structurally similar homologues is stored in a machine-readable storage medium, which is capable of displaying a graphical three-dimensional representation of the structure. Such data may be used for a variety of purposes, such as drug discovery.

[0264] For the first time, the present invention permits the use of structure-based or rational drug design techniques to design, select, and synthesize chemical entities that are capable of modulating the biological function of CAN-12.

[0265] Accordingly, the present invention is also directed to the design of small molecules which imitates the structure of the CAN-12 active site domain (SEQ ID NO:46), or a portion thereof, in accordance with the structure coordinates provided in Table IV. Alternatively, the present invention is directed to the design of small molecules which may bind to at least part of the CAN-12 active site domain (SEQ ID NO:25), or some portion thereof. For purposes of this invention, by CAN-12 active site domain, it is also meant to include mutants or homologues thereof. In a preferred embodiment, the mutants or homologues have at least 25% identity, more preferably 50% identity, more preferably 75% identity, and most preferably 90% identity to SEQ ID NO:46. In this context, the term “small molecule” may be construed to mean any molecule described known in the art or described elsewhere herein, though may include, for example, peptides, chemicals, carbohydrates, nucleic acids, PNAs, and any derivatives thereof.

[0266] The three-dimensional model structure of the CAN-12 will also provide methods for identifying modulators of biological function. Various methods or combination thereof can be used to identify these compounds.

[0267] For example, test compounds can be modeled that fit spatially into the active site domain in CAN-12 embodied by the sequence from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330, or some portion thereof, of SEQ ID NO:2 or SEQ ID NO:24 (corresponding to SEQ ID NO:46), in accordance with the structural coordinates of Table IV.

[0268] Structure coordinates of the active site domain in CAN-12 defined by the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330 of SEQ ID NO:2 or SEQ ID NO:24, can also be used to identify structural and chemical features. Identified structural or chemical features can then be employed to design or select compounds as potential CAN-12 modulators. By structural and chemical features it is meant to include, but is not limited to, van der Waals interactions, hydrogen bonding interactions, charge interaction, hydrophobic bonding interaction, and dipole interaction. Alternatively, or in conjunction with, the three-dimensional structural model can be employed to design or select compounds as potential CAN-12 modulators. Compounds identified as potential CAN-12 modulators can then be synthesized and screened in an assay characterized by binding of a test compound to the CAN-12, or in characterizing the ability of CAN-12 to modulate a protease target in the presence of a small molecule. Examples of assays useful in screening of potential CAN-12 modulators include, but are not limited to, screening in silico, in vitro assays and high throughput assays. Finally, these methods may also involve modifying or replacing one or more amino acids at amino acid positions, C101, H253, and/or N277 of SEQ ID NO:2 or SEQ ID NO:24 in accordance with the structure coordinates of Table IV.

[0269] However, as will be understood by those of skill in the art upon this disclosure, other structure based design methods can be used. Various computational structure based design methods have been disclosed in the art.

[0270] For example, a number computer modeling systems are available in which the sequence of the CAN-12 and the CAN-12 structure (i.e., atomic coordinates of CAN-12 and/or the atomic coordinates of the active site domain as provided in Table IV) can be input. This computer system then generates the structural details of one or more these regions in which a potential CAN-12 modulator binds so that complementary structural details of the potential modulators can be determined. Design in these modeling systems is generally based upon the compound being capable of physically and structurally associating with CAN-12. In addition, the compound must be able to assume a conformation that allows it to associate with CAN-12. Some modeling systems estimate the potential inhibitory or binding effect of a potential CAN-12 modulator prior to actual synthesis and testing.

[0271] Methods for screening chemical entities or fragments for their ability to associate with a given protein target are also well known. Often these methods begin by visual inspection of the binding site on the computer screen. Selected fragments or chemical entities are then positioned in the active site domain of CAN-12. Docking is accomplished using software such as INSIGHTII, QUANTA and SYBYL, following by energy minimization and molecular dynamics with standard molecular mechanic forcefields such as CHARMM and AMBER. Examples of computer programs which assist in the selection of chemical fragment or chemical entities useful in the present invention include, but are not limited to, GRID (Goodford, 1985), AUTODOCK (Goodsell, 1990), and DOCK (Kuntz et al. 1982).

[0272] Upon selection of preferred chemical entities or fragments, their relationship to each other and CAN-12 can be visualized and then assembled into a single potential modulator. Programs useful in assembling the individual chemical entities include, but are not limited to CAVEAT (Bartlett et al. 1989) and 3D Database systems (Martin1992).

[0273] Alternatively, compounds may be designed de novo using either an empty active site or optionally including some portion of a known inhibitor. Methods of this type of design include, but are not limited to LUDI (Bohm 1992) and LeapFrog (Tripos Associates, St. Louis Mo.).

[0274] In addition, CAN-12 is overall well suited to modern methods including combinatorial chemistry.

[0275] Programs such as DOCK (Kuntz et al. 1982) can be used with the atomic coordinates from the homology model to identify potential ligands from databases or virtual databases which potentially bind CAN-12 active site domain, and which may therefore be suitable candidates for synthesis and testing.

[0276] Additionally, the three-dimensional homology model of CAN-12 will aid in the design of mutants with altered biological activity.

[0277] The following are encompassed by the present invention: a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12 according to Table IV or a homologue of said model, wherein said homologue comprises backbone atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; and a machine-readable data storage medium, wherein said molecule is defined by the set of structure coordinates of the model for CAN-12 according to Table IV, or a homologue of said molecule, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; a model comprising all or any part of the model defined by structure coordinates of CAN-12 according to Table IV, or a mutant or homologue of said molecule or molecular complex.

[0278] In a further embodiment, the following are encompassed by the present invention: a method for identifying a mutant of CAN-12 with altered biological properties, function, or reactivity, the method comprising any combination of steps of: use of the model or a homologue of said model according to Table IV, for the design of protein mutants with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein; and use of the model or a homologue of said model, for the design of a protein with mutations in the active site domain comprised of the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330 of SEQ ID NO:2 or SEQ ID NO:24 according to Table IV with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein.

[0279] In further preferred embodiments, the following are encompassed by the present invention: a method for identifying modulators of CAN-12 biological properties, function, or reactivity, the method comprising any combination of steps of: modeling test compounds that overlay spatially into the active site domain defined by all or any portion of residues from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E251 to about amino acid Y255, from about amino acid N277 to about amino acid K281, from about amino acid V327 to about amino acid V330 of SEQ ID NO:2 or SEQ ID NO:24 and of the three-dimensional structural model according to Table IV, or using a homologue or portion thereof.

[0280] The present invention encompasses using the structure coordinates as set forth herein to identify structural and chemical features of the CAN-12 polypeptide; employing identified structural or chemical features to design or select compounds as potential CAN-12 modulators; employing the three-dimensional structural model to design or select compounds as potential CAN-12 modulators; synthesizing the potential CAN-12 modulators; screening the potential CAN-12 modulators in an assay characterized by binding of a protein to the CAN-12; selecting the potential CAN-12 modulator from a database; designing the CAN-12 modulator de novo; and/or designing said CAN-12 modulator from a known modulator activity.

[0281] Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO: 1 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides consisting of a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 4570 of SEQ ID NO:1, b is an integer between 15 to 4584, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:1, and where b is greater than or equal to a+14.

[0282] In one embodiment, a CAN12 polypeptide comprises a portion of the amino sequence depicted in FIGS. 1A-E. In another embodiment, a CAN12 polypeptide comprises at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids of the amino sequence depicted in FIGS. 1A-E. In further embodiments, the CAN12 polypeptide does not consist of the sequence ALLEKAYAKL (SEQ ID NO:141), and/or ALLEKAYAKLSGSYE. (SEQ ID NO:142).

[0283] Features of the Polypeptide Encoded by Gene No:2

[0284] The polypeptide of this gene provided as SEQ ID NO:54 (FIGS. 8A-C), encoded by the polynucleotide sequence according to SEQ ID NO:53 (FIGS. 8A-C), and/or encoded by the polynucleotide contained within the deposited clone, CAN-12v1, has significant homology at the nucleotide and amino acid level to a number of calpains, which include, for example, the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE ) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). An alignment of the CAN-12v1 polypeptide with these proteins is provided in FIGS. 2A-E. Based upon such strong conservation, the inventors have ascribed the CAN-12v1 polypeptide as having proteolytic activity, preferably calpain activity.

[0285] The CAN-12v1 polypeptide was determined to have 28.7% identity and 35.6% similarity with the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); to have 33.3% identity and 45.1% similarity with the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); to have 38.3% identity and 46.8% similarity with the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); to have 40.4% identity and 49.1% similarity with the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); to have 39.8% identity and 47.8% similarity with the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE ) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); to have 40.6% identity and 48.8% similarity with the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); to have 36.3% identity and 44.9% similarity with the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); to have 38.8% identity and 47.4% similarity with the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); to have 37.9% identity and 47.6% similarity with the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and to have 40.7% identity and 49.8% similarity with the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12).

[0286] The human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3)is a human calpain gene that encodes a large calpain subunit. CAN10 is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. CAN10 is similar in organization to calpains 5 and 6 and is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM) and located within the NIDDM1 chromosomal region (Nat. Genet. 26 (2), 163-175 (2000)).

[0287] The large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6) is a muscle-specific member of the calpain large subunit family. Loss of CAPN3 function has been associated with limb-girdle muscular dystrophies type 2A (Cell 81 (1), 27-40 (1995)).

[0288] The human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is a calpain that is expressed predominantly in stomach and small intestine and is thought to have specialized functions in the digestive tract, and be associated with gastric cancer.(Biol. Chem. 379 (2), 175-183 (1998); and Jpn. J. Cancer Res. 91 (5), 459-463 (2000)).

[0289] As described above, the CAN-12v1 polypeptide was found to have significant sequence homology with calpains, particularly members of the m-calpain family. A conserved peptide signature of Qx3(G,E)xC(Y,W)x2(S,T,A,G,C)(S,T,A,G,C,V) Qx{3}(G)xC(W)x{2}(A)(A) (referred to as a thiol (cysteine) protease active site domain) common to most calpain family members is found in the protein sequence of CAN-12v1 from amino acid 90 to amino acid 111 of SEQ ID NO:54 (FIGS. 1A-C). Protein threading and molecular modeling of CAN-12v1 suggests that CAN-12v1 has a structural fold similar to representative m-calpains. Moreover, the structural and threading alignments of the present invention suggest that amino acids 101 (“C”), 254 (“H”), and 278 (“N”) of SEQ ID NO:54 (FIGS. 8A-C) may represent the catalytic amino acids within the active site domain. Thus, based upon the sequence and structural homology to known calpains, particularly the presence of the thiol cysteine protease active site domain, the novel CAN-12v1 is believed to represent a novel human calpain.

[0290] In confirmation of the strong homology to known calpains, the CAN-12v1 polypeptide was determined to have several conserved catalytic amino acids at amino acid C101, H254, and N278 of SEQ ID NO:54 (FIGS. 8A-C). As discussed more particularly herein, calpains are a group of structurally diverse, high molecular weight (400 to 500 amino acids) proteins that have a catalytic cysteine amino acid and one or more calcium binding domains. Despite the structural heterogeneity, calpains share some well defined structural-functional characteristics, particularly in their active site domains.

[0291] In preferred embodiments, the CAN-12v1 polypeptide of the present invention is directed to a polypeptide having structural similarity to calpains.

[0292] Based upon the strong homology to members of the calpain family, the CAN-12v1 polypeptide is expected to share at least some biological activity with calpains, preferably with m-calpain family members, and more preferable to the large subunits of m-calpain family members, in addition to other calpains and calpain subunits referenced herein and/or otherwise known in the art.

[0293] Expression profiling designed to measure the steady state mRNA levels encoding the CAN-12 polypeptide showed predominately high expression levels in spinal cord tissue; significantly high expression in lymph node and thymus, and to a lesser extent, in spleen tissue (See FIG. 4).

[0294] Expanded analysis of CAN-12 expression levels by TaqMan™ quantitative PCR (see FIG. 6) confirmed that the CAN-12 polypeptide is expressed in the lymph gland. However, the TaqMan™ quantitative PCR determined that the CAN-12 polypeptide is primarily expressed in the eosophagus. In fact, with the exception of the lymph gland, the steady state mRNA level of CAN-12 was approximately 2700 times higher in the esophagus than in all other tissues tested. These data suggest modulators of the CAN-12 polynucleotides and polypeptides may be useful for the treatment, detection, and/or amelioration of the following, non-limiting diseases and disorders associated with the eosphagus: dysphagia, cricoharyngeal incoordination, esophageal carcinoma, esophageal webs, achalasia, symptomatic diffuse esophageal spasm, gastroesophageal reflux, and/or corrosive esophagitis.

[0295] The polynucleotides encoding the CAN-12 polypeptide of the present invention were used to determine the chromosomal localization of the calpain12 gene. Polynuclelotides corresponding to CAN-12 (SEQ ID NO:1) were shown to localize to chromosome 2, specifically 2p16-p21. The comparison of the chromosomal location of the calpain12 gene with the location of chromosomal regions which have been shown to be associated with specific diseases or conditions, e.g. by linkage analysis, can be indicative of diseases in which calpain12 may play a role. Interestingly, a whole-genome linkage scan in multiple sclerosis families (Ebers et al. A full genome search in multiple sclerosis. Nature Genet. 13: 472-476, 1996.) identified 5 susceptibility loci on chromosomes 2, 3, 5, 11, and X. In particular, an association was identified with marker D2S119 on chromosome 2 and MS. The localization of the D2S119 marker was further delimeated to 2p 16-p21 based on a radiation hybrid linkage map retrieved from an online query at NCBI web site: http:/www.ncbi.nlm.nih.gov/genome/sts/. Since the map of calpain 12 and the susceptibility marker D2S119 overlaps, it is reasonable to postulate that calpain 12 may contribute to MS. Furthermore, the transcription profile of calpain12 indicated a prominent expression in spinal cord, and implication of calpains in MS has been suggested (Shields DC et al. A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc Natl Acad Sci U S A. 96:11486-91.1999).

[0296] The CAN-12v1 polynucleotides and polypeptides of the present invention, including agonists and/or fragments thereof, have uses that include modulating cellular adhesion events, cellular proliferation, and inflammation, in various cells, tissues, and organisms, and particularly in mammalian spinal cord tissue, lymph node, thymus, and spleen tissue, preferably human tissue. CAN-12v1 polynucleotides and polypeptides of the present invention, including agonists and/or fragments thereof, may be useful in diagnosing, treating, prognosing, and/or preventing neural, immune, hematopoietic, and/or proliferative diseases or disorders.

[0297] The strong homology to human calpains, particularly m-calpains, combined with the predominate localized expression in esophagus tissue suggests the CAN-12v1 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing gastrointestinal diseases, particularly esophageal diseases and/or disorders which include the following non-limiting examples: aberrant transport of food bolus from the mouth to the stomach, aberrant prevention of retrograde flow of gastrointestinal contents, aberrant esophageal peristaltic contractions, pyrosis, painful swallowing, reflux esophagitis, esophageal motility disorders, esophageal spasms, diffuse esophageal spasm, atypical chest pain, regurgitation, oropharyngeal paralysis, nasal regurgitation, dysphagia, cricopharyngeal bar, globus pharyngeus, achalasia, motor disorders of the esophageal smooth muscle, scleroderma esophagus, gastroesophageal reflux disease (GERD), esophagitis, Barrett's esophagus, viral esophagitis, Herpes simplex virus mediated viral esophagitis, Varicella-zoster virus mediated viral esophagitis, Cytomegalovirus mediated viral esophagitis, bacterial esophagitis, Lactobacillus mediated bacterial esophagitis, Candida mediated esophagitis, radiation esophagitis, corrosive esophagitis, pill-induced esophagitis, esophagitis associated with mucocutaneous and systemic diseases, diverticula, lower esophageal mucosal ring, lower esophageal muscular ring, hiatal hernia, paraesophageal hernia, esophageal rupture, and/or Mallory-Weiss Syndrome.

[0298] Although calpains are typically associated primarily with neurogenerative conditions, their association in gastrointenstinal tissues has precedence. For example, the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is predominately expressed in the stomach and small intestine and is thought to be associated with gastric cancers.

[0299] The strong homology to human calpains, particularly m-calpains, combined with the localized expression in spinal cord tissue suggests the CAN-12v1 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing neural diseases, neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the “Neurological Diseases”, “Regeneration” and “Hyperproliferative Disorders” sections below, in the Examples, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0300] Alternatively, the strong homology to human calpains, particularly m-calpains, combined with the localized expression in lymph node, thymus, and spleen tissue suggests the CAN-12v1 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, ameliorating, and/or preventing immune diseases and/or disorders. Representative uses are described in the “Immune Activity” and “Infectious Disease” sections below, and elsewhere herein. Briefly, the strong expression in immune tissue indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. The CAN-12v1 polypeptide may also be useful as a preventative agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lense tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren's disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product may be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types.

[0301] Moreover, the protein would be useful in the detection, treatment, and/or prevention of a variety of vascular disorders and conditions, which include, but are not limited to miscrovascular disease, vascular leak syndrome, aneurysm, stroke, embolism, thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0302] In addition, antagonists of the CAN-12v1 polynucleotides and polypeptides may have uses that include diagnosing, treating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include immune and/or proliferative diseases or disorders, particularly thrombosis, embolism, and other blood disorders. Therapeutic and/or pharmaceutical compositions comprising the CAN-12v1 polypeptides may be formulated to comprise heparin.

[0303] In addition, antagonists of the CAN-12v1 polynucleotides and polypeptides may have uses that include diagnosing, treating, ameliorating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include neuronal excitotoxicity, ischemic stroke, hemoragic stroke, hypoxic stress, trauma, cell destruction, spinal cord injury following trauma, degeneration of vulnerable hippocampal neurons after ischemia, reovirus-induced apoptosis, viral-induced induced myocarditis, acute and chronic inflammation, cataract formation, multiple sclerosis, demylenating disorders, acoustic trauma, hearing loss caused by noise, neuronal damage, cardiac ischemic damage, and/or hepatocyte necrosis during and following anoxia.

[0304] CAN-12v1 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include modulating development, differentiation, cellular transformation in response to cell signaling, cell-cell and/or cell-extracellular matrix interactions, clustering of the integrin receptor aIIb3, modulating in long term potentiation (memory), modulating neurite outgrowth, modulating cortical lamination activation of protein kinases and phosphatases, remodeling and disassembling the cytoskeleton, cell cycle modulation, in addition, to ameliorating, preventing, and/or treating limb-girdle muscular dystrophy (LGMD), insulin resistance in diabetics, Alzheimer's disease, Multiple sclerosis, Huntington's disease, Parkinson's disease and amyotrophy.

[0305] Moreover, CAN-12v1 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include treating, diagnosing, prognosing, and/or preventing hyperproliferative disorders, particularly of the neural and immune systems. Such disorders may include, for example, cancers, and metastatic conditions.

[0306] CAN-12v1 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include identification of modulators of CAN-12v1 function including antibodies (for detection or neutralization), naturally-occurring modulators and small molecule modulators. Antibodies to domains (including CAN-12v1 epitopes provided herein) of the CAN-12v1 protein could be used as diagnostic agents of inflammatory conditions in patients, are useful in monitoring the activation and presence of cognate proteases, and can be used as a biomarker for the protease involvement in disease states and in the evaluation of inhibitors of the cognate protease in vivo.

[0307] CAN-12v1 polypeptides and polynucleotides are useful for diagnosing diseases related to over or under expression of CAN-12v1 proteins by identifying mutations in the CAN-12v1 gene using CAN-12v1 probes, or determining CAN-12v1 protein or mRNA expression levels. CAN-12v1 polypeptides are also useful for screening for compounds, which affect activity of the protein. Diseases that can be treated with CAN-12v1 include, the following, non-limiting examples: neuro-regeneration, neuropathic pain, obesity, anorexia, HIV infections, cancers, bulimia, asthma, Parkinson's disease, acute heart failure, hypotension, hypertension, osteoporosis, angina pectoris, myocardial infarction, psychotic, immune, metabolic, cardiovascular, and neurological disorders.

[0308] The predominate expression in neural tissues, combined with the significant expression in a number of other tissues, suggests the CAN-12v1 polynucleotide and polypeptide of the present invention may be involved in modulating nerve invasion, innervation, nerve maintenance, and potentially myeline sheath maintenance and integrity.

[0309] The CAN-12v1 polynucleotides and polypeptides, including fragments and antagonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing diseases and disorders of the neural system, particularly Alzheimer's disease, either directly or indirectly, in addition to other neural disorders known in the art or provided in the “Neurological Diseases” section herein, such as modulating nerve invasion, innervation, nerve maintenance, potentially myelin sheath maintenance and integrity, encephalomyelitis, autoimmune encephalomyelitis, human T cell leukemia virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP), and neuro-inflammatory diseases.

[0310] Molecular genetic manipulation of the structure of the active site domain, particularly the predicted catalytic amino acids, and of other functional domains in the calpain family (e.g., active site domain binding pocket) enables the production of calpains with tailor-made activities. Thus, the CAN-12v1 polypeptides, and fragments thereof, as well as any homologous product resulting from genetic manipulation of the structure, are useful for NMR-based design of modulators of CAN-12v1 biological activity, and calpains, in general.

[0311] CAN-12v1 polypeptides and polynucleotides have additional uses which include diagnosing diseases related to the over and/or under expression of CAN-12v1 by identifying mutations in the CAN-12v1 gene by using CAN-12v1 sequences as probes or by determining CAN-12v1 protein or mRNA expression levels. CAN-12v1 polypeptides may be useful for screening compounds that affect the activity of the protein. CAN-12v1 peptides can also be used for the generation of specific antibodies and as bait in yeast two hybrid screens to find proteins the specifically interact with CAN-12v1 (described elsewhere herein).

[0312] The CAN-12v1 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing metabolic diseases and disorders, such as diabetes. Moreover, expressed human CAN-12v1 may be useful in the detection of patients susceptible to diabetes. Also paradigms that would simulate intracellular CAN-12v1 activity would be useful in treating diabetes.

[0313] The CAN-12v1 polynucleotides and polypeptides, including fragments thereof, may have uses which include identifying inhibitors of intracellular calpain inhibitors (calpastatins) leading to an effective increase in calpain activity.

[0314] Various approaches to detect alterations or allelic variants at the genomic or mRNA level of CAN-12v 1, could be used as a diagnostic for identifying MS patients, or individuals susceptible to have MS. It is likely that the CAN-12v1 gene comprises polymorphic sites (i.e. SNPs), with specific alleles which may be associated with MS or other neurodegenerative disorders, or associated with an increased likelihood of developing these diseases. Therefore, the invention provides the CAN-12v1 sequence that can be used to design specific primers for the identification of polymorphisms or mutations in CAN-12v1 of patients affected with MS. The presence of a specific allele variant, such as a SNP allele or SNPs haplotype that renders the subject carrying it more susceptible to develop MS or other related diseases could be identified (e.g. a variant in the CAN-12v1 promoter region that increased transcript levels of CAN-12v1, or mutations in the coding sequence that increased the stability or half-life of the CAN-12v1 protein). Other methods such as Northern-blot analysis could be performed to measure transcript levels using a CAN-12v1 cDNA probe derived from the sequence of the invention.

[0315] Although it is believed the encoded polypeptide may share at least some biological activities with human calpains (particularly m-calpains), a number of methods of determining the exact biological function of this clone are either known in the art or are described elsewhere herein. Briefly, the function of this clone may be determined by applying microarray methodology. Nucleic acids corresponding to the CAN-12v1 polynucleotides, in addition to, other clones of the present invention, may be arrayed on microchips for expression profiling. Depending on which polynucleotide probe is used to hybridize to the slides, a change in expression of a specific gene may provide additional insight into the function of this gene based upon the conditions being studied. For example, an observed increase or decrease in expression levels when the polynucleotide probe used comes from diseased neural tissue, as compared to, normal tissue might indicate a function in modulating neural function, for example. In the case of CAN-12v1, spinal cord, lymph node, thymus, and/or spleen tissue should be used to extract RNA to prepare the probe.

[0316] In addition, the function of the protein may be assessed by applying quantitative PCR methodology, for example. Real time quantitative PCR would provide the capability of following the expression of the CAN-12v1 gene throughout development, for example. Quantitative PCR methodology requires only a nominal amount of tissue from each developmentally important step is needed to perform such experiments. Therefore, the application of quantitative PCR methodology to refining the biological function of this polypeptide is encompassed by the present invention. In the case of CAN-12v 1, a disease correlation related to CAN-12v 1 may be made by comparing the mRNA expression level of CAN-12v1 in normal tissue, as compared to diseased tissue (particularly diseased tissue isolated from the following: esophagus, spinal cord, lymph node, thymus, and/or spleen tissue). Significantly higher or lower levels of CAN-12v1 expression in the diseased tissue may suggest CAN-12v1 plays a role in disease progression, and antagonists against CAN-12v1 polypeptides would be useful therapeutically in treating, preventing, and/or ameliorating the disease. Alternatively, significantly higher or lower levels of CAN-12v1 expression in the diseased tissue may suggest CAN-12v1 plays a defensive role against disease progression, and agonists of CAN-12v1 polypeptides may be useful therapeutically in treating, preventing, and/or ameliorating the disease. Also encompassed by the present invention are quantitative PCR probes corresponding to the polynucleotide sequence provided as SEQ ID NO:53 (FIGS. 8A-C).

[0317] The function of the protein may also be assessed through complementation assays in yeast. For example, in the case of the CAN-12v1, transforming yeast deficient in calpain activity, particularly m-calpain activity, and assessing their ability to grow would provide convincing evidence the CAN-12v1 polypeptide has calpain activity, and possibly m-calpain activity. Additional assay conditions and methods that may be used in assessing the function of the polynucleotides and polypeptides of the present invention are known in the art, some of which are disclosed elsewhere herein.

[0318] Alternatively, the biological function of the encoded polypeptide may be determined by disrupting a homologue of this polypeptide in Mice and/or rats and observing the resulting phenotype. Such knock-out experiments are known in the art, some of which are disclosed elsewhere herein.

[0319] Moreover, the biological function of this polypeptide may be determined by the application of antisense and/or sense methodology and the resulting generation of transgenic mice and/or rats. Expressing a particular gene in either sense or antisense orientation in a transgenic mouse or rat could lead to respectively higher or lower expression levels of that particular gene. Altering the endogenous expression levels of a gene can lead to the observation of a particular phenotype that can then be used to derive indications on the function of the gene. The gene can be either over-expressed or under expressed in every cell of the organism at all times using a strong ubiquitous promoter, or it could be expressed in one or more discrete parts of the organism using a well characterized tissue-specific promoter (e.g., an esophagus, spinal cord, lymph node, thymus, or spleen specific promoter), or it can be expressed at a specified time of development using an inducible and/or a developmentally regulated promoter.

[0320] In the case of CAN-12v1 transgenic mice or rats, if no phenotype is apparent in normal growth conditions, observing the organism under diseased conditions (neural, immune, hematopoietic diseases or disorders, cancers, etc.) may lead to understanding the function of the gene. Therefore, the application of antisense and/or sense methodology to the creation of transgenic mice or rats to refine the biological function of the polypeptide is encompassed by the present invention.

[0321] In preferred embodiments, the following N-terminal CAN-12v1 deletion polypeptides are encompassed by the present invention: M1-L694, S2-L694, L3-L694, W4-L694, P5-L694, P6-L694, F7-L694, R8-L694, C9-L694, R10-L694, W11-L694, K12-L694, L13-L694, A14-L694, P15-L694, R16-L694, Y17-L694, S18-L694, R19-L694, R20-L694, A21-L694, S22-L694, P23-L694, Q24-L694, Q25-L694, P26-L694, Q27-L694, Q28-L694, D29-L694, F30-L694, E31-L694, A32-L694, L33-L694, L34-L694, A35-L694, E36-L694, C37-L694, L38-L694, R39-L694, N40-L694, G41-L694, C42-L694, L43-L694, F44-L694, E45-L694, D46-L694, T47-L694, S48-L694, F49-L694, P50-L694, A51-L694, T52-L694, L53-L694, S54-L694, S55-L694, 156-L694, G57-L694, S58-L694, G59-L694, S60-L694, L61-L694, L62-L694, Q63-L694, K64-L694, L65-L694, P66-L694, P67-L694, R68-L694, L69-L694, Q70-L694, W71-L694, K72-L694, R73-L694, P74-L694, P75-L694, E76-L694, L77-L694, H78-L694, S79-L694, N80-L694, P81-L694, Q82-L694, F83-L694, Y84-L694, F85-L694, A86-L694, K87-L694, A88-L694, K89-L694, R90-L694, L91-L694, D92-L694, L93-L694, C94-L694, Q95-L694, G96-L694, 197-L694, V98-L694, G99-L694, D100-L694, C101-L694, W102-L694, F103-L694, L104-L694, A 105-L694, A 106-L694, L107-L694, Q108-L694, A109-L694, L110-L694, A111-L694, L112-L694, H113-L694, Q114-L694, D115-L694, 1116-L694, L117-L694, S118-L694, R119-L694, V120-L694, V121-L694, P122-L694, L123-L694, N124-L694, Q125-L694, S126-L694, F127-L694, T128-L694, E129-L694, K130-L694, Y131-L694, A132-L694, G133-L694, 1134-L694, F135-L694, R136-L694, F137-L694, W138-L694, F139-L694, W140-L694, H141-L694, Y142-L694, G143-L694, N144-L694, W145-L694, V146-L694, P147-L694, V148-L694, V149-L694, 1150-L694, D151-L694, D152-L694, R153-L694, L154-L694, P155-L694, V156-L694, N157-L694, E158-L694, A159-L694, G160-L694, Q161-L694, L162-L694, V163-L694, F164-L694, V165-L694, S166-L694, S167-L694, T168-L694, Y169-L694, K170-L694, N171-L694, L172-L694, F173-L694, W174-L694, G175-L694, A176-L694, L177-L694, L178-L694, E179-L694, K180-L694, A181-L694, Y182-L694, A183-L694, K184-L694, L185-L694, S186-L694, G187-L694, S188-L694, Y189-L694, El 90-L694, D191-L694, L192-L694, Q193-L694, S194-L694, G195-L694, Q196-L694, V197-L694, S198-L694, E199-L694, A200-L694, L201-L694, V202-L694, D203-L694, F204-L694, T205-L694, G206-L694, G207-L694, V208-L694, T209-L694, M210-L694, T211-L694, 1212-L694, N213-L694, L214-L694, A215-L694, E216-L694, A217-L694, H218-L694, G219-L694, N220-L694, L221-L694, W222-L694, D223-L694, 1224-L694, L225-L694, 1226-L694, E227-L694, A228-L694, T229-L694, Y230-L694, N231-L694, R232-L694, T233-L694, L234-L694, 1235-L694, G236-L694, C237-L694, Q238-L694, T239-L694, H240-L694, S241-L694, G242-L694, E243-L694, K244-L694, 1245-L694, L246-L694, E247-L694, N248-L694, G249-L694, L250-L694, V251-L694, E252-L694, G253-L694, H254-L694, A255-L694, Y256-L694, T257-L694, L258-L694, T259-L694, G260-L694, 1261-L694, R262-L694, K263-L694, V264-L694, T265-L694, C266-L694, K267-L694, H268-L694, R269-L694, P270-L694, E271-L694, Y272-L694, L273-L694, V274-L694, K275-L694, L276-L694, R277-L694, N278-L694, P279-L694, W280-L694, G281-L694, K282-L694, V283-L694, E284-L694, W285-L694, K286-L694, G287-L694, D288-L694, W289-L694, S290-L694, D291-L694, S292-L694, S293-L694, S294-L694, K295-L694, W296-L694, E297-L694, L298-L694, L299-L694, S300-L694, P301-L694, K302-L694, E303-L694, K304-L694, 1305-L694, L306-L694, L307-L694, L308-L694, R309-L694, K310-L694, D311-L694, N312-L694, D313-L694, G314-L694, E315-L694, F316-L694, W317-L694, M318-L694, T319-L694, L320-L694, Q321-L694, D322-L694, F323-L694, K324-L694, T325-L694, H326-L694, F327-L694, V328-L694, L329-L694, L330-L694, V331-L694, 1332-L694, C333-L694, K334-L694, L335-L694, T336-L694, P337-L694, G338-L694, L339-L694, L340-L694, S341-L694, Q342-L694, E343-L694, A344-L694, A345-L694, Q346-L694, K347-L694, W348-L694, T349-L694, Y350-L694, T351-L694, M352-L694, R353-L694, E354-L694, G355-L694, R356-L694, W357-L694, E358-L694, K359-L694, R360-L694, S361-L694, T362-L694, A363-L694, G364-L694, G365-L694, Q366-L694, R367-L694, Q368-L694, L369-L694, L370-L694, Q371-L694, D372-L694, T373-L694, F374-L694, W375-L694, K376-L694, N377-L694, P378-L694, Q379-L694, F380-L694, L381-L694, L382-L694, S383-L694, V384-L694, W385-L694, R386-L694, P387-L694, E388-L694, E389-L694, G390-L694, R391-L694, R392-L694, S393-L694, L394-L694, R395-L694, P396-L694, C397-L694, S398-L694, V399-L694, L400-L694, V401-L694, S402-L694, L403-L694, L404-L694, Q405-L694, K406-L694, P407-L694, R408-L694, H409-L694, R410-L694, C411-L694, R412-L694, K413-L694, R414-L694, K415-L694, P416-L694, L417-L694, L418-L694, A419-L694, 1420-L694, G421-L694, F422-L694, Y423-L694, L424-L694, Y425-L694, R426-L694, Y427-L694, H428-L694, D429-L694, D430-L694, Q431-L694, R432-L694, R433-L694, L434-L694, P435-L694, P436-L694, E437-L694, F438-L694, F439-L694, Q440-L694, R441-L694, N442-L694, T443-L694, P444-L694, L445-L694, S446-L694, Q447-L694, P448-L694, D449-L694, R450-L694, F451-L694, L452-L694, K453-L694, E454-L694, K455-L694, E456-L694, V457-L694, S458-L694, Q459-L694, E460-L694, L461-L694, C462-L694, L463-L694, E464-L694, P465-L694, G466-L694, T467-L694, Y468-L694, L469-L694, 1470-L694, V471-L694, P472-L694, C473-L694, 1474-L694, L475-L694, E476-L694, A477-L694, H478-L694, Q479-L694, K480-L694, S481-L694, E482-L694, F483-L694, V484-L694, L485-L694, R486-L694, V487-L694, F488-L694, S489-L694, R490-L694, K491-L694, H492-L694, 1493-L694, F494-L694, Y495-L694, E496-L694, 1497-L694, G498-L694, S499-L694, N500-L694, S501-L694, G502-L694, V503-L694, V504-L694, F505-L694, S506-L694, K507-L694, E508-L694, 1509-L694, E510-L694, D511-L694, Q512-L694, N513-L694, E514-L694, R515-L694, Q516-L694, D517-L694, E518-L694, F519-L694, F520-L694, T521-L694, K522-L694, F523-L694, F524-L694, E525-L694, K526-L694, H527-L694, P528-L694, E529-L694, 1530-L694, N531-L694, A532-L694, V533-L694, Q534-L694, L535-L694, Q536-L694, N537-L694, L538-L694, L539-L694, N540-L694, Q541-L694, and/or M542-L694 of SEQ ID NO:54. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN -12v1 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0322] In preferred embodiments, the following C-terminal CAN-12v1 deletion polypeptides are encompassed by the present invention: M1-L694, M1-L693, M1-T692, M1-T691, M1-N690, M1-F689, M1-1688, M1-L687, M1-Y686, M1-S685, M1-T684, M1-S683, M1-H682, M1-A681, M1-V680, M1-G679, M1-G678, M1-D677, M1-I676, M1-N675, M1-A674, M1-L673, M1-1672, M1-V671, M1-P670, M1-V669, M1-1668, M1-M667, M1-F666, M1-F665, M1-T664, M1-P663, M1-T662, M1-S661, M1-Q660, M1-L659, M1-D658, M1-V657, M1-D656, M1-K655, M1-L654, M1-T653, M1-V652, M1-S651, M1-R650, M1-1649, M1-L648, M1-T647, M1-V646, M1-E645, M1-A644, M1-H643, M1-W642, M1-V641, M1-D640, M1-G639, M1-R638, M1-R637, M1-Q636, M1-R635, M1-1634, M1-L633, M1-T632, M1-C631, M1-G630, M1-A629, M1-R628, M1-T627, M1-H626, M1-G625, M1-C624, M1-S623, M1-W622, M1-S621, M1-K620, M1-R619, M1-H618, M1-R617, M1-G616, M1-A615, M1-E614, M1-R613, M1-M612, M1-A611, M1-A610, M1-H609, M1-L608, M1-Q607, M1-E606, M1-W605, M1-N604, M1-L603, M1-Y602, M1-G601, M1-S600, M1-G599, M1-R598, M1-D597, M1-Q596, M1-K595, M1-H594, M1-F593, M1-V592, M1-K591, M1-Q590, M1-S589, M1-L588, M1-K587, M1-L586, M1-Q585, M1-K584, M1-W583, M1-L582, M1-D581, M1-R580, M1-F579, M1-E578, M1-Q577, M1-1576, M1-S575, M1-M574, M1-T573, M1-G572, M1-S571, M1-A570, M1-N569, M1-L568, M1-D567, M1-L566, M1-L565, M1-A564, M1-L563, M1-1562, M1-G561, M1-Q560, M1-C559, M1-A558, M1-E557, M1-L556, M1-S555, M1-F554, M1-F553, M1-P552, M1-Q551, M1-R550, M1-S549, Ml-G548, M1-L547, M1-S546, M1-S545, M1-W544, M1-T543, M1-M542, M1-Q541, M1-N540, M1-L539, M1-L538, M1-N537, M1-Q536, M1-L535, M1-Q534, M1-V533, M1-A532, M1-N531, M1-1530, M1-E529, M1-P528, M1-H527, M1-K526, M1-E525, M1-F524, M1-F523, M1-K522, M1-T521, M1-F520, M1-F519, M1-E518, M1-D517, M1-Q516, M1-R515, M1-E514, M1-N513, M1-Q512, M1-D511, M1-E510, M1-1509, M1-E508, M1-K507, M1-S506, M1-F505, M1-V504, M1-V503, M1-G502, M1-S501, M1-N500, M1-S499, M1-G498, M1-1497, M1-E496, M1-Y495, M1-F494, M1-1493, M1-H492, M1-K491, M1-R490, M1-S489, M1-F488, M1-V487, M1-R486, M1-L485, M1-V484, M1-F483, M1-E482, M1-S481, M1-K480, M1-Q479, M1-H478, M1-A477, M1-E476, Ml-L475, M1-1474, M1-C473, M1-P472, M1-V471, M1-1470, M1-L469, M1-Y468, M1-T467, M1-G466, M1-P465, M1-E464, M1-L463, M1-C462, M1-L461, M1-E460, M1-Q459, M1-S458, M1-V457, M1-E456, M1-K455, M1-E454, M1-K453, M1-L452, M1-F451, M1-R450, M1-D449, M1-P448, M1-Q447, M1-S446, M1-L445, M1-P444, M1-T443, M1-N442, M1-R441, M1-Q440, M1-F439, M1-F438, M1-E437, M1-P436, M1-P435, M1-L434, M1-R433, M1-R432, M1-Q431, M1-D430, M1-D429, M1-H428, M1-Y427, M1-R426, M1-Y425, M1-L424, M1-Y423, M1-F422, M1-G421, M1-1420, M1-A419, M1-L418, M1-L417, M1-P416, M1-K415, M1-R414, M1-K413, M1-R412, M1-C411, M1-R410, M1-H409, M1-R408, M1-P407, M1-K406, M1-Q405, M1-L404, M1-L403, M1-S402, M1-V401, M1-L400, M1-V399, M1-S398, M1-C397, M1-P396, M1-R395, M1-L394, M1-S393, M1-R392, M1-R391, M1-G390, M1-E389, M1-E388, M1-P387, M1-R386, M1-W385, M1-V384, M1-S383, M1-L382, M1-L381, M1-F380, M1-Q379, M1-P378, M1-N377, M1-K376, M1-W375, M1-F374, M1-T373, M1-D372, M1-Q371, M1-L370, M1-L369, M1-Q368, M1-R367, M1-Q366, M1-G365, M1-G364, M1-A363, M1-T362, M1-S361, M1-R360, M1-K359, M1-E358, M1-W357, M1-R356, M1-G355, M1-E354; M1-R353, M1-M352, M1-T351, M1-Y350, M1-T349, M1-W348, M1-K347, M1-Q346, M1-A345, M1-A344, M1-E343, M1-Q342, M1-S341, M1-L340, M1-L339, M1-G338, M1-P337, M1-T336, M1-L335, M1-K334, M1-C333, M1-1332, M1-V331, M1-L330, M1-L329, M1-V328, M1-F327, M1-H326, M1-T325, M1-K324, M1-F323, M1-D322, M1-Q321, M1-L320, M1-T319, M1-M318, M1-W317, M1-F316, M1-E315, M1-G314, M1-D313, M1-N312, M1-D311, M1-K310, M1-R309, M1-L308, M1-L307, M1-L306, M1-1305, M1-K304, M1-E303, M1-K302, M1-P301, M1-S300, M1-L299, M1-L298, M1-E297, M1-W296, M1-K295, M1-S294, M1-S293, M1-S292, M1-D291, M1-S290, M1-W289, M1-D288, M1-G287, M1-K286, M1-W285, M1-E284, M1-V283, M1-K282, M1-G281, M1-W280, M1-P279, M1-N278, M1-R277, M1-L276, M1-K275, M1-V274, M1-L273, M1-Y272, M1-E271, M1-P270, M1-R269, M1-H268, M1-K267, M1-C266, M1-T265, M1-V264, M1-K263, M1-R262, M1-1261, M1-G260, M1-T259, M1-L258, M1-T257, M1-Y256, M1-A255, M1-H254, M1-G253, M1-E252, M1-V251, M1-L250, M1-G249, M1-N248, M1-E247, M1-L246, M1-1245, M1-K244, and/or M1-E243 of SEQ ID NO:54. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12v1 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0323] Alternatively, preferred polypeptides of the present invention may comprise polypeptide sequences corresponding to, for example, internal regions of the CAN-12v1 polypeptide (e.g., any combination of both N- and C-terminal CAN-12v1 polypeptide deletions) of SEQ ID NO:54. For example, internal regions could be defined by the equation: amino acid NX to amino acid CX, wherein NX refers to any N-terminal deletion polypeptide amino acid of CAN-12v1 (SEQ ID NO:54), and where CX refers to any C-terminal deletion polypeptide amino acid of CAN-12v1 (SEQ ID NO:54). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0324] The present invention also encompasses immunogenic and/or antigenic epitopes of the CAN-12v1 polypeptide.

[0325] The CAN-12v1 polypeptides of the present invention were determined to comprise several phosphorylation sites based upon the Motif algorithm (Genetics Computer Group, Inc.). The phosphorylation of such sites may regulate some biological activity of the CAN-12v1 polypeptide. For example, phosphorylation at specific sites may be involved in regulating the proteins ability to associate or bind to other molecules (e.g., proteins, ligands, substrates, DNA, etc.). In the present case, phosphorylation may modulate the ability of the CAN-12v1 polypeptide to associate with other polypeptides, particularly the serine protease substrate for CAN-12v1, or its ability to modulate serine protease function.

[0326] The CAN-12v1 polypeptide was predicted to comprise eleven PKC phosphorylation sites using the Motif algorithm (Genetics Computer Group, Inc.). In vivo, protein kinase C exhibits a preference for the phosphorylation of serine or threonine residues. The PKC phosphorylation sites have the following consensus pattern: [ST]-x-[RK], where S or T represents the site of phosphorylation and ‘x’ an intervening amino acid residue. Additional information regarding PKC phosphorylation sites can be found in Woodget J. R., Gould K. L., Hunter T., Eur. J. Biochem. 161:177-184(1986), and Kishimoto A., Nishiyama K., Nakanishi H., Uratsuji Y., Nomura H., Takeyama Y., Nishizuka Y., J. Biol. Chem. . . . 260:12492-12499(1985); which are hereby incorporated by reference herein.

[0327] In preferred embodiments, the following PKC phosphorylation site polypeptides are encompassed by the present invention: LAPRYSRRASPQQ (SEQ ID NO:58), LNQSFTEKYAGIF (SEQ ID NO:59), VFVSSTYKNLFWG (SEQ ID NO:60), GIRKVTCKHRPEY (SEQ ID NO:61), DWSDSSSKWELLS (SEQ ID NO:62), KWELLSPKEKILL (SEQ ID NO:63), QKWTYTMREGRWE (SEQ ID NO:64), EEGRRSLRPCSVL (SEQ ID NO:65), VLRVFSRKHIFYE (SEQ ID NO:66), KQLKLSQKVFHKQ (SEQ ID NO:67), and/or LIRSVTLKDVDLQ (SEQ ID NO:68). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of the CAN-12v1 PKC phosphorylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0328] The CAN-12v1 polypeptide has been shown to comprise four glycosylation site according to the Motif algorithm (Genetics Computer Group, Inc.). As discussed more specifically herein, protein glycosylation is thought to serve a variety of functions including: augmentation of protein folding, inhibition of protein aggregation, regulation of intracellular trafficking to organelles, increasing resistance to proteolysis, modulation of protein antigenicity, and mediation of intercellular adhesion.

[0329] In preferred embodiments, the following asparagine glycosylation site polypeptide is encompassed by the present invention: RVVPLNQSFTEKYA (SEQ ID NO:69), IEATYNRTLIGCQT (SEQ ID NO:70), ALLDLNASGTMSIQ (SEQ ID NO:71), and/or SYLIFNTTLL (SEQ ID NO:72). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12v1 asparagine glycosylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0330] The CAN-12v1 polypeptide has been shown to comprise one amidation site according to the Motif algorithm (Genetics Computer Group, Inc.). The precursor of hormones and other active peptides which are C-terminally amidated is always directly followed by a glycine residue which provides the amide group, and most often by at least two consecutive basic residues (Arg or Lys) which generally function as an active peptide precursor cleavage site. Although all amino acids can be amidated, neutral hydrophobic residues such as Val or Phe are good substrates, while charged residues such as Asp or Arg are much less reactive. A consensus pattern for amidation sites is the following: x-G-[RK]-[RK], wherein “X” represents the amidation site. Additional information relating to asparagine glycosylation may be found in reference to the following publications, which are hereby incorporated by reference herein: Kreil G., Meth. Enzymol. 106:218-223(1984); and Bradbury A. F., Smyth D. G., Biosci. Rep. 7:907-916(1987).

[0331] In preferred embodiments, the following amidation site polypeptide is encompassed by the present invention: VWRPEEGRRSLRPC (SEQ ID NO:73). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this CAN-12v1 amidation site polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0332] The CAN-12v1 polypeptide has been shown to comprise one RGD cell attachment site domain according to the Motif algorithm (Genetics Computer Group, Inc.). The sequence Arg-Gly-Asp, found in fibronectin, is crucial for its interaction with its cell surface receptor, an integrin. What has been called the ‘RGD’ tripeptide is also found in the sequences of a number of other proteins, where it has been shown to play a role in cell adhesion. Non-limiting examples of these proteins are the following: some forms of collagens, fibrinogen, vitronectin, von Willebrand factor (VWF), snake disintegrins, and slime mold discoidins. The ‘RGD’ tripeptide is also found in other proteins where it may serve the same purpose. A consensus pattern for RGD cell attachment sites is the following: R-G-D. Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Ruoslahti E., Pierschbacher M. D., Cell 44:517-518(1986); and d'Souza S. E., Ginsberg M. H., Plow E. F., Trends Biochem. Sci. 16:246-250(1991).

[0333] In preferred embodiments, the following RGD cell attachment site domain polypeptide is encompassed by the present invention: LIRQRRGDVWHAE (SEQ ID NO:74). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this RGD cell attachment site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0334] In confirmation of the CAN-12v1 polypeptide being a calpain, it has been shown to comprise one EF-hand calcium-binding domain according to the Motif algorithm (Genetics Computer Group, Inc.). Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Several representative proteins containing EF-hand regions are provided below: For each type of protein, the total number of EF-hand regions known or supposed to exist are provided in parenthesis: Aequorin and Renilla luciferin binding protein (LBP) (Ca=3); Alpha actinin (Ca=2); Calbindin (Ca=4); Calcineurin B subunit (protein phosphatase 2B regulatory subunit) (Ca=4); Calcium-binding protein from Streptomyces erythraeus (Ca=3?); Calcium-binding protein from Schistosoma mansoni (Ca=2?); Calcium-binding proteins TCBP-23 and TCBP-25 from Tetrahymena thermophila (Ca=4?); Calcium-dependent protein kinases (CDPK) from plants (Ca=4); Calcium vector protein from amphoxius (Ca=2); Calcyphosin (thyroid protein p24) (Ca=4?); Calmodulin (Ca=4, except in yeast where Ca=3); Calpain small and large chains (Ca=2); Calretinin (Ca=6); Calcyclin (prolactin receptor associated protein) (Ca=2); Caltractin (centrin) (Ca=2 or 4); Cell Division Control protein 31 (gene CDC31) from yeast (Ca=2?); Diacylglycerol kinase (EC 2.7.1.107) (DGK) (Ca=2); FAD-dependent glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) from mammals (Ca=1); Fimbrin (plastin) (Ca=2); Flagellar calcium-binding protein (1f8) from Trypanosoma cruzi (Ca=l or 2); Guanylate cyclase activating protein (GCAP) (Ca=3); Inositol phospholipid-specific phospholipase C isozymes gamma-1 and delta-1 (Ca=2) [10]; Intestinal calcium-binding protein (ICaBPs) (Ca=2); MIF related proteins 8 (MRP-8 or CFAG) and 14 (MRP-14) (Ca=2); Myosin regulatory light chains (Ca=1); Oncomodulin (Ca=2); Osteonectin (basement membrane protein BM-40) (SPARC) and proteins that contains an ‘osteonectin’ domain (QR1, matrix glycoprotein SCI) (Ca=1); Parvalbumins alpha and beta (Ca=2); Placental calcium-binding protein (18a2) (nerve growth factor induced protein 42a) (p9k) (Ca=2); Recoverins (visinin, hippocalcin, neurocalcin, S-modulin) (Ca=2 to 3); Reticulocalbin (Ca=4); S-100 protein, alpha and beta chains (Ca=2); Sarcoplasmic calcium-binding protein (SCPs) (Ca=2 to 3); Sea urchin proteins Spec 1 (Ca=4), Spec 2 (Ca=4?), Lps-1 (Ca=8); Serine/threonine protein phosphatase rdgc (EC 3.1.3.16) from Drosophila (Ca=2); Sorcin V19 from hamster (Ca=2); Spectrin alpha chain (Ca=2); Squidulin (optic lobe calcium-binding protein) from squid (Ca=4); and Troponins C; from skeletal muscle (Ca=4), from cardiac muscle (Ca=3), from arthropods and molluscs (Ca=2).

[0335] A consensus pattern for EF hand calcium binding domains is the following:

21 2 3 4 5 6 7 8 9 10 12 13X Y Z -Y -X -ZD-x-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]-x(2)-[DE]-[LIVMFYW],

[0336] wherein X, Y, Z, -Y, -X, and -Z are as defined above, and wherein “x” represents any amino acid. Amino acid residues within the consensus at positions 1 (X), 3 (Y) and 12 (-Z) are the most conserved. The 6th residue in an EF-hand loop is in most cases a Gly.

[0337] Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Kawasaki H., Kretsinger R. H., Protein Prof. 2:305-490(1995); Kretsinger R. H., Cold Spring Harbor Symp. Quant. Biol. 52:499-510(1987); Moncrief N. D., Kretsinger R. H., Goodman M., J. Mol. Evol. 30:522-562(1990); Nakayama S., Moncrief N. D., Kretsinger R. H., J. Mol. Evol. 34:416-448(1992); Heizmann C. W., Hunziker W., Trends Biochem. Sci. 16:98-103(1991); Kligman D., Hilt D. C., Trends Biochem. Sci. 13:437-443(1988); Strynadka N. C. J., James M. N. G., Annu. Rev. Biochem. 58:951-98(1989); Haiech J., Sallantin J., Biochimie 67:555-560(1985); Chauvaux S., Beguin P., Aubert J.-P., Bhat K. M., Gow L. A., Wood T. M., Bairoch A., Biochem. J. 265:261-265(1990); Bairoch A., Cox J. A., FEBS Lett. 269:454-456(1990).

[0338] In preferred embodiments, the following EF-hand calcium binding domain polypeptide is encompassed by the present invention: ILALLDLNASGTMSIQEFRDLWK (SEQ ID NO:75). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this EF-hand calcium binding domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0339] In further confirmation of the CAN-12v1 polypeptide being a calpain, it has been shown to comprise one eukaryotic thiol (cysteine) protease active site domain according to the Motif algorithm (Genetics Computer Group, Inc.). Eukaryotic thiol proteases (EC 3.4.22.-) are a family of proteolytic enzymes which contain an active site cysteine. Catalysis proceeds through a thioester intermediate and is facilitated by a nearby histidine side chain; an asparagine completes the essential catalytic triad. Non-limiting examples of proteases which are known to belong to this family are provided below: Vertebrate lysosomal cathepsins B (EC 3.4.22.1), H (EC 3.4.22.16), L (EC 3.4.22.15), and S (EC 3.4.22.27); Vertebrate lysosomal dipeptidyl peptidase I (EC 3.4.14.1) (also known as cathepsin C); Vertebrate calpains (EC 3.4.22.17) (Calpains are intracellular calcium-activated thiol protease that contain both a N-terminal catalytic domain and a C-terminal calcium-binding domain; Mammalian cathepsin K, which seems involved in osteoclastic bone resorption; Human cathepsin O; Bleomycin hydrolase (An enzyme that catalyzes the inactivation of the antitumor drug BLM (a glycopeptide); Plant enzymes: barley aleurain (EC 3.4.22.16), EP-B1/B4; kidney bean EP-C1, rice bean SH-EP; kiwi fruit actinidin (EC 3.4.22.14); papaya latex papain (EC 3.4.22.2), chymopapain (EC 3.4.22.6), caricain (EC 3.4.22.30), and proteinase IV (EC 3.4.22.25); pea turgor-responsive protein 15A; pineapple stem bromelain (EC 3.4.22.32); rape COT44; rice oryzain alpha, beta, and gamma; tomato low-temperature induced, Arabidopsis thaliana A494, RD19A and RD21A; House-dust mites allergens DerP1 and EurM1; Cathepsin B-like proteinases from the worms Caenorhabditis elegans (genes gcp-1, cpr-3, cpr-4, cpr-5 and cpr-6), Schistosoma mansoni (antigen SM31) and Japonica (antigen SJ31), Haemonchus contortus (genes AC-1 and AC-2), and Ostertagia ostertagi (CP-1 and CP-3); Slime mold cysteine proteinases CP1 and CP2; Cruzipain from Trypanosoma cruzi and brucei; Throphozoite cysteine proteinase (TCP) from various Plasmodium species; Proteases from Leishmania mexicana, Theileria annulata and Theileria parva; Baculoviruses cathepsin-like enzyme (v-cath); Drosophila small optic lobes protein (gene sol), a neuronal protein that contains a calpain-like domain; Yeast thiol protease BLH1/YCP1/LAP3; and Caenorhabditis elegans hypothetical protein CO6G4.2, a calpain-like protein; Two bacterial peptidases are also part of this family—Aminopeptidase C from Lactococcus lactis (gene pepC), and Thiol protease tpr from Porphyromonas gingivalis.

[0340] A consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: Q-x(3)-[GE]-x-C-[YW]-x(2)-[STAGC]-[STAGCV], wherein C is the active site residue, and “x” represents any amino acid. The residue in position 4 of the pattern is almost always cysteine; the only exceptions are calpains (Leu), bleomycin hydrolase (Ser) and yeast YCP1 (Ser); while the residue in position 5 of the pattern is always Gly except in papaya protease IV where it is Glu.

[0341] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [LIVMGSTAN]-x-H-[GSACE]-[LIVM]-x-[LIVMAT](2)-G-x-[GSADNH], wherein H is the active site residue, and “x” represents any amino acid.

[0342] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [FYCH]-[WI]-[LIVT]-x-[KRQAG]-N-[ST]-W-x(3)-[FYW]-G-x(2)-G-[LFYW]-[LIVMFYG]-x-[LIVMF], wherein N is the active site residue, and “x” represents any amino acid.

[0343] Additional information relating to for eukaryotic thiol (cysteine) protease active site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Dufour E., Biochirnie 70:1335-1342(1988); Kirschke H., Barrett A. J., Rawlings N. D., Protein Prof. 2:1587-1643(1995); Shi G.-P., Chapman H. A., Bhairi S. M., Deleeuw C., Reddy V. Y., Weiss S. J., FEBS Lett. 357:129-134(1995); Velasco G., Ferrando A. A., Puente X. S., Sanchez L. M., Lopez-Otin C., J. Biol. Chem. . . . 269:27136-27142(1994); Chapot-Chartier M. P., Nardi M., Chopin M. C., Chopin A., Gripon J. C., Appl. Environ. Microbiol. 59:330-333(1993); Higgins D. G., McConnell D. J., Sharp P. M., Nature 340:604-604(1989); Rawlings N. D., Barrett A. J., Meth. Enzymol. 244:461-486(1994), and http://www.expasy.ch/cgi-bin/lists?peptidas.txt, which are hereby incorporated by reference in their entirety herein.

[0344] In preferred embodiments, the following for eukaryotic thiol (cysteine) protease active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALA (SEQ ID NO:76). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this for eukaryotic thiol (cysteine) protease active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0345] As referenced elsewhere herein, calpains are organized in domains. As a point of reference, the larger catalytic subunit of the best characterized m-calpain is organized in four domains (I-IV)(Hosfield et al., Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation. EMBO J. 18:6880-9, 1999; Strobl et al., The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Proc Natl Acad Sci U S A. 97:588-92, 2000). The N-terminal domain I contains an alpha helical region. Domain II contains the catalytic active domain with the active site amino acids. Domain II contains the linker between the Ca2+ binding domain in domain IV to the active site domain II.

[0346] The CAN-12v1 calpain of the present invention has the same domain I and II as the CAN-12 calpain, but differ in domains III and IV. The N-terminal domain I consists of residues Met1-Arg20. Domain II of the present calpains (Ala2l-Lys333) contain the catalytic active site residues acids (Cys101, His254 and Asn278). As can be seen in the sequence alignments (FIGS. 2A-E), there is high amino acid sequence homology in the amino acid residues bracketing the active site amino acids. Combined domains I and II of the calpains of the present invention are 42-45% homologous to m-calpain.

[0347] The CAN-12v1 calpain of the present invention, have the same domain I and II, although they differ in composition and content of domains III and IV. The CAN-12 and CAN-12v1 calpain contains the linker (domain III) and the C-terminal domain IV, though the CAN-12v1 calpain is lacking residues Met426, Asn427 and Lys428 of SEQ ID NO54) in the “linker” domain.

[0348] The present invention also provides a three-dimensional homology model of the CAN-12 polypeptide (see FIG. 6). Although the CAN-12 polypeptide sequence is different than the CAN-12v1 polypeptide sequence, the fact that domain I and II are substantially the same suggests the homology model of CAN-12 may be used for designing potential ligands (including agonists and/or antagonists) for the CAN-12v1 polypeptide. A three-dimensional homology model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995). The homology model of the CAN-12 polypeptide, corresponding to amino acid residues 12 to 524 of SEQ ID NO:2, was based upon the homologous structure of CAN2, a m-calpain family member (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) and is defined by the set of structural coordinates set forth in Table IV herein.

[0349] A description of the headings in Table IV are as follows: “Atom No” refers to the atom number within the CAN-12 homology model; “Atom name” refers to the element whose coordinates are measured, the first letter in the column defines the element; “Residue” refers to the amino acid within which the atom resides, and the provided number after the amino acid refers to the amino acid number of the “residue”; “X Coord”, “Y Coord”, and “Z Coord” structurally define the atomic position of the element measured in three dimensions.

[0350] The CAN-12 homology model of the present invention may provide one basis for designing rational stimulators (agonists) and/or inhibitors (antagonists) of one or more of the biological functions of CAN-12v1, or of CAN-12v1 mutants having altered specificity (e.g., molecularly evolved CAN-12v1 polypeptides, engineered site-specific CAN-12v1 mutants, CAN-12v1 allelic variants, etc.).

[0351] Homology models are not only useful for designing rational agonists and/or antagonists, but are also useful in predicting the function of a particular polypeptide. The functional predictions from homology models are typically more accurate than the functional attributes derived from traditional polypeptide sequence homology alignments (e.g., CLUSTALW), particularly when the three dimensional structure of a related polypeptide is known (e.g., m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11). The increased prediction accuracy is based upon the fact that homology models approximate the three-dimensional structure of a protein, while homology based alignments only take into account the one dimension polypeptide sequence. Since the function of a particular polypeptide is determined not only by its primary, secondary, and tertiary structure, functional assignments derived solely upon homology alignments using the one dimensional protein sequence may be less reliable. A 3-dimensional model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995).

[0352] Prior to developing a homology model, those of skill in the art would appreciate that a template of a known protein, or model protein, must first be identified which will be used as a basis for constructing the homology model for the protein of unknown structure (query template). In the case of the CAN-12 polypeptide of the present invention, the model protein template used in constructing the CAN-12 homology model was the m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11).

[0353] Identifying a template can be accomplished using pairwise alignment of protein sequences using such programs as FASTA (Pearson, et al 1990) and BLAST (Altschul, et al, 1990). In cases where sequence similarity is high (greater than 30%), such pairwise comparison methods may be adequate for identifying an appropriate template. Likewise, multiple sequence alignments or profile-based methods can be used to align a query sequence to an alignment of multiple (structurally and biochemically) related proteins. When the sequence similarity is low, more advanced techniques may be used. Such techniques, include, for example, protein fold recognition (protein threading; Hendlich, et al, 1990), where the compatibility of a particular polypeptide sequence with the 3-dimensional fold of a potential template protein is gauged on the basis of a knowledge-based potential.

[0354] Following the initial sequence alignment, the second step would be to optimally align the query template to the model template by manual manipulation and/or by the incorporation of features specific to the polypeptides (e.g., motifs, secondary structure predictions, and allowed conservations). Preferably, the incorporated features are found within both the model and query template.

[0355] The third step would be to identify structurally conserved regions that could be used to construct secondary core structure (Sali, et al, 1995). Loops could be added using knowledge-based techniques, and by performing forcefield calculations (Sali, et al, 1995).

[0356] The term “structure coordinates” refers to Cartesian coordinates generated from the building of a homology model. In this invention, the homology model of residues 12 to 524 of CAN-12 was derived from generating a sequence alignment with m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) using the COMPOSER suite of software within SYBYL6.6 (Tripos Associates, St. Louis, Mo.) and then generating the backbone and side chain conformations. In the original crystal structure (pdb code 1dkv) as well as the crystal structure reported elsewhere (Hosfield et al, 1999), the active site of the enzyme comprising a cysteine, a histidine and an asparagine residue was not “formed”. The helix that contains the active site C101 was altered by moving the helix down one pitch so that the active site geometry could match that found in Papain (pdb code 1b4). This modified structure of human m-calpain was used as the template for construction of the homology model (illustrated in FIG. 6 herein).

[0357] The skilled artisan would appreciate that a set of structure coordinates for a protein represents a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates, as emanate from the generation of similar homology models using different alignment templates (i.e., other than the m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11), and/or using different methods in generating the homology model, will likely have minor effects on the overall shape. Variations in coordinates may also be generated because of mathematical manipulations of the structure coordinates. For example, the structure coordinates set forth in Table IV could be manipulated by fractionalization of the structure coordinates; integer additions, or integer subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above.

[0358] Therefore, various computational analyses are necessary to determine whether a template molecule or a portion thereof is sufficiently similar to all or part of a query template (e.g., CAN-12) in order to be considered the same. Such analyses may be carried out in current software applications, such as SYBYL version 6.6 or INSIGHTII (Molecular Simulations Inc., San Diego, Calif.) version 2000 and as described in the accompanying User's Guides.

[0359] Using the superimposition tool in the program SYBYL, comparisons can be made between different structures and different conformations of the same structure. The procedure used in SYBYL to compare structures is divided into four steps: 1) load the structures to be compared; 2) define the atom equivalencies in these structures; 3) perform a fitting operation; and 4) analyze the results. Each structure is identified by a name. One structure is identified as the target (i.e., the fixed structure); the second structure (i.e., moving structure) is identified as the source structure. The atom equivalency within SYBYL is defined by user input. For the purpose of this invention, we will define equivalent atoms as protein backbone atoms (N, Cα, C and O) for all conserved residues between the two structures being compared. We will also consider only rigid fitting operations. When a rigid fitting method is used, the working structure is translated and rotated to obtain an optimum fit with the target structure. The fitting operation uses an algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atoms is an absolute minimum. This number, given in angstroms, is reported by the SYBYL program. For the purpose of the present invention, any homology model of a CAN-12 that has a root mean square deviation of conserved residue backbone atoms (N, Cα, C, O) of less than 3.0 A when superimposed on the relevant backbone atoms described by structure coordinates listed in Table IV are considered identical. More preferably, the root mean square deviation for the CAN-12 polypeptide is less than 2.0 Å.

[0360] The homology model of the present invention is useful for the structure-based design of modulators of the CAN-12 biological function, as well as mutants with altered biological function and/or specificity.

[0361] In accordance with the structural coordinates provided in Table IV and the three dimensional homology model of CAN-12, the CAN-12v1 polypeptide has been shown to comprise a an active site region embodied by the following amino acids: from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:54 (FIGS. 8A-C). In this context, the term “about” may be construed to mean 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids more in either the N- or C-terminal direction of the above referenced amino acids.

[0362] Also more preferred are polypeptides comprising all or any part of the CAN-12v1 active site domain, or a mutant or homologue of said polypeptide or molecular complex. By mutant or homologue of the molecule is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12 amino acids of not more than about 4.5 Angstroms, and preferably not more than about 3.5 Angstroms.

[0363] In preferred embodiments, the following CAN-12v1 active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALALHQDILSRVVPLNQSFTEKYAGIFRFWFWH YGNWVPVVIDDRLPVNEAGQLVFVSSTYKNLFWGALLEKAYAKLSGSYEDL QSGQVSEALVDFTGGVTMTINLAEAHGNLWDILIEATYNRTLIGCQTHSGKIL ENGLVEGHAYTLTGIRKVTCKHRPEYLVKLRNPWGKVEWKGDWSDSSSKW ELLSPKEKILLLRKDNDGEFWMTLQDFKTHFVLLV (SEQ ID NO:92). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12v1 active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0364] The present invention also encompasses polypeptides comprising at least a portion of the CAN-12 active site domain (SEQ ID NO: 92). Such polypeptides may correspond, for example, to the N- and/or C-terminal deletions of the active site domain.

[0365] In preferred embodiments, the following N-terminal CAN-12v1 active site domain deletion polypeptides are encompassed by the present invention: R1-V242, L2-V242, D3-V242, L4-V242, C5-V242, Q6-V242, G7-V242, 18-V242, V9-V242, G10-V242, D11-V242, C12-V242, W13-V242, F14-V242, L15-V242, A16-V242, A17-V242, L18-V242, Q19-V242, A20-V242, L21-V242, A22-V242, L23-V242, H24-V242, Q25-V242, D26-V242, 127-V242, L28-V242, S29-V242, R30-V242, V31-V242, V32-V242, P33-V242, L34-V242, N35-V242, Q36-V242, S37-V242, F38-V242, T39-V242, E40-V242, K41-V242, Y42-V242, A43-V242, G44-V242, 145-V242, F46-V242, R47-V242, F48-V242, W49-V242, F50-V242, W51-V242, H52-V242, Y53-V242, G54-V242, N55-V242, W56-V242, V57-V242, P58-V242, V59-V242, V60-V242, 161-V242, D62-V242, D63-V242, R64-V242, L65-V242, P66-V242, V67-V242, N68-V242, E69-V242, A70-V242, G71-V242, Q72-V242, L73-V242, V74-V242, F75-V242, V76-V242, S77-V242, S78-V242, T79-V242, Y80-V242, K81-V242, N82-V242, L83-V242, F84-V242, W85-V242, G86-V242, A87-V242, L88-V242, L89-V242, E90-V242, K91-V242, A92-V242, Y93-V242, A94-V242, K95-V242, L96-V242, S97-V242, G98-V242, S99-V242, Y100-V242, E101-V242, D102-V242, L103-V242, Q104-V242, S105-V242, G106-V242, Q107-V242, V108-V242, S109-V242, E110-V242, A111-V242, L112-V242, V113-V242, D 114-V242, F115-V242, T116-V242, G117-V242, G118-V242, V119-V242, T120-V242, M121-V242, T122-V242, I123-V242, N124-V242, L125-V242, A126-V242, E127-V242, A128-V242, H129-V242, G130-V242, N131-V242, L132-V242, W133-V242, D134-V242, I135-V242,-L136-V242, 1137-V242, E138-V242, A139-V242, T140-V242, Y141-V242, N142-V242, R143-V242, T144-V242, L145-V242, 1146-V242, G147-V242, C148-V242, Q149-V242, T150-V242, H151-V242, S152-V242, G153-V242, E154-V242, K155-V242, 1156-V242, L157-V242, E158-V242, N159-V242, G160-V242, L161-V242, V162-V242, E163-V242, G164-V242, H165-V242, A166-V242, Y167-V242, T168-V242, L169-V242, T170-V242, G171-V242, 1172-V242, R173-V242, K174-V242, V175-V242, T176-V242, C177-V242, K178-V242, H179-V242, R180-V242, P181-V242, E182-V242, Y183-V242, L184-V242, V185-V242, K186-V242, L187-V242, R188-V242, N189-V242, P190-V242, W191-V242, G192-V242, K193-V242, V194-V242, E195-V242, W196-V242, K197-V242, G198-V242, D199-V242, W200-V242, S201-V242, D202-V242, S203-V242, S204-V242, S205-V242, K206-V242, W207-V242, E208-V242, L209-V242, L210-V242, S211-V242, P212-V242, K213-V242, E214-V242, K215-V242, 1216-V242, L217-V242, L218-V242, L219-V242, R220-V242, K221-V242, D222-V242, N223-V242, D224-V242, G225-V242, E226-V242, F227-V242, W228-V242, M229-V242, T230-V242, L231-V242, Q232-V242, D233-V242, F234-V242, K235-V242, and/or T236-V242 of SEQ ID NO:92. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN-12v1 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0366] In preferred embodiments, the following C-terminal CAN-12v1 active site domain deletion polypeptides are encompassed by the present invention: R1-V242, R1-L241, R1-L240, R1-V239, R1-F238, R1-H237, R1-T236, R1-K235, R1-F234, R1-D233, R1-Q232, R1-L231, R1-T230, R1-M229, R1-W228, R1-F227, R1-E226, R1-G225, R1-D224, R1-N223, R1-D222, R1-K221, R1-R220, R1-L219, R1-L218, R1-L217, R1-1216, R1-K215, R1-E214, R1-K213, R1-P212, R1-S211, R1-L210, R1-L209, R1-E208, R1-W207, R1-K206, R1-S205, R1-S204, R1-S203, R1-D202, R1-S201, R1-W200, R1-D199, R1-G198, R1-K197, R1-W196, R1-E195, R1-V194, R1-K193, R1-G192, R1-W191, R1-P190, R1-N189, R1-R188, R1-L187, R1-K186, R1-V185, R1-L184, R1-Y183, R1-E182, R1-P181, R1-R180, R1-H179, R1-K178, R1-C177, R1-T176, R1-V175, R1-K174, R1-R173, R1-I172, R1-G171, R1-T170, R1-L169, R1-T168, R1-Y167, R1-A166, R1-H165, R1-G164, R1-E163, R1-V162, R1-L161, R1-G160, R1-N159, R1-E158, R1-L157, R1-I156, R1-K155, R1-E154, R1-G153, R1-S152, R1-H151, R1-T150, R1-Q149, R1-C148, R1-G147, R1-I146, R1-L145, R1-T144, R1-R143, R1-N142, R1-Y141, R1-T140, R1-A139, R1-E138, R1-I137, R1-L136, R1-I135, R1-D134, R1-W133, R1-L132, R1-N131, R1-G130, R1-H129, R1-A128, R1-E127, R1-A126, R1-L125, R1-N124, R1-I123, R1-T122, R1-M121, R1-T120, R1-V119, R1-G118, R1-G117, R1-T116, R1-F115, R1-D114, R1-V113, R1-L112, R1-A111, R1-E110, R1-S109, R1-V108, R1-Q107, R1-G106, R1-S105, R1-Q104, R1-L103, R1-D102, R1-E101, R1-Y100, R1-S99, R1-G98, R1-S97, R1-L96, R1-K95, R1-A94, R1-Y93, R1-A92, R1-K91, R1-E90, R1-L89, R1-L88, R1-A87, R1-G86, R1-W85, R1-F84, R1-L83, R1-N82, R1-K81, R1-Y80, R1-T79, R1-S78, R1-S77, R1-V76, R1-F75, R1-V74, R1-L73, R1-Q72, R1-G71, R1-A70, R1-E69, R1-N68, R1-V67, R1-P66, R1-L65, R1-R64, R1-D63, R1-D62, R1-161, R1-V60, R1-V59, R1-P58, R1-V57, R1-W56, R1-N55, R1-G54, R1-Y53, R1-H52, R1-W51, R1-F50, R1-W49, R1-F48, R1-R47, R1-F46, R1-145, R1-G44, R1-A43, R1-Y42, R1-K41, R1-E40, R1-T39, R1-F38, R1-S37, R1-Q36, R1-N35, R1-L34, R1-P33, R1-V32, R1-V31, R1-R30, R1-S29, R1-L28, R1-127, R1-D26, R1-Q25, R1-H24, R1-L23, R1-A22, R1-L21, R1-A20, R1-Q19, R1-L18, R1-A17, R1-A16, R1-L15, R1-F14, R1-W13, R1-C12, R1-D11, R1-G10, R1-V9, R1-I8, and/or R1-G7 of SEQ ID NO:92. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12v1 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0367] Alternatively, such polypeptides may comprise polypeptide sequences corresponding, for example, to internal regions of the CAN-12v1 active site domain (e.g., any combination of both N- and C-terminal CAN-12v1 active site domain deletions) of SEQ ID NO:92. For example, internal regions could be defined by the equation NX to CX, where NX refers to any N-terminal amino acid position of the CAN-12v1 active site domain (SEQ ID NO:92), and where CX refers to any C-terminal amino acid position of the CAN-12v1 active site domain (SEQ ID NO:92). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0368] In preferred embodiments, the following CAN-12v1 active site domain amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L91 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein D92 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L93 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein C94 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q95 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein G96 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I97 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V98 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein G99 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D100 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C101 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W102 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F103 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L104 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A105 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A106 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L107 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q108 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein A109 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L110 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A 111 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L112 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein H113 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q114 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D115 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I116 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L117 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S118 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein R119 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein V120 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V121 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P122 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein L123 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein N124 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein Q125 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S126 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein F127 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T128 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein E129 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K130 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y131 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A132 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G133 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I134 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F135 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R136 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein F137 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W138 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F139 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W140 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein H141 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y142 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein G143 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N144 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein W145 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein V146 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P147 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V148 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V149 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein I150 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D151 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D152 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R153 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L154 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein P155 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V156 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein N157 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein E158 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A159 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G160 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q161 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein L162 is substituted with either an A, C, D, E, F, G, H, 1, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V163 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein F164 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V165 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S166 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S167 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein T168 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y169 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein K170 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N171 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L172 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein F173 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W174 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G175 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A176 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L177 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L178 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E179 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K180 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A181 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y182 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A183 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K184 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L185 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S186 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G187 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S188 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein Y189 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein E190 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D191 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L192 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q193 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S194 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G195 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q196 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein V197 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S198 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein E199 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A200 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L201 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V202 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein D203 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F204 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T205 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G206 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G207 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V208 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T209 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein M210 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T211 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein I212 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N213 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L214 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A215 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E216 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A217 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H218 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G219 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N220 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L221 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein W222 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein D223 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I224 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L225 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein I226 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E227 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A228 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T229 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y230 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein N231 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein R232 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein T233 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L234 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein I235 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G236 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C237 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q238 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein T239 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H240 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S241 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G242 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E243 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K244 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein 1245 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L246 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E247 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N248 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein G249 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L250 is substituted with either an A, C, D, E, F, G, H, 1, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V251 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E252 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G253 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H254 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A255 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y256 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein T257 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L258 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein T259 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G260 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I261 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R262 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K263 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V264 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T265 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein C266 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K267 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H268 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R269 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein P270 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein E271 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y272 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein L273 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V274 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein K275 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L276 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R277 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein N278 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein P279 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein W280 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G281 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K282 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V283 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E284 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W285 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein K286 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G287 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D288 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W289 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein S290 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein D291 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S292 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S293 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S294 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein K295 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W296 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein E297 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L298 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L299 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S300 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein P301 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein K302 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E303 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K304 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I305 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L306 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L307 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L308 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R309 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K310 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D311 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N312 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein D313 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G314 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E315 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F316 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W317 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein M318 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T319 is substituted with either an A, C, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L320 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q321 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D322 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F323 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K324 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T325 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H326 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F327 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V328 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein L329 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L330 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; and/or wherein V331 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y of SEQ ID NO:54, in addition to any combination thereof. The present invention also encompasses the use of these CAN-12v1 active site domain amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0369] In preferred embodiments, the following CAN-12v1 active site domain conservative amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either a K, or H; wherein L91 is substituted with either an A, I, or V; wherein D92 is substituted with an E; wherein L93 is substituted with either an A, I, or V; wherein C94 is a C; wherein Q95 is substituted with a N; wherein G96 is substituted with either an A, M, S, or T; wherein 197 is substituted with either an A, V, or L; wherein V98 is substituted with either an A, I, or L; wherein G99 is substituted with either an A, M, S, or T; wherein D100 is substituted with an E; wherein C101 is a C; wherein W102 is either an F, or Y; wherein F103 is substituted with either a W, or Y; wherein L104 is substituted with either an A, I, or V; wherein A105 is substituted with either a G, I, L, M, S, T, or V; wherein A106 is substituted with either a G, I, L, M, S, T, or V; wherein L107 is substituted with either an A, I, or V; wherein Q108 is substituted with a N; wherein A109 is substituted with either a G, I, L, M, S, T, or V; wherein L110 is substituted with either an A, I, or V; wherein A111 is substituted with either a G, I, L, M, S, T, or V; wherein L112 is substituted with either an A, I, or V; wherein H113 is substituted with either a K, or R; wherein Q114 is substituted with a N; wherein D115 is substituted with an E; wherein I116 is substituted with either an A, V, or L; wherein L117 is substituted with either an A, I, or V; wherein S118 is substituted with either an A, G, M, or T; wherein R119 is substituted with either a K, or H; wherein V120 is substituted with either an A, I, or L; wherein V121 is substituted with either an A, I, or L; wherein P122 is a P; wherein L123 is substituted with either an A, I, or V; wherein N124 is substituted with a Q; wherein Q125 is substituted with a N; wherein S126 is substituted with either an A, G, M, or T; wherein F127 is substituted with either a W, or Y; wherein T128 is substituted with either an A, G, M, or S; wherein E129 is substituted with a D; wherein K130 is substituted with either a R, or H; wherein Y131 is either an F, or W; wherein A132 is substituted with either a G, I, L, M, S, T, or V; wherein G133 is substituted with either an A, M, S, or T; wherein I134 is substituted with either an A, V, or L; wherein F135 is substituted with either a W, or Y; wherein R136 is substituted with either a K, or H; wherein F137 is substituted with either a W, or Y; wherein W138 is either an F, or Y; wherein F139 is substituted with either a W, or Y; wherein W140 is either an F, or Y; wherein H141 is substituted with either a K, or R; wherein Y142 is either an F, or W; wherein G143 is substituted with either an A, M, S, or T; wherein N144 is substituted with a Q; wherein W145 is either an F, or Y; wherein V146 is substituted with either an A, I, or L; wherein P147 is a P; wherein V148 is substituted with either an A, I, or L; wherein V149 is substituted with either an A, I, or L; wherein 1150 is substituted with either an A, V, or L; wherein D151 is substituted with an E; wherein D152 is substituted with an E; wherein R153 is substituted with either a K, or H; wherein L154 is substituted with either an A, I, or V; wherein P155 is a P; wherein V156 is substituted with either an A, I, or L; wherein N157 is substituted with a Q; wherein E158 is substituted with a D; wherein A159 is substituted with either a G, I, L, M, S, T, or V; wherein G160 is substituted with either an A, M, S, or T; wherein Q161 is substituted with a N; wherein L162 is substituted with either an A, I, or V; wherein V163 is substituted with either an A, I, or L; wherein F164 is substituted with either a W, or Y; wherein V165 is substituted with either an A, I, or L; wherein S166 is substituted with either an A, G, M, or T; wherein S167 is substituted with either an A, G, M, or T; wherein T168 is substituted with either an A, G, M, or S; wherein Y169 is either an F, or W; wherein K170 is substituted with either a R, or H; wherein N171 is substituted with a Q; wherein L172 is substituted with either an A, I, or V; wherein F173 is substituted with either a W, or Y; wherein W174 is either an F, or Y; wherein G175 is substituted with either an A, M, S, or T; wherein A176 is substituted with either a G, I, L, M, S, T, or V; wherein L177 is substituted with either an A, I, or V; wherein L178 is substituted with either an A, I, or V; wherein E179 is substituted with a D; wherein K180 is substituted with either a R, or H; wherein A181 is substituted with either a G, I, L, M, S, T, or V; wherein Y182 is either an F, or W; wherein A183 is substituted with either a G, I, L, M, S, T, or V; wherein K184 is substituted with either a R, or H; wherein L185 is substituted with either an A, I, or V; wherein S186 is substituted with either an A, G, M, or T; wherein G187 is substituted with either an A, M, S, or T; wherein S188 is substituted with either an A, G, M, or T; wherein Y189 is either an F, or W; wherein E190 is substituted with a D; wherein D191 is substituted with an E; wherein L192 is substituted with either an A, I, or V; wherein Q193 is substituted with a N; wherein S194 is substituted with either an A, G, M, or T; wherein G195 is substituted with either an A, M, S, or T; wherein Q196 is substituted with a N; wherein V197 is substituted with either an A, I, or L; wherein S198 is substituted with either an A, G, M, or T; wherein E199 is substituted with a D; wherein A200 is substituted with either a G, I, L, M, S, T, or V; wherein L201 is substituted with either an A, I, or V; wherein V202 is substituted with either an A, I, or L; wherein D203 is substituted with an E; wherein F204 is substituted with either a W, or Y; wherein T205 is substituted with either an A, G, M, or S; wherein G206 is substituted with either an A, M, S, or T; wherein G207 is substituted with either an A, M, S, or T; wherein V208 is substituted with either an A, I, or L; wherein T209 is substituted with either an A, G, M, or S; wherein M210 is substituted with either an A, G, S, or T; wherein T211 is substituted with either an A, G, M, or S; wherein I212 is substituted with either an A, V, or L; wherein N213 is substituted with a Q; wherein L214 is substituted with either an A, I, or V; wherein A215 is substituted with either a G, I, L, M, S, T, or V; wherein E216 is substituted with a D; wherein A217 is substituted with either a G, I, L, M, S, T, or V; wherein H218 is substituted with either a K, or R; wherein G219 is substituted with either an A, M, S, or T; wherein N220 is substituted with a Q; wherein L221 is substituted with either an A, I, or V; wherein W222 is either an F, or Y; wherein D223 is substituted with an E; wherein 1224 is substituted with either an A, V, or L; wherein L225 is substituted with either an A, I, or V; wherein 1226 is substituted with either an A, V, or L; wherein E227 is substituted with a D; wherein A228 is substituted with either a G, I, L, M, S, T, or V; wherein T229 is substituted with either an A, G, M, or S; wherein Y230 is either an F, or W; wherein N231 is substituted with a Q; wherein R232 is substituted with either a K, or H; wherein T233 is substituted with either an A, G, M, or S; wherein L234 is substituted with either an A, I, or V; wherein I235 is substituted with either an A, V, or L; wherein G236 is substituted with either an A, M, S, or T; wherein C237 is a C; wherein Q238 is substituted with a N; wherein T239 is substituted with either an A, G, M, or S; wherein H240 is substituted with either a K, or R; wherein S241 is substituted with either an A, G, M, or T; wherein G242 is substituted with either an A, M, S, or T; wherein E243 is substituted with a D; wherein K244 is substituted with either a R, or H; wherein I245 is substituted with either an A, V, or L; wherein L246 is substituted with either an A, I, or V; wherein E247 is substituted with a D; wherein N248 is substituted with a Q; wherein G249 is substituted with either an A, M, S, or T; wherein L250 is substituted with either an A, I, or V; wherein V251 is substituted with either an A, I, or L; wherein E252 is substituted with a D; wherein G253 is substituted with either an A, M, S, or T; wherein H254 is substituted with either a K, or R; wherein A255 is substituted with either a G, I, L, M, S, T, or V; wherein Y256 is either an F, or W; wherein T257 is substituted with either an A, G, M, or S; wherein L258 is substituted with either an A, I, or V; wherein T259 is substituted with either an A, G, M, or S; wherein G260 is substituted with either an A, M, S, or T; wherein I261 is substituted with either an A, V, or L; wherein R262 is substituted with either a K, or H; wherein K263 is substituted with either a R, or H; wherein V264 is substituted with either an A, I, or L; wherein T265 is substituted with either an A, G, M, or S; wherein C266 is a C; wherein K267 is substituted with either a R, or H; wherein H268 is substituted with either a K, or R; wherein R269 is substituted with either a K, or H; wherein P270 is a P; wherein E271 is substituted with a D; wherein Y272 is either an F, or W; wherein L273 is substituted with either an A, I, or V; wherein V274 is substituted with either an A, I, or L; wherein K275 is substituted with either a R, or H; wherein L276 is substituted with either an A, I, or V; wherein R277 is substituted with either a K, or H; wherein N278 is substituted with a Q; wherein P279 is a P; wherein W280 is either an F, or Y; wherein G281 is substituted with either an A, M, S, or T; wherein K282 is substituted with either a R, or H; wherein V283 is substituted with either an A, I, or L; wherein E284 is substituted with a D; wherein W285 is either an F, or Y; wherein K286 is substituted with either a R, or H; wherein G287 is substituted with either an A, M, S, or T; wherein D288 is substituted with an E; wherein W289 is either an F, or Y; wherein S290 is substituted with either an A, G, M, or T; wherein D291 is substituted with an E; wherein S292 is substituted with either an A, G, M, or T; wherein S293 is substituted with either an A, G, M, or T; wherein S294 is substituted with either an A, G, M, or T; wherein K295 is substituted with either a R, or H; wherein W296 is either an F, or Y; wherein E297 is substituted with a D; wherein L298 is substituted with either an A, I, or V; wherein L299 is substituted with either an A, I, or V; wherein S300 is substituted with either an A, G, M, or T; wherein P301 is a P; wherein K302 is substituted with either a R, or H; wherein E303 is substituted with a D; wherein K304 is substituted with either a R, or H; wherein I305 is substituted with either an A, V, or L; wherein L306 is substituted with either an A, I, or V; wherein L307 is substituted with either an A, I, or V; wherein L308 is substituted with either an A, I, or V; wherein R309 is substituted with either a K, or H; wherein K310 is substituted with either a R, or H; wherein D311 is substituted with an E; wherein N312 is substituted with a Q; wherein D313 is substituted with an E; wherein G314 is substituted with either an A, M, S, or T; wherein E315 is substituted with a D; wherein F316 is substituted with either a W, or Y; wherein W317 is either an F, or Y; wherein M318 is substituted with either an A, G, S, or T; wherein T319 is substituted with either an A, G, M, or S; wherein L320 is substituted with either an A, I, or V; wherein Q321 is substituted with a N; wherein D322 is substituted with an E; wherein F323 is substituted with either a W, or Y; wherein K324 is substituted with either a R, or H; wherein T325 is substituted with either an A, G, M, or S; wherein H326 is substituted with either a K, or R; wherein F327 is substituted with either a W, or Y; wherein V328 is substituted with either an A, I, or L; wherein L329 is substituted with either an A, I, or V; wherein L330 is substituted with either an A, I, or V; and/or wherein V331 is substituted with either an A, I, or L of SEQ ID NO:54 in addition to any combination thereof. Other suitable substitutions within the CAN-12v1 active site domain are encompassed by the present invention and are referenced elsewhere herein. The present invention also encompasses the use of these CAN-12v1 active site domain conservative amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0370] For purposes of the present invention, by “at least a portion of” is meant all or any part of the CAN-12v1 active site domain corresponding to the analogous amino acids of the CAN-12 active site domain defined by the structure coordinates according to Table IV (e.g., fragments thereof). More preferred are molecules comprising all or any parts of the CAN-12v1 active site domain, corresponding to the analogous amino acids of the CAN-12 active site domain defined by the structure coordinates according to Table IV, or a mutant or homologue of said molecule or molecular complex. By mutant or homologue of the molecule it is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12v1 amino acids of not more than 4.5 Angstroms, and preferably not more than 3.5 Angstroms.

[0371] The term “root mean square deviation” means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a term that expresses the deviation or variation from a trend or object. For the purposes of the present invention, the “root mean square deviation” defines the variation in the backbone of a protein from the relevant portion of the backbone of the AR portion of the complex as defined by the structure coordinates described herein.

[0372] A preferred embodiment is a machine-readable data storage medium that is capable of displaying a graphical three-dimensional representation of a molecule or molecular complex that is defined by the structure coordinates of all of the amino acids in Table IV +/−a root mean square deviation from the backbone atoms of those amino acids of not more than 4.0 ANG, preferably 3.0 ANG.

[0373] The structure coordinates of a CAN-12 homology model, including portions thereof, is stored in a machine-readable storage medium. Such data may be used for a variety of purposes, such as drug discovery.

[0374] Accordingly, in one embodiment of this invention is provided a machine-readable data storage medium comprising a data storage material encoded with the structure coordinates set forth in Table IV.

[0375] One embodiment utilizes System 10 as disclosed in WO 98/11134, the disclosure of which is incorporated herein by reference in its entirety. Briefly, one version of these embodiments comprises a computer comprising a central processing unit (“CPU”), a working memory which may be, e.g, RAM (random-access memory) or “core” memory, mass storage memory (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals, one or more keyboards, one or more input lines, and one or more output lines, all of which are interconnected by a conventional bidirectional system bus.

[0376] Input hardware, coupled to the computer by input lines, may be implemented in a variety of ways. Machine-readable data of this invention may be inputted via the use of a modem or modems connected by a telephone line or dedicated data line. Alternatively or additionally, the input hardware may comprise CD-ROM drives or disk drives. In conjunction with a display terminal, keyboard may also be used as an input device.

[0377] Output hardware, coupled to the computer by output lines, may similarly be implemented by conventional devices. By way of example, output hardware may include a CRT display terminal for displaying a graphical representation of a region or domain of the present invention using a program such as QUANTA as described herein. Output hardware might also include a printer, so that hard copy output may be produced, or a disk drive, to store system output for later use.

[0378] In operation, the CPU coordinates the use of the various input and output devices, coordinates data accesses from mass storage, and accesses to and from the working memory, and determines the sequence of data processing steps. A number of programs may be used to process the machine-readable data of this invention. Such programs are discussed in reference to the computational methods of drug discovery as described herein. Specific references to components of the hardware system are included as appropriate throughout the following description of the data storage medium.

[0379] For the purpose of the present invention, any magnetic data storage medium which can be encoded with machine-readable data would be sufficient for carrying out the storage requirements of the system. The medium could be a conventional floppy diskette or hard disk, having a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, on one or both sides, containing magnetic domains whose polarity or orientation could be altered magnetically, for example. The medium may also have an opening for receiving the spindle of a disk drive or other data storage device.

[0380] The magnetic domains of the coating of a medium may be polarized or oriented so as to encode in a manner which may be conventional, machine readable data such as that described herein, for execution by a system such as the system described herein.

[0381] Another example of a suitable storage medium which could also be encoded with such machine-readable data, or set of instructions, which could be carried out by a system such as the system described herein, could be an optically-readable data storage medium. The medium could be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk which is optically readable and magneto-optically writable. The medium preferably has a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, usually of one side of substrate.

[0382] In the case of a CD-ROM, as is well known, the coating is reflective and is impressed with a plurality of pits to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of the coating. A protective coating, which preferably is substantially transparent, is provided on top of the reflective coating.

[0383] In the case of a magneto-optical disk, as is well known, the coating has no pits, but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser. The orientation of the domains can be read by measuring the polarization of laser light reflected from the coating. The arrangement of the domains encodes the data as described above.

[0384] Thus, in accordance with the present invention, data capable of displaying the three dimensional structure of the CAN-12 homology model, or portions thereof and their structurally similar homologues is stored in a machine-readable storage medium, which is capable of displaying a graphical three-dimensional representation of the structure. Such data may be used for a variety of purposes, such as drug discovery.

[0385] For the first time, the present invention permits the use of structure-based or rational drug design techniques to design, select, and synthesize chemical entities that are capable of modulating the biological function of CAN-12v 1.

[0386] Accordingly, the present invention is also directed to the design of small molecules which imitates the structure of the CAN-12v1 active site domain (SEQ ID NO:92), or a portion thereof, corresponding to the analogous amino acids of the CAN-12 active site domain defined by the structure provided in Table IV. Alternatively, the present invention is directed to the design of small molecules which may bind to at least part of the CAN-12v1 active site domain (SEQ ID NO:92), or some portion thereof. For purposes of this invention, by CAN-12v1 active site domain, it is also meant to include mutants or homologues thereof. In a preferred embodiment, the mutants or homologues have at least 25% identity, more preferably 50% identity, more preferably 75% identity, and most preferably 90% identity to SEQ ID NO:92. In this context, the term “small molecule” may be construed to mean any molecule described known in the art or described elsewhere herein, though may include, for example, peptides, chemicals, carbohydrates, nucleic acids, PNAs, and any derivatives thereof.

[0387] The three-dimensional model structure of CAN-12v1, corresponding to the structure coordinates of the analogous amino acids of the CAN-12 polypeptide, will also provide methods for identifying modulators of biological function. Various methods or combination thereof can be used to identify these compounds.

[0388] For example, test compounds can be modeled that fit spatially into the active site domain in CAN-12v1 embodied by the sequence from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331, or some portion thereof, of SEQ ID NO:54 (corresponding to SEQ ID NO:92), in accordance with the structural coordinates of the corresponding amino acids of the CAN-12 polypeptide of Table IV.

[0389] Structure coordinates of the active site domain in CAN-12v1 defined by the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:54, can also be used to identify structural and chemical features. Identified structural or chemical features can then be employed to design or select compounds as potential CAN-12v1 modulators. By structural and chemical features it is meant to include, but is not limited to, van der Waals interactions, hydrogen bonding interactions, charge interaction, hydrophobic bonding interaction, and dipole interaction. Alternatively, or in conjunction with, the three-dimensional structural model can be employed to design or select compounds as potential CAN-12v1 modulators. Compounds identified as potential CAN-12v1 modulators can then be synthesized and screened in an assay characterized by binding of a test compound to the CAN-12v1, or in characterizing the ability of CAN-12v1 to modulate a protease target in the presence of a small molecule. Examples of assays useful in screening of potential CAN-12v1 modulators include, but are not limited to, screening in silico, in vitro assays and high throughput assays. Finally, these methods may also involve modifying or replacing one or more amino acids at amino acid positions, C101, H254, and/or N278 of SEQ ID NO:54 in accordance with the structure coordinates of the corresponding amino acids of CAN-12 as provided in Table IV.

[0390] However, as will be understood by those of skill in the art upon this disclosure, other structure based design methods can be used. Various computational structure based design methods have been disclosed in the art.

[0391] For example, a number of computer modeling systems are available in which the sequence of the CAN-12v1 and the CAN-12 structure (i.e., atomic coordinates of CAN-12 and/or the atomic coordinates of the active site domain as provided in Table IV, or the corresponding amino acids of CAN-12v1 which are identical to the same region of CAN-12 and for which the same coordinates may be relied thereon) can be input. This computer system then generates the structural details of one or more these regions in which a potential CAN-12v1 modulator binds so that complementary structural details of the potential modulators can be determined. Design in these modeling systems is generally based upon the compound being capable of physically and structurally associating with CAN-12v1. In addition, the compound must be able to assume a conformation that allows it to associate with CAN-12v1. Some modeling systems estimate the potential inhibitory or binding effect of a potential CAN-12v1 modulator prior to actual synthesis and testing.

[0392] Methods for screening chemical entities or fragments for their ability to associate with a given protein target are also well known. Often these methods begin by visual inspection of the binding site on the computer screen. Selected fragments or chemical entities are then positioned in the active site domain of CAN-12v1. Docking is accomplished using software such as INSIGHTII, QUANTA and SYBYL, following by energy minimization and molecular dynamics with standard molecular mechanic forcefields such as CHARMM and AMBER. Examples of computer programs which assist in the selection of chemical fragment or chemical entities useful in the present invention include, but are not limited to, GRID (Goodford, 1985), AUTODOCK (Goodsell, 1990), and DOCK (Kuntz et al. 1982).

[0393] Upon selection of preferred chemical entities or fragments, their relationship to each other and CAN-12v1 can be visualized and then assembled into a single potential modulator. Programs useful in assembling the individual chemical entities include, but are not limited to CAVEAT (Bartlett et al. 1989) and 3D Database systems (Martin1992).

[0394] Alternatively, compounds may be designed de novo using either an empty active site or optionally including some portion of a known inhibitor. Methods of this type of design include, but are not limited to LUDI (Bohm 1992) and LeapFrog (Tripos Associates, St. Louis Mo.).

[0395] In addition, CAN-12v1 is overall well suited to modern methods including combinatorial chemistry.

[0396] Programs such as DOCK (Kuntz et al. 1982) can be used with the atomic coordinates from the homology model to identify potential ligands from databases or virtual databases which potentially bind CAN-12 active site domain, and which may therefore be suitable candidates for synthesis and testing.

[0397] Additionally, the three-dimensional homology model of CAN-12 will aid in the design of mutants with altered biological activity for the CAN-12v1 polypeptide.

[0398] The following are encompassed by the present invention: a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12 according to Table IV or a homologue of said model, wherein said homologue comprises backbone atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; and a machine-readable data storage medium, wherein said molecule is defined by the set of structure coordinates of the model for CAN-12 according to Table IV, or a homologue of said molecule, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; a model comprising all or any part of the model defined by structure coordinates of CAN-12 according to Table IV, or a mutant or homologue of said molecule or molecular complex.

[0399] In a further embodiment, the following are encompassed by the present invention: a method for identifying a mutant of CAN-12v1 with altered biological properties, function, or reactivity, the method comprising any combination of steps of: use of the model or a homologue of said model according to Table IV, for the design of protein mutants with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein; and use of the model or a homologue of said model, for the design of a protein with mutations in the active site domain comprised of the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:54 according to the corresponding amino acids of CAN-12 as provided in Table IV with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein.

[0400] In further preferred embodiments, the following are encompassed by the present invention: a method for identifying modulators of CAN-12v1 biological properties, function, or reactivity, the method comprising any combination of steps of: modeling test compounds that overlay spatially into the active site domain defined by all or any portion of residues from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:54 in reference to the corresponding amino acids of CAN-12 according to Table IV, or using a homologue or portion thereof.

[0401] The present invention encompasses using the structure coordinates as set forth herein to identify structural and chemical features of the CAN-12v1 polypeptide; employing identified structural or chemical features to design or select compounds as potential CAN-12v1 modulators; employing the three-dimensional structural model to design or select compounds as potential CAN-12v1 modulators; synthesizing the potential CAN-12v1 modulators; screening the potential CAN-12v1 modulators in an assay characterized by binding of a protein to the CAN-12v1; selecting the potential CAN-12v1 modulator from a database; designing the CAN-12v1 modulator de novo; and/or designing said CAN-12v1 modulator from a known modulator activity.

[0402] Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO: 53 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides consisting of a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2081 of SEQ ID NO:53, b is an integer between 15 to 2095, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:53, and where b is greater than or equal to a+14.

[0403] In one embodiment, a CAN12.v1 polypeptide comprises a portion of the amino sequence depicted in FIGS. 8A-C. In another embodiment, a CAN12.v1 polypeptide comprises at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids of the amino sequence depicted in FIGS. 8A-C. In further embodiments, the CAN12.v1 polypeptide does not consist of the sequence ALLEKAYAKL (SEQ ID NO:141), and/or ALLEKAYAKLSGSYE. (SEQ ID NO:142).

[0404] Features of the Polypeptide Encoded by Gene No:3

[0405] The polypeptide of this gene provided as SEQ ID NO:56 (FIGS. 9A-C), encoded by the polynucleotide sequence according to SEQ ID NO:55 (FIGS. 9A-C), and/or encoded by the polynucleotide contained within the deposited clone, CAN-12v2, has significant homology at the nucleotide and amino acid level to a number of calpains, which include, for example, the human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) μ-TYPE ) (mCALPAIN 1; Genbank Accession No: gilO88666; SEQ ID NO:7); the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); the human CAN11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12). An alignment of the CAN-12v2 polypeptide with these proteins is provided in FIGS. 2A-E. Based upon such strong conservation, the inventors have ascribed the CAN-12v2 polypeptide as having proteolytic activity, preferably calpain activity.

[0406] The CAN-12v2 polypeptide was determined to have 28.8% identity and 35.7% similarity with the human CAN10 protein (type, II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3); to have 33.3% identity and 45.1% similarity with the human CAN5 protein (hCAN5; Genbank Accession No: gilNP—004046; SEQ ID NO:4); to have 38.3% identity and 46.6% similarity with the large catalytic subunit of the human CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase, CANP, μ-TYPE) (hCAN1; Genbank Accession No: gil12408656; SEQ ID NO:5); to have 41.3% identity and 49.8% similarity with the large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6); to have 39.6% identity and 47.6% similarity with the large catalytic subunit of the mouse CALPAIN 1 protein (also referred to as Calcium-Activated Neutral Proteinase) (CANP) 1-TYPE ) (mCALPAIN1; Genbank Accession No: gilO88666; SEQ ID NO:7); to have 40.6% identity and 48.8% similarity with the mouse CALPAIN LP82 (mLP82; Genbank Accession No: gil3661585; SEQ ID NO:8); to have 36.3% identity and 44.9% similarity with the rat stomach-specific calcium-activated neutral protease large subunit, NCL2 protein (rNCL2; Genbank Accession No: gilNP—006606; SEQ ID NO:9); to have 38.8% identity and 47.3% similarity with the human CAN 11 protein (hCAN11; Genbank Accession No: gilNP—008989; SEQ ID NO:10); to have 37.9% identity and 47.3% similarity with the human CAN2 protein (hCAN2; Genbank Accession No: gil4502563; SEQ ID NO:11); and to have 40.7% identity and 49.8% similarity with the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12).

[0407] The human CAN10 protein (type II diabetes linked) (hCAN10; Genbank Accession No: gilNP—075574; SEQ ID NO:3)is a human calpain gene that encodes a large calpain subunit. CAN10 is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. CAN10 is similar in organization to calpains 5 and 6 and is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM) and located within the NIDDM1 chromosomal region (Nat. Genet. 26 (2), 163-175 (2000)).

[0408] The large subunit of the human calpain 3 protein (EC 3.4.22.17) (also referred to as CALPAIN L3, CALPAIN P94, Calcium-Activated Neutral Proteinase 3, CANP 3; muscle-specific calcium-activated neutral protease 3 large subunit) (hCAN3; Genbank Accession No: gil4557405; SEQ ID NO:6) is a muscle-specific member of the calpain large subunit family. Loss of CAPN3 function has been associated with limb-girdle muscular dystrophies type 2A (Cell 81 (1), 27-40 (1995)).

[0409] The human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is a calpain that is expressed predominantly in stomach and small intestine and is thought to have specialized functions in the digestive tract, and be associated with gastric cancer.(Biol. Chem. 379 (2), 175-183 (1998); and Jpn. J. Cancer Res. 91 (5), 459-463 (2000)).

[0410] As described-above, the CAN-12v2 polypeptide was found to have significant sequence homology with calpains, particularly members of the m-calpain family. A conserved peptide signature of Qx3(G,E)xC(Y,W)x2(S,T,A,G,C)(S,T,A,G,C,V) Qx{3}(G)xC(W)x{2}(A)(A) (referred to as a thiol (cysteine) protease active site domain) common to most calpain family members is found in the protein sequence of CAN-12v2 from amino acid 90 to amino acid 111 of SEQ ID NO:56 (FIGS. 9A-C). Protein threading and molecular modeling of CAN-12v2 suggests that CAN-12v2 has a structural fold similar to representative m-calpains. Moreover, the structural and threading alignments of the present invention suggest that amino acids 101 (“C”), 254 (“H”), and 278 (“N”) of SEQ ID NO:56 (FIGS. 9A-C) may represent the catalytic amino acids within the active site domain. Thus, based upon the sequence and structural homology to known calpains, particularly the presence of the thiol cysteine protease active site domain, the novel CAN-12v2 is believed to represent a novel human calpain.

[0411] In confirmation of the strong homology to known calpains, the CAN-12v2 polypeptide was determined to have several conserved catalytic amino acids at amino acid C101, H254, and N278 of SEQ ID NO:56 (FIGS. 9A-C). As discussed more particularly herein, calpains are a group of structurally diverse, high molecular weight (400 to 500 amino acids) proteins that have a catalytic cysteine amino acid and one or more calcium binding domains. Despite the structural heterogeneity, calpains share some well defined structural-functional characteristics, particularly in their active site domains.

[0412] In preferred embodiments, the CAN-12v2 polypeptide of the present invention is directed to a polypeptide having structural similarity to calpains.

[0413] Based upon the strong homology to members of the calpain family, the CAN-12v2 polypeptide is expected to share at least some biological activity with calpains, preferably with m-calpain family members, and more preferable to the large subunits of m-calpain family members, in addition to other calpains and calpain subunits referenced herein and/or otherwise known in the art.

[0414] Expression profiling designed to measure the steady state mRNA levels encoding the CAN-12 polypeptide showed predominately high expression levels in spinal cord tissue; significantly high expression in lymph node and thymus, and to a lesser extent, in spleen tissue (See FIG. 4).

[0415] Expanded analysis of CAN-12 expression levels by TaqMan™ quantitative PCR (see FIG. 6) confirmed that the CAN-12 polypeptide is expressed in the lymph gland. However, the TaqMan™ quantitative PCR determined that the CAN-12 polypeptide is primarily expressed in the eosophagus. In fact, with the exception of the lymph gland, the steady state mRNA level of CAN-12 was approximately 2700 times higher in the esophagus than in all other tissues tested. These data suggest modulators of the CAN-12 polynucleotides and polypeptides may be useful for the treatment, detection, and/or amelioration of the following, non-limiting diseases and disorders associated with the eosphagus: dysphagia, cricoharyngeal incoordination, esophageal carcinoma, esophageal webs, achalasia, symptomatic diffuse esophageal spasm, gastroesophageal reflux, and/or corrosive esophagitis.

[0416] The polynucleotides encoding the CAN-12 polypeptide of the present invention were used to determine the chromosomal localization of the calpain12 gene. Polynuclelotides corresponding to CAN-12 (SEQ ID NO:1) were shown to localize to chromosome 2, specifically 2p16-p21. The comparison of the chromosomal location of the calpain12 gene with the location of chromosomal regions which have been shown to be associated with specific diseases or conditions, e.g. by linkage analysis, can be indicative of diseases in which calpain12 may play a role. Interestingly, a whole-genome linkage scan in multiple sclerosis families (Ebers et al. A full genome search in multiple sclerosis. Nature Genet. 13: 472-476, 1996.) identified 5 susceptibility loci on chromosomes 2, 3, 5, 11, and X. In particular, an association was identified with marker D2S119 on chromosome 2 and MS. The localization of the D2S119 marker was further delimeated to 2p16-p21 based on a radiation hybrid linkage map retrieved from an online query at NCBI web site: http:/www.ncbi.nlm.nih.gov/genome/sts/. Since the map of calpain 12 and the susceptibility marker D2S119 overlaps, it is reasonable to postulate that calpain 12 may contribute to MS. Furthermore, the transcription profile of calpain12 indicated a prominent expression in spinal cord, and implication of calpains in MS has been suggested (Shields DC et al. A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc Natl Acad Sci U S A. 96:11486-91.1999).

[0417] The CAN-12v2 polynucleotides and polypeptides of the present invention, including agonists and/or fragments thereof, have uses that include modulating cellular adhesion events, cellular proliferation, and inflammation, in various cells, tissues, and organisms, and particularly in mammalian spinal cord tissue, lymph node, thymus, and spleen tissue, preferably human tissue. CAN-12v2 polynucleotides and polypeptides of the present invention, including agonists and/or fragments thereof, may be useful in diagnosing, treating, prognosing, and/or preventing neural, immune, hematopoietic, and/or proliferative diseases or disorders.

[0418] The strong homology to human calpains, particularly m-calpains, combined with the predominate localized expression in esophagus tissue suggests the CAN-12 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing gastrointestinal diseases, particularly esophageal diseases and/or disorders which include the following non-limiting examples: aberrant transport of food bolus from the mouth to the stomach, aberrant prevention of retrograde flow of gastrointestinal contents, aberrant esophageal peristaltic contractions, pyrosis, painful swallowing, reflux esophagitis, esophageal motility disorders, esophageal spasms, diffuse esophageal spasm, atypical chest pain, regurgitation, oropharyngeal paralysis, nasal regurgitation, dysphagia, cricopharyngeal bar, globus pharyngeus, achalasia, motor disorders of the esophageal smooth muscle, scleroderma esophagus, gastroesophageal reflux disease (GERD), esophagitis, Barrett's esophagus, viral esophagitis, Herpes simplex virus mediated viral esophagitis, Varicella-zoster virus mediated viral esophagitis, Cytomegalovirus mediated viral esophagitis, bacterial esophagitis, Lactobacillus mediated bacterial esophagitis, Candida mediated esophagitis, radiation esophagitis, corrosive esophagitis, pill-induced esophagitis, esophagitis associated with mucocutaneous and systemic diseases, diverticula, lower esophageal mucosal ring, lower esophageal muscular ring, hiatal hernia, paraesophageal hernia, esophageal rupture, and/or Mallory-Weiss Syndrome.

[0419] Although calpains are typically associated primarily with neurogenerative conditions, their association in gastrointenstinal tissues has precedence. For example, the human CAN9 protein (hCAN9; Genbank Accession No: gil5729758; SEQ ID NO:12) is predominately expressed in the stomach and small intestine and is thought to be associated with gastric cancers.

[0420] The strong homology to human calpains, particularly m-calpains, combined with the localized expression in spinal cord tissue suggests the CAN-12v2 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, and/or preventing neural diseases, neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the “Neurological Diseases”, “Regeneration” and “Hyperproliferative Disorders” sections below, in the Examples, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0421] Alternatively, the strong homology to human calpains, particularly m-calpains, combined with the localized expression in lymph node, thymus, and spleen tissue suggests the CAN-12v2 polynucleotides and polypeptides may be useful in treating, diagnosing, prognosing, ameliorating, and/or preventing immune diseases and/or disorders. Representative uses are described in the “Immune Activity” and “Infectious Disease” sections below, and elsewhere herein. Briefly, the strong expression in immune tissue indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. The CAN-12v2 polypeptide may also be useful as a preventative agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lense tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren's disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product may be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types.

[0422] Moreover, the protein would be useful in the detection, treatment, and/or prevention of a variety of vascular disorders and conditions, which include, but are not limited to miscrovascular disease, vascular leak syndrome, aneurysm, stroke, embolism, thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.

[0423] In addition, antagonists of the CAN-12v2 polynucleotides and polypeptides may have uses that include diagnosing, treating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include immune and/or proliferative diseases or disorders, particularly thrombosis, embolism, and other blood disorders. Therapeutic and/or pharmaceutical compositions comprising the CAN-12v2 polypeptides may be formulated to comprise heparin.

[0424] In addition, antagonists of the CAN-12v2 polynucleotides and polypeptides may have uses that include diagnosing, treating, ameliorating, prognosing, and/or preventing diseases or disorders related to hyper calpain activity, which may include neuronal excitotoxicity, ischemic stroke, hemoragic stroke, hypoxic stress, trauma, cell destruction, spinal cord injury following trauma, degeneration of vulnerable hippocampal neurons after ischemia, reovirus-induced apoptosis, viral-induced induced myocarditis, acute and chronic inflammation, cataract formation, multiple sclerosis, demylenating disorders, acoustic trauma, hearing loss caused by noise, neuronal damage, cardiac ischemic damage, and/or hepatocyte necrosis during and following anoxia.

[0425] CAN-12v2 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include modulating development, differentiation, cellular transformation in response to cell signaling, cell-cell and/or cell-extracellular matrix interactions, clustering of the integrin receptor aIIb3, modulating in long term potentiation (memory), modulating neurite outgrowth, modulating cortical lamination activation of protein kinases and phosphatases, remodeling and disassembling the cytoskeleton, cell cycle modulation, in addition, to ameliorating, preventing, and/or treating limb-girdle muscular dystrophy (LGMD), insulin resistance in diabetics, Alzheimer's disease, Multiple sclerosis, Huntington's disease, Parkinson's disease and amyotrophy.

[0426] Moreover, CAN-12v2 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include treating, diagnosing, prognosing, and/or preventing hyperproliferative disorders, particularly of the neural and immune systems. Such disorders may include, for example, cancers, and metastatic conditions.

[0427] CAN-12v2 polynucleotides and polypeptides, including fragments and/or antagonsists thereof, may have uses which include identification of modulators of CAN-12v2 function including antibodies (for detection or neutralization), naturally-occurring modulators and small molecule modulators. Antibodies to domains (including CAN-12v2 epitopes provided herein) of the CAN-12v2 protein could be used as diagnostic agents of inflammatory conditions in patients, are useful in monitoring the activation and presence of cognate proteases, and can be used as a biomarker for the protease involvement in disease states and in the evaluation of inhibitors of the cognate protease in vivo.

[0428] CAN-12v2 polypeptides and polynucleotides are useful for diagnosing diseases related to over or under expression of CAN-12v2 proteins by identifying mutations in the CAN-12v2 gene using CAN-12v2 probes, or determining CAN-12v2 protein or mRNA expression levels. CAN-12v2 polypeptides are also useful for screening for compounds, which affect activity of the protein. Diseases that can be treated with CAN-12v2 include, the following, non-limiting examples: neuro-regeneration, neuropathic pain, obesity, anorexia, HIV infections, cancers, bulimia, asthma, Parkinson's disease, acute heart failure, hypotension, hypertension, osteoporosis, angina pectoris, myocardial infarction, psychotic, immune, metabolic, cardiovascular, and neurological disorders.

[0429] The predominate expression in neural tissues, combined with the significant expression in a number of other tissues, suggests the CAN-12v2 polynucleotide and polypeptide of the present invention may be involved in modulating nerve invasion, innervation, nerve maintenance, and potentially myeline sheath maintenance and integrity.

[0430] The CAN-12v2 polynucleotides and polypeptides, including fragments and antagonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing diseases and disorders of the neural system, particularly Alzheimer's disease, either directly or indirectly, in addition to other neural disorders known in the art or provided in the “Neurological Diseases” section herein, such as modulating nerve invasion, innervation, nerve maintenance, potentially myelin sheath maintenance and integrity, encephalomyelitis, autoimmune encephalomyelitis, human T cell leukemia virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP), and neuro-inflammatory diseases.

[0431] Molecular genetic manipulation of the structure of the active site domain, particularly the predicted catalytic amino acids, and of other functional domains in the calpain family (e.g., active site domain binding pocket) enables the production of calpains with tailor-made activities. Thus, the CAN-12v2 polypeptides, and fragments thereof, as well as any homologous product resulting from genetic manipulation of the structure, are useful for NMR-based design of modulators of CAN-12v2 biological activity, and calpains, in general.

[0432] CAN-12v2 polypeptides and polynucleotides have additional uses which include diagnosing diseases related to the over and/or under expression of CAN-12v2 by identifying mutations in the CAN-12v2 gene by using CAN-12v2 sequences as probes or by determining CAN-12v2 protein or mRNA expression levels. CAN-12v2 polypeptides may be useful for screening compounds that affect the activity of the protein. CAN-12v2 peptides can also be used for the generation of specific antibodies and as bait in yeast two hybrid screens to find proteins the specifically interact with CAN-12v2 (described elsewhere herein).

[0433] The CAN-12v2 polynucleotides and polypeptides, including fragments and agonists thereof, may have uses which include detecting, diagnosing, treating, ameliorating, and/or preventing metabolic diseases and disorders, such as diabetes. Moreover, expressed human CAN-12v2 may be useful in the detection of patients susceptible to diabetes. Also paradigms that would simulate intracellular CAN-12v2 activity would be useful in treating diabetes.

[0434] The CAN-12v2 polynucleotides and polypeptides, including fragments thereof, may have uses which include identifying inhibitors of intracellular calpain inhibitors (calpastatins) leading to an effective increase in calpain activity.

[0435] Various approaches to detect alterations or allelic variants at the genomic or mRNA level of CAN-12v2, could be used as a diagnostic for identifying MS patients, or individuals susceptible to have MS. It is likely that the CAN-12v2 gene comprises polymorphic sites (i.e. SNPs), with specific alleles which may be associated with MS or other neurodegenerative disorders, or associated with an increased likelihood of developing these diseases. Therefore, the invention provides the CAN-12v2 sequence that can be used to design specific primers for the identification of polymorphisms or mutations in CAN-12v2 of patients affected with MS. The presence of a specific allele variant, such as a SNP allele or SNPs haplotype that renders the subject carrying it more susceptible to develop MS or other related diseases could be identified (e.g. a variant in the CAN-12v2 promoter region that increased transcript levels of CAN-12v2, or mutations in the coding sequence that increased the stability or half-life of the CAN-12v2 protein). Other methods such as Northern-blot analysis could be performed to measure transcript levels using a CAN-12v2 cDNA probe derived from the sequence of the invention.

[0436] Although it is believed the encoded polypeptide may share at least some biological activities with human calpains (particularly m-calpains), a number of methods of determining the exact biological function of this clone are either known in the art or are described elsewhere herein. Briefly, the function of this clone may be determined by applying microarray methodology. Nucleic acids corresponding to the CAN-12v2 polynucleotides, in addition to, other clones of the present invention, may be arrayed on microchips for expression profiling. Depending on which polynucleotide probe is used to hybridize to the slides, a change in expression of a specific gene may provide additional insight into the function of this gene based upon the conditions being studied. For example, an observed increase or decrease in expression levels when the polynucleotide probe used comes from diseased neural tissue, as compared to, normal tissue might indicate a function in modulating neural function, for example. In the case of CAN-12v2, spinal cord, lymph node, thymus, and/or spleen tissue should be used to extract RNA to prepare the probe.

[0437] In addition, the function of the protein may be assessed by applying quantitative PCR methodology, for example. Real time quantitative PCR would provide the capability of following the expression of the CAN-12v2 gene throughout development, for example. Quantitative PCR methodology requires only a nominal amount of tissue from each developmentally important step is needed to perform such experiments. Therefore, the application of quantitative PCR methodology to refining the biological function of this polypeptide is encompassed by the present invention. In the case of CAN-12v2, a disease correlation related to CAN-12v2 may be made by comparing the mRNA expression level of CAN-I 2v2 in normal tissue, as compared to diseased tissue (particularly diseased tissue isolated from the following: esophagus, spinal cord, lymph node, thymus, and/or spleen tissue). Significantly higher or lower levels of CAN-12v2 expression in the diseased tissue may suggest CAN-12v2 plays a role in disease progression, and antagonists against CAN-12v2 polypeptides would be useful therapeutically in treating, preventing, and/or ameliorating the disease. Alternatively, significantly higher or lower levels of CAN-12v2 expression in the diseased tissue may suggest CAN-12v2 plays a defensive role against disease progression, and agonists of CAN-12v2 polypeptides may be useful therapeutically in treating, preventing, and/or ameliorating the disease. Also encompassed by the present invention are quantitative PCR probes corresponding to the polynucleotide sequence provided as SEQ ID NO:55 (FIGS. 9A-C).

[0438] The function of the protein may also be assessed through complementation assays in yeast. For example, in the case of the CAN-12v2, transforming yeast deficient in calpain activity, particularly m-calpain activity, and assessing their ability to grow would provide convincing evidence the CAN-12v2 polypeptide has calpain activity, and possibly m-calpain activity. Additional assay conditions and methods that may be used in assessing the function of the polynucleotides and polypeptides of the present invention are known in the art, some of which are disclosed elsewhere herein.

[0439] Alternatively, the biological function of the encoded polypeptide may be determined by disrupting a homologue of this polypeptide in Mice and/or rats and observing the resulting phenotype. Such knock-out experiments are known in the art, some of which are disclosed elsewhere herein.

[0440] Moreover, the biological function of this polypeptide may be determined by the application of antisense and/or sense methodology and the resulting generation of transgenic mice and/or rats. Expressing a particular gene in either sense or antisense orientation in a transgenic mouse or rat could lead to respectively higher or lower expression levels of that particular gene. Altering the endogenous expression levels of a gene can lead to the observation of a particular phenotype that can then be used to derive indications on the function of the gene. The gene can be either over-expressed or under expressed in every cell of the organism at all times using a strong ubiquitous promoter, or it could be expressed in one or more discrete parts of the organism using a well characterized tissue-specific promoter (e.g., an esophagus, spinal cord, lymph node, thymus, or spleen specific promoter), or it can be expressed at a specified time of development using an inducible and/or a developmentally regulated promoter.

[0441] In the case of CAN-12v2 transgenic mice or rats, if no phenotype is apparent in normal growth conditions, observing the organism under diseased conditions (neural, immune, hematopoietic diseases or disorders, cancers, etc.) may lead to understanding the function of the gene. Therefore, the application of antisense and/or sense methodology to the creation of transgenic mice or rats to refine the biological function of the polypeptide is encompassed by the present invention.

[0442] In preferred embodiments, the following N-terminal CAN-12v2 deletion polypeptides are encompassed by the present invention: M1-L697, S2-L697, L3-L697, W4-L697, P5-L697, P6-L697, F7-L697, R8-L697, C9-L697, R10-L697, W11-L697, K12-L697, L13-L697, A14-L697, P15-L697, R16-L697, Y17-L697, S18-L697, R19-L697, R20-L697, A21-L697, S22-L697, P23-L697, Q24-L697, Q25-L697, P26-L697, Q27-L697, Q28-L697, D29-L697, F30-L697, E31-L697, A32-L697, L33-L697, L34-L697, A35-L697, E36-L697, C37-L697, L38-L697, R39-L697, N40-L697, G41-L697, C42-L697, I43-L697, F44-L697, E45-L697, D46-L697, T47-L697, S48-L697, F49-L697, P50-L697, A51-L697, T52-L697, L53-L697, S54-L697, S55-L697, 156-L697, G57-L697, S58-L697, G59-L697, S60-L697, L61-L697, L62-L697, Q63-L697, K64-L697, L65-L697, P66-L697, P67-L697, R68-L697, L69-L697, Q70-L697, W71-L697, K72-L697, R73-L697, P74-L697, P75-L697, E76-L697, L77-L697, H78-L697, S79-L697, N80-L697, P81-L697, Q82-L697, F83-L697, Y84-L697, F85-L697, A86-L697, K87-L697, A88-L697, K89-L697, R90-L697, L91-L697, D92-L697, L93-L697, C94-L697, Q95-L697, G96-L697, 197-L697, V98-L697, G99-L697, D100-L697, C101-L697, W102-L697, F103-L697, L104-L697, A105-L697, A 106-L697, L107-L697, Q108-L697, A109-L697, L110-L697, A111-L697, L112-L697, H113-L697, Q114-L697, D115-L697, 1116-L697, L117-L697, S118-L697, R119-L697, V120-L697, V121-L697, P122-L697, L123-L697, N124-L697, Q125-L697, S126-L697, F127-L697, T128-L697, E129-L697, K130-L697, Y131-L697, A132-L697, G133-L697, 1134-L697, F135-L697, R136-L697, F137-L697, W138-L697, F139-L697, W140-L697, H141-L697, Y142-L697, G143-L697, N144-L697, W145-L697, V146-L697, P147-L697, V148-L697, V149-L697, 1150-L697, D151-L697, D152-L697, R153-L697, L154-L697, P155-L697, V156-L697, N157-L697, E158-L697, A159-L697, G160-L697, Q161-L697, L162-L697, V163-L697, F164-L697, V165-L697, S166-L697, S167-L697, T168-L697, Y169-L697, K170-L697, N171-L697, L172-L697, F173-L697, W174-L697, G175-L697, A176-L697, L177-L697, L178-L697, E179-L697, K180-L697, A181-L697, Y182-L697, A183-L697, K184-L697, L185-L697, S186-L697, G187-L697, S188-L697, Y189-L697, E190-L697, D191-L697, L192-L697, Q193-L697, S194-L697, G195-L697, Q196-L697, V197-L697, S198-L697, E199-L697, A200-L697, L201-L697, V202-L697, D203-L697, F204-L697, T205-L697, G206-L697, G207-L697, V208-L697, T209-L697, M210-L697, T211-L697, 1212-L697, N213-L697, L214-L697, A215-L697, E216-L697, A217-L697, H218-L697, G219-L697, N220-L697, L221-L697, W222-L697, D223-L697, 1224-L697, L225-L697, 1226-L697, E227-L697, A228-L697, T229-L697, Y230-L697, N231-L697, R232-L697, T233-L697, L234-L697, 1235-L697, G236-L697, C237-L697, Q238-L697, T239-L697, H240-L697, S241-L697, G242-L697, E243-L697, K244-L697, 1245-L697, L246-L697, E247-L697, N248-L697, G249-L697, L250-L697, V251-L697, E252-L697, G253-L697, H254-L697, A255-L697, Y256-L697, T257-L697, L258-L697, T259-L697, G260-L697, 1261-L697, R262-L697, K263-L697, V264-L697, T265-L697, C266-L697, K267-L697, H268-L697, R269-L697, P270-L697, E271-L697, Y272-L697, L273-L697, V274-L697, K275-L697, L276-L697, R277-L697, N278-L697, P279-L697, W280-L697, G281-L697, K282-L697, V283-L697, E284-L697, W285-L697, K286-L697, G287-L697, D288-L697, W289-L697, S290-L697, D291-L697, S292-L697, S293-L697, S294-L697, K295-L697, W296-L697, E297-L697, L298-L697, L299-L697, S300-L697, P301-L697, K302-L697, E303-L697, K304-L697, 1305-L697, L306-L697, L307-L697, L308-L697, R309-L697, K310-L697, D311-L697, N312-L697, D313-L697, G314-L697, E315-L697, F316-L697, W317-L697, M318-L697, T319-L697, L320-L697, Q321-L697, D322-L697, F323-L697, K324-L697, T325-L697, H326-L697, F327-L697, V328-L697, L329-L697, L330-L697, V331-L697, 1332-L697, C333-L697, K334-L697, L335-L697, T336-L697, P337-L697, G338-L697, L339-L697, L340-L697, S341-L697, Q342-L697, E343-L697, A344-L697, A345-L697, Q346-L697, K347-L697, W348-L697, T349-L697, Y350-L697, T351-L697, M352-L697, R353-L697, E354-L697, G355-L697, R356-L697, W357-L697, E358-L697, K359-L697, R360-L697, S361-L697, T362-L697, A363-L697, G364-L697, G365-L697, Q366-L697, R367-L697, Q368-L697, L369-L697, L370-L697, Q371-L697, D372-L697, T373-L697, F374-L697, W375-L697, K376-L697, N377-L697, P378-L697, Q379-L697, F380-L697, L381-L697, L382-L697, S383-L697, V384-L697, W385-L697, R386-L697, P387-L697, E388-L697, E389-L697, G390-L697, R391-L697, R392-L697, S393-L697, L394-L697, R395-L697, P396-L697, C397-L697, S398-L697, V399-L697, L400-L697, V401-L697, S402-L697, L403-L697, L404-L697, Q405-L697, K406-L697, P407-L697, R408-L697, H409-L697, R410-L697, C411-L697, R412-L697, K413-L697, R414-L697, K415-L697, P416-L697, L417-L697, L418-L697, A419-L697, 1420-L697, G421-L697, F422-L697, Y423-L697, L424-L697, Y425-L697, R426-L697, M427-L697, N428-L697, K429-L697, Y430-L697, H431-L697, D432-L697, D433-L697, Q434-L697, R435-L697, R436-L697, L437-L697, P438-L697, P439-L697, E440-L697, F441-L697, F442-L697, Q443-L697, R444-L697, N445-L697, T446-L697, P447-L697, L448-L697, S449-L697, Q450-L697, P451-L697, D452-L697, R453-L697, F454-L697, L455-L697, K456-L697, E457-L697, K458-L697, E459-L697, V460-L697, S461-L697, Q462-L697, E463-L697, L464-L697, C465-L697, L466-L697, E467-L697, P468-L697, G469-L697, T470-L697, Y471-L697, L472-L697, 1473-L697, V474-L697, P475-L697, C476-L697, 1477-L697, L478-L697, E479-L697, A480-L697, H481-L697, Q482-L697, K483-L697, S484-L697, E485-L697, F486-L697, V487-L697, L488-L697, R489-L697, V490-L697, F491-L697, S492-L697, R493-L697, K494-L697, H495-L697, 1496-L697, F497-L697, Y498-L697, E499-L697, 1500-L697, G501-L697, S502-L697, N503-L697, S504-L697, G505-L697, V506-L697, V507-L697, F508-L697, S509-L697, K510-L697, E511-L697, 1512-L697, E513-L697, D514-L697, Q515-L697, N516-L697, E517-L697, R518-L697, Q519-L697, D520-L697, E521-L697, F522-L697, F523-L697, T524-L697, K525-L697, F526-L697, F527-L697, E528-L697, K529-L697, H530-L697, P531-L697, E532-L697, 1533-L697, N534-L697, A535-L697, V536-L697, Q537-L697, L538-L697, Q539-L697, N540-L697, L541-L697, L542-L697, N543-L697, Q544-L697, and/or M545-L697 of SEQ ID NO:56. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN-12v2 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0443] In preferred embodiments, the following C-terminal CAN-12v2 deletion polypeptides are encompassed by the present invention: M1-L697, M1-L696, M1-T695, M1-T694, M1-N693, M1-F692, M1-1691, M1-L690, M1-Y689, M1-S688, M1-T687, M1-S686, M1-H685, M1-A684, M1-V683, M1-G682, M1-G681, M1-D680, M1-1679, M1-N678, M1-A677, M1-L676, M1-I675, M1-V674, M1-P673, M1-V672, M1-I671, M1-M670, M1-F669, M1-F668, M1-T667, M1-P666, M1-T665, M1-S664, M1-Q663, M1-L662, M1-D661, M1-V660, M1-D659, M1-K658, M1-L657, M1-T656, M1-V655, M1-S654, M1-R653, M1-I652, M1-L651, M1-T650, M1-V649, M1-E648, M1-A647, M1-H646, M1-W645, M1-V644, M1-D643, M1-G642, M1-R641, M1-R640, M1-Q639, M1-R638, M1-I637, M1-L636, M1-T635, M1-C634, M1-G633, M1-A632, M1-R631, M1-T630, M1-H629, M1-G628, M1-C627, M1-S626, M1-W625, M1-S624, M1-K623, M1-R622, M1-H621, M1-R620, M1-G619, M1-A618, M1-E617, M1-R616, M1-M615, M1-A614, M1-A613, M1-H612, M1-L611, M1-Q610, M1-E609, M1-W608, M1-N607, M1-L606, M1-Y605, M1-G604, M1-S603, M1-G602, M1-R601, M1-D600, M1-Q599, M1-K598, M1-H597, M1-F596, M1-V595, M1-K594, M1-Q593, M1-S592, M1-L591, M1-K590, M1-L589, M1-Q588, M1-K587, M1-W586, M1-L585, M1-D584, M1-R583, M1-F582, M1-E581, M1-Q580, M1-I579, M1-S578, M1-M577, M1-T576, M1-G575, M1-S574, M1-A573, M1-N572, M1-L571, M1-D570, M1-L569, M1-L568, M1-A567, M1-L566, M1-1565, M1-G564, M1-Q563, M1-C562, M1-A561, M1-E560, M1-L559, M1-S558, M1-F557, M1-F556, M1-P555, M1-Q554, M1-R553, M1-S552, M1-G551, M1-L550, M1-S549, M1-S548, M1-W547, M1-T546, M1-M545, M1-Q544, M1-N543, M1-L542, M1-L541, M1-N540, M1-Q539, M1-L538, M1-Q537, M1-V536, M1-A535, M1-N534, M1-1533, M1-E532, M1-P531, M1-H530, M1-K529, M1-E528, M1-F527, M1-F526, M1-K525, M1-T524, M1-F523, M1-F522, M1-E521, M1-D520, M1-Q519, M1-R518, M1-E517, M1-N516, M1-Q515, M1-D514, M1-E513, M1-I512, M1-E511, M1-K510, M1-S509, M1-F508, M1-V507, M1-V506, M1-G505, M1-S504, M1-N503, M1-S502, M1-G501, M1-I500, M1-E499, M1-Y498, M1-F497, M1-I496, M1-H495, M1-K494, M1-R493, M1-S492, M1-F491, M1-V490, M1-R489, M1-L488, M1-V487, M1-F486, M1-E485, M1-S484, M1-K483, M1-Q482, M1-H481, M1-A480, M1-E479, M1-L478, M1-1477, M1-C476, M1-P475, M1-V474, M1-I473, M1-L472, M1-Y471, M1-T470, M1-G469, M1-P468, M1-E467, M1-L466, M1-C465, M1-L464, M1-E463, M1-Q462, M1-S461, M1-V460, M1-E459, M1-K458, M1-E457, M1-K456, M1-L455, M1-F454, M1-R453, M1-D452, M1-P451, M1-Q450, M1-S449, M1-L448, M1-P447, M1-T446, M1-N445, M1-R444, M1-Q443, M1-F442, M1-F441, M1-E440, M1-P439, M1-P438, M1-I437, M1-R436, M1-R435, M1-Q434, M1-D433, M1-D432, M1-H431, M1-Y430, M1-K429, M1-N428, and/or M1-M427 of SEQ ID NO:56. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12v2 deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0444] Alternatively, preferred polypeptides of the present invention may comprise polypeptide sequences corresponding to, for example, internal regions of the CAN-12v2 polypeptide (e.g., any combination of both N- and C-terminal CAN-12v2 polypeptide deletions) of SEQ ID NO:56. For example, internal regions could be defined by the equation: amino acid NX to amino acid CX, wherein NX refers to any N-terminal deletion polypeptide amino acid of CAN-12v2 (SEQ ID NO:56), and where CX refers to any C-terminal deletion polypeptide amino acid of CAN-12v2 (SEQ ID NO:56). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0445] The present invention also encompasses immunogenic and/or antigenic epitopes of the CAN-12v2 polypeptide.

[0446] The CAN-12v2 polypeptides of the present invention were determined to comprise several phosphorylation sites based upon the Motif algorithm (Genetics Computer Group, Inc.). The phosphorylation of such sites may regulate some biological activity of the CAN-12v2 polypeptide. For example, phosphorylation at specific sites may be involved in regulating the proteins ability to associate or bind to other molecules (e.g., proteins, ligands, substrates, DNA, etc.). In the present case, phosphorylation may modulate the ability of the CAN-12v2 polypeptide to associate with other polypeptides, particularly the serine protease substrate for CAN-12v2, or its ability to modulate serine protease function.

[0447] The CAN-12v2 polypeptide was predicted to comprise eleven PKC phosphorylation sites using the Motif algorithm (Genetics Computer Group, Inc.). In vivo, protein kinase C exhibits a preference for the phosphorylation of serine or threonine residues. The PKC phosphorylation sites have the following consensus pattern: [ST]-x-[RK], where S or T represents the site of phosphorylation and ‘x’ an intervening amino acid residue. Additional information regarding PKC phosphorylation sites can be found in Woodget J. R., Gould K. L., Hunter T., Eur. J. Biochem. 161:177-184(1986), and Kishimoto A., Nishiyama K., Nakanishi H., Uratsuji Y., Nomura H., Takeyama Y., Nishizuka Y., J. Biol. Chem. . . . 260:12492-12499(1985); which are hereby incorporated by reference herein.

[0448] In preferred embodiments, the following PKC phosphorylation site polypeptides are encompassed by the present invention: LAPRYSRRASPQQ (SEQ ID NO:76), LNQSFTEKYAGIF (SEQ ID NO:77), VFVSSTYKNLFWG (SEQ ID NO:78), GIRKVTCKHRPEY (SEQ ID NO:79), DWSDSSSKWELLS (SEQ ID NO:80), KWELLSPKEKILL (SEQ ID NO:81), QKWTYTMREGRWE (SEQ ID NO:82), EEGRRSLRPCSVL (SEQ ID NO:83), VLRVFSRKHIFYE (SEQ ID NO:84), KQLKLSQKVFHKQ (SEQ ID NO:85), and/or LIRSVTLKDVDLQ (SEQ ID NO:86). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of the CAN-12v2 PKC phosphorylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0449] The CAN-12v2 polypeptide has been shown to comprise four glycosylation site according to the Motif algorithm (Genetics Computer Group, Inc.). As discussed more specifically herein, protein glycosylation is thought to serve a variety of functions including: augmentation of protein folding, inhibition of protein aggregation, regulation of intracellular trafficking to organelles, increasing resistance to proteolysis, modulation of protein antigenicity, and mediation of intercellular adhesion.

[0450] In preferred embodiments, the following asparagine glycosylation site polypeptide is encompassed by the present invention: RVVPLNQSFTEKYA (SEQ ID NO:87), IEATYNRTLIGCQT (SEQ ID NO:102), ALLDLNASGTMSIQ (SEQ ID NO:103), and/or SYLIFNTTLL (SEQ ID NO:104). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12v2 asparagine glycosylation site polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0451] The CAN-12v2 polypeptide has been shown to comprise one amidation site according to the Motif algorithm (Genetics Computer Group, Inc.). The precursor of hormones and other active peptides which are C-terminally amidated is always directly followed by a glycine residue which provides the amide group, and most often by at least two consecutive basic residues (Arg or Lys) which generally function as an active peptide precursor cleavage site. Although all amino acids can be amidated, neutral hydrophobic residues such as Val or Phe are good substrates, while charged residues such as Asp or Arg are much less reactive. A consensus pattern for amidation sites is the following: x-G-[RK]-[RK], wherein “X” represents the amidation site. Additional information relating to asparagine glycosylation may be found in reference to the following publications, which are hereby incorporated by reference herein: Kreil G., Meth. Enzymol. 106:218-223(1984); and Bradbury A. F., Smyth D. G., Biosci. Rep. 7:907-916(1987).

[0452] In preferred embodiments, the following amidation site polypeptide is encompassed by the present invention: VWRPEEGRRSLRPC (SEQ ID NO:88). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this CAN-12v2 amidation site polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0453] The CAN-12v2 polypeptide has been shown to comprise one RGD cell attachment site domain according to the Motif algorithm (Genetics Computer Group, Inc.). The sequence Arg-Gly-Asp, found in fibronectin, is crucial for its interaction with its cell surface receptor, an integrin. What has been called the ‘RGD’ tripeptide is also found in the sequences of a number of other proteins, where it has been shown to play a role in cell adhesion. Non-limiting examples of these proteins are the following: some forms of collagens, fibrinogen, vitronectin, von Willebrand factor (VWF), snake disintegrins, and slime mold discoidins. The ‘RGD’ tripeptide is also found in other proteins where it may serve the same purpose. A consensus pattern for RGD cell attachment sites is the following: R-G-D. Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Ruoslahti E., Pierschbacher M. D., Cell 44:517-518(1986); and d'Souza S. E., Ginsberg M. H., Plow E. F., Trends Biochem. Sci. 16:246-250(1991).

[0454] In preferred embodiments, the following RGD cell attachment site domain polypeptide is encompassed by the present invention: LIRQRRGDVWHAE (SEQ ID NO:89). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this RGD cell attachment site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0455] In confirmation of the CAN-12v2 polypeptide being a calpain, it has been shown to comprise one EF-hand calcium-binding domain according to the Motif algorithm (Genetics Computer Group, Inc.). Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Several representative proteins containing EF-hand regions are provided below: For each type of protein, the total number of EF-hand regions known or supposed to exist are provided in parenthesis: Aequorin and Renilla luciferin binding protein (LBP) (Ca=3); Alpha actinin (Ca=2); Calbindin (Ca=4); Calcineurin B subunit (protein phosphatase 2B regulatory subunit) (Ca=4); Calcium-binding protein from Streptomyces erythraeus (Ca=3?); Calcium-binding protein from Schistosoma mansoni (Ca=2?); Calcium-binding proteins TCBP-23 and TCBP-25 from Tetrahymena thermophila (Ca=4?); Calcium-dependent protein kinases (CDPK) from plants (Ca=4); Calcium vector protein from amphoxius (Ca=2); Calcyphosin (thyroid protein p24) (Ca=4?); Calmodulin (Ca=4, except in yeast where Ca=3); Calpain small and large chains (Ca=2); Calretinin (Ca=6); Calcyclin (prolactin receptor associated protein) (Ca=2); Caltractin (centrin) (Ca=2 or 4); Cell Division Control protein 31 (gene CDC31) from yeast (Ca=2?); Diacylglycerol kinase (EC 2.7.1.107) (DGK) (Ca=2); FAD-dependent glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) from mammals (Ca=1); Fimbrin (plastin) (Ca=2); Flagellar calcium-binding protein (1f8) from Trypanosoma cruzi (Ca=1 or 2); Guanylate cyclase activating protein (GCAP) (Ca=3); Inositol phospholipid-specific phospholipase C isozymes gamma-1 and delta-1 (Ca=2) [10]; Intestinal calcium-binding protein (ICaBPs) (Ca=2); MIF related proteins 8 (MRP-8 or CFAG) and 14 (MRP-14) (Ca=2); Myosin regulatory light chains (Ca=1); Oncomodulin (Ca=2); Osteonectin (basement membrane protein BM-40) (SPARC) and proteins that contains an ‘osteonectin’ domain (QR1, matrix glycoprotein SCI) (Ca=1); Parvalbumins alpha and beta (Ca=2); Placental calcium-binding protein (18a2) (nerve growth factor induced protein 42a) (p9k) (Ca=2); Recoverins (visinin, hippocalcin, neurocalcin, S-modulin) (Ca=2 to 3); Reticulocalbin (Ca=4); S-100 protein, alpha and beta chains (Ca=2); Sarcoplasmic calcium-binding protein (SCPs) (Ca=2 to 3); Sea urchin proteins Spec 1 (Ca=4), Spec 2 (Ca=4?), Lps-1 (Ca=8); Serine/threonine protein phosphatase rdgc (EC 3.1.3.16) from Drosophila (Ca=2); Sorcin V19 from hamster (Ca=2); Spectrin alpha chain (Ca=2); Squidulin (optic lobe calcium-binding protein) from squid (Ca=4); and Troponins C; from skeletal muscle (Ca=4), from cardiac muscle (Ca=3), from arthropods and molluscs (Ca=2).

[0456] A consensus pattern for EF hand calcium binding domains is the following:

31 2 3 4 5 6 7 8 9 10 12 13X Y Z -Y -X -ZD-x-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]-x(2)-[DE]-[LIVMFYW],

[0457] wherein X, Y, Z, -Y, -X, and -Z are as defined above, and wherein “x” represents any amino acid. Amino acid residues within the consensus at positions 1 (X), 3 (Y) and 12 (-Z) are the most conserved. The 6th residue in an EF-hand loop is in most cases a Gly.

[0458] Additional information relating to RGD cell attachment site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Kawasaki H., Kretsinger R. H., Protein Prof. 2:305-490(1995); Kretsinger R. H., Cold Spring Harbor Symp. Quant. Biol. 52:499-510(1987); Moncrief N. D., Kretsinger R. H., Goodman M., J. Mol. Evol. 30:522-562(1990); Nakayama S., Moncrief N. D., Kretsinger R. H., J. Mol. Evol. 34:416-448(1992); Heizmann C. W., Hunziker W., Trends Biochem. Sci. 16:98-103(1991); Kligman D., Hilt D. C., Trends Biochem. Sci. 13:437-443(1988); Strynadka N. C. J., James M. N. G., Annu. Rev. Biochem. 58:951-98(1989); Haiech J., Sallantin J., Biochimie 67:555-560(1985); Chauvaux S., Beguin P., Aubert J.-P., Bhat K. M., Gow L. A., Wood T. M., Bairoch A., Biochem. J. 265:261-265(1990); Bairoch A., Cox J. A., FEBS Lett. 269:454-456(1990).

[0459] In preferred embodiments, the following EF-hand calcium binding domain polypeptide is encompassed by the present invention: ILALLDLNASGTMSIQEFRDLWK (SEQ ID NO:90). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this EF-hand calcium binding domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0460] In further confirmation of the CAN-12v2 polypeptide being a calpain, it has been shown to comprise one eukaryotic thiol (cysteine) protease active site domain according to the Motif algorithm (Genetics Computer Group, Inc.). Eukaryotic thiol proteases (EC 3.4.22.-) are a family of proteolytic enzymes which contain an active site cysteine. Catalysis proceeds through a thioester intermediate and is facilitated by a nearby histidine side chain; an asparagine completes the essential catalytic triad. Non-limiting examples of proteases which are known to belong to this family are provided below: Vertebrate lysosomal cathepsins B (EC 3.4.22.1), H (EC 3.4.22.16), L (EC 3.4.22.15), and S (EC 3.4.22.27); Vertebrate lysosomal dipeptidyl peptidase I (EC 3.4.14.1) (also known as cathepsin C); Vertebrate calpains (EC 3.4.22.17) (Calpains are intracellular calcium-activated thiol protease that contain both a N-terminal catalytic domain and a C-terminal calcium-binding domain; Mammalian cathepsin K, which seems involved in osteoclastic bone resorption; Human cathepsin O; Bleomycin hydrolase (An enzyme that catalyzes the inactivation of the antitumor drug BLM (a glycopeptide); Plant enzymes: barley aleurain (EC 3.4.22.16), EP-B1/B4; kidney bean EP-C1, rice bean SH-EP; kiwi fruit actinidin (EC 3.4.22.14); papaya latex papain (EC 3.4.22.2), chymopapain (EC 3.4.22.6), caricain (EC 3.4.22.30), and proteinase IV (EC 3.4.22.25); pea turgor-responsive protein 15A; pineapple stem bromelain (EC 3.4.22.32); rape COT44; rice oryzain alpha, beta, and gamma; tomato low-temperature induced, Arabidopsis thaliana A494, RD19A and RD21A; House-dust mites allergens DerP1 and EurM1; Cathepsin B-like proteinases from the worms Caenorhabditis elegans (genes gcp-1, cpr-3, cpr-4, cpr-5 and cpr-6), Schistosoma mansoni (antigen SM31) and Japonica (antigen SJ31), Haemonchus contortus (genes AC-1 and AC-2), and Ostertagia ostertagi (CP-1 and CP-3); Slime mold cysteine proteinases CP1 and CP2; Cruzipain from Trypanosoma cruzi and brucei; Throphozoite cysteine proteinase (TCP) from various Plasmodium species; Proteases from Leishmania mexicana, Theileria annulata and Theileria parva; Baculoviruses cathepsin-like enzyme (v-cath); Drosophila small optic lobes protein (gene sol), a neuronal protein that contains a calpain-like domain; Yeast thiol protease BLH1/YCP1/LAP3; and Caenorhabditis elegans hypothetical protein CO6G4.2, a calpain-like protein; Two bacterial peptidases are also part of this family—Aminopeptidase C from Lactococcus lactis (gene pepC), and Thiol protease tpr from Porphyromonas gingivalis.

[0461] A consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: Q-x(3)-[GE]-x-C-[YW]-x(2)-[STAGC]-[STAGCV], wherein C is the active site residue, and “x” represents any amino acid. The residue in position 4 of the pattern is almost always cysteine; the only exceptions are calpains (Leu), bleomycin hydrolase (Ser) and yeast YCP1 (Ser); while the residue in position 5 of the pattern is always Gly except in papaya protease IV where it is Glu.

[0462] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [LIVMGSTAN]-x-H-[GSACE]-[LIVM]-x-[LIVMAT](2)-G-x-[GSADNH], wherein H is the active site residue, and “x” represents any amino acid.

[0463] An additional consensus pattern for eukaryotic thiol (cysteine) protease active site domains is the following: [FYCH]-[WI]-[LIVT]-x-[KRQAG]-N-[ST]-W-x(3)-[FYW]-G-x(2)-G-[LFYW]-[LIVMFYG]-x-[LIVMF], wherein N is the active site residue, and “x” represents any amino acid.

[0464] Additional information relating to for eukaryotic thiol (cysteine) protease active site domains may be found in reference to the following publications, which are hereby incorporated by reference herein: Dufour E., Biochimie 70:1335-1342(1988); Kirschke H., Barrett A. J., Rawlings N. D., Protein Prof. 2:1587-1643(1995); Shi G. -P., Chapman H. A., Bhairi S. M., Deleeuw C., Reddy V. Y., Weiss S. J., FEBS Lett. 357:129-134(1995); Velasco G., Ferrando A. A., Puente X. S., Sanchez L. M., Lopez-Otin C., J. Biol. Chem. . . . 269:27136-27142(1994); Chapot-Chartier M. P., Nardi M., Chopin M. C., Chopin A., Gripon J. C., Appl. Environ. Microbiol. 59:330-333(1993); Higgins D. G., McConnell D. J., Sharp P. M., Nature 340:604-604(1989); Rawlings N. D., Barrett A. J., Meth. Enzymol. 244:461-486(1994), and http://www.expasy.ch/cgi-bin/lists?peptidas.txt, which are hereby incorporated by reference in their entirety herein.

[0465] In preferred embodiments, the following for eukaryotic thiol (cysteine) protease active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALA (SEQ ID NO:91). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of this for eukaryotic thiol (cysteine) protease active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0466] As referenced elsewhere herein, calpains are organized in domains. As a point of reference, the larger catalytic subunit of the best characterized m-calpain is organized in four domains (I-IV)(Hosfield et al., Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation. EMBO J. 18:6880-9, 1999; Strobl et al., The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Proc Natl Acad Sci U S A. 97:588-92, 2000). The N-terminal domain I contains an alpha helical region. Domain II contains the catalytic active domain with the active site amino acids. Domain III contains the linker between the Ca2+binding domain in domain IV to the active site domain II.

[0467] The CAN-12v2 calpain of the present invention has the same domain I and II as the CAN-12 calpain, but differs in domains III and IV. The N-terminal domain I consists of residues Met1-Arg20. Domain II of the CAN-12v2 calpain (Ala21-Lys333) contain the catalytic active site residue acids (Cys101, His254 and Asn278). As can be seen in the sequence alignments (FIGS. 2A-E), there is high amino acid sequence homology in the amino acid residues bracketing the active site amino acids. Combined domains I and II of the calpains of the present invention are 42-45% homologous to m-calpain.

[0468] The CAN-12v2 calpain of the present invention, have the same domain I and II, although they differ in composition and content of domains III and IV. The CAN-12 and CAN-12v2 calpains contain both the linker (domain III) and C-terminal domain IV. The “linker” domain also contains residues Met426, Asn427 and Lys428 of SEQ ID NO56).

[0469] The present invention also provides a three-dimensional homology model of the CAN-12v2 polypeptide (see FIG. 11). The three-dimensional homology model of the CAN-12 polypeptide may also be applicable to the CAN-12v2 polypeptide. Although the CAN-12 polypeptide sequence is different than the CAN-12v2 polypeptide sequence, the fact that domain I and II are substantially the same suggests the homology model of CAN-12 may be used for designing potential ligands (including agonists and/or antagonists) for the CAN-12v2 polypeptide. A three-dimensional homology model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995). The homology model of the CAN-12v2 polypeptide, corresponding to amino acid residues 12 to 428 and from amino acid residues 543 to 639 of SEQ ID NO:56, was based upon the homologous structure of CAN2, a m-calpain family member (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) and is defined by the set of structural coordinates set forth in Table V herein. Note that amino acids 429 to 542 of SEQ ID NO:56 were omitted from the homology model. As a result, the amino acid residue numbers in Table V do not correspond to the amino acid residue numbers as provided in SEQ ID NO:56 (FIGS. 9A-C). Rather, the amino acid residue numbers in Table V for amino acid residues 12 to 428 correspond to amino acid residues 12 to 428 of SEQ ID NO:56 (FIGS. 9A-C), while amino acid residue numbers in Table V for amino acid residues 429 to 512 correspond to amino acid residues 543 to 639 of SEQ ID NO:56 (FIGS. 9A-C).

[0470] A description of the headings in Table V are as follows: “Atom No” refers to the atom number within the CAN-12v2 homology model; “Atom name” refers to the element whose coordinates are measured, the first letter in the column defines the element; “Residue” refers to the amino acid within which the atom resides, and the provided number after the amino acid refers to the amino acid number of the “residue”; “X Coord”, “Y Coord”, and “Z Coord” structurally define the atomic position of the element measured in three dimensions.

[0471] The CAN-12v2 homology model of the present invention may provide one basis for designing rational stimulators (agonists) and/or inhibitors (antagonists) of one or more of the biological functions of CAN-12v2, or of CAN-12v2 mutants having altered specificity (e.g., molecularly evolved CAN-12v2 polypeptides, engineered site-specific CAN-12v2 mutants, CAN-12v2 allelic variants, etc.).

[0472] Homology models are not only useful for designing rational agonists and/or antagonists, but are also useful in predicting the function of a particular polypeptide. The functional predictions from homology models are typically more accurate than the functional attributes derived from traditional polypeptide sequence homology alignments (e.g., CLUSTALW), particularly when the three dimensional structure of a related polypeptide is known (e.g., m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11). The increased prediction accuracy is based upon the fact that homology models approximate the three-dimensional structure of a protein, while homology based alignments only take into account the one dimension polypeptide sequence. Since the function of a particular polypeptide is determined not only by its primary, secondary, and tertiary structure, functional assignments derived solely upon homology alignments using the one dimensional protein sequence may be less reliable. A 3-dimensional model can be constructed on the basis of the known structure of a homologous protein (Greer et al, 1991, Lesk, et al, 1992, Cardozo, et al, 1995, Yuan, et al, 1995).

[0473] Prior to developing a homology model, those of skill in the art would appreciate that a template of a known protein, or model protein, must first be identified which will be used as a basis for constructing the homology model for the protein of unknown structure (query template). In the case of the CAN-12v2 polypeptide of the present invention, the model protein template used in constructing the CAN-12v2 homology model was the m-calpain family member CAN2 protein; Genbank Accession No. gil7546423; SEQ ID NO:11).

[0474] Identifying a template can be accomplished using pairwise alignment of protein sequences using such programs as FASTA (Pearson, et al 1990) and BLAST (Altschul, et al, 1990). In cases where sequence similarity is high (greater than 30%), such pairwise comparison methods may be adequate for identifying an appropriate template. Likewise, multiple sequence alignments or profile-based methods can be used to align a query sequence to an alignment of multiple (structurally and biochemically) related proteins. When the sequence similarity is low, more advanced techniques may be used. Such techniques, include, for example, protein fold recognition (protein threading; Hendlich, et al, 1990), where the compatibility of a particular polypeptide sequence with the 3-dimensional fold of a potential template protein is gauged on the basis of a knowledge-based potential.

[0475] Following the initial sequence alignment, the second step would be to optimally align the query template to the model template by manual manipulation and/or by the incorporation of features specific to the polypeptides (e.g., motifs, secondary structure predictions, and allowed conservations). Preferably, the incorporated features are found within both the model and query template.

[0476] The third step would be to identify structurally conserved regions that could be used to construct secondary core structure (SalI, et al, 1995). Loops could be added using knowledge-based techniques, and by performing forcefield calculations (Sali, et al, 1995).

[0477] In order to recognize errors in a three-dimensional structure, knowledge based mean fields can be used to judge the quality of protein folds (Sippl 1993). The methods can be used to recognize misfolded structures as well as faulty parts of structural models. The technique generates an energy graph where the energy distribution for a given protein fold is displayed on the y-axis and residue position in the protein fold is displayed on the x-axis. The knowledge based mean fields compose a force field derived from a set of globular protein structures taken as a subset from the Protein Data Bank (Bernstein et. al. 1977). To analyze the quality of a model the energy distribution is plotted and compared to the energy distribution of the template from which the model was generated. FIG. 13 shows the energy graph for the CAN-12.v2 model (dotted line) and the template (1dkv, m-calpain) from which the model was generated. This graph supports the motif and sequence alignments in confirming that the three dimensional structure coordinates of CAN-12.v2 are an accurate and useful representation for the polypeptide.

[0478] The term “structure coordinates” refers to Cartesian coordinates generated from the building of a homology model. In this invention, the homology model of residues 12 to 525 of CAN-12v2 was derived from generating a sequence alignment with m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11) using the COMPOSER suite of software within SYBYL6.6 (Tripos Associates, St. Louis, Mo.) and then generating the backbone and side chain conformations. In the original crystal structure (pdb code I dkv) as well as the crystal structure reported elsewhere (Hosfield et al, 1999), the active site of the enzyme comprising a cysteine, a histidine and an asparagine residue was not “formed”. The helix that contains the active site C101 was altered by moving the helix down one pitch so that the active site geometry could match that found in Papain (pdb code 1b4). This modified structure of human m-calpain was used as the template for construction of the homology model (illustrated in FIG. 11 herein).

[0479] The skilled artisan would appreciate that a set of structure coordinates for a protein represents a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates, as emanate from the generation of similar homology models using different alignment templates (i.e., other than the m-calpain (Strobl et al, 2000; hCAN2; Genbank Accession No. gil7546423; SEQ ID NO:11), and/or using different methods in generating the homology model, will likely have minor effects on the overall shape. Variations in coordinates may also be generated because of mathematical manipulations of the structure coordinates. For example, the structure coordinates set forth in Table V could be manipulated by fractionalization of the structure coordinates; integer additions, or integer subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above.

[0480] Therefore, various computational analyses are necessary to determine whether a template molecule or a portion thereof is sufficiently similar to all or part of a query template (e.g., CAN-12v2) in order to be considered the same. Such analyses may be carried out in current software applications, such as SYBYL version 6.6 or INSIGHTII (Molecular Simulations Inc., San Diego, Calif.) version 2000 and as described in the accompanying User's Guides.

[0481] Using the superimposition tool in the program SYBYL, comparisons can be made between different structures and different conformations of the same structure. The procedure used in SYBYL to compare structures is divided into four steps: 1) load the structures to be compared; 2) define the atom equivalencies in these structures; 3) perform a fitting operation; and 4) analyze the results. Each structure is identified by a name. One structure is identified as the target (i.e., the fixed structure); the second structure (i.e., moving structure) is identified as the source structure. The atom equivalency within SYBYL is defined by user input. For the purpose of this invention, we will define equivalent atoms as protein backbone atoms (N, Cα, C and O) for all conserved residues between the two structures being compared. We will also consider only rigid fitting operations. When a rigid fitting method is used, the working structure is translated and rotated to obtain an optimum fit with the target structure. The fitting operation uses an algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atoms is an absolute minimum. This number, given in angstroms, is reported by the SYBYL program. For the purpose of the present invention, any homology model of a CAN-12v2 that has a root mean square deviation of conserved residue backbone atoms (N, Cα, C, O) of less than 3.0 A when superimposed on the relevant backbone atoms described by structure coordinates listed in Table V are considered identical. More preferably, the root mean square deviation for the CAN-12v2 polypeptide is less than 2.0 A.

[0482] The homology model of the present invention is useful for the structure-based design of modulators of the CAN-12v2 biological function, as well as mutants with altered biological function and/or specificity.

[0483] In accordance with the structural coordinates provided in Table V and the three dimensional homology model of CAN-12v2, the CAN-12v2 polypeptide has been shown to comprise a an active site region embodied by the following amino acids: from about amino acid R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:56 (FIGS. 8A-C). In this context, the term “about” may be construed to mean 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids more in either the N- or C-terminal direction of the above referenced amino acids.

[0484] Also more preferred are polypeptides comprising all or any part of the CAN-12v2 active site domain, or a mutant or homologue of said polypeptide or molecular complex. By mutant or homologue of the molecule is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12v2 amino acids of not more than about 4.5 Angstroms, and preferably not more than about 3.5 Angstroms.

[0485] In preferred embodiments, the following CAN-12v2 active site domain polypeptide is encompassed by the present invention: RLDLCQGIVGDCWFLAALQALALHQDILSRVVPLNQSFTEKYAGIFRFWFWH YGNWVPVVIDDRLPVNEAGQLVFVSSTYKNLFWGALLEKAYAKLSGSYEDL QSGQVSEALVDFTGGVTMTINLAEAHGNLWDILIEATYNRTLIGCQTHSGEKI LENGLVEGHAYTLTGIRKVTCKHRPEYLVKLRNPWGKVEWKGDWSDSSSK WELLSPKEKILLLRKDNDGEFWMTLQDFKTHFVLLV (SEQ ID NO:93). Polynucleotides encoding this polypeptide are also provided. The present invention also encompasses the use of the CAN-12v2 active site domain polypeptide as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0486] The present invention also encompasses polypeptides comprising at least a portion of the CAN-12v2 active site domain (SEQ ID NO: 93). Such polypeptides may correspond, for example, to the N- and/or C-terminal deletions of the active site domain.

[0487] In preferred embodiments, the following N-terminal CAN-12v2 active site domain deletion polypeptides are encompassed by the present invention: R1-V242, L2-V242, D3-V242, L4-V242, C5-V242, Q6-V242, G7-V242, 18-V242, V9-V242, G1O-V242, D11-V242, C12-V242, W13-V242, F14-V242, L15-V242, A16-V242, A17-V242, L18-V242, Q19-V242, A20-V242, L21-V242, A22-V242, L23-V242, H24-V242, Q25-V242, D26-V242, 127-V242, L28-V242, S29-V242, R30-V242, V31-V242, V32-V242, P33-V242, L34-V242, N35-V242, Q36-V242, S37-V242, F38-V242, T39-V242, E40-V242, K41-V242, Y42-V242, A43-V242, G44-V242, 145-V242, F46-V242, R47-V242, F48-V242, W49-V242, F50-V242, W51-V242, H52-V242, Y53-V242, G54-V242, N55-V242, W56-V242, V57-V242, P58-V242, V59-V242, V60-V242, 161-V242, D62-V242, D63-V242, R64-V242, L65-V242, P66-V242, V67-V242, N68-V242, E69-V242, A70-V242, G71-V242, Q72-V242, L73-V242, V74-V242, F75-V242, V76-V242, S77-V242, S78-V242, T79-V242, Y80-V242, K81-V242, N82-V242, L83-V242, F84-V242, W85-V242, G86-V242, A87-V242, L88-V242, L89-V242, E90-V242, K91-V242, A92-V242, Y93-V242, A94-V242, K95-V242, L96-V242, S97-V242, G98-V242, S99-V242, Y100-V242, E101-V242, D102-V242, L103-V242, Q104-V242, S105-V242, G106-V242, Q107-V242, V108-V242, S109-V242, E110-V242, A111-V242, L112-V242, V113-V242, D114-V242, F115-V242, T116-V242, G117-V242, G118-V242, V119-V242, T120-V242, M121-V242, T122-V242, 1123-V242, N124-V242, L125-V242, A126-V242, E127-V242, A128-V242, H129-V242, G130-V242, N131-V242, L132-V242, W133-V242, D134-V242, 1135-V242, L136-V242, 1137-V242, E138-V242, A139-V242, T140-V242, Y141-V242, N142-V242, R143-V242, T144-V242, L145-V242, 1146-V242, G147-V242, C148-V242, Q149-V242, T150-V242, H151-V242, S152-V242, G153-V242, E154-V242, K155-V242, 1156-V242, L157-V242, E158-V242, N159-V242, G160-V242, L161-V242, V162-V242, E163-V242, G164-V242, H165-V242, A166-V242, Y167-V242, T168-V242, L169-V242, T170-V242, G171-V242, 1172-V242, R173-V242, K174-V242, V175-V242, T176-V242, C177-V242, K178-V242, H179-V242, R180-V242, P181-V242, E182-V242, Y183-V242, L184-V242, V185-V242, K186-V242, L187-V242, R188-V242, N189-V242, P190-V242, W191-V242, G192-V242, K193-V242, V194-V242, E195-V242, W196-V242, K197-V242, G198-V242, D199-V242, W200-V242, S201-V242, D202-V242, S203-V242, S204-V242, S205-V242, K206-V242, W207-V242, E208-V242, L209-V242, L210-V242, S211-V242, P212-V242, K213-V242, E214-V242, K215-V242, 1216-V242, L217-V242, L218-V242, L219-V242, R220-V242, K221-V242, D222-V242, N223-V242, D224-V242, G225-V242, E226-V242, F227-V242, W228-V242, M229-V242, T230-V242, L231-V242, Q232-V242, D233-V242, F234-V242, K235-V242, and/or T236-V242 of SEQ ID NO:93. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these N-terminal CAN-12v2 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0488] In preferred embodiments, the following C-terminal CAN-12v2 active site domain deletion polypeptides are encompassed by the present invention: R1-V242, R1-L241, R1-L240, R1-V239, R1-F238, R1-H237, R1-T236, R1-K235, R1-F234, R1-D233, R1-Q232, R1-L231, R1-T230, R1-M229, R1-W228, R1-F227, R1-E226, R1-G225, R1-D224, R1-N223, R1-D222, R1-K221, R1-R220, R1-L219, R1-L218, R1-L217, R1-1216, R1-K215, R1-E214, R1-K213, R1-P212, R1-S211, R1-L210, R1-L209, R1-E208, R1-W207, R1-K206, R1-S205, R1-S204, R1-S203, R1-D202, R1-S201, R1-W200, R1-D199, R1-G198, R1-K197, R1-W196, R1-E195, R1-V194, R1-K193, R1-G192, R1-W191, R1-P190, R1-N189, R1-R188, R1-L187, R1-K186, R1-V185, R1-L184, R1-Y183, R1-E182, R1-P181, R1-R180, R1-H179, R1-K178, R1-C177, R1-T176, R1-V175, R1-K174, R1-R173, R1-1172, R1-G171, R1-T170, R1-L169, R1-T168, R1-Y167, R1-A166, R1-H165, R1-G164, R1-E163, R1-V162, R1-L161, R1-G160, R1-N159, R1-E158, R1-L157, R1-1156, R1-K155, R1-E154, R1-G153, R1-S152, R1-H151, R1-T150, R1-Q149, R1-C148, R1-G147, R1-I146, R1-L145, R1-T144, R1-R143, R1-N142, R1-Y141, R1-T140, R1-A139, R1-E138, R1-I137, R1-L136, R1-I135, R1-D134, R1-W133, R1-L132, R1-N131, R1-G130, R1-H129, R1-A128, R1-E127, R1-A126, R1-L125, R1-N124, R1-I123, R1-T122, R1-M121, R1-T120, R1-V119, R1-G118, R1-G117, R1-T116, R1-F115, R1-D114, R1-V113, R1-L112, R1-A111, R1-E110, R1-S109, R1-V108, R1-Q107, R1-G106, R1-S105, R1-Q104, R1-L103, R1-D102, R1-E101, R1-Y100, R1-S99, R1-G98, R1-S97, R1-L96, R1-K95, R1-A94, R1-Y93, R1-A92, R1-K91, R1-E90, R1-L89, R1-L88, R1-A87, R1-G86, R1-W85, R1-F84, R1-L83, R1-N82, R1-K81, R1-Y80, R1-T79, R1-S78, R1-S77, R1-V76, R1-F75, R1-V74, R1-L73, R1-Q72, R1-G71, R1-A70, R1-E69, R1-N68, R1-V67, R1-P66, R1-L65, R1-R64, R1-D63, R1-D62, R1-161, R1-V60, R1-V59, R1-P58, R1-V57, R1-W56, R1-N55, R1-G54, R1-Y53, R1-H52, R1-W51, R1-F50, R1-W49, R1-F48, R1-R47, R1-F46, R1-145, R1-G44, R1-A43, R1-Y42, R1-K41, R1-E40, R1-T39, R1-F38, R1-S37, R1-Q36, R1-N35, R1-L34, R1-P33, R1-V32, R1-V31, R1-R30, R1-S29, R1-L28, R1-I27, R1-D26, R1-Q25, R1-H24, R1-L23, R1-A22, R1-L21, R1-A20, R1-Q19, R1-L18, R1-A17, R1-A16, R1-L15, R1-F14, R1-W13, R1-C12, R1-D11, R1-G10, R1-V9, R1-18, and/or R1-G7 of SEQ ID NO:93. Polynucleotide sequences encoding these polypeptides are also provided. The present invention also encompasses the use of these C-terminal CAN-12v2 active site domain deletion polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0489] Alternatively, such polypeptides may comprise polypeptide sequences corresponding, for example, to internal regions of the CAN-12v2 active site domain (e.g., any combination of both N- and C-terminal CAN-12v2 active site domain deletions) of SEQ ID NO:93. For example, internal regions could be defined by the equation NX to CX, where NX refers to any N-terminal amino acid position of the CAN-12v2 active site domain (SEQ ID NO:93), and where CX refers to any C-terminal amino acid position of the CAN-12v2 active site domain (SEQ ID NO:93). Polynucleotides encoding these polypeptides are also provided. The present invention also encompasses the use of these polypeptides as an immunogenic and/or antigenic epitope as described elsewhere herein.

[0490] In preferred embodiments, the following CAN-I 2v2 active site domain amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L91 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein D92 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L93 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein C94 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q95 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein G96 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I97 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V98 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein G99 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D100 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C101 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W102 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F103 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L104 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A105 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A106 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L107 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q108 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein A109 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L110 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A 111 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L112 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein H113 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q114 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D115 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I116 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L117 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S118 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein R119 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein V120 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V121 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P122 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein L123 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein N124 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein Q125 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S126 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein F127 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T128 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein E129 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K130 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y131 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A132 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G133 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I134 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F135 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R136 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein F137 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W138 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein F139 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W140 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein H141 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y142 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein G143 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N144 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein W145 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein V146 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein P147 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V148 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein V149 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein I150 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D151 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D152 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R153 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein L154 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein P155 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein V156 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein N157 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein E158 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A159 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G160 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q161 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein L162 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V163 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein F164 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V165 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S166 is substituted with either an A, C, D, E, F, G, H, 1, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S167 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein T168 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y169 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein K170 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N171 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L172 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein F173 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W174 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G175 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A176 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L177 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L178 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E179 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K180 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A181 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y182 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein A183 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K184 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L185 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S186 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G187 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S188 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein Y189 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein E190 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D191 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L192 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q193 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein S194 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G195 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q196 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein V197 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein S198 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein E199 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A200 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L201 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V202 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein D203 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F204 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T205 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G206 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G207 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V208 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T209 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein M210 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T211 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein I212 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N213 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L214 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein A215 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E216 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A217 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H218 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G219 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N220 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein L221 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein W222 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein D223 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I224 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L225 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein I226 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E227 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A228 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T229 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein Y230 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein N231 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein R232 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein T233 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L234 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein I235 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G236 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein C237 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Q238 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein T239 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H240 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S241 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein G242 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E243 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K244 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I245 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L246 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein E247 is substituted with either an A, C, D, F, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N248 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein G249 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L250 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V251 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E252 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G253 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H254 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein A255 is substituted with either a C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y256 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein T257 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L258 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein T259 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein G260 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I261 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R262 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K263 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V264 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein T265 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein C266 is substituted with either an A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K267 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein H268 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein R269 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein P270 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein E271 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein Y272 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or W; wherein L273 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein V274 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein K275 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L276 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R277 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein N278 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein P279 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein W280 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein G281 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K282 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V283 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein E284 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W285 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein K286 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G287 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D288 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W289 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein S290 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein D291 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein S292 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S293 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein S294 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein K295 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W296 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein E297 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L298 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L299 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein S300 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, or Y; wherein P301 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, or Y; wherein K302 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E303 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K304 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein I305 is substituted with either an A, C, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein L306 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L307 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L308 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein R309 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y; wherein K310 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein D311 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein N312 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, or Y; wherein D313 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein G314 is substituted with either an A, C, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein E315 is substituted with either an A, C, D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F316 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein W317 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y; wherein M318 is substituted with either an A, C, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, or Y; wherein T319 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V, W, or Y; wherein L320 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein Q321 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, or Y; wherein D322 is substituted with either an A, C, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F323 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein K324 is substituted with either an A, C, D, E, F, G, H, I, L, M, N, P, Q, R, S, T, V, W, or Y; wherein T325 is substituted with either an A, C, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, V, W, or Y; wherein H326 is substituted with either an A, C, D, E, F, G, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein F327 is substituted with either an A, C, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y; wherein V328 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y; wherein L329 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; wherein L330 is substituted with either an A, C, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V, W, or Y; and/or wherein V331 is substituted with either an A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, or Y of SEQ ID NO:56, in addition to any combination thereof. The present invention also encompasses the use of these CAN-12v2 active site domain amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0491] In preferred embodiments, the following CAN-12v2 active site domain conservative amino acid substitutions are encompassed by the present invention: wherein R90 is substituted with either a K, or H; wherein L91 is substituted with either an A, I, or V; wherein D92 is substituted with an E; wherein L93 is substituted with either an A, I, or V; wherein C94 is a C; wherein Q95 is substituted with a N; wherein G96 is substituted with either an A, M, S, or T; wherein 197 is substituted with either an A, V, or L; wherein V98 is substituted with either an A, I, or L; wherein G99 is substituted with either an A, M, S, or T; wherein D100 is substituted with an E; wherein C101 is a C; wherein W102 is either an F, or Y; wherein F103 is substituted with either a W, or Y; wherein L104 is substituted with either an A, I, or V; wherein A105 is substituted with either a G, I, L, M, S, T, or V; wherein A106 is substituted with either a G, I, L, M, S, T, or V; wherein L107 is substituted with either an A, I, or V; wherein Q108 is substituted with a N; wherein A109 is substituted with either a G, I, L, M, S, T, or V; wherein L110 is substituted with either an A, I, or V; wherein A111 is substituted with either a G, I, L, M, S, T, or V; wherein L112 is substituted with either an A, I, or V; wherein H113 is substituted with either a K, or R; wherein Q114 is substituted with a N; wherein D115 is substituted with an E; wherein I116 is substituted with either an A, V, or L; wherein L117 is substituted with either an A, I, or V; wherein S118 is substituted with either an A, G, M, or T; wherein R119 is substituted with either a K, or H; wherein V120 is substituted with either an A, I, or L; wherein V121 is substituted with either an A, I, or L; wherein P122 is a P; wherein L123 is substituted with either an A, I, or V; wherein N124 is substituted with a Q; wherein Q125 is substituted with a N; wherein S126 is substituted with either an A, G, M, or T; wherein F127 is substituted with either a W, or Y; wherein T128 is substituted with either an A, G, M, or S; wherein E129 is substituted with a D; wherein K130 is substituted with either a R, or H; wherein Y131 is either an F, or W; wherein A132 is substituted with either a G, I, L, M, S, T, or V; wherein G133 is substituted with either an A, M, S, or T; wherein I134 is substituted with either an A, V, or L; wherein F135 is substituted with either a W, or Y; wherein R136 is substituted with either a K, or H; wherein F137 is substituted with either a W, or Y; wherein W138 is either an F, or Y; wherein F139 is substituted with either a W, or Y; wherein W140 is either an F, or Y; wherein H141 is substituted with either a K, or R; wherein Y142 is either an F, or W; wherein G143 is substituted with either an A, M, S, or T; wherein N144 is substituted with a Q; wherein W145 is either an F, or Y; wherein V146 is substituted with either an A, I, or L; wherein P147 is a P; wherein V148 is substituted with either an A, I, or L; wherein V149 is substituted with either an A, I, or L; wherein I150 is substituted with either an A, V, or L; wherein D151 is substituted with an E; wherein D152 is substituted with an E; wherein R153 is substituted with either a K, or H; wherein L154 is substituted with either an A, I, or V; wherein P155 is a P; wherein V156 is substituted with either an A, I, or L; wherein N157 is substituted with a Q; wherein E158 is substituted with a D; wherein A159 is substituted with either a G, I, L, M, S, T, or V; wherein G160 is substituted with either an A, M, S, or T; wherein Q161 is substituted with a N; wherein L162 is substituted with either an A, I, or V; wherein V163 is substituted with either an A, I, or L; wherein F164 is substituted with either a W, or Y; wherein V165 is substituted with either an A, I, or L; wherein S166 is substituted with either an A, G, M, or T; wherein S167 is substituted with either an A, G, M, or T; wherein T168 is substituted with either an A, G, M, or S; wherein Y169 is either an F, or W; wherein K170 is substituted with either a R, or H; wherein N171 is substituted with a Q; wherein L172 is substituted with either an A, I, or V; wherein F173 is substituted with either a W, or Y; wherein W174 is either an F, or Y; wherein G175 is substituted with either an A, M, S, or T; wherein A176 is substituted with either a G, I, L, M, S, T, or V; wherein L177 is substituted with either an A, I, or V; wherein L178 is substituted with either an A, I, or V; wherein E179 is substituted with a D; wherein K180 is substituted with either a R, or H; wherein A181 is substituted with either a G, I, L, M, S, T, or V; wherein Y182 is either an F, or W; wherein A183 is substituted with either a G, I, L, M, S, T, or V; wherein K184 is substituted with either a R, or H; wherein L185 is substituted with either an A, I, or V; wherein S186 is substituted with either an A, G, M, or T; wherein G187 is substituted with either an A, M, S, or T; wherein S188 is substituted with either an A, G, M, or T; wherein Y189 is either an F, or W; wherein E190 is substituted with a D; wherein D191 is substituted with an E; wherein L192 is substituted with either an A, I, or V; wherein Q193 is substituted with a N; wherein S194 is substituted with either an A, G, M, or T; wherein G195 is substituted with either an A, M, S, or T; wherein Q196 is substituted with a N; wherein V197 is substituted with either an A, I, or L; wherein S198 is substituted with either an A, G, M, or T; wherein E199 is substituted with a D; wherein A200 is substituted with either a G, I, L, M, S, T, or V; wherein L201 is substituted with either an A, I, or V; wherein V202 is substituted with either an A, I, or L; wherein D203 is substituted with an E; wherein F204 is substituted with either a W, or Y; wherein T205 is substituted with either an A, G, M, or S; wherein G206 is substituted with either an A, M, S, or T; wherein G207 is substituted with either an A, M, S, or T; wherein V208 is substituted with either an A, I, or L; wherein T209 is substituted with either an A, G, M, or S; wherein M210 is substituted with either an A, G, S, or T; wherein T211 is substituted with either an A, G, M, or S; wherein I212 is substituted with either an A, V, or L; wherein N213 is substituted with a Q; wherein L214 is substituted with either an A, I, or V; wherein A215 is substituted with either a G, I, L, M, S, T, or V; wherein E216 is substituted with a D; wherein A217 is substituted with either a G, I, L, M, S, T, or V; wherein H218 is substituted with either a K, or R; wherein G219 is substituted with either an A, M, S, or T; wherein N220 is substituted with a Q; wherein L221 is substituted with either an A, I, or V; wherein W222 is either an F, or Y; wherein D223 is substituted with an E; wherein I224 is substituted with either an A, V, or L; wherein L225 is substituted with either an A, I, or V; wherein I226 is substituted with either an A, V, or L; wherein E227 is substituted with a D; wherein A228 is substituted with either a G, I, L, M, S, T, or V; wherein T229 is substituted with either an A, G, M, or S; wherein Y230 is either an F, or W; wherein N231 is substituted with a Q; wherein R232 is substituted with either a K, or H; wherein T233 is substituted with either an A, G, M, or S; wherein L234 is substituted with either an A, I, or V; wherein I235 is substituted with either an A, V, or L; wherein G236 is substituted with either an A, M, S, or T; wherein C237 is a C; wherein Q238 is substituted with a N; wherein T239 is substituted with either an A, G, M, or S; wherein H240 is substituted with either a K, or R; wherein S241 is substituted with either an A, G, M, or T; wherein G242 is substituted with either an A, M, S, or T; wherein E243 is substituted with a D; wherein K244 is substituted with either a R, or H; wherein I245 is substituted with either an A, V, or L; wherein L246 is substituted with either an A, I, or V; wherein E247 is substituted with a D; wherein N248 is substituted with a Q; wherein G249 is substituted with either an A, M, S, or T; wherein L250 is substituted with either an A, I, or V; wherein V251 is substituted with either an A, I, or L; wherein E252 is substituted with a D; wherein G253 is substituted with either an A, M, S, or T; wherein H254 is substituted with either a K, or R; wherein A255 is substituted with either a G, I, L, M, S, T, or V; wherein Y256 is either an F, or W; wherein T257 is substituted with either an A, G, M, or S; wherein L258 is substituted with either an A, I, or V; wherein T259 is substituted with either an A, G, M, or S; wherein G260 is substituted with either an A, M, S, or T; wherein I261 is substituted with either an A, V, or L; wherein R262 is substituted with either a K, or H; wherein K263 is substituted with either a R, or H; wherein V264 is substituted with either an A, I, or L; wherein T265 is substituted with either an A, G, M, or S; wherein C266 is a C; wherein K267 is substituted with either a R, or H; wherein H268 is substituted with either a K, or R; wherein R269 is substituted with either a K, or H; wherein P270 is a P; wherein E271 is substituted with a D; wherein Y272 is either an F, or W; wherein L273 is substituted with either an A, I, or V; wherein V274 is substituted with either an A, I, or L; wherein K275 is substituted with either a R, or H; wherein L276 is substituted with either an A, I, or V; wherein R277 is substituted with either a K, or H; wherein N278 is substituted with a Q; wherein P279 is a P; wherein W280 is either an F, or Y; wherein G281 is substituted with either an A, M, S, or T; wherein K282 is substituted with either a R, or H; wherein V283 is substituted with either an A, I, or L; wherein E284 is substituted with a D; wherein W285 is either an F, or Y; wherein K286 is substituted with either a R, or H; wherein G287 is substituted with either an A, M, S, or T; wherein D288 is substituted with an E; wherein W289 is either an F, or Y; wherein S290 is substituted with either an A, G, M, or T; wherein D291 is substituted with an E; wherein S292 is substituted with either an A, G, M, or T; wherein S293 is substituted with either an A, G, M, or T; wherein S294 is substituted with either an A, G, M, or T; wherein K295 is substituted with either a R, or H; wherein W296 is either an F, or Y; wherein E297 is substituted with a D; wherein L298 is substituted with either an A, I, or V; wherein L299 is substituted with either an A, I, or V; wherein S300 is substituted with either an A, G, M, or T; wherein P301 is a P; wherein K302 is substituted with either a R, or H; wherein E303 is substituted with a D; wherein K304 is substituted with either a R, or H; wherein I305 is substituted with either an A, V, or L; wherein L306 is substituted with either an A, I, or V; wherein L307 is substituted with either an A, I, or V; wherein L308 is substituted with either an A, I, or V; wherein R309 is substituted with either a K, or H; wherein K310 is substituted with either a R, or H; wherein D311 is substituted with an E; wherein N312 is substituted with a Q; wherein D313 is substituted with an E; wherein G314 is substituted with either an A, M, S, or T; wherein E315 is substituted with a D; wherein F316 is substituted with either a W, or Y; wherein W317 is either an F, or Y; wherein M318 is substituted with either an A, G, S, or T; wherein T319 is substituted with either an A, G, M, or S; wherein L320 is substituted with either an A, I, or V; wherein Q321 is substituted with a N; wherein D322 is substituted with an E; wherein F323 is substituted with either a W, or Y; wherein K324 is substituted with either a R, or H; wherein T325 is substituted with either an A, G, M, or S; wherein H326 is substituted with either a K, or R; wherein F327 is substituted with either a W, or Y; wherein V328 is substituted with either an A, I, or L; wherein L329 is substituted with either an A, I, or V; wherein L330 is substituted with either an A, I, or V; and/or wherein V331 is substituted with either an A, I, or L of SEQ ID NO:56 in addition to any combination thereof. Other suitable substitutions within the CAN-12v2 active site domain are encompassed by the present invention and are referenced elsewhere herein. The present invention also encompasses the use of these CAN-12v2 active site domain conservative amino acid substituted polypeptides as immunogenic and/or antigenic epitopes as described elsewhere herein.

[0492] For purposes of the present invention, by “at least a portion of” is meant all or any part of the CAN-12v2 active site domain defined by the structure coordinates according to Table V (e.g., fragments thereof). More preferred are molecules comprising all or any parts of the CAN-12v2 active site domain defined by the structure coordinates according to Table V, or a mutant or homologue of said molecule or molecular complex. By mutant or homologue of the molecule it is meant a molecule that has a root mean square deviation from the backbone atoms of said CAN-12v2 amino acids of not more than 4.5 Angstroms, and preferably not more than 3.5 Angstroms.

[0493] The term “root mean square deviation” means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a term that expresses the deviation or variation from a trend or object. For the purposes of the present invention, the “root mean square deviation” defines the variation in the backbone of a protein from the relevant portion of the backbone of the AR portion of the complex as defined by the structure coordinates described herein.

[0494] A preferred embodiment is a machine-readable data storage medium that is capable of displaying a graphical three-dimensional representation of a molecule or molecular complex that is defined by the structure coordinates of all of the amino acids in Table V +/−a root mean square deviation from the backbone atoms of those amino acids of not more than 4.0 ANG, preferably 3.0 ANG.

[0495] The structure coordinates of a CAN-12v2 homology model, including portions thereof, is stored in a machine-readable storage medium. Such data may be used for a variety of purposes, such as drug discovery.

[0496] Accordingly, in one embodiment of this invention is provided a machine-readable data storage medium comprising a data storage material encoded with the structure coordinates set forth in Table V.

[0497] One embodiment utilizes System 10 as disclosed in WO 98/11134, the disclosure of which is incorporated herein by reference in its entirety. Briefly, one version of these embodiments comprises a computer comprising a central processing unit (“CPU”), a working memory which may be, e.g, RAM (random-access memory) or “core” memory, mass storage memory (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals, one or more keyboards, one or more input lines, and one or more output lines, all of which are interconnected by a conventional bidirectional system bus.

[0498] Input hardware, coupled to the computer by input lines, may be implemented in a variety of ways. Machine-readable data of this invention may be inputted via the use of a modem or modems connected by a telephone line or dedicated data line. Alternatively or additionally, the input hardware may comprise CD-ROM drives or disk drives. In conjunction with a display terminal, keyboard may also be used as an input device.

[0499] Output hardware, coupled to the computer by output lines, may similarly be implemented by conventional devices. By way of example, output hardware may include a CRT display terminal for displaying a graphical representation of a region or domain of the present invention using a program such as QUANTA as described herein. Output hardware might also include a printer, so that hard copy output may be produced, or a disk drive, to store system output for later use.

[0500] In operation, the CPU coordinates the use of the various input and output devices, coordinates data accesses from mass storage, and accesses to and from the working memory, and determines the sequence of data processing steps. A number of programs may be used to process the machine-readable data of this invention. Such programs are discussed in reference to the computational methods of drug discovery as described herein. Specific references to components of the hardware system are included as appropriate throughout the following description of the data storage medium.

[0501] For the purpose of the present invention, any magnetic data storage medium which can be encoded with machine-readable data would be sufficient for carrying out the storage requirements of the system. The medium could be a conventional floppy diskette or hard disk, having a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, on one or both sides, containing magnetic domains whose polarity or orientation could be altered magnetically, for example. The medium may also have an opening for receiving the spindle of a disk drive or other data storage device.

[0502] The magnetic domains of the coating of a medium may be polarized or oriented so as to encode in a manner which may be conventional, machine readable data such as that described herein, for execution by a system such as the system described herein.

[0503] Another example of a suitable storage medium which could also be encoded with such machine-readable data, or set of instructions, which could be carried out by a system such as the system described herein, could be an optically-readable data storage medium. The medium could be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk which is optically readable and magneto-optically writable. The medium preferably has a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, usually of one side of substrate.

[0504] In the case of a CD-ROM, as is well known, the coating is reflective and is impressed with a plurality of pits to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of the coating. A protective coating, which preferably is substantially transparent, is provided on top of the reflective coating.

[0505] In the case of a magneto-optical disk, as is well known, the coating has no pits, but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser. The orientation of the domains can be read by measuring the polarization of laser light reflected from the coating. The arrangement of the domains encodes the data as described above.

[0506] Thus, in accordance with the present invention, data capable of displaying the three dimensional structure of the CAN-12v2 homology model, or portions thereof and their structurally similar homologues is stored in a machine-readable storage medium, which is capable of displaying a graphical three-dimensional representation of the structure. Such data may be used for a variety of purposes, such as drug discovery.

[0507] For the first time, the present invention permits the use of structure-based or rational drug design techniques to design, select, and synthesize chemical entities that are capable of modulating the biological function of CAN-12v2.

[0508] Accordingly, the present invention is also directed to the design of small molecules which imitates the structure of the CAN-12v2 active site domain (SEQ ID NO:93), or a portion thereof defined by the structure provided in Table V. Alternatively, the present invention is directed to the design of small molecules which may bind to at least part of the CAN-12v2 active site domain (SEQ ID NO:93), or some portion thereof. For purposes of this invention, by CAN-12v2 active site domain, it is also meant to include mutants or homologues thereof. In a preferred embodiment, the mutants or homologues have at least 25% identity, more preferably 50% identity, more preferably 75% identity, and most preferably 90% identity to SEQ ID NO:93. In this context, the term “small molecule” may be construed to mean any molecule described known in the art or described elsewhere herein, though may include, for example, peptides, chemicals, carbohydrates, nucleic acids, PNAs, and any derivatives thereof.

[0509] The three-dimensional model structure of CAN-12v2 will also provide methods for identifying modulators of biological function. Various methods or combination thereof can be used to identify these compounds.

[0510] For example, test compounds can be modeled that fit spatially into the active site domain in CAN-12v2 embodied by the sequence from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331, or some portion thereof, of SEQ ID NO:56 (corresponding to SEQ ID NO:93), in accordance with the structural coordinates of Table V.

[0511] Structure coordinates of the active site domain in CAN-12v2 defined by the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:56, can also be used to identify structural and chemical features. Identified structural or chemical features can then be employed to design or select compounds as potential CAN-12v2 modulators. By structural and chemical features it is meant to include, but is not limited to, van der Waals interactions, hydrogen bonding interactions, charge interaction, hydrophobic bonding interaction, and dipole interaction. Alternatively, or in conjunction with, the three-dimensional structural model can be employed to design or select compounds as potential CAN-12v2 modulators. Compounds identified as potential CAN-12v2 modulators can then be synthesized and screened in an assay characterized by binding of a test compound to the CAN-12v2, or in characterizing the ability of CAN-12v2 to modulate a protease target in the presence of a small molecule. Examples of assays useful in screening of potential CAN-12v2 modulators include, but are not limited to, screening in silico, in vitro assays and high throughput assays. Finally, these methods may also involve modifying or replacing one or more amino acids at amino acid positions, C101, H254, and/or N278 of SEQ ID NO:56 in accordance with the structure coordinates of Table V.

[0512] However, as will be understood by those of skill in the art upon this disclosure, other structure based design methods can be used. Various computational structure based design methods have been disclosed in the art.

[0513] For example, a number of computer modeling systems are available in which the sequence of the CAN-12v2 and the CAN-12v2 structure (i.e., atomic coordinates of CAN-12v2 and/or the atomic coordinates of the active site domain as provided in Table V, can be input. This computer system then generates the structural details of one or more these regions in which a potential CAN-12v2 modulator binds so that complementary structural details of the potential modulators can be determined. Design in these modeling systems is generally based upon the compound being capable of physically and structurally associating with CAN-12v2. In addition, the compound must be able to assume a conformation that allows it to associate with CAN-12v2. Some modeling systems estimate the potential inhibitory or binding effect of a potential CAN-12v2 modulator prior to actual synthesis and testing.

[0514] Methods for screening chemical entities or fragments for their ability to associate with a given protein target are also well known. Often these methods begin by visual inspection of the binding site on the computer screen. Selected fragments or chemical entities are then positioned in the active site domain of CAN-12v2. Docking is accomplished using software such as INSIGHTII, QUANTA and SYBYL, following by energy minimization and molecular dynamics with standard molecular mechanic forcefields such as CHARMM and AMBER. Examples of computer programs which assist in the selection of chemical fragment or chemical entities useful in the present invention include, but are not limited to, GRID (Goodford, 1985), AUTODOCK (Goodsell, 1990), and DOCK (Kuntz et al. 1982).

[0515] Upon selection of preferred chemical entities or fragments, their relationship to each other and CAN-12v2 can be visualized and then assembled into a single potential modulator. Programs useful in assembling the individual chemical entities include, but are not limited to CAVEAT (Bartlett et al. 1989) and 3D Database systems (Martin 1992).

[0516] Alternatively, compounds may be designed de novo using either an empty active site or optionally including some portion of a known inhibitor. Methods of this type of design include, but are not limited to LUDI (Bohm 1992) and LeapFrog (Tripos Associates, St. Louis Mo.).

[0517] In addition, CAN-12v2 is overall well suited to modern methods including combinatorial chemistry.

[0518] Programs such as DOCK (Kuntz et al. 1982) can be used with the atomic coordinates from the homology model to identify potential ligands from databases or virtual databases which potentially bind CAN-12v2 active site domain, and which may therefore be suitable candidates for synthesis and testing.

[0519] Additionally, the three-dimensional homology model of CAN-12v2 will aid in the design of mutants with altered biological activity for the CAN-12v2 polypeptide.

[0520] The following are encompassed by the present invention: a machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein the data is defined by the structure coordinates of the model CAN-12v2 according to Table V or a homologue of said model, wherein said homologue comprises backbone atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; and a machine-readable data storage medium, wherein said molecule is defined by the set of structure coordinates of the model for CAN-12v2 according to Table V, or a homologue of said molecule, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 4.5 Å, preferably not more than 4.0 Å, most preferably not more than 3.5 Å, and even more preferably not more than 3.0 Å; a model comprising all or any part of the model defined by structure coordinates of CAN-12v2 according to Table V, or a mutant or homologue of said molecule or molecular complex.

[0521] In a further embodiment, the following are encompassed by the present invention: a method for identifying a mutant of CAN-12v2 with altered biological properties, function, or reactivity, the method comprising any combination of steps of: use of the model or a homologue of said model according to Table V, for the design of protein mutants with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein; and use of the model or a homologue of said model, for the design of a protein with mutations in the active site domain comprised of the amino acids from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid I212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:56 according to Table V with altered biological function or properties which exhibit any combination of therapeutic effects provided elsewhere herein.

[0522] In further preferred embodiments, the following are encompassed by the present invention: a method for identifying modulators of CAN-12v2 biological properties, function, or reactivity, the method comprising any combination of steps of: modeling test compounds that overlay spatially into the active site domain defined by all or any portion of residues from about R90 to about amino acid C94, from about amino acid G99 to about amino acid L104, from about amino acid Q196 to about amino acid S198, from about amino acid M210 to about amino acid 1212, from about amino acid G236 to about amino acid H240, from about amino acid E252 to about amino acid Y256, from about amino acid N278 to about amino acid K282, from about amino acid V328 to about amino acid V331 of SEQ ID NO:56 according to Table V, or using a homologue or portion thereof.

[0523] The present invention encompasses using the structure coordinates as set forth herein to identify structural and chemical features of the CAN-12v2 polypeptide; employing identified structural or chemical features to design or select compounds as potential CAN-12v2 modulators; employing the three-dimensional structural model to design or select compounds as potential CAN-12v2 modulators; synthesizing the potential CAN-12v2 modulators; screening the potential CAN-12v2 modulators in an assay characterized by binding of a protein to the CAN-12v2; selecting the potential CAN-12v2 modulator from a database; designing the CAN-12v2 modulator de novo; and/or designing said CAN-12v2 modulator from a known modulator activity.

[0524] Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO: 55 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides consisting of a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2090 of SEQ ID NO:55, b is an integer between 15 to 2104, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:55, and where b is greater than or equal to a+14.

[0525] In one embodiment, a CAN12.v2 polypeptide comprises a portion of the amino sequence depicted in FIGS. 9A-C. In another embodiment, a CAN12.v2 polypeptide comprises at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids of the amino sequence depicted in FIGS. 9A-C. In further embodiments, the CAN12.v2 polypeptide does not consist of the sequence ALLEKAYAKL (SEQ ID NO:141), and/or ALLEKAYAKLSGSYE. (SEQ ID NO:142)

4TABLE IATCCNTTotal5′ NTDepositSEQNTof Start3′ NTAATotalGeneCDNANo. Z andID.Seq ofCodonofSeq IDAA ofNo.CloneIDDateVectorNo. XCloneof ORFORFNo. YORF1.CAN-12XXXXXpSport 11 and 234584114139724428(proteaseXx/Xx/Xx5, clone70)1.CAN-12XXXXXpSport 1 1458411419952581(proteaseXx/Xx/Xx5, clone70, CAN-12+) +spliceaminoacids2.CAN-PTA-3434pSport 1532095920905469412v1Jun. 07, 2001(protease5, clone1e)3.CAN-PTA-3434pSport 1552104920995669712v2Jun. 07, 2001(protease5, clone1e1b-1)

[0526] Table I summarizes the information corresponding to each “Gene No.” described above. The nucleotide sequence identified as “NT SEQ ID NO:X” was assembled from partially homologous (“overlapping”) sequences obtained from the “cDNA clone ID” identified in Table I and, in some cases, from additional related DNA clones. The overlapping sequences were assembled into a single contiguous sequence of high redundancy (usually several overlapping sequences at each nucleotide position), resulting in a final sequence identified as SEQ ID NO:X.

[0527] The cDNA Clone ID was deposited on the date and given the corresponding deposit number listed in “ATCC Deposit No:Z and Date.” “Vector” refers to the type of vector contained in the cDNA Clone ID.

[0528] “Total NT Seq. Of Clone” refers to the total number of nucleotides in the clone contig identified by “Gene No.” The deposited clone may contain all or most of the sequence of SEQ ID NO:X. The nucleotide position of SEQ ID NO:X of the putative start codon (methionine) is identified as “5′ NT of Start Codon of ORF.”

[0529] The translated amino acid sequence, beginning with the methionine, is identified as “AA SEQ ID NO:Y,” although other reading frames can also be easily translated using known molecular biology techniques. The polypeptides produced by these alternative open reading frames are specifically contemplated by the present invention.

[0530] The total number of amino acids within the open reading frame of SEQ ID NO:Y is identified as “Total AA of ORF”.

[0531] SEQ ID NO:X (where X may be any of the polynucleotide sequences disclosed in the sequence listing) and the translated SEQ ID NO:Y (where Y may be any of the polypeptide sequences disclosed in the sequence listing) are sufficiently accurate and otherwise suitable for a variety of uses well known in the art and described further herein. For instance, SEQ ID NO:X is useful for designing nucleic acid hybridization probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the cDNA contained in the deposited clone. These probes will also hybridize to nucleic acid molecules in biological samples, thereby enabling a variety of forensic and diagnostic methods of the invention. Similarly, polypeptides identified from SEQ ID NO:Y may be used, for example, to generate antibodies which bind specifically to proteins containing the polypeptides and the proteins encoded by the cDNA clones identified in Table I.

[0532] Nevertheless, DNA sequences generated by sequencing reactions can contain sequencing errors. The errors exist as misidentified nucleotides, or as insertions or deletions of nucleotides in the generated DNA sequence. The erroneously inserted or deleted nucleotides may cause frame shifts in the reading frames of the predicted amino acid sequence. In these cases, the predicted amino acid sequence diverges from the actual amino acid sequence, even though the generated DNA sequence may be greater than 99.9% identical to the actual DNA sequence (for example, one base insertion or deletion in an open reading frame of over 1000 bases).

[0533] Accordingly, for those applications requiring precision in the nucleotide sequence or the amino acid sequence, the present invention provides not only the generated nucleotide sequence identified as SEQ ID NO:1, 23, 53, and/or 55 and the predicted translated amino acid sequence identified as SEQ ID NO:2, 24, 54, and/or 56, but also a sample of plasmid DNA containing a cDNA of the invention deposited with the ATCC, as set forth in Table I. The nucleotide sequence of each deposited clone can readily be determined by sequencing the deposited clone in accordance with known methods. The predicted amino acid sequence can then be verified from such deposits. Moreover, the amino acid sequence of the protein encoded by a particular clone can also be directly determined by peptide sequencing or by expressing the protein in a suitable host cell containing the deposited cDNA, collecting the protein, and determining its sequence.

[0534] The present invention also relates to the genes corresponding to SEQ ID NO:1, 23, 53, and/or 55, SEQ ID NO:2, 24, 54, and/or 56, or the deposited clone. The corresponding gene can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material.

[0535] Also provided in the present invention are species homologs, allelic variants, and/or orthologs. The skilled artisan could, using procedures well-known in the art, obtain the polynucleotide sequence corresponding to full-length genes (including, but not limited to the full-length coding region), allelic variants, splice variants, orthologs, and/or species homologues of genes corresponding to SEQ ID NO:1, 23, 53, and/or 55, SEQ ID NO:2, 24, 54, and/or 56, or a deposited clone, relying on the sequence from the sequences disclosed herein or the clones deposited with the ATCC. For example, allelic variants and/or species homologues may be isolated and identified by making suitable probes or primers which correspond to the 5′, 3′, or internal regions of the sequences provided herein and screening a suitable nucleic acid source for allelic variants and/or the desired homologue.

[0536] The polypeptides of the invention can be prepared in any suitable manner. Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.

[0537] The polypeptides may be in the form of the protein, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification, such as multiple histidine residues, or an additional sequence for stability during recombinant production.

[0538] The polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified. A recombinantly produced version of a polypeptide, can be substantially purified using techniques described herein or otherwise known in the art, such as, for example, by the one-step method described in Smith and Johnson, Gene 67:31-40 (1988). Polypeptides of the invention also can be purified from natural, synthetic or recombinant sources using protocols described herein or otherwise known in the art, such as, for example, antibodies of the invention raised against the full-length form of the protein.

[0539] The present invention provides a polynucleotide comprising, or alternatively consisting of, the sequence identified as SEQ ID NO:1, 23, 53, and/or 55, and/or a cDNA provided in ATCC Deposit No. Z:. The present invention also provides a polypeptide comprising, or alternatively consisting of, the sequence identified as SEQ ID NO:2, 24, 54, and/or 56, and/or a polypeptide encoded by the cDNA provided in ATCC Deposit NO:Z. The present invention also provides polynucleotides encoding a polypeptide comprising, or alternatively consisting of the polypeptide sequence of SEQ ID NO:2, 24, 54, and/or 56, and/or a polypeptide sequence encoded by the cDNA contained in ATCC Deposit No:Z.

[0540] Preferably, the present invention is directed to a polynucleotide comprising, or alternatively consisting of, the sequence identified as SEQ ID NO:1, 23, 53, and/or 55, and/or a cDNA provided in ATCC Deposit No.: that is less than, or equal to, a polynucleotide sequence that is 5 mega basepairs, 1 mega basepairs, 0.5 mega basepairs, 0.1 mega basepairs, 50,000 basepairs, 20,000 basepairs, or 10,000 basepairs in length.

[0541] The present invention encompasses polynucleotides with sequences complementary to those of the polynucleotides of the present invention disclosed herein. Such sequences may be complementary to the sequence disclosed as SEQ ID NO:1, 23, 53, and/or 55, the sequence contained in a deposit, and/or the nucleic acid sequence encoding the sequence disclosed as SEQ ID NO:2, 24, 54, and/or 56.

[0542] The present invention also encompasses polynucleotides capable of hybridizing, preferably under reduced stringency conditions, more preferably under stringent conditions, and most preferably under highly stringent conditions, to polynucleotides described herein. Examples of stringency conditions are shown in Table II below: highly stringent conditions are those that are at least as stringent as, for example, conditions A-F; stringent conditions are at least as stringent as, for example, conditions G-L; and reduced stringency conditions are at least as stringent as, for example, conditions M-R.

5TABLE IIStrin-gencyHybridizationWashCon-PolynucleotideHybridTemperatureTemperatureditionHybrid ±Length (bp) ‡and Buffer †and Buffer †ADNA:DNA> or equal to65° C.; 1xSSC -65° C.;50or- 42° C.;0.3xSSC1xSSC, 50%formamideBDNA:DNA<50Tb*; 1xSSCTb*; 1xSSCCDNA:RNA> or equal to67° C.; 1xSSC -67° C.;50or- 45° C.;0.3xSSC1xSSC, 50%formamideDDNA:RNA<50Td*; 1xSSCTd*; 1xSSCERNA:RNA> or equal to70° C.; 1xSSC -70° C.;50or- 50° C.;0.3xSSC1xSSC, 50%formamideFRNA:RNA<50Tf*; 1xSSCTf*; 1xSSCGDNA:DNA> or equal to65° C.; 4xSSC -65° C.;50or- 45° C.;1xSSC4xSSC, 50%formamideHDNA:DNA<50Th*; 4xSSCTh*; 4xSSCIDNA:RNA> or equal to67° C.; 4xSSC -67° C.;50or- 45° C.;1xSSC4xSSC, 50%formamideJDNA:RNA<50Tj*; 4xSSCTj*; 4xSSCKRNA:RNA> or equal to70° C.; 4xSSC -67° C.;50or- 40° C.;1xSSC6xSSC, 50%formamideLRNA:RNA<50Tl*; 2xSSCTl*; 2xSSCMDNA:DNA> or equal to50° C.; 4xSSC -50° C.;50or- 40° C.2xSSC6xSSC, 50%formamideNDNA:DNA<50Tn*; 6xSSCTn*; 6xSSCODNA:RNA> or equal to55° C.; 4xSSC -55° C.;50or- 42° C.;2xSSC6xSSC, 50%formamidePDNA:RNA<50Tp*; 6xSSCTp*; 6xSSCQRNA:RNA> or equal to60° C.; 4xSSC -60° C.;50or- 45° C.;2xSSC6xSSC, 50%formamideRRNA:RNA<50Tr*; 4xSSCTr*; 4xSSC‡ The “hybrid length” is the anticipated length for the hybridized region(s) of the hybridizing polynucleotides. When hybridizing a polynucleotide of unknown sequence, the hybrid is assumed to be that of the hybridizing plynucleotide of the present invention. When polynucletides of known sequence are hybridized, the hybrid length can be determined by aligning the sequences of the polynucleotides and identifying the region or regions of optimal sequence complementarity. Methods of # aligning two or more polynucleotide sequences and/or determining the percent identity between two polynucleotide sequences are well known in the art (e.g., MegAlign program of the DNA*Star suite of programs, etc). † SSPE (1xSSPE is 0.15M NaCl, 10 mM NaH2PO4, and 1.25 mM EDTA, pH 7.4) can be substituted for SSC (1xSSC is 0.15 M NaCl and 15 mM sodium citrate) in the hybridization and wash buffers; washes are performed for 15 minutes after hybridization is complete. The hydridizations and washes may additionally include 5X Denhardt's reagent, .5-1.0% SDS, 100 ug/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate, and up to 50% formamide. *Tb-Tr: The hybridization temperature for hybrids anticipated to be less than 50 base pairs in length should be 5-10° C. less than the melting temperature Tm of the hybrids there Tm is determined according to the following equations. For hybrids less than 18 base pairs in length, Tm(° C.) = 2(# of A + T bases) + 4(# of G + C bases). For hybrids between 18 and 49 base pairs in length, # Tm(° C.) = 81.5 + 16.6(log10[Na+]) + 0.41(% G + C) − (600/N), where N is the number of bases in the hybrid, and [Na+] is the concentration of sodium ions in the hybridization buffer ([NA+] for 1xSSC = .165 M). ± The present invention encompasses the substitution of any one, or more DNA or RNA hybrid partners with either a PNA, or a modified polynucleotide. Such modified polynucleotides are known in the art and are more particularly described elsewhere herein.

[0543] Additional examples of stringency conditions for polynucleotide hybridization are provided, for example, in Sambrook, J., E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., chapters 9 and 11, and Current Protocols in Molecular Biology, 1995, F. M., Ausubel et al., eds, John Wiley and Sons, Inc., sections 2.10 and 6.3-6.4, which are hereby incorporated by reference herein.

[0544] Preferably, such hybridizing polynucleotides have at least 70% sequence identity (more preferably, at least 80% identity; and most preferably at least 90% or 95% identity) with the polynucleotide of the present invention to which they hybridize, where sequence identity is determined by comparing the sequences of the hybridizing polynucleotides when aligned so as to maximize overlap and identity while minimizing sequence gaps. The determination of identity is well known in the art, and discussed more specifically elsewhere herein.

[0545] The invention encompasses the application of PCR methodology to the polynucleotide sequences of the present invention, the clone deposited with the ATCC, and/or the cDNA encoding the polypeptides of the present invention. PCR techniques for the amplification of nucleic acids are described in U.S. Pat. No. 4,683,195 and Saiki et al., Science, 239:487-491 (1988). PCR, for example, may include the following steps, of denaturation of template nucleic acid (if double-stranded), annealing of primer to target, and polymerization. The nucleic acid probed or used as a template in the amplification reaction may be genomic DNA, cDNA, RNA, or a PNA. PCR may be used to amplify specific sequences from genomic DNA, specific RNA sequence, and/or cDNA transcribed from mRNA. References for the general use of PCR techniques, including specific method parameters, include Mullis et al., Cold Spring Harbor Symp. Quant. Biol., 51:263, (1987), Ehrlich (ed), PCR Technology, Stockton Press, NY, 1989; Ehrlich et al., Science, 252:1643-1650, (1991); and “PCR Protocols, A Guide to Methods and Applications”, Eds., Innis et al., Academic Press, New York, (1990).

[0546] Signal Sequences

[0547] The present invention also encompasses mature forms of the polypeptide comprising, or alternatively consisting of, the polypeptide sequence of SEQ ID NO:2, 24, 54, and/or 56, the polypeptide encoded by the polynucleotide described as SEQ ID NO:1, 23, 53, and/or 55, and/or the polypeptide sequence encoded by a cDNA in the deposited clone. The present invention also encompasses polynucleotides encoding mature forms of the present invention, such as, for example the polynucleotide sequence of SEQ ID NO:1, 23, 53, and/or 55, and/or the polynucleotide sequence provided in a cDNA of the deposited clone.

[0548] According to the signal hypothesis, proteins secreted by eukaryotic cells have a signal or secretary leader sequence which is cleaved from the mature protein once export of the growing protein chain across the rough endoplasmic reticulum has been initiated. Most eukaryotic cells cleave secreted proteins with the same specificity. However, in some cases, cleavage of a secreted protein is not entirely uniform, which results in two or more mature species of the protein. Further, it has long been known that cleavage specificity of a secreted protein is ultimately determined by the primary structure of the complete protein, that is, it is inherent in the amino acid sequence of the polypeptide.

[0549] Methods for predicting whether a protein has a signal sequence, as well as the cleavage point for that sequence, are available. For instance, the method of McGeoch, Virus Res. 3:271-286 (1985), uses the information from a short N-terminal charged region and a subsequent uncharged region of the complete (uncleaved) protein. The method of von Heinje, Nucleic Acids Res. 14:4683-4690 (1986) uses the information from the residues surrounding the cleavage site, typically residues -13 to +2, where +1 indicates the amino terminus of the secreted protein. The accuracy of predicting the cleavage points of known mammalian secretory proteins for each of these methods is in the range of 75-80%. (von Heinje, supra.) However, the two methods do not always produce the same predicted cleavage point(s) for a given protein.

[0550] The established method for identifying the location of signal sequences, in addition, to their cleavage sites has been the SignalP program (v1.1) developed by Henrik Nielsen et al., Protein Engineering 10: 1-6 (1997). The program relies upon the algorithm developed by von Heinje, though provides additional parameters to increase the prediction accuracy.

[0551] More recently, a hidden Markov model has been developed (H. Neilson, et al., Ismb 1998;6: 122-30), which has been incorporated into the more recent SignalP (v2.0). This new method increases the ability to identify the cleavage site by discriminating between signal peptides and uncleaved signal anchors. The present invention encompasses the application of the method disclosed therein to the prediction of the signal peptide location, including the cleavage site, to any of the polypeptide sequences of the present invention.

[0552] As one of ordinary skill would appreciate, however, cleavage sites sometimes vary from organism to organism and cannot be predicted with absolute certainty. Accordingly, the polypeptide of the present invention may contain a signal sequence. Polypeptides of the invention which comprise a signal sequence have an N-terminus beginning within 5 residues (i.e., +or −5 residues, or preferably at the −5, −4, −3, −2, −1, +1, +2, +3, +4, or +5 residue) of the predicted cleavage point. Similarly, it is also recognized that in some cases, cleavage of the signal sequence from a secreted protein is not entirely uniform, resulting in more than one secreted species. These polypeptides, and the polynucleotides encoding such polypeptides, are contemplated by the present invention.

[0553] Moreover, the signal sequence identified by the above analysis may not necessarily predict the naturally occurring signal sequence. For example, the naturally occurring signal sequence may be further upstream from the predicted signal sequence. However, it is likely that the predicted signal sequence will be capable of directing the secreted protein to the ER. Nonetheless, the present invention provides the mature protein produced by expression of the polynucleotide sequence of SEQ ID NO:1, 23, 53, and/or 55 and/or the polynucleotide sequence contained in the cDNA of a deposited clone, in a mammalian cell (e.g., COS cells, as described below). These polypeptides, and the polynucleotides encoding such polypeptides, are contemplated by the present invention.

[0554] Polynucleotide and Polypeptide Variants

[0555] The present invention also encompasses variants (e.g., allelic variants, orthologs, etc.) of the polynucleotide sequence disclosed herein in SEQ ID NO:1, 23, 53, and/or 55, the complementary strand thereto, and/or the cDNA sequence contained in the deposited clone.

[0556] The present invention also encompasses variants of the polypeptide sequence, and/or fragments therein, disclosed in SEQ ID NO:2, 24, 54, and/or 56, a polypeptide encoded by the polynucleotide sequence in SEQ ID NO:1, 23, 53, and/or 55, and/or a polypeptide encoded by a cDNA in the deposited clone.

[0557] “Variant” refers to a polynucleotide or polypeptide differing from the polynucleotide or polypeptide of the present invention, but retaining essential properties thereof. Generally, variants are overall closely similar, and, in many regions, identical to the polynucleotide or polypeptide of the present invention.

[0558] Thus, one aspect of the invention provides an isolated nucleic acid molecule comprising, or alternatively consisting of, a polynucleotide having a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a CAN-12 related polypeptide having an amino acid sequence as shown in the sequence listing and described in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (b) a nucleotide sequence encoding a mature CAN-12 related polypeptide having the amino acid sequence as shown in the sequence listing and described in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (c) a nucleotide sequence encoding a biologically active fragment of a CAN-12 related polypeptide having an amino acid sequence shown in the sequence listing and described in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (d) a nucleotide sequence encoding an antigenic fragment of a CAN-12 related polypeptide having an amino acid sequence sown in the sequence listing and described in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (e) a nucleotide sequence encoding a CAN-12 related polypeptide comprising the complete amino acid sequence encoded by a human cDNA plasmid contained in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (f) a nucleotide sequence encoding a mature CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA plasmid contained in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (g) a nucleotide sequence encoding a biologically active fragment of a CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA plasmid contained in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (h) a nucleotide sequence encoding an antigenic fragment of a CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA plasmid contained in SEQ ID NO:1, 23, 53, and/or 55 or the cDNA contained in ATCC deposit No:PTA-3434; (I) a nucleotide sequence complimentary to any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), or (h), above.

[0559] The present invention is also directed to polynucleotide sequences which comprise, or alternatively consist of, a polynucleotide sequence which is at least about 80%, 85%, 90%, 91%, 92%, 92.4%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to, for example, any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), or (h), above. Polynucleotides encoded by these nucleic acid molecules are also encompassed by the invention. In another embodiment, the invention encompasses nucleic acid molecules which comprise, or alternatively, consist of a polynucleotide which hybridizes under stringent conditions, or alternatively, under lower stringency conditions, to a polynucleotide in (a), (b), (c), (d), (e), (f), (g), or (h), above. Polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention, as are polypeptides encoded by these polypeptides.

[0560] Another aspect of the invention provides an isolated nucleic acid molecule comprising, or alternatively, consisting of, a polynucleotide having a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a CAN-12 related polypeptide having an amino acid sequence as shown in the sequence listing and descried in Table I; (b) a nucleotide sequence encoding a mature CAN-12 related polypeptide having the amino acid sequence as shown in the sequence listing and descried in Table I; (c) a nucleotide sequence encoding a biologically active fragment of a CAN-12 related polypeptide having an amino acid sequence as shown in the sequence listing and descried in Table I; (d) a nucleotide sequence encoding an antigenic fragment of a CAN-12 related polypeptide having an amino acid sequence as shown in the sequence listing and descried in Table I; (e) a nucleotide sequence encoding a CAN-12 related polypeptide comprising the complete amino acid sequence encoded by a human cDNA in a cDNA plasmid contained in the ATCC Deposit and described in Table I; (f) a nucleotide sequence encoding a mature CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA in a cDNA plasmid contained in the ATCC Deposit and described in Table I: (g) a nucleotide sequence encoding a biologically active fragment of a CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA in a cDNA plasmid contained in the ATCC Deposit and described in Table I; (h) a nucleotide sequence encoding an antigenic fragment of a CAN-12 related polypeptide having an amino acid sequence encoded by a human cDNA in a cDNA plasmid contained in the ATCC deposit and described in Table I; (i) a nucleotide sequence complimentary to any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), or (h) above.

[0561] The present invention is also directed to nucleic acid molecules which comprise, or alternatively, consist of, a nucleotide sequence which is at least about 80%, 85%,90%,91%,92%,92.4%,93%,94%, 95%,96%,97%,98%, 99%,99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to, for example, any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), or (h), above.

[0562] The present invention encompasses polypeptide sequences which comprise, or alternatively consist of, an amino acid sequence which is at least about 60.3%, 61.4%, 80%, 81.8%, 82.2%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to, the following non-limited examples, the polypeptide sequence identified as SEQ ID NO:2, 24, 54, and/or 56, the polypeptide sequence encoded by a cDNA provided in the deposited clone, and/or polypeptide fragments of any of the polypeptides provided herein. Polynucleotides encoded by these nucleic acid molecules are also encompassed by the invention. In another embodiment, the invention encompasses nucleic acid molecules which comprise, or alternatively, consist of a polynucleotide which hybridizes under stringent conditions, or alternatively, under lower stringency conditions, to a polynucleotide in (a), (b), (c), (d), (e), (f), (g), or (h), above. Polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention, as are polypeptides encoded by these polypeptides.

[0563] The present invention is also directed to polypeptides which comprise, or alternatively consist of, an amino acid sequence which is at least about 60.3%, 61.4%, 80%, 81.8%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to, for example, the polypeptide sequence shown in SEQ ID NO:2, 24, 54, and/or 56, a polypeptide sequence encoded by the nucleotide sequence in SEQ ID NO:1, 23, 53, and/or 55, a polypeptide sequence encoded by the cDNA in cDNA plasmid:Z, and/or polypeptide fragments of any of these polypeptides (e.g., those fragments described herein). Polynucleotides which hybridize to the complement of the nucleic acid molecules encoding these polypeptides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompasses by the present invention, as are the polypeptides encoded by these polynucleotides.

[0564] By a nucleic acid having a nucleotide sequence at least, for example, 95% “identical” to a reference nucleotide sequence of the present invention, it is intended that the nucleotide sequence of the nucleic acid is identical to the reference sequence except that the nucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the polypeptide. In other words, to obtain a nucleic acid having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. The query sequence may be an entire sequence referenced in Table I, the ORF (open reading frame), or any fragment specified as described herein.

[0565] As a practical matter, whether any particular nucleic acid molecule or polypeptide is at least about 60.3%, 61.4%, 80%, 81.8%, 80%, 85%, 90%, 91%, 92%, 92.4%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a nucleotide sequence of the present invention can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the CLUSTALW computer program (Thompson, J. D., et al., Nucleic Acids Research, 2(22):4673-4680, (1994)), which is based on the algorithm of Higgins, D. G., et al., Computer Applications in the Biosciences (CABIOS), 8(2):189-191, (1992). In a sequence alignment the query and subject sequences are both DNA sequences. An RNA sequence can be compared by converting U's to T's. However, the CLUSTALW algorithm automatically converts U's to T's when comparing RNA sequences to DNA sequences. The result of said global sequence alignment is in percent identity. Preferred parameters used in a CLUSTALW alignment of DNA sequences to calculate percent identity via pairwise alignments are: Matrix=IUB, k-tuple=1, Number of Top Diagonals=5, Gap Penalty=3, Gap Open Penalty 10, Gap Extension Penalty=0.1, Scoring Method=Percent, Window Size=5 or the length of the subject nucleotide sequence, whichever is shorter. For multiple alignments, the following CLUSTALW parameters are preferred: Gap Opening Penalty=10; Gap Extension Parameter=0.05; Gap Separation Penalty Range=8; End Gap Separation Penalty=Off; % Identity for Alignment Delay=40%; Residue Specific Gaps:Off; Hydrophilic Residue Gap=Off; and Transition Weighting=0. The pairwise and multple alignment parameters provided for CLUSTALW above represent the default parameters as provided with the AlignX software program (Vector NTI suite of programs, version 6.0).

[0566] The present invention encompasses the application of a manual correction to the percent identity results, in the instance where the subject sequence is shorter than the query sequence because of 5′ or 3′ deletions, not because of internal deletions. If only the local pairwise percent identity is required, no manual correction is needed. However, a manual correction may be applied to determine the global percent identity from a global polynucleotide alignment. Percent identity calculations based upon global polynucleotide alignments are often preferred since they reflect the percent identity between the polynucleotide molecules as a whole (i.e., including any polynucleotide overhangs, not just overlapping regions), as opposed to, only local matching polynucleotides. Manual corrections for global percent identity determinations are required since the CLUSTALW program does not account for 5′ and 3′ truncations of the subject sequence when calculating percent identity. For subject sequences truncated at the 5′ or 3′ ends, relative to the query sequence, the percent identity is corrected by calculating the number of bases of the query sequence that are 5′ and 3′ of the subject sequence, which are not matched/aligned, as a percent of the total bases of the query sequence. Whether a nucleotide is matched/aligned is determined by results of the CLUSTALW sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above CLUSTALW program using the specified parameters, to arrive at a final percent identity score. This corrected score may be used for the purposes of the present invention. Only bases outside the 5′ and 3′ bases of the subject sequence, as displayed by the CLUSTALW alignment, which are not matched/aligned with the query sequence, are calculated for the purposes of manually adjusting the percent identity score.

[0567] For example, a 90 base subject sequence is aligned to a 100 base query sequence to determine percent identity. The deletions occur at the 5′ end of the subject sequence and therefore, the CLUSTALW alignment does not show a matched/alignment of the first 10 bases at 5′ end. The 10 unpaired bases represent 10% of the sequence (number of bases at the 5′ and 3′ ends not matched/total number of bases in the query sequence) so 10% is subtracted from the percent identity score calculated by the CLUSTALW program. If the remaining 90 bases were perfectly matched the final percent identity would be 90%. In another example, a 90 base subject sequence is compared with a 100 base query sequence. This time the deletions are internal deletions so that there are no bases on the 5′ or 3′ of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by CLUSTALW is not manually corrected. Once again, only bases 5′ and 3′ of the subject sequence which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are required for the purposes of the present invention.

[0568] By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a query amino acid sequence of the present invention, it is intended that the amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a query amino acid sequence, up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, or substituted with another amino acid. These alterations of the reference sequence may occur at the amino- or carboxy-terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.

[0569] As a practical matter, whether any particular polypeptide is at least about 60.3%, 61.4%, 80%, 81.8%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to, for instance, an amino acid sequence referenced in Table 1 (SEQ ID NO:2) or to the amino acid sequence encoded by cDNA contained in a deposited clone, can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the CLUSTALW computer program (Thompson, J. D., et al., Nucleic Acids Research, 2(22):4673-4680, (1994)), which is based on the algorithm of Higgins, D. G., et al., Computer Applications in the Biosciences (CABIOS), 8(2):189-191, (1992). In a sequence alignment the query and subject sequences are both amino acid sequences. The result of said global sequence alignment is in percent identity. Preferred parameters used in a CLUSTALW alignment of DNA sequences to calculate percent identity via pairwise alignments are: Matrix=BLOSUM, k-tuple=1, Number of Top Diagonals=5, Gap Penalty=3, Gap Open Penalty 10, Gap Extension Penalty=0.1, Scoring Method=Percent, Window Size=5 or the length of the subject nucleotide sequence, whichever is shorter. For multiple alignments, the following CLUSTALW parameters are preferred: Gap Opening Penalty=10; Gap Extension Parameter=0.05; Gap Separation Penalty Range=8; End Gap Separation Penalty=Off; % Identity for Alignment Delay=40%; Residue Specific Gaps:Off; Hydrophilic Residue Gap=Off; and Transition Weighting=0. The pairwise and multple alignment parameters provided for CLUSTALW above represent the default parameters as provided with the AlignX software program (Vector NTI suite of programs, version 6.0).

[0570] The present invention encompasses the application of a manual correction to the percent identity results, in the instance where the subject sequence is shorter than the query sequence because of N- or C-terminal deletions, not because of internal deletions. If only the local pairwise percent identity is required, no manual correction is needed. However, a manual correction may be applied to determine the global percent identity from a global polypeptide alignment. Percent identity calculations based upon global polypeptide alignments are often preferred since they reflect the percent identity between the polypeptide molecules as a whole (i.e., including any polypeptide overhangs, not just overlapping regions), as opposed to, only local matching polypeptides. Manual corrections for global percent identity determinations are required since the CLUSTALW program does not account for N- and C-terminal truncations of the subject sequence when calculating percent identity. For subject sequences truncated at the N- and C-termini, relative to the query sequence, the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C-terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the CLUSTALW sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above CLUSTALW program using the specified parameters, to arrive at a final percent identity score. This final percent identity score is what may be used for the purposes of the present invention. Only residues to the N- and C-termini of the subject sequence, which are not matched/aligned with the query sequence, are considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C-terminal residues of the subject sequence.

[0571] For example, a 90 amino acid residue subject sequence is aligned with a 100 residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence and therefore, the CLUSTALW alignment does not show a matching/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the CLUSTALW program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%. In another example, a 90 residue subject sequence is compared with a 100 residue query sequence. This time the deletions are internal deletions so there are no residues at the N- or C-termini of the subject sequence, which are not matched/aligned with the query. In this case the percent identity calculated by CLUSTALW is not manually corrected. Once again, only residue positions outside the N- and C-terminal ends of the subject sequence, as displayed in the CLUSTALW alignment, which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are required for the purposes of the present invention.

[0572] In addition to the above method of aligning two or more polynucleotide or polypeptide sequences to arrive at a percent identity value for the aligned sequences, it may be desirable in some circumstances to use a modified version of the CLUSTALW algorithm which takes into account known structural features of the sequences to be aligned, such as for example, the SWISS-PROT designations for each sequence. The result of such a modifed CLUSTALW algorithm may provide a more accurate value of the percent identity for two polynucleotide or polypeptide sequences. Support for such a modified version of CLUSTALW is provided within the CLUSTALW algorithm and would be readily appreciated to one of skill in the art of bioinformatics.

[0573] The variants may contain alterations in the coding regions, non-coding regions, or both. Especially preferred are polynucleotide variants containing alterations which produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded polypeptide. Nucleotide variants produced by silent substitutions due to the degeneracy of the genetic code are preferred. Moreover, variants in which 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination are also preferred. Polynucleotide variants can be produced for a variety of reasons, e.g., to optimize codon expression for a particular host (change codons in the mRNA to those preferred by a bacterial host such as E. coli).

[0574] Naturally occurring variants are called “allelic variants,” and refer to one of several alternate forms of a gene occupying a given locus on a chromosome of an organism. (Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985).) These allelic variants can vary at either the polynucleotide and/or polypeptide level and are included in the present invention. Alternatively, non-naturally occurring variants may be produced by mutagenesis techniques or by direct synthesis.

[0575] Using known methods of protein engineering and recombinant DNA technology, variants may be generated to improve or alter the characteristics of the polypeptides of the present invention. For instance, one or more amino acids can be deleted from the N-terminus or C-terminus of the protein without substantial loss of biological function. The authors of Ron et al., J. Biol. Chem. 268: 2984-2988 (1993), reported variant KGF proteins having heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino acid residues. Similarly, Interferon gamma exhibited up to ten times higher activity after deleting 8-10 amino acid residues from the carboxy terminus of this protein (Dobeli et al., J. Biotechnology 7:199-216 (1988)).

[0576] Moreover, ample evidence demonstrates that variants often retain a biological activity similar to that of the naturally occurring protein. For example, Gayle and coworkers (J. Biol. Chem. . . . 268:22105-22111 (1993)) conducted extensive mutational analysis of human cytokine IL-1a. They used random mutagenesis to generate over 3,500 individual IL-1a mutants that averaged 2.5 amino acid changes per variant over the entire length of the molecule. Multiple mutations were examined at every possible amino acid position. The investigators found that “[m]ost of the molecule could be altered with little effect on either [binding or biological activity].” In fact, only 23 unique amino acid sequences, out of more than 3,500 nucleotide sequences examined, produced a protein that significantly differed in activity from wild-type.

[0577] Furthermore, even if deleting one or more amino acids from the N-terminus or C-terminus of a polypeptide results in modification or loss of one or more biological functions, other biological activities may still be retained. For example, the ability of a deletion variant to induce and/or to bind antibodies which recognize the protein will likely be retained when less than the majority of the residues of the protein are removed from the N-terminus or C-terminus. Whether a particular polypeptide lacking N- or C-terminal residues of a protein retains such immunogenic activities can readily be determined by routine methods described herein and otherwise known in the art.

[0578] Alternatively, such N-terminus or C-terminus deletions of a polypeptide of the present invention may, in fact, result in a significant increase in one or more of the biological activities of the polypeptide(s). For example, biological activity of many polypeptides are governed by the presence of regulatory domains at either one or both termini. Such regulatory domains effectively inhibit the biological activity of such polypeptides in lieu of an activation event (e.g., binding to a cognate ligand or receptor, phosphorylation, proteolytic processing, etc.). Thus, by eliminating the regulatory domain of a polypeptide, the polypeptide may effectively be rendered biologically active in the absence of an activation event.

[0579] Thus, the invention further includes polypeptide variants that show substantial biological activity. Such variants include deletions, insertions, inversions, repeats, and substitutions selected according to general rules known in the art so as have little effect on activity. For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie et al., Science 247:1306-1310 (1990), wherein the authors indicate that there are two main strategies for studying the tolerance of an amino acid sequence to change.

[0580] The first strategy exploits the tolerance of amino acid substitutions by natural selection during the process of evolution. By comparing amino acid sequences in different species, conserved amino acids can be identified. These conserved amino acids are likely important for protein function. In contrast, the amino acid positions where substitutions have been tolerated by natural selection indicates that these positions are not critical for protein function. Thus, positions tolerating amino acid substitution could be modified while still maintaining biological activity of the protein.

[0581] The second strategy uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene to identify regions critical for protein function. For example, site directed mutagenesis or alanine-scanning mutagenesis (introduction of single alanine mutations at every residue in the molecule) can be used. (Cunningham and Wells, Science 244:1081-1085 (1989).) The resulting mutant molecules can then be tested for biological activity.

[0582] As the authors state, these two strategies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which amino acid changes are likely to be permissive at certain amino acid positions in the protein. For example, most buried (within the tertiary structure of the protein) amino acid residues require nonpolar side chains, whereas few features of surface side chains are generally conserved.

[0583] The invention encompasses polypeptides having a lower degree of identity but having sufficient similarity so as to perform one or more of the same functions performed by the polypeptide of the present invention. Similarity is determined by conserved amino acid substitution. Such substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics (e.g., chemical properties). According to Cunningham et al above, such conservative substitutions are likely to be phenotypically silent. Additional guidance concerning which amino acid changes are likely to be phenotypically silent are found in Bowie et al., Science 247:1306-1310 (1990).

[0584] Tolerated conservative amino acid substitutions of the present invention involve replacement of the aliphatic or hydrophobic amino acids Ala, Val, Leu and Ile; replacement of the hydroxyl residues Ser and Thr; replacement of the acidic residues Asp and Glu; replacement of the amide residues Asn and Gln, replacement of the basic residues Lys, Arg, and His; replacement of the aromatic residues Phe, Tyr, and Trp, and replacement of the small-sized amino acids Ala, Ser, Thr, Met, and Gly.

[0585] In addition, the present invention also encompasses the conservative substitutions provided in Table III below.

6TABLE IIIFor Amino AcidCodeReplace with any of:AlanineAD-Ala, Gly, beta-Ala, L-Cys, D-CysArginineRD-Arg, Lys, D-Lys, homo-Arg, D-homo-Arg,Met, Ile, D-Met, D-Ile, Orn, D-OrnAsparagineND-Asn, Asp, D-Asp, Glu, D-Glu, Gln, D-GlnAspartic AcidDD-Asp, D-Asn, Asn, Glu, D-Glu, Gln, D-GlnCysteineCD-Cys, S-Me-Cys, Met, D-Met, Thr, D-ThrGlutamineQD-Gln, Asn, D-Asn, Glu, D-Glu, Asp, D-AspGlutamic AcidED-Glu, D-Asp, Asp, Asn, D-Asn, Gln, D-GlnGlycineGAla, D-Ala, Pro, D-Pro, β-Ala, AcpIsoleucineID-Ile, Val, D-Val, Leu, D-Leu, Met, D-MetLeucineLD-Leu, Val, D-Val, Met, D-MetLysineKD-Lys, Arg, D-Arg, homo-Arg, D-homo-Arg,Met, D-Met, Ile, D-Ile, Orn, D-OrnMethionineMD-Met, S-Me-Cys, Ile, D-Ile, Leu, D-Leu,Val, D-ValPhenylalanineFD-Phe, Tyr, D-Thr, L-Dopa, His, D-His, Trp,D-Trp, Trans-3,4, or 5-phenylproline,cis-3,4, or 5-phenylprolineProlinePD-Pro, L-1-thioazolidine-4-carboxylic acid,D- or L-1-oxazolidine-4-carboxylic acidSerineSD-Ser, Thr, D-Thr, allo-Thr, Met, D-Met,Met(O), D-Met(O), L-Cys, D-CysThreonineTD-Thr, Ser, D-Ser, allo-Thr, Met, D-Met,Met(O), D-Met(O), Val, D-ValTyrosineYD-Tyr, Phe, D-Phe, L-Dopa, His, D-HisValineVD-Val, Leu, D-Leu, Ile, D-Ile, Met, D-Met

[0586] Aside from the uses described above, such amino acid substitutions may also increase protein or peptide stability. The invention encompasses amino acid substitutions that contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the protein or peptide sequence. Also included are substitutions that include amino acid residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., β or γ amino acids.

[0587] Both identity and similarity can be readily calculated by reference to the following publications: Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Informatics Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991.

[0588] In addition, the present invention also encompasses substitution of amino acids based upon the probability of an amino acid substitution resulting in conservation of function. Such probabilities are determined by aligning multiple genes with related function and assessing the relative penalty of each substitution to proper gene function. Such probabilities are often described in a matrix and are used by some algorithms (e.g., BLAST, CLUSTALW, GAP, etc.) in calculating percent similarity wherein similarity refers to the degree by which one amino acid may substitute for another amino acid without lose of function. An example of such a matrix is the PAM250 or BLOSUM62 matrix.

[0589] Aside from the canonical chemically conservative substitutions referenced above, the invention also encompasses substitutions which are typically not classified as conservative, but that may be chemically conservative under certain circumstances. Analysis of enzymatic catalysis for proteases, for example, has shown that certain amino acids within the active site of some enzymes may have highly perturbed pKa's due to the unique microenvironment of the active site. Such perturbed pKa's could enable some amino acids to substitute for other amino acids while conserving enzymatic structure and function. Examples of amino acids that are known to have amino acids with perturbed pKa's are the Glu-35 residue of Lysozyme, the Ile-16 residue of Chymotrypsin, the His-159 residue of Papain, etc. The conservation of function relates to either anomalous protonation or anomalous deprotonation of such amino acids, relative to their canonical, non-perturbed pKa. The pKa perturbation may enable these amino acids to actively participate in general acid-base catalysis due to the unique ionization environment within the enzyme active site. Thus, substituting an amino acid capable of serving as either a general acid or general base within the microenvironment of an enzyme active site or cavity, as may be the case, in the same or similar capacity as the wild-type amino acid, would effectively serve as a conservative amino substitution.

[0590] Besides conservative amino acid substitution, variants of the present invention include, but are not limited to, the following: (i) substitutions with one or more of the non-conserved amino acid residues, where the substituted amino acid residues may or may not be one encoded by the genetic code, or (ii) substitution with one or more of amino acid residues having a substituent group, or (iii) fusion of the mature polypeptide with another compound, such as a compound to increase the stability and/or solubility of the polypeptide (for example, polyethylene glycol), or (iv) fusion of the polypeptide with additional amino acids, such as, for example, an IgG Fc fusion region peptide, or leader or secretory sequence, or a sequence facilitating purification. Such variant polypeptides are deemed to be within the scope of those skilled in the art from the teachings herein.

[0591] For example, polypeptide variants containing amino acid substitutions of charged amino acids with other charged or neutral amino acids may produce proteins with improved characteristics, such as less aggregation. Aggregation of pharmaceutical formulations both reduces activity and increases clearance due to the aggregate's immunogenic activity. (Pinckard et al., Clin. Exp. Immunol. 2:331-340 (1967); Robbins et al., Diabetes 36: 838-845 (1987); Cleland et al., Crit. Rev. Therapeutic Drug Carrier Systems 10:307-377 (1993).)

[0592] Moreover, the invention further includes polypeptide variants created through the application of molecular evolution (“DNA Shuffling”) methodology to the polynucleotide disclosed as SEQ ID NO:1, 23, 53, and/or 55, the sequence of the clone submitted in a deposit, and/or the cDNA encoding the polypeptide disclosed as SEQ ID NO:2, 24, 54, and/or 56. Such DNA Shuffling technology is known in the art and more particularly described elsewhere herein (e.g., WPC, Stemmer, PNAS, 91:10747, (1994)), and in the Examples provided herein).

[0593] A further embodiment of the invention relates to a polypeptide which comprises the amino acid sequence of the present invention having an amino acid sequence which contains at least one amino acid substitution, but not more than 50 amino acid substitutions, even more preferably, not more than 40 amino acid substitutions, still more preferably, not more than 30 amino acid substitutions, and still even more preferably, not more than 20 amino acid substitutions. Of course, in order of ever-increasing preference, it is highly preferable for a peptide or polypeptide to have an amino acid sequence which comprises the amino acid sequence of the present invention, which contains at least one, but not more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid substitutions. In specific embodiments, the number of additions, substitutions, and/or deletions in the amino acid sequence of the present invention or fragments thereof (e.g., the mature form and/or other fragments described herein), is 1-5,5-10, 5-25, 5-50, 10-50 or 50-150, conservative amino acid substitutions are preferable.

[0594] Polynucleotide and Polypeptide Fragments

[0595] The present invention is directed to polynucleotide fragments of the polynucleotides of the invention, in addition to polypeptides encoded therein by said polynucleotides and/or fragments.

[0596] In the present invention, a “polynucleotide fragment” refers to a short polynucleotide having a nucleic acid sequence which: is a portion of that contained in a deposited clone, or encoding the polypeptide encoded by the cDNA in a deposited clone; is a portion of that shown in SEQ ID NO:1, 23, 53, and/or 55 or the complementary strand thereto, or is a portion of a polynucleotide sequence encoding the polypeptide of SEQ ID NO:2, 24, 54, and/or 56. The nucleotide fragments of the invention are preferably at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt, at least about 50 nt, at least about 75 nt, or at least about 150 nt in length. A fragment “at least 20 nt in length,” for example, is intended to include 20 or more contiguous bases from the cDNA sequence contained in a deposited clone or the nucleotide sequence shown in SEQ ID NO:1, 23, 53, and/or 55. In this context “about” includes the particularly recited value, a value larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus, or at both termini. These nucleotide fragments have uses that include, but are not limited to, as diagnostic probes and primers as discussed herein. Of course, larger fragments (e.g., 50, 150, 500, 600, 2000 nucleotides) are preferred.

[0597] Moreover, representative examples of polynucleotide fragments of the invention, include, for example, fragments comprising, or alternatively consisting of, a sequence from about nucleotide number 1-50, 51-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 651-700, 701-750, 751-800, 800-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, or 2001 to the end of SEQ ID NO:1, 23, 53, and/or 55, or the complementary strand thereto, or the cDNA contained in a deposited clone. In this context “about” includes the particularly recited ranges, and ranges larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini. Preferably, these fragments encode a polypeptide which has biological activity. More preferably, these polynucleotides can be used as probes or primers as discussed herein. Also encompassed by the present invention are polynucleotides which hybridize to these nucleic acid molecules under stringent hybridization conditions or lower stringency conditions, as are the polypeptides encoded by these polynucleotides.

[0598] In the present invention, a “polypeptide fragment” refers to an amino acid sequence which is a portion of that contained in SEQ ID NO:2, 24, 54, and/or 56 or encoded by the cDNA contained in a deposited clone. Protein (polypeptide) fragments may be “free-standing,” or comprised within a larger polypeptide of which the fragment forms a part or region, most preferably as a single continuous region. Representative examples of polypeptide fragments of the invention, include, for example, fragments comprising, or alternatively consisting of, from about amino acid number 1-20, 21-40, 41-60, 61-80, 81-100, 102-120, 121-140, 141-160, or 161 to the end of the coding region. Moreover, polypeptide fragments can be about 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150 amino acids in length. In this context “about” includes the particularly recited ranges or values, and ranges or values larger or smaller by several (5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes. Polynucleotides encoding these polypeptides are also encompassed by the invention.

[0599] Preferred polypeptide fragments include the full-length protein. Further preferred polypeptide fragments include the full-length protein having a continuous series of deleted residues from the amino or the carboxy terminus, or both. For example, any number of amino acids, ranging from 1-60, can be deleted from the amino terminus of the full-length polypeptide. Similarly, any number of amino acids, ranging from 1-30, can be deleted from the carboxy terminus of the full-length protein. Furthermore, any combination of the above amino and carboxy terminus deletions are preferred. Similarly, polynucleotides encoding these polypeptide fragments are also preferred.

[0600] Also preferred are polypeptide and polynucleotide fragments characterized by structural or functional domains, such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. Polypeptide fragments of SEQ ID NO:2, 24, 54, and/or 56 falling within conserved domains are specifically contemplated by the present invention. Moreover, polynucleotides encoding these domains are also contemplated.

[0601] Other preferred polypeptide fragments are biologically active fragments. Biologically active fragments are those exhibiting activity similar, but not necessarily identical, to an activity of the polypeptide of the present invention. The biological activity of the fragments may include an improved desired activity, or a decreased undesirable activity. Polynucleotides encoding these polypeptide fragments are also encompassed by the invention.

[0602] In a preferred embodiment, the functional activity displayed by a polypeptide encoded by a polynucleotide fragment of the invention may be one or more biological activities typically associated with the full-length polypeptide of the invention. Illustrative of these biological activities includes the fragments ability to bind to at least one of the same antibodies which bind to the full-length protein, the fragments ability to interact with at lease one of the same proteins which bind to the full-length, the fragments ability to elicit at least one of the same immune responses as the full-length protein (i.e., to cause the immune system to create antibodies specific to the same epitope, etc.), the fragments ability to bind to at least one of the same polynucleotides as the full-length protein, the fragments ability to bind to a receptor of the full-length protein, the fragments ability to bind to a ligand of the full-length protein, and the fragments ability to multimerize with the full-length protein. However, the skilled artisan would appreciate that some fragments may have biological activities which are desirable and directly inapposite to the biological activity of the full-length protein. The functional activity of polypeptides of the invention, including fragments, variants, derivatives, and analogs thereof can be determined by numerous methods available to the skilled artisan, some of which are described elsewhere herein.

[0603] The present invention encompasses polypeptides comprising, or alternatively consisting of, an epitope of the polypeptide having an amino acid sequence of SEQ ID NO:2, 24, 54, and/or 56, or an epitope of the polypeptide sequence encoded by a polynucleotide sequence contained in ATCC deposit No. Z or encoded by a polynucleotide that hybridizes to the complement of the sequence of SEQ ID NO:1, 23, 53, and/or 55 or contained in ATCC deposit No. Z under stringent hybridization conditions or lower stringency hybridization conditions as defined supra. The present invention further encompasses polynucleotide sequences encoding an epitope of a polypeptide sequence of the invention (such as, for example, the sequence disclosed in SEQ ID NO:1), polynucleotide sequences of the complementary strand of a polynucleotide sequence encoding an epitope of the invention, and polynucleotide sequences which hybridize to the complementary strand under stringent hybridization conditions or lower stringency hybridization conditions defined supra.

[0604] The term “epitopes,” as used herein, refers to portions of a polypeptide having antigenic or immunogenic activity in an animal, preferably a mammal, and most preferably in a human. In a preferred embodiment, the present invention encompasses a polypeptide comprising an epitope, as well as the polynucleotide encoding this polypeptide. An “immunogenic epitope,” as used herein, is defined as a portion of a protein that elicits an antibody response in an animal, as determined by any method known in the art, for example, by the methods for generating antibodies described infra. (See, for example, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983)). The term “antigenic epitope,” as used herein, is defined as a portion of a protein to which an antibody can immunospecifically bind its antigen as determined by any method well known in the art, for example, by the immunoassays described herein. Immunospecific binding excludes non-specific binding but does not necessarily exclude cross-reactivity with other antigens. Antigenic epitopes need not necessarily be immunogenic.

[0605] Fragments which function as epitopes may be produced by any conventional means. (See, e.g., Houghten, Proc. Natl. Acad. Sci. USA 82:5131-5135 (1985), further described in U.S. Pat. No. 4,631,211).

[0606] In the present invention, antigenic epitopes preferably contain a sequence of at least 4, at least 5, at least 6, at least 7, more preferably at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25, at least 30, at least 40, at least 50, and, most preferably, between about 15 to about 30 amino acids. Preferred polypeptides comprising immunogenic or antigenic epitopes are at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acid residues in length, or longer. Additional non-exclusive preferred antigenic epitopes include the antigenic epitopes disclosed herein, as well as portions thereof. Antigenic epitopes are useful, for example, to raise antibodies, including monoclonal antibodies, that specifically bind the epitope. Preferred antigenic epitopes include the antigenic epitopes disclosed herein, as well as any combination of two, three, four, five or more of these antigenic epitopes. Antigenic epitopes can be used as the target molecules in immunoassays. (See, for instance, Wilson et al., Cell 37:767-778 (1984); Sutcliffe et al., Science 219:660-666 (1983)).

[0607] Similarly, immunogenic epitopes can be used, for example, to induce antibodies according to methods well known in the art. (See, for instance, Sutcliffe et al., supra; Wilson et al., supra; Chow et al., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle et al., J. Gen. Virol. 66:2347-2354 (1985). Preferred immunogenic epitopes include the immunogenic epitopes disclosed herein, as well as any combination of two, three, four, five or more of these immunogenic epitopes. The polypeptides comprising one or more immunogenic epitopes may be presented for eliciting an antibody response together with a carrier protein, such as an albumin, to an animal system (such as rabbit or mouse), or, if the polypeptide is of sufficient length (at least about 25 amino acids), the polypeptide may be presented without a carrier. However, immunogenic epitopes comprising as few as 8 to 10 amino acids have been shown to be sufficient to raise antibodies capable of binding to, at the very least, linear epitopes in a denatured polypeptide (e.g., in Western blotting).

[0608] Epitope-bearing polypeptides of the present invention may be used to induce antibodies according to methods well known in the art including, but not limited to, in vivo immunization, in vitro immunization, and phage display methods. See, e.g., Sutcliffe et al., supra; Wilson et al., supra, and Bittle et al., J. Gen. Virol., 66:2347-2354 (1985). If in vivo immunization is used, animals may be immunized with free peptide; however, anti-peptide antibody titer may be boosted by coupling the peptide to a macromolecular carrier, such as keyhole limpet hemacyanin (KLH) or tetanus toxoid. For instance, peptides containing cysteine residues may be coupled to a carrier using a linker such as maleimidobenzoyl-N-hydroxysuccinimide ester (MBS), while other peptides may be coupled to carriers using a more general linking agent such as glutaraldehyde. Animals such as rabbits, rats and mice are immunized with either free or carrier-coupled peptides, for instance, by intraperitoneal and/or intradermal injection of emulsions containing about 100 μg of peptide or carrier protein and Freund's adjuvant or any other adjuvant known for stimulating an immune response. Several booster injections may be needed, for instance, at intervals of about two weeks, to provide a useful titer of anti-peptide antibody which can be detected, for example, by ELISA assay using free peptide adsorbed to a solid surface. The titer of anti-peptide antibodies in serum from an immunized animal may be increased by selection of anti-peptide antibodies, for instance, by adsorption to the peptide on a solid support and elution of the selected antibodies according to methods well known in the art.

[0609] As one of skill in the art will appreciate, and as discussed above, the polypeptides of the present invention comprising an immunogenic or antigenic epitope can be fused to other polypeptide sequences. For example, the polypeptides of the present invention may be fused with the constant domain of immunoglobulins (IgA, IgE, IgG, IgM), or portions thereof (CH1, CH2, CH3, or any combination thereof and portions thereof) resulting in chimeric polypeptides. Such fusion proteins may facilitate purification and may increase half-life in vivo. This has been shown for chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. See, e.g., EP 394,827; Traunecker et al., Nature, 331:84-86 (1988). Enhanced delivery of an antigen across the epithelial barrier to the immune system has been demonstrated for antigens (e.g., insulin) conjugated to an FcRn binding partner such as IgG or Fe fragments (see, e.g., PCT Publications WO 96/22024 and WO 99/04813). IgG Fusion proteins that have a disulfide-linked dimeric structure due to the IgG portion disulfide bonds have also been found to be more efficient in binding and neutralizing other molecules than monomeric polypeptides or fragments thereof alone. See, e.g., Fountoulakis et al., J. Biochem., 270:3958-3964 (1995). Nucleic acids encoding the above epitopes can also be recombined with a gene of interest as an epitope tag (e.g., the hemagglutinin (“HA”) tag or flag tag) to aid in detection and purification of the expressed polypeptide. For example, a system described by Janknecht et al. allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al., 1991, Proc. Natl. Acad. Sci. USA 88:8972-897). In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the open reading frame of the gene is translationally fused to an amino-terminal tag consisting of six histidine residues. The tag serves as a matrix binding domain for the fusion protein. Extracts from cells infected with the recombinant vaccinia virus are loaded onto Ni2+ nitriloacetic acid-agarose column and histidine-tagged proteins can be selectively eluted with imidazole-containing buffers.

[0610] Additional fusion proteins of the invention may be generated through the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as “DNA shuffling”). DNA shuffling may be employed to modulate the activities of polypeptides of the invention, such methods can be used to generate polypeptides with altered activity, as well as agonists and antagonists of the polypeptides. See, generally, U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; 5,834,252; and 5,837,458, and Patten et al., Curr. Opinion Biotechnol. 8:724-33 (1997); Harayama, Trends Biotechnol. 16(2):76-82 (1998); Hansson, et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo and Blasco, Biotechniques 24(2):308-13 (1998) (each of these patents and publications are hereby incorporated by reference in its entirety). In one embodiment, alteration of polynucleotides corresponding to SEQ ID NO:1, 23, 53, and/or 55 and the polypeptides encoded by these polynucleotides may be achieved by DNA shuffling. DNA shuffling involves the assembly of two or more DNA segments by homologous or site-specific recombination to generate variation in the polynucleotide sequence. In another embodiment, polynucleotides of the invention, or the encoded polypeptides, may be altered by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods prior to recombination. In another embodiment, one or more components, motifs, sections, parts, domains, fragments, etc., of a polynucleotide encoding a polypeptide of the invention may be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous molecules.

[0611] Antibodies

[0612] Further polypeptides of the invention relate to antibodies and T-cell antigen receptors (TCR) which immunospecifically bind a polypeptide, polypeptide fragment, or variant of SEQ ID NO:2, 24, 54, and/or 56, and/or an epitope, of the present invention (as determined by immunoassays well known in the art for assaying specific antibody-antigen binding). Antibodies of the invention include, but are not limited to, polyclonal, monoclonal, monovalent, bispecific, heteroconjugate, multispecific, human, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′) fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the invention), and epitope-binding fragments of any of the above. The term “antibody,” as used herein, refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that immunospecifically binds an antigen. The immunoglobulin molecules of the invention can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of immunoglobulin molecule. Moreover, the term “antibody” (Ab) or “monoclonal antibody” (Mab) is meant to include intact molecules, as well as, antibody fragments (such as, for example, Fab and F(ab′)2 fragments) which are capable of specifically binding to protein. Fab and F(ab′)2 fragments lack the Fc fragment of intact antibody, clear more rapidly from the circulation of the animal or plant, and may have less non-specific tissue binding than an intact antibody (Wahl et al., J. Nucl. Med. . . . 24:316-325 (1983)). Thus, these fragments are preferred, as well as the products of a FAB or other immunoglobulin expression library. Moreover, antibodies of the present invention include chimeric, single chain, and humanized antibodies.

[0613] Most preferably the antibodies are human antigen-binding antibody fragments of the present invention and include, but are not limited to, Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (sdFv) and fragments comprising either a VL or VH domain. Antigen-binding antibody fragments, including single-chain antibodies, may comprise the variable region(s) alone or in combination with the entirety or a portion of the following: hinge region, CH1, CH2, and CH3 domains. Also included in the invention are antigen-binding fragments also comprising any combination of variable region(s) with a hinge region, CH1, CH2, and CH3 domains. The antibodies of the invention may be from any animal origin including birds and mammals. Preferably, the antibodies are human, murine (e.g., mouse and rat), donkey, ship rabbit, goat, guinea pig, camel, horse, or chicken. As used herein, “human” antibodies include antibodies having the amino acid sequence of a human immunoglobulin and include antibodies isolated from human immunoglobulin libraries or from animals transgenic for one or more human immunoglobulin and that do not express endogenous immunoglobulins, as described infra and, for example in, U.S. Pat. No. 5,939,598 by Kucherlapati et al.

[0614] The antibodies of the present invention may be monospecific, bispecific, trispecific or of greater multispecificity. Multispecific antibodies may be specific for different epitopes of a polypeptide of the present invention or may be specific for both a polypeptide of the present invention as well as for a heterologous epitope, such as a heterologous polypeptide or solid support material. See, e.g., PCT publications WO 93/17715; WO 92/08802; WO 91/00360; WO 92/05793; Tutt, et al., J. Immunol. 147:60-69 (1991); U.S. Pat. Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920; 5,601,819; Kostelny et al., J. Immunol. 148:1547-1553 (1992).

[0615] Antibodies of the present invention may be described or specified in terms of the epitope(s) or portion(s) of a polypeptide of the present invention which they recognize or specifically bind. The epitope(s) or polypeptide portion(s) may be specified as described herein, e.g., by N-terminal and C-terminal positions, by size in contiguous amino acid residues, or listed in the Tables and Figures. Antibodies which specifically bind any epitope or polypeptide of the present invention may also be excluded. Therefore, the present invention includes antibodies that specifically bind polypeptides of the present invention, and allows for the exclusion of the same.

[0616] Antibodies of the present invention may also be described or specified in terms of their cross-reactivity. Antibodies that do not bind any other analog, ortholog, or homologue of a polypeptide of the present invention are included. Antibodies that bind polypeptides with at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, and at least 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In specific embodiments, antibodies of the present invention cross-react with murine, rat and/or rabbit homologues of human proteins and the corresponding epitopes thereof. Antibodies that do not bind polypeptides with less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, and less than 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In a specific embodiment, the above-described cross-reactivity is with respect to any single specific antigenic or immunogenic polypeptide, or combination(s) of 2, 3, 4, 5, or more of the specific antigenic and/or immunogenic polypeptides disclosed herein. Further included in the present invention are antibodies which bind polypeptides encoded by polynucleotides which hybridize to a polynucleotide of the present invention under stringent hybridization conditions (as described herein). Antibodies of the present invention may also be described or specified in terms of their binding affinity to a polypeptide of the invention. Preferred binding affinities include those with a dissociation constant or Kd less than 5×10-2 M, 10-2 M, 5×10-3 M, 10-3 M, 5×10-4 M, 10-4 M, 5×10-5 M, 10-5 M, 5×10-6 M, 10-6M, 5×10-7 M, 107 M, 5×10-8 M, 10-8 M, 5×10-9 M, 10-9 M, 5×10-10 M, 10-10 M, 5×10-11 M, 10-11 M, 5×10-12 M, 10-12 M, 5×10-13 M, 10-13 M, 5×10-14 M, 10-14 M, 5×10-15 M, or 10-15 M.

[0617] The invention also provides antibodies that competitively inhibit binding of an antibody to an epitope of the invention as determined by any method known in the art for determining competitive binding, for example, the immunoassays described herein. In preferred embodiments, the antibody competitively inhibits binding to the epitope by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50%.

[0618] Antibodies of the present invention may act as agonists or antagonists of the polypeptides of the present invention. For example, the present invention includes antibodies which disrupt the receptor/ligand interactions with the polypeptides of the invention either partially or fully. Preferably, antibodies of the present invention bind an antigenic epitope disclosed herein, or a portion thereof. The invention features both receptor-specific antibodies and ligand-specific antibodies. The invention also features receptor-specific antibodies which do not prevent ligand binding but prevent receptor activation. Receptor activation (i.e., signaling) may be determined by techniques described herein or otherwise known in the art. For example, receptor activation can be determined by detecting the phosphorylation (e.g., tyrosine or serine/threonine) of the receptor or its substrate by immunoprecipitation followed by western blot analysis (for example, as described supra). In specific embodiments, antibodies are provided that inhibit ligand activity or receptor activity by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50% of the activity in absence of the antibody.

[0619] The invention also features receptor-specific antibodies which both prevent ligand binding and receptor activation as well as antibodies that recognize the receptor-ligand complex, and, preferably, do not specifically recognize the unbound receptor or the unbound ligand. Likewise, included in the invention are neutralizing antibodies which bind the ligand and prevent binding of the ligand to the receptor, as well as antibodies which bind the ligand, thereby preventing receptor activation, but do not prevent the ligand from binding the receptor. Further included in the invention are antibodies which activate the receptor. These antibodies may act as receptor agonists, i.e., potentiate or activate either all or a subset of the biological activities of the ligand-mediated receptor activation, for example, by inducing dimerization of the receptor. The antibodies may be specified as agonists, antagonists or inverse agonists for biological activities comprising the specific biological activities of the peptides of the invention disclosed herein. The above antibody agonists can be made using methods known in the art. See, e.g., PCT publication WO 96/40281; U.S. Pat. No. 5,811,097; Deng et al., Blood 92(6):1981-1988 (1998); Chen et al., Cancer Res. 58(16):3668-3678 (1998); Harrop et al., J. Immunol. 161(4):1786-1794 (1998); Zhu et al., Cancer Res. 58(15):3209-3214 (1998); Yoon et al., J. Immunol. 160(7):3170-3179 (1998); Prat et al., J. Cell. Sci. 111(Pt2):237-247 (1998); Pitard et al., J. Immunol. Methods 205(2):177-190 (1997); Liautard et al., Cytokine 9(4):233-241 (1997); Carlson et al., J. Biol. Chem. 272(17):11295-11301 (1997); Taryman et al., Neuron 14(4):755-762 (1995); Muller et al., Structure 6(9):1153-1167 (1998); Bartunek et al., Cytokine 8(1):14-20 (1996) (which are all incorporated by reference herein in their entireties).

[0620] Antibodies of the present invention may be used, for example, but not limited to, to purify, detect, and target the polypeptides of the present invention, including both in vitro and in vivo diagnostic and therapeutic methods. For example, the antibodies have use in immunoassays for qualitatively and quantitatively measuring levels of the polypeptides of the present invention in biological samples. See, e.g., Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988) (incorporated by reference herein in its entirety).

[0621] As discussed in more detail below, the antibodies of the present invention may be used either alone or in combination with other compositions. The antibodies may further be recombinantly fused to a heterologous polypeptide at the N- or C-terminus or chemically conjugated (including covalently and non-covalently conjugations) to polypeptides or other compositions. For example, antibodies of the present invention may be recombinantly fused or conjugated to molecules useful as labels in detection assays and effector molecules such as heterologous polypeptides, drugs, radionucleotides, or toxins. See, e.g., PCT publications WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No. 5,314,995; and EP 396,387.

[0622] The antibodies of the invention include derivatives that are modified, i.e., by the covalent attachment of any type of molecule to the antibody such that covalent attachment does not prevent the antibody from generating an anti-idiotypic response. For example, but not by way of limitation, the antibody derivatives include antibodies that have been modified, e.g., by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. Additionally, the derivative may contain one or more non-classical amino acids.

[0623] The antibodies of the present invention may be generated by any suitable method known in the art.

[0624] The antibodies of the present invention may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan (Harlow, et al., Antibodies: A Laboratory Manual, (Cold spring Harbor Laboratory Press, 2nd ed. (1988); and Current Protocols, Chapter 2; which are hereby incorporated herein by reference in its entirety). In a preferred method, a preparation of the XXXXX protein is prepared and purified to render it substantially free of natural contaminants. Such a preparation is then introduced into an animal in order to produce polyclonal antisera of greater specific activity. For example, a polypeptide of the invention can be administered to various host animals including, but not limited to, rabbits, mice, rats, etc. to induce the production of sera containing polyclonal antibodies specific for the antigen. The administration of the polypeptides of the present invention may entail one or more injections of an immunizing agent and, if desired, an adjuvant. Various adjuvants may be used to increase the immunological response, depending on the host species, and include but are not limited to, Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and corynebacterium parvum. Such adjuvants are also well known in the art. For the purposes of the invention, “immunizing agent” may be defined as a polypeptide of the invention, including fragments, variants, and/or derivatives thereof, in addition to fusions with heterologous polypeptides and other forms of the polypeptides described herein.

[0625] Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections, though they may also be given intramuscularly, and/or through IV). The immunizing agent may include polypeptides of the present invention or a fusion protein or variants thereof. Depending upon the nature of the polypeptides (i.e., percent hydrophobicity, percent hydrophilicity, stability, net charge, isoelectric point etc.), it may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Such conjugation includes either chemical conjugation by derivitizing active chemical functional groups to both the polypeptide of the present invention and the immunogenic protein such that a covalent bond is formed, or through fusion-protein based methodology, or other methods known to the skilled artisan. Examples of such immunogenic proteins include, but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. Additional examples of adjuvants which may be employed includes the MPL-TDM adjuvant (monophosphoryl lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.

[0626] The antibodies of the present invention may comprise monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975) and U.S. Pat. No. 4,376,110, by Harlow, et al., Antibodies: A Laboratory Manual, (Cold spring Harbor Laboratory Press, 2nd ed. (1988), by Hammerling, et al., Monoclonal Antibodies and T-Cell Hybridomas (Elsevier, N.Y., pp. 563-681 (1981); Kohler et al., Eur. J. Immunol. 6:511 (1976); Kohler et al., Eur. J. Immunol. 6:292 (1976), or other methods known to the artisan. Other examples of methods which may be employed for producing monoclonal antibodies includes, but are not limited to, the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cole et al., 1983, Proc. Natl. Acad. Sci. USA 80:2026-2030), and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAb of this invention may be cultivated in vitro or in vivo. Production of high titers of mAbs in vivo makes this the presently preferred method of production.

[0627] In a hybridoma method, a mouse, a humanized mouse, a mouse with a human immune system, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.

[0628] The immunizing agent will typically include polypeptides of the present invention or a fusion protein thereof. Preferably, the immunizing agent consists of an XXXXX polypeptide or, more preferably, with a XXXXX polypeptide-expressing cell. Such cells may be cultured in any suitable tissue culture medium; however, it is preferable to culture cells in Earle's modified Eagle's medium supplemented with 10% fetal bovine serum (inactivated at about 56 degrees C.), and supplemented with about 10 g/l of nonessential amino acids, about 1,000 U/ml of penicillin, and about 100 ug/ml of streptomycin. Generally, either peripheral blood lymphocytes (“PBLs”) are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986), pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.

[0629] Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. More preferred are the parent myeloma cell line (SP2O) as provided by the ATCC. As inferred throughout the specification, human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63).

[0630] The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the polypeptides of the present invention. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbant assay (ELISA). Such techniques are known in the art and within the skill of the artisan. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollart, Anal. Biochem., 107:220 (1980).

[0631] After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, supra, and/or according to Wands et al. (Gastroenterology 80:225-232 (1981)). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.

[0632] The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-sepharose, hydroxyapatite chromatography, gel exclusion chromatography, gel electrophoresis, dialysis, or affinity chromatography.

[0633] The skilled artisan would acknowledge that a variety of methods exist in the art for the production of monoclonal antibodies and thus, the invention is not limited to their sole production in hydridomas. For example, the monoclonal antibodies may be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. In this context, the term “monoclonal antibody” refers to an antibody derived from a single eukaryotic, phage, or prokaryotic clone. The DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies, or such chains from human, humanized, or other sources). The hydridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transformed into host cells such as Simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison et al, supra) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

[0634] The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fe region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.

[0635] In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. Monoclonal antibodies can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof. For example, monoclonal antibodies can be produced using hybridoma techniques including those known in the art and taught, for example, in Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling, et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563-681 (Elsevier, N.Y., 1981) (said references incorporated by reference in their entireties). The term “monoclonal antibody” as used herein is not limited to antibodies produced through hybridoma technology. The term “monoclonal antibody” refers to an antibody that is derived from a single clone, including any eukaryotic, prokaryotic, or phage clone, and not the method by which it is produced.

[0636] Methods for producing and screening for specific antibodies using hybridoma technology are routine and well known in the art and are discussed in detail in the Examples described herein. In a non-limiting example, mice can be immunized with a polypeptide of the invention or a cell expressing such peptide. Once an immune response is detected, e.g., antibodies specific for the antigen are detected in the mouse serum, the mouse spleen is harvested and splenocytes isolated. The splenocytes are then fused by well known techniques to any suitable myeloma cells, for example cells from cell line SP20 available from the ATCC. Hybridomas are selected and cloned by limited dilution. The hybridoma clones are then assayed by methods known in the art for cells that secrete antibodies capable of binding a polypeptide of the invention. Ascites fluid, which generally contains high levels of antibodies, can be generated by immunizing mice with positive hybridoma clones.

[0637] Accordingly, the present invention provides methods of generating monoclonal antibodies as well as antibodies produced by the method comprising culturing a hybridoma cell secreting an antibody of the invention wherein, preferably, the hybridoma is generated by fusing splenocytes isolated from a mouse immunized with an antigen of the invention with myeloma cells and then screening the hybridomas resulting from the fusion for hybridoma clones that secrete an antibody able to bind a polypeptide of the invention.

[0638] Antibody fragments which recognize specific epitopes may be generated by known techniques. For example, Fab and F(ab′)2 fragments of the invention may be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab′)2 fragments). F(ab′)2 fragments contain the variable region, the light chain constant region and the CH1 domain of the heavy chain.

[0639] For example, the antibodies of the present invention can also be generated using various phage display methods known in the art. In phage display methods, functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them. In a particular embodiment, such phage can be utilized to display antigen binding domains expressed from a repertoire or combinatorial antibody library (e.g., human or murine). Phage expressing an antigen binding domain that binds the antigen of interest can be selected or identified with antigen, e.g., using labeled antigen or antigen bound or captured to a solid surface or bead. Phage used in these methods are typically filamentous phage including fd and M13 binding domains expressed from phage with Fab, Fv or disulfide stabilized Fv antibody domains recombinantly fused to either the phage gene III or gene VIII protein. Examples of phage display methods that can be used to make the antibodies of the present invention include those disclosed in Brinkman et al., J. Inmunol. Methods 182:41-50 (1995); Ames et al., J. Immunol. Methods 184:177-186 (1995); Kettleborough et al., Eur. J. Immunol. 24:952-958 (1994); Persic et al., Gene 1879-18 (1997); Burton et al., Advances in Immunology 57:191-280 (1994); PCT application No. PCT/GB91/01134; PCT publications WO 90/02809; WO 91/10737; WO 92/01047; WO 92/18619; WO 93/11236; WO 95/15982; WO 95/20401; and U.S. Pat. Nos. 5,698,426; 5,223,409; 5,403,484; 5,580,717; 5,427,908; 5,750,753; 5,821,047; 5,571,698; 5,427,908; 5,516,637; 5,780,225; 5,658,727; 5,733,743 and 5,969,108; each of which is incorporated herein by reference in its entirety.

[0640] As described in the above references, after phage selection, the antibody coding regions from the phage can be isolated and used to generate whole antibodies, including human antibodies, or any other desired antigen binding fragment, and expressed in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, e.g., as described in detail below. For example, techniques to recombinantly produce Fab, Fab′ and F(ab′)2 fragments can also be employed using methods known in the art such as those disclosed in PCT publication WO 92/22324; Mullinax et al., BioTechniques 12(6):864-869 (1992); and Sawai et al., AJRI 34:26-34 (1995); and Better et al., Science 240:1041-1043 (1988) (said references incorporated by reference in their entireties). Examples of techniques which can be used to produce single-chain Fvs and antibodies include those described in U.S. Pat. Nos. 4,946,778 and 5,258,498; Huston et al., Methods in Enzymology 203:46-88 (1991); Shu et al., PNAS 90:7995-7999 (1993); and Skerra et al., Science 240:1038-1040 (1988).

[0641] For some uses, including in vivo use of antibodies in humans and in vitro detection assays, it may be preferable to use chimeric, humanized, or human antibodies. A chimeric antibody is a molecule in which different portions of the antibody are derived from different animal species, such as antibodies having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region. Methods for producing chimeric antibodies are known in the art. See e.g., Morrison, Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Gillies et al., (1989) J. Immunol. Methods 125:191-202; Cabilly et al., Taniguchi et al., EP 171496; Morrison et al., EP 173494; Neuberger et al., WO 8601533; Robinson et al., WO 8702671; Boulianne et al., Nature 312:643 (1984); Neuberger et al., Nature 314:268 (1985); U.S. Pat. Nos. 5,807,715; 4,816,567; and 4,816397, which are incorporated herein by reference in their entirety. Humanized antibodies are antibody molecules from non-human species antibody that binds the desired antigen having one or more complementarity determining regions (CDRs) from the non-human species and a framework regions from a human immunoglobulin molecule. Often, framework residues in the human framework regions will be substituted with the corresponding residue from the CDR donor antibody to alter, preferably improve, antigen binding. These framework substitutions are identified by methods well known in the art, e.g., by modeling of the interactions of the CDR and framework residues to identify framework residues important for antigen binding and sequence comparison to identify unusual framework residues at particular positions. (See, e.g., Queen et al., U.S. Pat. No. 5,585,089; Riechmann et al., Nature 332:323 (1988), which are incorporated herein by reference in their entireties.) Antibodies can be humanized using a variety of techniques known in the art including, for example, CDR-grafting (EP 239,400; PCT publication WO 91/09967; U.S. Pat. Nos. 5,225,539; 5,530,101; and 5,585,089), veneering or resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology 28(4/5):489-498 (1991); Studnicka et al., Protein Engineering 7(6):805-814 (1994); Roguska. et al., PNAS 91:969-973 (1994)), and chain shuffling (U.S. Pat. No. 5,565,332). Generally, a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization can be essentially performed following the methods of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Reichmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such “humanized” antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possible some FR residues are substituted from analogous sites in rodent antibodies.

[0642] In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988)1 and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992).

[0643] Completely human antibodies are particularly desirable for therapeutic treatment of human patients. Human antibodies can be made by a variety of methods known in the art including phage display methods described above using antibody libraries derived from human immunoglobulin sequences. See also, U.S. Pat. Nos. 4,444,887 and 4,716,111; and PCT publications WO 98/46645, WO 98/50433, WO 98/24893, WO 98/16,654, WO 96/34096, WO 96/33735, and WO 91/10741; each of which is incorporated herein by reference in its entirety. The techniques of cole et al., and Boerder et al., are also available for the preparation of human monoclonal antibodies (cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Riss, (1985); and Boerner et al., J. Immunol., 147(1):86-95, (1991)).

[0644] Human antibodies can also be produced using transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes. For example, the human heavy and light chain immunoglobulin gene complexes may be introduced randomly or by homologous recombination into mouse embryonic stem cells. Alternatively, the human variable region, constant region, and diversity region may be introduced into mouse embryonic stem cells in addition to the human heavy and light chain genes. The mouse heavy and light chain immunoglobulin genes may be rendered non-functional separately or simultaneously with the introduction of human immunoglobulin loci by homologous recombination. In particular, homozygous deletion of the JH region prevents endogenous antibody production. The modified embryonic stem cells are expanded and microinjected into blastocysts to produce chimeric mice. The chimeric mice are then bred to produce homozygous offspring which express human antibodies. The transgenic mice are immunized in the normal fashion with a selected antigen, e.g., all or a portion of a polypeptide of the invention. Monoclonal antibodies directed against the antigen can be obtained from the immunized, transgenic mice using conventional hybridoma technology. The human immunoglobulin transgenes harbored by the transgenic mice rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation. Thus, using such a technique, it is possible to produce therapeutically useful IgG, IgA, IgM and IgE antibodies. For an overview of this technology for producing human antibodies, see Lonberg and Huszar, Int. Rev. Immunol. 13:65-93 (1995). For a detailed discussion of this technology for producing human antibodies and human monoclonal antibodies and protocols for producing such antibodies, see, e.g., PCT publications WO 98/24893; WO 92/01047; WO 96/34096; WO 96/33735; European Patent No. 0 598 877; U.S. Pat. Nos. 5,413,923; 5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793; 5,916,771; and 5,939,598, which are incorporated by reference herein in their entirety. In addition, companies such as Abgenix, Inc. (Freemont, Calif.), Genpharm (San Jose, Calif.), and Medarex, Inc. (Princeton, N.J.) can be engaged to provide human antibodies directed against a selected antigen using technology similar to that described above.

[0645] Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and creation of an antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,106, and in the following scientific publications: Marks et al., Biotechnol., 10:779-783 (1992); Lonberg et al., Nature 368:856-859 (1994); Fishwild et al., Nature Biotechnol., 14:845-51 (1996); Neuberger, Nature Biotechnol., 14:826 (1996); Lonberg and Huszer, Intern. Rev. Immunol., 13:65-93 (1995).

[0646] Completely human antibodies which recognize a selected epitope can be generated using a technique referred to as “guided selection.” In this approach a selected non-human monoclonal antibody, e.g., a mouse antibody, is used to guide the selection of a completely human antibody recognizing the same epitope. (Jespers et al., Bio/technology 12:899-903 (1988)).

[0647] Further, antibodies to the polypeptides of the invention can, in turn, be utilized to generate anti-idiotype antibodies that “mimic” polypeptides of the invention using techniques well known to those skilled in the art. (See, e.g., Greenspan & Bona, FASEB J. 7(5):437-444; (1989) and Nissinoff, J. Immunol. 147(8):2429-2438 (1991)). For example, antibodies which bind to and competitively inhibit polypeptide multimerization and/or binding of a polypeptide of the invention to a ligand can be used to generate anti-idiotypes that “mimic” the polypeptide multimerization and/or binding domain and, as a consequence, bind to and neutralize polypeptide and/or its ligand. Such neutralizing anti-idiotypes or Fab fragments of such anti-idiotypes can be used in therapeutic regimens to neutralize polypeptide ligand. For example, such anti-idiotypic antibodies can be used to bind a polypeptide of the invention and/or to bind its ligands/receptors, and thereby block its biological activity.

[0648] Such anti-idiotypic antibodies capable of binding to the XXXXX polypeptide can be produced in a two-step procedure. Such a method makes use of the fact that antibodies are themselves antigens, and therefore, it is possible to obtain an antibody that binds to a second antibody. In accordance with this method, protein specific antibodies are used to immunize an animal, preferably a mouse. The splenocytes of such an animal are then used to produce hybridoma cells, and the hybridoma cells are screened to identify clones that produce an antibody whose ability to bind to the protein-specific antibody can be blocked by the polypeptide. Such antibodies comprise anti-idiotypic antibodies to the protein-specific antibody and can be used to immunize an animal to induce formation of further protein-specific antibodies.

[0649] The antibodies of the present invention may be bispecific antibodies. Bispecific antibodies are monoclonal, Preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present invention, one of the binding specificities may be directed towards a polypeptide of the present invention, the other may be for any other antigen, and preferably for a cell-surface protein, receptor, receptor subunit, tissue-specific antigen, virally derived protein, virally encoded envelope protein, bacterially derived protein, or bacterial surface protein, etc.

[0650] Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991).

[0651] Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transformed into a suitable host organism. For further details of generating bispecific antibodies see, for example Suresh et al., Meth. In Enzym., 121:210 (1986).

[0652] Heteroconjugate antibodies are also contemplated by the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for the treatment of HIV infection (WO 91/00360; WO 92/20373; and EP03089). It is contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioester bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.

[0653] Polynucleotides Encoding Antibodies

[0654] The invention further provides polynucleotides comprising a nucleotide sequence encoding an antibody of the invention and fragments thereof. The invention also encompasses polynucleotides that hybridize under stringent or lower stringency hybridization conditions, e.g., as defined supra, to polynucleotides that encode an antibody, preferably, that specifically binds to a polypeptide of the invention, preferably, an antibody that binds to a polypeptide having the amino acid sequence of SEQ ID NO:2, 24, 54, and/or 56.

[0655] The polynucleotides may be obtained, and the nucleotide sequence of the polynucleotides determined, by any method known in the art. For example, if the nucleotide sequence of the antibody is known, a polynucleotide encoding the antibody may be assembled from chemically synthesized oligonucleotides (e.g., as described in Kutmeier et al., BioTechniques 17:242 (1994)), which, briefly, involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, annealing and ligating of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR.

[0656] Alternatively, a polynucleotide encoding an antibody may be generated from nucleic acid from a suitable source. If a clone containing a nucleic acid encoding a particular antibody is not available, but the sequence of the antibody molecule is known, a nucleic acid encoding the immunoglobulin may be chemically synthesized or obtained from a suitable source (e.g., an antibody cDNA library, or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the antibody, such as hybridoma cells selected to express an antibody of the invention) by PCR amplification using synthetic primers hybridizable to the 3′ and 5′ ends of the sequence or by cloning using an oligonucleotide probe specific for the particular gene sequence to identify, e.g., a cDNA clone from a cDNA library that encodes the antibody. Amplified nucleic acids generated by PCR may then be cloned into replicable cloning vectors using any method well known in the art.

[0657] Once the nucleotide sequence and corresponding amino acid sequence of the antibody is determined, the nucleotide sequence of the antibody may be manipulated using methods well known in the art for the manipulation of nucleotide sequences, e.g., recombinant DNA techniques, site directed mutagenesis, PCR, etc. (see, for example, the techniques described in Sambrook et al., 1990, Molecular Cloning, A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. and Ausubel et al., eds., 1998, Current Protocols in Molecular Biology, John Wiley & Sons, NY, which are both incorporated by reference herein in their entireties ), to generate antibodies having a different amino acid sequence, for example to create amino acid substitutions, deletions, and/or insertions.

[0658] In a specific embodiment, the amino acid sequence of the heavy and/or light chain variable domains may be inspected to identify the sequences of the complementarity determining regions (CDRs) by methods that are well know in the art, e.g., by comparison to known amino acid sequences of other heavy and light chain variable regions to determine the regions of sequence hypervariability. Using routine recombinant DNA techniques, one or more of the CDRs may be inserted within framework regions, e.g., into human framework regions to humanize a non-human antibody, as described supra. The framework regions may be naturally occurring or consensus framework regions, and preferably human framework regions (see, e.g., Chothia et al., J. Mol. Biol. 278: 457-479 (1998) for a listing of human framework regions). Preferably, the polynucleotide generated by the combination of the framework regions and CDRs encodes an antibody that specifically binds a polypeptide of the invention. Preferably, as discussed supra, one or more amino acid substitutions may be made within the framework regions, and, preferably, the amino acid substitutions improve binding of the antibody to its antigen. Additionally, such methods may be used to make amino acid substitutions or deletions of one or more variable region cysteine residues participating in an intrachain disulfide bond to generate antibody molecules lacking one or more intrachain disulfide bonds. Other alterations to the polynucleotide are encompassed by the present invention and within the skill of the art.

[0659] In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., Proc. Natl. Acad. Sci. 81:851-855 (1984); Neuberger et al., Nature 312:604-608 (1984); Takeda et al., Nature 314:452-454 (1985)) by splicing genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. As described supra, a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region, e.g., humanized antibodies.

[0660] Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778; Bird, Science 242:423-42 (1988); Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988); and Ward et al., Nature 334:544-54 (1989)) can be adapted to produce single chain antibodies. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide. Techniques for the assembly of functional Fv fragments in E. coli may also be used (Skerra et al., Science 242:1038-1041 (1988)).

[0661] More preferably, a clone encoding an antibody of the present invention may be obtained according to the method described in the Example section herein.

[0662] Methods of Producing Antibodies

[0663] The antibodies of the invention can be produced by any method known in the art for the synthesis of antibodies, in particular, by chemical synthesis or preferably, by recombinant expression techniques.

[0664] Recombinant expression of an antibody of the invention, or fragment, derivative or analog thereof, (e.g., a heavy or light chain of an antibody of the invention or a single chain antibody of the invention), requires construction of an expression vector containing a polynucleotide that encodes the antibody. Once a polynucleotide encoding an antibody molecule or a heavy or light chain of an antibody, or portion thereof (preferably containing the heavy or light chain variable domain), of the invention has been obtained, the vector for the production of the antibody molecule may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. The invention, thus, provides replicable vectors comprising a nucleotide sequence encoding an antibody molecule of the invention, or a heavy or light chain thereof, or a heavy or light chain variable domain, operably linked to a promoter. Such vectors may include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., PCT Publication WO 86/05807; PCT Publication WO 89/01036; and U.S. Pat. No. 5,122,464) and the variable domain of the antibody may be cloned into such a vector for expression of the entire heavy or light chain.

[0665] The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce an antibody of the invention. Thus, the invention includes host cells containing a polynucleotide encoding an antibody of the invention, or a heavy or light chain thereof, or a single chain antibody of the invention, operably linked to a heterologous promoter. In preferred embodiments for the expression of double-chained antibodies, vectors encoding both the heavy and light chains may be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.

[0666] A variety of host-expression vector systems may be utilized to express the antibody molecules of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody molecule of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing antibody coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). Preferably, bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule. For example, mammalian cells such as Chinese hamster ovary cells (CHO), in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus is an effective expression system for antibodies (Foecking et al., Gene 45:101 (1986); Cockett et al., Bio/Technology 8:2 (1990)).

[0667] In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the antibody molecule being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of an antibody molecule, vectors which direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., EMBO J. 2:1791 (1983)), in which the antibody coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, Nucleic Acids Res. 13:3101-3109 (1985); Van Heeke & Schuster, J. Biol. Chem. 24:5503-5509 (1989)); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to matrix glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.

[0668] In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The antibody coding sequence may be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter).

[0669] In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, the antibody coding sequence of interest may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts. (e.g., see Logan & Shenk, Proc. Natl. Acad. Sci. USA 81:355-359 (1984)). Specific initiation signals may also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences: Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see Bittner et al., Methods in Enzymol. 153:51-544 (1987)).

[0670] In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. Such mammalian host cells include but are not limited to CHO, VERY, BHK, Hela, COS, MDCK, 293, 3T3, WI38, and in particular, breast cancer cell lines such as, for example, BT483, Hs578T, HTB2, BT20 and T47D, and normal mammary gland cell line such as, for example, CRL7030 and Hs578Bst.

[0671] For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the antibody molecule may be engineered. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells may be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method may advantageously be used to engineer cell lines which express the antibody molecule. Such engineered cell lines may be particularly useful in screening and evaluation of compounds that interact directly or indirectly with the antibody molecule.

[0672] A number of selection systems may be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223 (1977)), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, Proc. Natl. Acad. Sci. USA 48:202 (1992)), and adenine phosphoribosyltransferase (Lowy et al., Cell 22:817 (1980)) genes can be employed in tk-, hgprt- or aprt-cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al., Natl. Acad. Sci. USA 77:357 (1980); O'Hare et al., Proc. Natl. Acad. Sci. USA 78:1527 (1981)); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA 78:2072 (1981)); neo, which confers resistance to the aminoglycoside G-418 Clinical Pharmacy 12:488-505; Wu and Wu, Biotherapy 3:87-95 (1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217 (1993); May, 1993, TIB TECH 11(5):155-215); and hygro, which confers resistance to hygromycin (Santerre et al., Gene 30:147 (1984)). Methods commonly known in the art of recombinant DNA technology may be routinely applied to select the desired recombinant clone, and such methods are described, for example, in Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993); Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990); and in Chapters 12 and 13, Dracopoli et al. (eds), Current Protocols in Human Genetics, John Wiley & Sons, NY (1994); Colberre-Garapin et al., J. Mol. Biol. 150:1 (1981), which are incorporated by reference herein in their entireties.

[0673] The expression levels of an antibody molecule can be increased by vector amplification (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol.3. (Academic Press, New York, 1987)). When a marker in the vector system expressing antibody is amplifiable, increase in the level of inhibitor present in culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody will also increase (Crouse et al., Mol. Cell. Biol. 3:257 (1983)).

[0674] The host cell may be co-transfected with two expression vectors of the invention, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide. The two vectors may contain identical selectable markers which enable equal expression of heavy and light chain polypeptides. Alternatively, a single vector may be used which encodes, and is capable of expressing, both heavy and light chain polypeptides. In such situations, the light chain should be placed before the heavy chain to avoid an excess of toxic free heavy chain (Proudfoot, Nature 322:52 (1986); Kohler, Proc. Natl. Acad. Sci. USA 77:2197 (1980)). The coding sequences for the heavy and light chains may comprise cDNA or genomic DNA.

[0675] Once an antibody molecule of the invention has been produced by an animal, chemically synthesized, or recombinantly expressed, it may be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. In addition, the antibodies of the present invention or fragments thereof can be fused to heterologous polypeptide sequences described herein or otherwise known in the art, to facilitate purification.

[0676] The present invention encompasses antibodies recombinantly fused or chemically conjugated (including both covalently and non-covalently conjugations) to a polypeptide (or portion thereof, preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids of the polypeptide) of the present invention to generate fusion proteins. The fusion does not necessarily need to be direct, but may occur through linker sequences. The antibodies may be specific for antigens other than polypeptides (or portion thereof, preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids of the polypeptide) of the present invention. For example, antibodies may be used to target the polypeptides of the present invention to particular cell types, either in vitro or in vivo, by fusing or conjugating the polypeptides of the present invention to antibodies specific for particular cell surface receptors. Antibodies fused or conjugated to the polypeptides of the present invention may also be used in in vitro immunoassays and purification methods using methods known in the art. See e.g., Harbor et al., supra, and PCT publication WO 93/21232; EP 439,095; Naramura et al., Immunol. Lett. 39:91-99 (1994); U.S. Pat. No. 5,474,981; Gillies et al., PNAS 89:1428-1432 (1992); Fell et al., J. Immunol. 146:2446-2452(1991), which are incorporated by reference in their entireties.

[0677] The present invention further includes compositions comprising the polypeptides of the present invention fused or conjugated to antibody domains other than the variable regions. For example, the polypeptides of the present invention may be fused or conjugated to an antibody Fc region, or portion thereof. The antibody portion fused to a polypeptide of the present invention may comprise the constant region, hinge region, CH1 domain, CH2 domain, and CH3 domain or any combination of whole domains or portions thereof. The polypeptides may also be fused or conjugated to the above antibody portions to form multimers. For example, Fc portions fused to the polypeptides of the present invention can form dimers through disulfide bonding between the Fc portions. Higher multimeric forms can be made by fusing the polypeptides to portions of IgA and IgM. Methods for fusing or conjugating the polypeptides of the present invention to antibody portions are known in the art. See, e.g., U.S. Pat. Nos. 5,336,603; 5,622,929; 5,359,046; 5,349,053; 5,447,851; 5,112,946; EP 307,434; EP 367,166; PCT publications WO 96/04388; WO 91/06570; Ashkenazi et al., Proc. Natl. Acad. Sci. USA 88:10535-10539 (1991); Zheng et al., J. Immunol. 154:5590-5600 (1995); and Vil et al., Proc. Natl. Acad. Sci. USA 89:11337-11341(1992) (said references incorporated by reference in their entireties).

[0678] As discussed, supra, the polypeptides corresponding to a polypeptide, polypeptide fragment, or a variant of SEQ ID NO:2, 24, 54, and/or 56 may be fused or conjugated to the above antibody portions to increase the in vivo half life of the polypeptides or for use in immunoassays using methods known in the art. Further, the polypeptides corresponding to SEQ ID NO:2, 24, 54, and/or 56 may be fused or conjugated to the above antibody portions to facilitate purification. One reported example describes chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. (EP 394,827; Traunecker et al., Nature 331:84-86 (1988). The polypeptides of the present invention fused or conjugated to an antibody having disulfide-linked dimeric structures (due to the IgG) may also be more efficient in binding and neutralizing other molecules, than the monomeric secreted protein or protein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964 (1995)). In many cases, the Fc part in a fusion protein is beneficial in therapy and diagnosis, and thus can result in, for example, improved pharmacokinetic properties. (EP A 232,262). Alternatively, deleting the Fc part after the fusion protein has been expressed, detected, and purified, would be desired. For example, the Fc portion may hinder therapy and diagnosis if the fusion protein is used as an antigen for immunizations. In drug discovery, for example, human proteins, such as hIL-5, have been fused with Fc portions for the purpose of high-throughput screening assays to identify antagonists of hIL-5. (See, Bennett et al., J. Molecular Recognition 8:52-58 (1995); Johanson et al., J. Biol. Chem. 270:9459-9471 (1995).

[0679] Moreover, the antibodies or fragments thereof of the present invention can be fused to marker sequences, such as a peptide to facilitate purification. In preferred embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance, hexa-histidine provides for convenient purification of the fusion protein. Other peptide tags useful for purification include, but are not limited to, the “HA” tag, which corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson et al., Cell 37:767 (1984)) and the “flag” tag.

[0680] The present invention further encompasses antibodies or fragments thereof conjugated to a diagnostic or therapeutic agent. The antibodies can be used diagnostically to, for example, monitor the development or progression of a tumor as part of a clinical testing procedure to, e.g., determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals using various positron emission tomographies, and nonradioactive paramagnetic metal ions. The detectable substance may be coupled or conjugated either directly to the antibody (or fragment thereof) or indirectly, through an intermediate (such as, for example, a linker known in the art) using techniques known in the art. See, for example, U.S. Pat. No. 4,741,900 for metal ions which can be conjugated to antibodies for use as diagnostics according to the present invention. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include 125I, 131I, 111In or 99Tc.

[0681] Further, an antibody or fragment thereof may be conjugated to a therapeutic moiety such as a cytotoxin, e.g., a cytostatic or cytocidal agent, a therapeutic agent or a radioactive metal ion, e.g., alpha-emitters such as, for example, 213Bi. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include paclitaxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologues thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and vinblastine).

[0682] The conjugates of the invention can be used for modifying a given biological response, the therapeutic agent or drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, a-interferon, β-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator, an apoptotic agent, e.g., TNF-alpha, TNF-beta, AIM I (See, International Publication No. WO 97/33899), AIM II (See, International Publication No. WO 97/34911), Fas Ligand (Takahashi et al., Int. Immunol., 6:1567-1574 (1994)), VEGI (See, International Publication No. WO 99/23105), a thrombotic agent or an anti-angiogenic agent, e.g., angiostatin or endostatin; or, biological response modifiers such as, for example, lymphokines, interleukin-1 (“1-1”), interleukin-2 (“1L-2”), interleukin-6 (“1L-6”), granulocyte macrophage colony stimulating factor (“GM-CSF”), granulocyte colony stimulating factor (“G-CSF”), or other growth factors.

[0683] Antibodies may also be attached to solid supports, which are particularly useful for immunoassays or purification of the target antigen. Such solid supports include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyinyl chloride or polypropylene.

[0684] Techniques for conjugating such therapeutic moiety to antibodies are well known, see, e.g., Arnon et al., “Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy”, in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., “Antibodies For Drug Delivery”, in Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe, “Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review”, in Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); “Analysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapy”, in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp. 303-16 (Academic Press 1985), and Thorpe et al., “The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates”, Immunol. Rev. 62:119-58 (1982).

[0685] Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Pat. No. 4,676,980, which is incorporated herein by reference in its entirety.

[0686] An antibody, with or without a therapeutic moiety conjugated to it, administered alone or in combination with cytotoxic factor(s) and/or cytokine(s) can be used as a therapeutic.

[0687] The present invention also encompasses the creation of synthetic antibodies directed against the polypeptides of the present invention. One example of synthetic antibodies is described in Radrizzani, M., et al., Medicina, (Aires), 59(6):753-8, (1999)). Recently, a new class of synthetic antibodies has been described and are referred to as molecularly imprinted polymers (MIPs) (Semorex, Inc.). Antibodies, peptides, and enzymes are often used as molecular recognition elements in chemical and biological sensors. However, their lack of stability and signal transduction mechanisms limits their use as sensing devices. Molecularly imprinted polymers (MIPs) are capable of mimicking the function of biological receptors but with less stability constraints. Such polymers provide high sensitivity and selectivity while maintaining excellent thermal and mechanical stability. MIPs have the ability to bind to small molecules and to target molecules such as organics and proteins' with equal or greater potency than that of natural antibodies. These “super” MIPs have higher affinities for their target and thus require lower concentrations for efficacious binding.

[0688] During synthesis, the MIPs are imprinted so as to have complementary size, shape, charge and functional groups of the selected target by using the target molecule itself (such as a polypeptide, antibody, etc.), or a substance having a very similar structure, as its “print” or “template.” MIPs can be derivatized with the same reagents afforded to antibodies. For example, fluorescent ‘super’ MIPs can be coated onto beads or wells for use in highly sensitive separations or assays, or for use in high throughput screening of proteins.

[0689] Moreover, MIPs based upon the structure of the polypeptide(s) of the present invention may be useful in screening for compounds that bind to the polypeptide(s) of the invention. Such a MIP would serve the role of a synthetic “receptor” by minimicking the native architecture of the polypeptide. In fact, the ability of a MIP to serve the role of a synthetic receptor has already been demonstrated for the estrogen receptor (Ye, L., Yu, Y., Mosbach, K, Analyst., 126(6):760-5, (2001); Dickert, F, L., Hayden, O., Halikias, K, P, Analyst., 126(6):766-71, (2001)). A synthetic receptor may either be mimicked in its entirety (e.g., as the entire protein), or mimicked as a series of short peptides corresponding to the protein (Rachkov, A., Minoura, N, Biochim, Biophys, Acta., 1544(1-2):255-66, (2001)). Such a synthetic receptor MIPs may be employed in any one or more of the screening methods described elsewhere herein.

[0690] MIPs have also been shown to be useful in “sensing” the presence of its mimicked molecule (Cheng, Z., Wang, E., Yang, X, Biosens, Bioelectron., 16(3): 179-85, (2001); Jenkins, A, L., Yin, R., Jensen, J. L, Analyst., 126(6):798-802, (2001); Jenkins, A, L., Yin, R., Jensen, J. L, Analyst., 126(6):798-802, (2001)). For example, a MIP designed using a polypeptide of the present invention may be used in assays designed to identify, and potentially quantitate, the level of said polypeptide in a sample. Such a MIP may be used as a substitute for any component described in the assays, or kits, provided herein (e.g., ELISA, etc.).

[0691] A number of methods may be employed to create MIPs to a specific receptor, ligand, polypeptide, peptide, organic molecule. Several preferred methods are described by Esteban et al in J. Anal, Chem., 370(7):795-802, (2001), which is hereby incorporated herein by reference in its entirety in addition to any references cited therein. Additional methods are known in the art and are encompassed by the present invention, such as for example, Hart, B, R., Shea, K, J. J. Am. Chem, Soc., 123(9):2072-3, (2001); and Quaglia, M., Chenon, K., Hall, A, J., De, Lorenzi, E., Sellergren, B, J. Am. Chem, Soc., 123(10):2146-54, (2001); which are hereby incorporated by reference in their entirety herein.

[0692] Uses for Antibodies Directed Against Polypeptides of the Invention

[0693] The antibodies of the present invention have various utilities. For example, such antibodies may be used in diagnostic assays to detect the presence or quantification of the polypeptides of the invention in a sample. Such a diagnostic assay may be comprised of at least two steps. The first, subjecting a sample with the antibody, wherein the sample is a tissue (e.g., human, animal, etc.), biological fluid (e.g., blood, urine, sputum, semen, amniotic fluid, saliva, etc.), biological extract (e.g., tissue or cellular homogenate, etc.), a protein microchip (e.g., See Arenkov P, et al., Anal Biochem., 278(2):123-131 (2000)), or a chromatography column, etc. And a second step involving the quantification of antibody bound to the substrate. Alternatively, the method may additionally involve a first step of attaching the antibody, either covalently, electrostatically, or reversibly, to a solid support, and a second step of subjecting the bound antibody to the sample, as defined above and elsewhere herein.

[0694] Various diagnostic assay techniques are known in the art, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogenous phases (Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc., (1987), pp147-158). The antibodies used in the diagnostic assays can be labeled with a detectable moiety. The detectable moiety should be capable of producing, either directly or indirectly, a detectable signal. For example, the detectable moiety may be a radioisotope, such as 2H, 14C, 32P, or 125I, a florescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase, green fluorescent protein, or horseradish peroxidase. Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144:945 (1962); Dafvid et al., Biochem., 13:1014 (1974); Pain et al., J. Immunol. Metho., 40:219(1981); and Nygren, J. Histochem. And Cytochem., 30:407 (1982).

[0695] Antibodies directed against the polypeptides of the present invention are useful for the affinity purification of such polypeptides from recombinant cell culture or natural sources. In this process, the antibodies against a particular polypeptide are immobilized on a suitable support, such as a Sephadex resin or filter paper, using methods well known in the art. The immobilized antibody then is contacted with a sample containing the polypeptides to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except for the desired polypeptides, which are bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the desired polypeptide from the antibody.

[0696] Immunophenotyping

[0697] The antibodies of the invention may be utilized for immunophenotyping of cell lines and biological samples. The translation product of the gene of the present invention may be useful as a cell specific marker, or more specifically as a cellular marker that is differentially expressed at various stages of differentiation and/or maturation of particular cell types. Monoclonal antibodies directed against a specific epitope, or combination of epitopes, will allow for the screening of cellular populations expressing the marker. Various techniques can be utilized using monoclonal antibodies to screen for cellular populations expressing the marker(s), and include magnetic separation using antibody-coated magnetic beads, “panning” with antibody attached to a solid matrix (i.e., plate), and flow cytometry (See, e.g., U.S. Pat. No. 5,985,660; and Morrison et al., Cell, 96:737-49 (1999)).

[0698] These techniques allow for the screening of particular populations of cells, such as might be found with hematological malignancies (i.e. minimal residual disease (MRD) in acute leukemic patients) and “non-self” cells in transplantations to prevent Graft-versus-Host Disease (GVHD). Alternatively, these techniques allow for the screening of hematopoietic stem and progenitor cells capable of undergoing proliferation and/or differentiation, as might be found in human umbilical cord blood.

[0699] Assays for Antibody Binding

[0700] The antibodies of the invention may be assayed for immunospecific binding by any method known in the art. The immunoassays which can be used include but are not limited to competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to name but a few. Such assays are routine and well known in the art (see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York, which is incorporated by reference herein in its entirety). Exemplary immunoassays are described briefly below (but are not intended by way of limitation).

[0701] Immunoprecipitation protocols generally comprise lysing a population of cells in a lysis buffer such as RIPA buffer (1% NP-40 or Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 0.15 M NaCl, 0.01 M sodium phosphate at pH 7.2, 1% Trasylol) supplemented with protein phosphatase and/or protease inhibitors (e.g., EDTA, PMSF, aprotinin, sodium vanadate), adding the antibody of interest to the cell lysate, incubating for a period of time (e.g., 1-4 hours) at 4° C., adding protein A and/or protein G sepharose beads to the cell lysate, incubating for about an hour or more at 4° C., washing the beads in lysis buffer and resuspending the beads in SDS/sample buffer. The ability of the antibody of interest to immunoprecipitate a particular antigen can be assessed by, e.g., western blot analysis. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the binding of the antibody to an antigen and decrease the background (e.g., pre-clearing the cell lysate with sepharose beads). For further discussion regarding immunoprecipitation protocols see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York at 10.16.1.

[0702] Western blot analysis generally comprises preparing protein samples, electrophoresis of the protein samples in a polyacrylamide gel (e.g., 8%-20% SDS-PAGE depending on the molecular weight of the antigen), transferring the protein sample from the polyacrylamide gel to a membrane such as nitrocellulose, PVDF or nylon, blocking the membrane in blocking solution (e.g., PBS with 3% BSA or non-fat milk), washing the membrane in washing buffer (e.g., PBS-Tween 20), blocking the membrane with primary antibody (the antibody of interest) diluted in blocking buffer, washing the membrane in washing buffer, blocking the membrane with a secondary antibody (which recognizes the primary antibody, e.g., an anti-human antibody) conjugated to an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) or radioactive molecule (e.g., 32P or 125I) diluted in blocking buffer, washing the membrane in wash buffer, and detecting the presence of the antigen. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected and to reduce the background noise. For further discussion regarding western blot protocols see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York at 10.8.1.

[0703] ELISAs comprise preparing antigen, coating the well of a 96 well microtiter plate with the antigen, adding the antibody of interest conjugated to a detectable compound such as an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) to the well and incubating for a period of time, and detecting the presence of the antigen. In ELISAs the antibody of interest does not have to be conjugated to a detectable compound; instead, a second antibody (which recognizes the antibody of interest) conjugated to a detectable compound may be added to the well. Further, instead of coating the well with the antigen, the antibody may be coated to the well. In this case, a second antibody conjugated to a detectable compound may be added following the addition of the antigen of interest to the coated well. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected as well as other variations of ELISAs known in the art. For further discussion regarding ELISAs see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York at 11.2.1.

[0704] The binding affinity of an antibody to an antigen and the off-rate of an antibody-antigen interaction can be determined by competitive binding assays. One example of a competitive binding assay is a radioimmunoassay comprising the incubation of labeled antigen (e.g., 3H or 125I) with the antibody of interest in the presence of increasing amounts of unlabeled antigen, and the detection of the antibody bound to the labeled antigen. The affinity of the antibody of interest for a particular antigen and the binding off-rates can be determined from the data by scatchard plot analysis. Competition with a second antibody can also be determined using radioimmunoassays. In this case, the antigen is incubated with antibody of interest conjugated to a labeled compound (e.g., 3H or 125I) in the presence of increasing amounts of an unlabeled second antibody.

[0705] Therapeutic Uses of Antibodies

[0706] The present invention is further directed to antibody-based therapies which involve administering antibodies of the invention to an animal, preferably a mammal, and most preferably a human, patient for treating one or more of the disclosed diseases, disorders, or conditions. Therapeutic compounds of the invention include, but are not limited to, antibodies of the invention (including fragments, analogs and derivatives thereof as described herein) and nucleic acids encoding antibodies of the invention (including fragments, analogs and derivatives thereof and anti-idiotypic antibodies as described herein). The antibodies of the invention can be used to treat, inhibit or prevent diseases, disorders or conditions associated with aberrant expression and/or activity of a polypeptide of the invention, including, but not limited to, any one or more of the diseases, disorders, or conditions described herein. The treatment and/or prevention of diseases, disorders, or conditions associated with aberrant expression and/or activity of a polypeptide of the invention includes, but is not limited to, alleviating symptoms associated with those diseases, disorders or conditions. Antibodies of the invention may be provided in pharmaceutically acceptable compositions as known in the art or as described herein.

[0707] A summary of the ways in which the antibodies of the present invention may be used therapeutically includes binding polynucleotides or polypeptides of the present invention locally or systemically in the body or by direct cytotoxicity of the antibody, e.g. as mediated by complement (CDC) or by effector cells (ADCC). Some of these approaches are described in more detail below. Armed with the teachings provided herein, one of ordinary skill in the art will know how to use the antibodies of the present invention for diagnostic, monitoring or therapeutic purposes without undue experimentation.

[0708] The antibodies of this invention may be advantageously utilized in combination with other monoclonal or chimeric antibodies, or with lymphokines or hematopoietic growth factors (such as, e.g., IL-2, IL-3 and IL-7), for example, which serve to increase the number or activity of effector cells which interact with the antibodies.

[0709] The antibodies of the invention may be administered alone or in combination with other types of treatments (e.g., radiation therapy, chemotherapy, hormonal therapy, immunotherapy and anti-tumor agents). Generally, administration of products of a species origin or species reactivity (in the case of antibodies) that is the same species as that of the patient is preferred. Thus, in a preferred embodiment, human antibodies, fragments derivatives, analogs, or nucleic acids, are administered to a human patient for therapy or prophylaxis.

[0710] It is preferred to use high affinity and/or potent in vivo inhibiting and/or neutralizing antibodies against polypeptides or polynucleotides of the present invention, fragments or regions thereof, for both immunoassays directed to and therapy of disorders related to polynucleotides or polypeptides, including fragments thereof, of the present invention. Such antibodies, fragments, or regions, will preferably have an affinity for polynucleotides or polypeptides of the invention, including fragments thereof. Preferred binding affinities include those with a dissociation constant or Kd less than 5×10-2 M, 10-2 M, 5×10-3 M, 10-3 M, 5×10-4 M, 10-4 M, 5×10-5 M, 10-5 M, 5×10-6 M, 10-6 M, 5×10-7 M, 10-7 M, 5×10−8 M, 10-8 M, 5×10-9 M, 10-9 M, 5×10-10 M, 10-10 M, 5×10-11 M, 10-11 M, 5×10-12 M, 10-12 M, 5×10-13 M, 10-13 M, 5×10-14 M, 10-14 M, 5×10-15 M, and 10-15 M.

[0711] Antibodies directed against polypeptides of the present invention are useful for inhibiting allergic reactions in animals. For example, by administering a therapeutically acceptable dose of an antibody, or antibodies, of the present invention, or a cocktail of the present antibodies, or in combination with other antibodies of varying sources, the animal may not elicit an allergic response to antigens.

[0712] Likewise, one could envision cloning the gene encoding an antibody directed against a polypeptide of the present invention, said polypeptide having the potential to elicit an allergic and/or immune response in an organism, and transforming the organism with said antibody gene such that it is expressed (e.g., constitutively, inducibly, etc.) in the organism. Thus, the organism would effectively become resistant to an allergic response resulting from the ingestion or presence of such an immune/allergic reactive polypeptide. Moreover, such a use of the antibodies of the present invention may have particular utility in preventing and/or ameliorating autoimmune diseases and/or disorders, as such conditions are typically a result of antibodies being directed against endogenous proteins. For example, in the instance where the polypeptide of the present invention is responsible for modulating the immune response to auto-antigens, transforming the organism and/or individual with a construct comprising any of the promoters disclosed herein or otherwise known in the art, in addition, to a polynucleotide encoding the antibody directed against the polypeptide of the present invention could effective inhibit the organisms immune system from eliciting an immune response to the auto-antigen(s). Detailed descriptions of therapeutic and/or gene therapy applications of the present invention are provided elsewhere herein.

[0713] Alternatively, antibodies of the present invention could be produced in a plant (e.g., cloning the gene of the antibody directed against a polypeptide of the present invention, and transforming a plant with a suitable vector comprising said gene for constitutive expression of the antibody within the plant), and the plant subsequently ingested by an animal, thereby conferring temporary immunity to the animal for the specific antigen the antibody is directed towards (See, for example, U.S. Pat. Nos. 5,914,123 and 6,034,298).

[0714] In another embodiment, antibodies of the present invention, preferably polyclonal antibodies, more preferably monoclonal antibodies, and most preferably single-chain antibodies, can be used as a means of inhibiting gene expression of a particular gene, or genes, in a human, mammal, and/or other organism. See, for example, International Publication Number WO 00/05391, published Feb. 3, 2000, to Dow Agrosciences LLC. The application of such methods for the antibodies of the present invention are known in the art, and are more particularly described elsewhere herein.

[0715] In yet another embodiment, antibodies of the present invention may be useful for multimerizing the polypeptides of the present invention. For example, certain proteins may confer enhanced biological activity when present in a multimeric state (i.e., such enhanced activity may be due to the increased effective concentration of such proteins whereby more protein is available in a localized location).

[0716] Antibody-Based Gene Therapy

[0717] In a specific embodiment, nucleic acids comprising sequences encoding antibodies or functional derivatives thereof, are administered to treat, inhibit or prevent a disease or disorder associated with aberrant expression and/or activity of a polypeptide of the invention, by way of gene therapy. Gene therapy refers to therapy performed by the administration to a subject of an expressed or expressible nucleic acid. In this embodiment of the invention, the nucleic acids produce their encoded protein that mediates a therapeutic effect.

[0718] Any of the methods for gene therapy available in the art can be used according to the present invention. Exemplary methods are described below.

[0719] For general reviews of the methods of gene therapy, see Goldspiel et al., Clinical Pharmacy 12:488-505 (1993); Wu and Wu, Biotherapy 3:87-95 (1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217 (1993); May, TIBTECH 11(5):155-215 (1993). Methods commonly known in the art of recombinant DNA technology which can be used are described in Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993); and Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990).

[0720] In a preferred aspect, the compound comprises nucleic acid sequences encoding an antibody, said nucleic acid sequences being part of expression vectors that express the antibody or fragments or chimeric proteins or heavy or light chains thereof in a suitable host. In particular, such nucleic acid sequences have promoters operably linked to the antibody coding region, said promoter being inducible or constitutive, and, optionally, tissue-specific. In another particular embodiment, nucleic acid molecules are used in which the antibody coding sequences and any other desired sequences are flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for intrachromosomal expression of the antibody encoding nucleic acids (Koller and Smithies, Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438 (1989). In specific embodiments, the expressed antibody molecule is a single chain antibody; alternatively, the nucleic acid sequences include sequences encoding both the heavy and light chains, or fragments thereof, of the antibody.

[0721] Delivery of the nucleic acids into a patient may be either direct, in which case the patient is directly exposed to the nucleic acid or nucleic acid-carrying vectors, or indirect, in which case, cells are first transformed with the nucleic acids in vitro, then transplanted into the patient. These two approaches are known, respectively, as in vivo or ex vivo gene therapy.

[0722] In a specific embodiment, the nucleic acid sequences are directly administered in vivo, where it is expressed to produce the encoded product. This can be accomplished by any of numerous methods known in the art, e.g., by constructing them as part of an appropriate nucleic acid expression vector and administering it so that they become intracellular, e.g., by infection using defective or attenuated retrovirals or other viral vectors (see U.S. Pat. No. 4,980,286), or by direct injection of naked DNA, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, encapsulation in liposomes, microparticles, or microcapsules, or by administering them in linkage to a peptide which is known to enter the nucleus, by administering it in linkage to a ligand subject to receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)) (which can be used to target cell types specifically expressing the receptors), etc. In another embodiment, nucleic acid-ligand complexes can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation. In yet another embodiment, the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., PCT Publications WO 92/06180; WO 92/22635; WO92/20316; WO93/14188, WO 93/20221). Alternatively, the nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination (Koller and Smithies, Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438 (1989)).

[0723] In a specific embodiment, viral vectors that contains nucleic acid sequences encoding an antibody of the invention are used. For example, a retroviral vector can be used (see Miller et al., Meth. Enzymol. 217:581-599 (1993)). These retroviral vectors contain the components necessary for the correct packaging of the viral genome and integration into the host cell DNA. The nucleic acid sequences encoding the antibody to be used in gene therapy are cloned into one or more vectors, which facilitates delivery of the gene into a patient. More detail about retroviral vectors can be found in Boesen et al., Biotherapy 6:291-302 (1994), which describes the use of a retroviral vector to deliver the mdr1 gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy. Other references illustrating the use of retroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest. 93:644-651 (1994); Kiem et al., Blood 83:1467-1473 (1994); Salmons and Gunzberg, Human Gene Therapy 4:129-141 (1993); and Grossman and Wilson, Curr. Opin. in Genetics and Devel. 3:110-114 (1993).

[0724] Adenoviruses are other viral vectors that can be used in gene therapy. Adenoviruses are especially attractive vehicles for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, Current Opinion in Genetics and Development 3:499-503 (1993) present a review of adenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10 (1994) demonstrated the use of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus monkeys. Other instances of the use of adenoviruses in gene therapy can be found in Rosenfeld et al., Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143-155 (1992); Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT Publication WO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). In a preferred embodiment, adenovirus vectors are used.

[0725] Adeno-associated virus (AAV) has also been proposed for use in gene therapy (Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300 (1993); U.S. Pat. No. 5,436,146).

[0726] Another approach to gene therapy involves transferring a gene to cells in tissue culture by such methods as electroporation, lipofection, calcium phosphate mediated transfection, or viral infection. Usually, the method of transfer includes the transfer of a selectable marker to the cells. The cells are then placed under selection to isolate those cells that have taken up and are expressing the transferred gene. Those cells are then delivered to a patient.

[0727] In this embodiment, the nucleic acid is introduced into a cell prior to administration in vivo of the resulting recombinant cell. Such introduction can be carried out by any method known in the art, including but not limited to transfection, electroporation, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc. Numerous techniques are known in the art for the introduction of foreign genes into cells (see, e.g., Loeffler and Behr, Meth. Enzymol. 217:599-618 (1993); Cohen et al., Meth. Enzymol. 217:618-644 (1993); Cline, Pharmac. Ther. 29:69-92m (1985) and may be used in accordance with the present invention, provided that the necessary developmental and physiological functions of the recipient cells are not disrupted. The technique should provide for the stable transfer of the nucleic acid to the cell, so that the nucleic acid is expressible by the cell and preferably heritable and expressible by its cell progeny.

[0728] The resulting recombinant cells can be delivered to a patient by various methods known in the art. Recombinant blood cells (e.g., hematopoietic stem or progenitor cells) are preferably administered intravenously. The amount of cells envisioned for use depends on the desired effect, patient state, etc., and can be determined by one skilled in the art.

[0729] Cells into which a nucleic acid can be introduced for purposes of gene therapy encompass any desired, available cell type, and include but are not limited to epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells, hepatocytes; blood cells such as Tlymphocytes, Blymphocytes, monocytes, macrophages, neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or progenitor cells, in particular hematopoietic stem or progenitor cells, e.g., as obtained from bone marrow, umbilical cord blood, peripheral blood, fetal liver, etc.

[0730] In a preferred embodiment, the cell used for gene therapy is autologous to the patient.

[0731] In an embodiment in which recombinant cells are used in gene therapy, nucleic acid sequences encoding an antibody are introduced into the cells such that they are expressible by the cells or their progeny, and the recombinant cells are then administered in vivo for therapeutic effect. In a specific embodiment, stem or progenitor cells are used. Any stem and/or progenitor cells which can be isolated and maintained in vitro can potentially be used in accordance with this embodiment of the present invention (see e.g. PCT Publication WO 94/08598; Stemple and Anderson, Cell 71:973-985 (1992); Rheinwald, Meth. Cell Bio. 21A:229 (1980); and Pittelkow and Scott, Mayo Clinic Proc. 61:771 (1986)).

[0732] In a specific embodiment, the nucleic acid to be introduced for purposes of gene therapy comprises an inducible promoter operably linked to the coding region, such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription. Demonstration of Therapeutic or Prophylactic Activity.

[0733] The compounds or pharmaceutical compositions of the invention are preferably tested in vitro, and then in vivo for the desired therapeutic or prophylactic activity, prior to use in humans. For example, in vitro assays to demonstrate the therapeutic or prophylactic utility of a compound or pharmaceutical composition include, the effect of a compound on a cell line or a patient tissue sample. The effect of the compound or composition on the cell line and/or tissue sample can be determined utilizing techniques known to those of skill in the art including, but not limited to, rosette formation assays and cell lysis assays. In accordance with the invention, in vitro assays which can be used to determine whether administration of a specific compound is indicated, include in vitro cell culture assays in which a patient tissue sample is grown in culture, and exposed to or otherwise administered a compound, and the effect of such compound upon the tissue sample is observed.

[0734] Therapeutic/Prophylactic Administration and Compositions

[0735] The invention provides methods of treatment, inhibition and prophylaxis by administration to a subject of an effective amount of a compound or pharmaceutical composition of the invention, preferably an antibody of the invention. In a preferred aspect, the compound is substantially purified (e.g., substantially free from substances that limit its effect or produce undesired side-effects). The subject is preferably an animal, including but not limited to animals such as cows, pigs, horses, chickens, cats, dogs, etc., and is preferably a mammal, and most preferably human.

[0736] Formulations and methods of administration that can be employed when the compound comprises a nucleic acid or an immunoglobulin are described above; additional appropriate formulations and routes of administration can be selected from among those described herein below.

[0737] Various delivery systems are known and can be used to administer a compound of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. . . . 262:4429-4432 (1987)), construction of a nucleic acid as part of a retroviral or other vector, etc. Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The compounds or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. In addition, it may be desirable to introduce the pharmaceutical compounds or compositions of the invention into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.

[0738] In a specific embodiment, it may be desirable to administer the pharmaceutical compounds or compositions of the invention locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. Preferably, when administering a protein, including an antibody, of the invention, care must be taken to use materials to which the protein does not absorb.

[0739] In another embodiment, the compound or composition can be delivered in a vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.)

[0740] In yet another embodiment, the compound or composition can be delivered in a controlled release system. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321:574 (1989)). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol. Chem. 23:61 (1983); see also Levy et al., Science 228:190 (1985); During et al., Ann. Neurol. 25:351 (1989); Howard et al., J. Neurosurg. 71:105 (1989)). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)).

[0741] Other controlled release systems are discussed in the review by Langer (Science 249:1527-1533 (1990)).

[0742] In a specific embodiment where the compound of the invention is a nucleic acid encoding a protein, the nucleic acid can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see U.S. Pat. No. 4,980,286), or by direct injection, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al., Proc. Natl. Acad. Sci. USA 88:1864-1868 (1991)), etc. Alternatively, a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination.

[0743] The present invention also provides pharmaceutical compositions. Such compositions comprise a therapeutically effective amount of a compound, and a pharmaceutically acceptable carrier. In a specific embodiment, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin. Such compositions will contain a therapeutically effective amount of the compound, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.

[0744] In a preferred embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.

[0745] The compounds of the invention can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.

[0746] The amount of the compound of the invention which will be effective in the treatment, inhibition and prevention of a disease or disorder associated with aberrant expression and/or activity of a polypeptide of the invention can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.

[0747] For antibodies, the dosage administered to a patient is typically 0.1 mg/kg to 100 mg/kg of the patient's body weight. Preferably, the dosage administered to a patient is between 0.1 mg/kg and 20 mg/kg of the patient's body weight, more preferably 1 mg/kg to 10 mg/kg of the patient's body weight. Generally, human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides. Thus, lower dosages of human antibodies and less frequent administration is often possible. Further, the dosage and frequency of administration of antibodies of the invention may be reduced by enhancing uptake and tissue penetration (e.g., into the brain) of the antibodies by modifications such as, for example, lipidation.

[0748] The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

[0749] Diagnosis and Imaging with Antibodies

[0750] Labeled antibodies, and derivatives and analogs thereof, which specifically bind to a polypeptide of interest can be used for diagnostic purposes to detect, diagnose, or monitor diseases, disorders, and/or conditions associated with the aberrant expression and/or activity of a polypeptide of the invention. The invention provides for the detection of aberrant expression of a polypeptide of interest, comprising (a) assaying the expression of the polypeptide of interest in cells or body fluid of an individual using one or more antibodies specific to the polypeptide interest and (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of aberrant expression.

[0751] The invention provides a diagnostic assay for diagnosing a disorder, comprising (a) assaying the, expression of the polypeptide of interest in cells or body fluid of an individual using one or more antibodies specific to the polypeptide interest and (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of a particular disorder. With respect to cancer, the presence of a relatively high amount of transcript in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.

[0752] Antibodies of the invention can be used to assay protein levels in a biological sample using classical immunohistological methods known to those of skill in the art (e.g., see Jalkanen, et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, et al., J. Cell. Biol. 105:3087-3096 (1987)). Other antibody-based methods useful for detecting protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels are known in the art and include enzyme labels, such as, glucose oxidase; radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99Tc); luminescent labels, such as luminol; and fluorescent labels, such as fluorescein and rhodamine, and biotin.

[0753] One aspect of the invention is the detection and diagnosis of a disease or disorder associated with aberrant expression of a polypeptide of interest in an animal, preferably a mammal and most preferably a human. In one embodiment, diagnosis comprises: a) administering (for example, parenterally, subcutaneously, or intraperitoneally) to a subject an effective amount of a labeled molecule which specifically binds to the polypeptide of interest; b) waiting for a time interval following the administering for permitting the labeled molecule to preferentially concentrate at sites in the subject where the polypeptide is expressed (and for unbound labeled molecule to be cleared to background level); c) determining background level; and d) detecting the labeled molecule in the subject, such that detection of labeled molecule above the background level indicates that the subject has a particular disease or disorder associated with aberrant expression of the polypeptide of interest. Background level can be determined by various methods including, comparing the amount of labeled molecule detected to a standard value previously determined for a particular system.

[0754] It will be understood in the art that the size of the subject and the imaging system used will determine the quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope moiety, for a human subject, the quantity of radioactivity injected will normally range from about 5 to 20 millicuries of 99mTc. The labeled antibody or antibody fragment will then preferentially accumulate at the location of cells which contain the specific protein. In vivo tumor imaging is described in S. W. Burchiel et al., “Immunopharmacokinetics of Radiolabeled Antibodies and Their Fragments.” (Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, S. W. Burchiel and B. A. Rhodes, eds., Masson Publishing Inc. (1982).

[0755] Depending on several variables, including the type of label used and the mode of administration, the time interval following the administration for permitting the labeled molecule to preferentially concentrate at sites in the subject and for unbound labeled molecule to be cleared to background level is 6 to 48 hours or 6 to 24 hours or 6 to 12 hours. In another embodiment the time interval following administration is 5 to 20 days or 5 to 10 days.

[0756] In an embodiment, monitoring of the disease or disorder is carried out by repeating the method for diagnosing the disease or disease, for example, one month after initial diagnosis, six months after initial diagnosis, one year after initial diagnosis, etc.

[0757] Presence of the labeled molecule can be detected in the patient using methods known in the art for in vivo scanning. These methods depend upon the type of label used. Skilled artisans will be able to determine the appropriate method for detecting a particular label. Methods and devices that may be used in the diagnostic methods of the invention include, but are not limited to, computed tomography (CT), whole body scan such as position emission tomography (PET), magnetic resonance imaging (MRI), and sonography.

[0758] In a specific embodiment, the molecule is labeled with a radioisotope and is detected in the patient using a radiation responsive surgical instrument (Thurston et al., U.S. Pat. No. 5,441,050). In another embodiment, the molecule is labeled with a fluorescent compound and is detected in the patient using a fluorescence responsive scanning instrument. In another embodiment, the molecule is labeled with a positron emitting metal and is detected in the patent using positron emission-tomography. In yet another embodiment, the molecule is labeled with a paramagnetic label and is detected in a patient using magnetic resonance imaging (MRI).

[0759] Kits

[0760] The present invention provides kits that can be used in the above methods. In one embodiment, a kit comprises an antibody of the invention, preferably a purified antibody, in one or more containers. In a specific embodiment, the kits of the present invention contain a substantially isolated polypeptide comprising an epitope which is specifically immunoreactive with an antibody included in the kit. Preferably, the kits of the present invention further comprise a control antibody which does not react with the polypeptide of interest. In another specific embodiment, the kits of the present invention contain a means for detecting the binding of an antibody to a polypeptide of interest (e.g., the antibody may be conjugated to a detectable substrate such as a fluorescent compound, an enzymatic substrate, a radioactive compound or a luminescent compound, or a second antibody which recognizes the first antibody may be conjugated to a detectable substrate).

[0761] In another specific embodiment of the present invention, the kit is a diagnostic kit for use in screening serum containing antibodies specific against proliferative and/or cancerous polynucleotides and polypeptides. Such a kit may include a control antibody that does not react with the polypeptide of interest. Such a kit may include a substantially isolated polypeptide antigen comprising an epitope which is specifically immunoreactive with at least one anti-polypeptide antigen antibody. Further, such a kit includes means for detecting the binding of said antibody to the antigen (e.g., the antibody may be conjugated to a fluorescent compound such as fluorescein or rhodamine which can be detected by flow cytometry). In specific embodiments, the kit may include a recombinantly produced or chemically synthesized polypeptide antigen. The polypeptide antigen of the kit may also be attached to a solid support.

[0762] In a more specific embodiment the detecting means of the above-described kit includes a solid support to which said polypeptide antigen is attached. Such a kit may also include a non-attached reporter-labeled anti-human antibody. In this embodiment, binding of the antibody to the polypeptide antigen can be detected by binding of the said reporter-labeled antibody.

[0763] In an additional embodiment, the invention includes a diagnostic kit for use in screening serum containing antigens of the polypeptide of the invention. The diagnostic kit includes a substantially isolated antibody specifically immunoreactive with polypeptide or polynucleotide antigens, and means for detecting the binding of the polynucleotide or polypeptide antigen to the antibody. In one embodiment, the antibody is attached to a solid support. In a specific embodiment, the antibody may be a monoclonal antibody. The detecting means of the kit may include a second, labeled monoclonal antibody. Alternatively, or in addition, the detecting means may include a labeled, competing antigen.

[0764] In one diagnostic configuration, test serum is reacted with a solid phase reagent having a surface-bound antigen obtained by the methods of the present invention. After binding with specific antigen antibody to the reagent and removing unbound serum components by washing, the reagent is reacted with reporter-labeled anti-human antibody to bind reporter to the reagent in proportion to the amount of bound anti-antigen antibody on the solid support. The reagent is again washed to remove unbound labeled antibody, and the amount of reporter associated with the reagent is determined. Typically, the reporter is an enzyme which is detected by incubating the solid phase in the presence of a suitable fluorometric, luminescent or calorimetric substrate (Sigma, St. Louis, Mo.).

[0765] The solid surface reagent in the above assay is prepared by known techniques for attaching protein material to solid support material, such as polymeric beads, dip sticks, 96-well plate or filter material. These attachment methods generally include non-specific adsorption of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activated carboxyl, hydroxyl, or aldehyde group. Alternatively, streptavidin coated plates can be used in conjunction with biotinylated antigen(s).

[0766] Thus, the invention provides an assay system or kit for carrying out this diagnostic method. The kit generally includes a support with surface-bound recombinant antigens, and a reporter-labeled anti-human antibody for detecting surface-bound anti-antigen antibody.

[0767] Fusion Proteins

[0768] Any polypeptide of the present invention can be used to generate fusion proteins. For example, the polypeptide of the present invention, when fused to a second protein, can be used as an antigenic tag. Antibodies raised against the polypeptide of the present invention can be used to indirectly detect the second protein by binding to the polypeptide. Moreover, because certain proteins target cellular locations based on trafficking signals, the polypeptides of the present invention can be used as targeting molecules once fused to other proteins.

[0769] Examples of domains that can be fused to polypeptides of the present invention include not only heterologous signal sequences, but also other heterologous functional regions. The fusion does not necessarily need to be direct, but may occur through linker sequences.

[0770] Moreover, fusion proteins may also be engineered to improve characteristics of the polypeptide of the present invention. For instance, a region of additional amino acids, particularly charged amino acids, may be added to the N-terminus of the polypeptide to improve stability and persistence during purification from the host cell or subsequent handling and storage. Peptide moieties may be added to the polypeptide to facilitate purification. Such regions may be removed prior to final preparation of the polypeptide. Similarly, peptide cleavage sites can be introduced in-between such peptide moieties, which could additionally be subjected to protease activity to remove said peptide(s) from the protein of the present invention. The addition of peptide moieties, including peptide cleavage sites, to facilitate handling of polypeptides are familiar and routine techniques in the art.

[0771] Moreover, polypeptides of the present invention, including fragments, and specifically epitopes, can be combined with parts of the constant domain of immunoglobulins (IgA, IgE, IgG, IgM) or portions thereof (CH1, CH2, CH3, and any combination thereof, including both entire domains and portions thereof), resulting in chimeric polypeptides. These fusion proteins facilitate purification and show an increased half-life in vivo. One reported example describes chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. (EP A 394,827; Traunecker et al., Nature 331:84-86 (1988).) Fusion proteins having disulfide-linked dimeric structures (due to the IgG) can also be more efficient in binding and neutralizing other molecules, than the monomeric secreted protein or protein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964 (1995).)

[0772] Similarly, EP-A-O 464 533 (Canadian counterpart 2045869) discloses fusion proteins comprising various portions of the constant region of immunoglobulin molecules together with another human protein or part thereof. In many cases, the Fe part in a fusion protein is beneficial in therapy and diagnosis, and thus can result in, for example, improved pharmacokinetic properties. (EP-A 0232 262.) Alternatively, deleting the Fe part after the fusion protein has been expressed, detected, and purified, would be desired. For example, the Fe portion may hinder therapy and diagnosis if the fusion protein is used as an antigen for immunizations. In drug discovery, for example, human proteins, such as hIL-5, have been fused with Fe portions for the purpose of high-throughput screening assays to identify antagonists of hIL-5. (See, D. Bennett et al., J. Molecular Recognition 8:52-58 (1995); K. Johanson et al., J. Biol. Chem. 270:9459-9471 (1995).)

[0773] Moreover, the polypeptides of the present invention can be fused to marker sequences (also referred to as “tags”). Due to the availability of antibodies specific to such “tags”, purification of the fused polypeptide of the invention, and/or its identification is significantly facilitated since antibodies specific to the polypeptides of the invention are not required. Such purification may be in the form of an affinity purification whereby an anti-tag antibody or another type of affinity matrix (e.g., anti-tag antibody attached to the matrix of a flow-thru column) that binds to the epitope tag is present. In preferred embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance, hexa-histidine provides for convenient purification of the fusion protein. Another peptide tag useful for purification, the “HA” tag, corresponds to an epitope derived from the influenza hemagglutinin protein. (Wilson et al., Cell 37:767 (1984)).

[0774] The skilled artisan would acknowledge the existence of other “tags” which could be readily substituted for the tags referred to supra for purification and/or identification of polypeptides of the present invention (Jones C., et al., J Chromatogr A. 707(1):3-22 (1995)). For example, the c-myc tag and the 8F9, 3C7, 6E10, G4m B7 and 9E10 antibodies thereto (Evan et al., Molecular and Cellular Biology 5:3610-3616 (1985)); the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky et al., Protein Engineering, 3(6):547-553 (1990), the Flag-peptide—i.e., the octapeptide sequence DYKDDDDK (SEQ ID NO:47), (Hopp et al., Biotech. 6:1204-1210 (1988); the KT3 epitope peptide (Martin et al., Science, 255:192-194 (1992)); a-tubulin epitope peptide (Skinner et al., J. Biol. Chem., 266:15136-15166, (1991)); the T7 gene 10 protein peptide tag (Lutz-Freyermuth et al., Proc. Natl. Sci. USA, 87:6363-6397 (1990)), the FITC epitope (Zymed, Inc.), the GFP epitope (Zymed, Inc.), and the Rhodamine epitope (Zymed, Inc.).

[0775] The present invention also encompasses the attachment of up to nine codons encoding a repeating series of up to nine arginine amino acids to the coding region of a polynucleotide of the present invention. The invention also encompasses chemically derivitizing a polypeptide of the present invention with a repeating series of up to nine arginine amino acids. Such a tag, when attached to a polypeptide, has recently been shown to serve as a universal pass, allowing compounds access to the interior of cells without additional derivitization or manipulation (Wender, P., et al., unpublished data).

[0776] Protein fusions involving polypeptides of the present invention, including fragments and/or variants thereof, can be used for the following, non-limiting examples, subcellular localization of proteins, determination of protein-protein interactions via immunoprecipitation, purification of proteins via affinity chromatography, functional and/or structural characterization of protein. The present invention also encompasses the application of hapten specific antibodies for any of the uses referenced above for epitope fusion proteins. For example, the polypeptides of the present invention could be chemically derivatized to attach hapten molecules (e.g., DNP, (Zymed, Inc.)). Due to the availability of monoclonal antibodies specific to such haptens, the protein could be readily purified using immunoprecipation, for example.

[0777] Polypeptides of the present invention, including fragments and/or variants thereof, in addition to, antibodies directed against such polypeptides, fragments, and/or variants, may be fused to any of a number of known, and yet to be determined, toxins, such as ricin, saporin (Mashiba H, et al., Ann. N.Y. Acad. Sci. 1999;886:233-5), or HC toxin (Tonukari N J, et al., Plant Cell. 2000 Feb;12(2):237-248), for example. Such fusions could be used to deliver the toxins to desired tissues for which a ligand or a protein capable of binding to the polypeptides of the invention exists.

[0778] The invention encompasses the fusion of antibodies directed against polypeptides of the present invention, including variants and fragments thereof, to said toxins for delivering the toxin to specific locations in a cell, to specific tissues, and/or to specific species. Such bifunctional antibodies are known in the art, though a review describing additional advantageous fusions, including citations for methods of production, can be found in P. J. Hudson, Curr. Opp. In. Imm. 11:548-557, (1999); this publication, in addition to the references cited therein, are hereby incorporated by reference in their entirety herein. In this context, the term “toxin” may be expanded to include any heterologous protein, a small molecule, radionucleotides, cytotoxic drugs, liposomes, adhesion molecules, glycoproteins, ligands, cell or tissue-specific ligands, enzymes, of bioactive agents, biological response modifiers, anti-fungal agents, hormones, steroids, vitamins, peptides, peptide analogs, anti-allergenic agents, anti-tubercular agents, anti-viral agents, antibiotics, anti-protozoan agents, chelates, radioactive particles, radioactive ions, X-ray contrast agents, monoclonal antibodies, polyclonal antibodies and genetic material. In view of the present disclosure, one skilled in the art could determine whether any particular “toxin” could be used in the compounds of the present invention. Examples of suitable “toxins” listed above are exemplary only and are not intended to limit the “toxins” that may be used in the present invention.

[0779] Thus, any of these above fusions can be engineered using the polynucleotides or the polypeptides of the present invention.

[0780] Vectors, Host Cells, and Protein Production

[0781] The present invention also relates to vectors containing the polynucleotide of the present invention, host cells, and the production of polypeptides by recombinant techniques. The vector may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.

[0782] The polynucleotides may be joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.

[0783] The polynucleotide insert should be operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and tac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.

[0784] As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase, G418 or neomycin resistance for eukaryotic cell culture and tetracycline, kanamycin or ampicillin resistance genes for culturing in E. coli and other bacteria. Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and conditions for the above-described host cells are known in the art.

[0785] Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE9, available from QIAGEN, Inc; pBluescript vectors, Phagescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available from Stratagene Cloning Systems, Inc; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Preferred expression vectors for use in yeast systems include, but are not limited to pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalph, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, pPIC9K, and PA0815 (all available from Invitrogen, Carlsbad, Calif.). Other suitable vectors will be readily apparent to the skilled artisan.

[0786] Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides of the present invention may in fact be expressed by a host cell lacking a recombinant vector.

[0787] A polypeptide of this invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography (“HPLC”) is employed for purification.

[0788] Polypeptides of the present invention, and preferably the secreted form, can also be recovered from: products purified from natural sources, including bodily fluids, tissues and cells, whether directly isolated or cultured; products of chemical synthetic procedures; and products produced by recombinant techniques from a prokaryotic or eukaryotic host, including, for example, bacterial, yeast, higher plant, insect, and mammalian cells. Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. In addition, polypeptides of the invention may also include an initial modified methionine residue, in some cases as a result of host-mediated processes. Thus, it is well known in the art that the N-terminal methionine encoded by the translation initiation codon generally is removed with high efficiency from any protein after translation in all eukaryotic cells. While the N-terminal methionine on most proteins also is efficiently removed in most prokaryotes, for some proteins, this prokaryotic removal process is inefficient, depending on the nature of the amino acid to which the N-terminal methionine is covalently linked.

[0789] In one embodiment, the yeast Pichia pastoris is used to express the polypeptide of the present invention in a eukaryotic system. Pichia pastoris is a methylotrophic yeast which can metabolize methanol as its sole carbon source. A main step in the methanol metabolization pathway is the oxidation of methanol to formaldehyde using O2. This reaction is catalyzed by the enzyme alcohol oxidase. In order to metabolize methanol as its sole carbon source, Pichia pastoris must generate high levels of alcohol oxidase due, in part, to the relatively low affinity of alcohol oxidase for O2. Consequently, in a growth medium depending on methanol as a main carbon source, the promoter region of one of the two alcohol oxidase genes (AOX1) is highly active. In the presence of methanol, alcohol oxidase produced from the AOX1 gene comprises up to approximately 30% of the total soluble protein in Pichia pastoris. See, Ellis, S. B., et al., Mol. Cell. Biol. 5:1111-21 (1985); Koutz, P. J, et al., Yeast 5:167-77 (1989); Tschopp, J. F., et al., Nucl. Acids Res. 15:3859-76 (1987). Thus, a heterologous coding sequence, such as, for example, a polynucleotide of the present invention, under the transcriptional regulation of all or part of the AOX1 regulatory sequence is expressed at exceptionally high levels in Pichia yeast grown in the presence of methanol.

[0790] In one example, the plasmid vector pPIC9K is used to express DNA encoding a polypeptide of the invention, as set forth herein, in a Pichea yeast system essentially as described in “Pichia Protocols: Methods in Molecular Biology,” D. R. Higgins and J. Cregg, eds. The Humana Press, Totowa, N.J., 1998. This expression vector allows expression and secretion of a protein of the invention by virtue of the strong AOX1 promoter linked to the Pichia pastoris alkaline phosphatase (PHO) secretory signal peptide (i.e., leader) located upstream of a multiple cloning site.

[0791] Many other yeast vectors could be used in place of pPIC9K, such as, pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalpha, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, and PAO815, as one skilled in the art would readily appreciate, as long as the proposed expression construct provides appropriately located signals for transcription, translation, secretion (if desired), and the like, including an in-frame AUG, as required.

[0792] In another embodiment, high-level expression of a heterologous coding sequence, such as, for example, a polynucleotide of the present invention, may be achieved by cloning the heterologous polynucleotide of the invention into an expression vector such as, for example, pGAPZ or pGAPZalpha, and growing the yeast culture in the absence of methanol.

[0793] In addition to encompassing host cells containing the vector constructs discussed herein, the invention also encompasses primary, secondary, and immortalized host cells of vertebrate origin, particularly mammalian origin, that have been engineered to delete or replace endogenous genetic material (e.g., coding sequence), and/or to include genetic material (e.g., heterologous polynucleotide sequences) that is operably associated with the polynucleotides of the invention, and which activates, alters, and/or amplifies endogenous polynucleotides. For example, techniques known in the art may be used to operably associate heterologous control regions (e.g., promoter and/or enhancer) and endogenous polynucleotide sequences via homologous recombination, resulting in the formation of a new transcription unit (see, e.g., U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; U.S. Pat. No. 5,733,761, issued Mar. 31, 1998; International Publication No. WO 96/29411, published Sep. 26, 1996; International Publication No. WO 94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al., Nature 342:435-438 (1989), the disclosures of each of which are incorporated by reference in their entireties).

[0794] In addition, polypeptides of the invention can be chemically synthesized using techniques known in the art (e.g., see Creighton, 1983, Proteins: Structures and Molecular Principles, W.H. Freeman & Co., N.Y., and Hunkapiller et al., Nature, 310:105-111 (1984)). For example, a polypeptide corresponding to a fragment of a polypeptide sequence of the invention can be synthesized by use of a peptide synthesizer. Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the polypeptide sequence. Non-classical amino acids include, but are not limited to, to the D-isomers of the common amino acids, 2,4-diaminobutyric acid, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, b-alanine, fluoro-amino acids, designer amino acids such as b-methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).

[0795] The invention encompasses polypeptides which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc. Any of numerous chemical modifications may be carried out by known techniques, including but not limited, to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4; acetylation, formylation, oxidation, reduction; metabolic synthesis in the presence of tunicamycin; etc.

[0796] Additional post-translational modifications encompassed by the invention include, for example, e.g., N-linked or O-linked carbohydrate chains, processing of N-terminal or C-terminal ends), attachment of chemical moieties to the amino acid backbone, chemical modifications of N-linked or O-linked carbohydrate chains, and addition or deletion of an N-terminal methionine residue as a result of prokaryotic host cell expression. The polypeptides may also be modified with a detectable label, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the protein, the addition of epitope tagged peptide fragments (e.g., FLAG, HA, GST, thioredoxin, maltose binding protein, etc.), attachment of affinity tags such as biotin and/or streptavidin, the covalent attachment of chemical moieties to the amino acid backbone, N- or C-terminal processing of the polypeptides ends (e.g., proteolytic processing), deletion of the N-terminal methionine residue, etc.

[0797] Also provided by the invention are chemically modified derivatives of the polypeptides of the invention which may provide additional advantages such as increased solubility, stability and circulating time of the polypeptide, or decreased immunogenicity (see U.S. Pat. No. 4,179,337). The chemical moieties for derivitization may be selected from water soluble polymers such as polyethylene glycol, ethylene glycol/propylene glycol copolymers, carboxymethylcellulose, dextran, polyinyl alcohol and the like. The polypeptides may be modified at random positions within the molecule, or at predetermined positions within the molecule and may include one, two, three or more attached chemical moieties.

[0798] The invention further encompasses chemical derivitization of the polypeptides of the present invention, preferably where the chemical is a hydrophilic polymer residue. Exemplary hydrophilic polymers, including derivatives, may be those that include polymers in which the repeating units contain one or more hydroxy groups (polyhydroxy polymers), including, for example, poly(vinyl alcohol); polymers in which the repeating units contain one or more amino groups (polyamine polymers), including, for example, peptides, polypeptides, proteins and lipoproteins, such as albumin and natural lipoproteins; polymers in which the repeating units contain one or more carboxy groups (polycarboxy polymers), including, for example, carboxymethylcellulose, alginic acid and salts thereof, such as sodium and calcium alginate, glycosaminoglycans and salts thereof, including salts of hyaluronic acid, phosphorylated and sulfonated derivatives of carbohydrates, genetic material, such as interleukin-2 and interferon, and phosphorothioate oligomers; and polymers in which the repeating units contain one or more saccharide moieties (polysaccharide polymers), including, for example, carbohydrates.

[0799] The molecular weight of the hydrophilic polymers may vary, and is generally about 50 to about 5,000,000, with polymers having a molecular weight of about 100 to about 50,000 being preferred. The polymers may be branched or unbranched. More preferred polymers have a molecular weight of about 150 to about 10,000, with molecular weights of 200 to about 8,000 being even more preferred.

[0800] For polyethylene glycol, the preferred molecular weight is between about 1 kDa and about 100 kDa (the term “about” indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight) for ease in handling and manufacturing. Other sizes may be used, depending on the desired therapeutic profile (e.g., the duration of sustained release desired, the effects, if any on biological activity, the ease in handling, the degree or lack of antigenicity and other known effects of the polyethylene glycol to a therapeutic protein or analog).

[0801] Additional preferred polymers which may be used to derivatize polypeptides of the invention, include, for example, poly(ethylene glycol) (PEG), poly(vinylpyrrolidine), polyoxomers, polysorbate and poly(vinyl alcohol), with PEG polymers being particularly preferred. Preferred among the PEG polymers are PEG polymers having a molecular weight of from about 100 to about 10,000. More preferably, the PEG polymers have a molecular weight of from about 200 to about 8,000, with PEG 2,000, PEG 5,000 and PEG 8,000, which have molecular weights of 2,000, 5,000 and 8,000, respectively, being even more preferred. Other suitable hydrophilic polymers, in addition to those exemplified above, will be readily apparent to one skilled in the art based on the present disclosure. Generally, the polymers used may include polymers that can be attached to the polypeptides of the invention via alkylation or acylation reactions.

[0802] The polyethylene glycol molecules (or other chemical moieties) should be attached to the protein with consideration of effects on functional or antigenic domains of the protein. There are a number of attachment methods available to those skilled in the art, e.g., EP 0 401 384, herein incorporated by reference (coupling PEG to G-CSF), see also Malik et al., Exp. Hematol. 20:1028-1035 (1992) (reporting pegylation of GM-CSF using tresyl chloride). For example, polyethylene glycol may be covalently bound through amino acid residues via a reactive group, such as, a free amino or carboxyl group. Reactive groups are those to which an activated polyethylene glycol molecule may be bound. The amino acid residues having a free amino group may include lysine residues and the N-terminal amino acid residues; those having a free carboxyl group may include aspartle acid residues glutamic acid residues and the C-terminal amino acid residue. Sulfhydryl groups may also be used as a reactive group for attaching the polyethylene glycol molecules. Preferred for therapeutic purposes is attachment at an amino group, such as attachment at the N-terminus or lysine group.

[0803] One may specifically desire proteins chemically modified at the N-terminus. Using polyethylene glycol as an illustration of the present composition, one may select from a variety of polyethylene glycol molecules (by molecular weight, branching, etc.), the proportion of polyethylene glycol molecules to protein (polypeptide) molecules in the reaction mix, the type of pegylation reaction to be performed, and the method of obtaining the selected N-terminally pegylated protein. The method of obtaining the N-terminally pegylated preparation (i.e., separating this moiety from other monopegylated moieties if necessary) may be by purification of the N-terminally pegylated material from a population of pegylated protein molecules. Selective proteins chemically modified at the N-terminus modification may be accomplished by reductive alkylation which exploits differential reactivity of different types of primary amino groups (lysine versus the N-terminus) available for derivatization in a particular protein. Under the appropriate reaction conditions, substantially selective derivatization of the protein at the N-terminus with a carbonyl group containing polymer is achieved.

[0804] As with the various polymers exemplified above, it is contemplated that the polymeric residues may contain functional groups in addition, for example, to those typically involved in linking the polymeric residues to the polypeptides of the present invention. Such functionalities include, for example, carboxyl, amine, hydroxy and thiol groups. These functional groups on the polymeric residues can be further reacted, if desired, with materials that are generally reactive with such functional groups and which can assist in targeting specific tissues in the body including, for example, diseased tissue. Exemplary materials which can be reacted with the additional functional groups include, for example, proteins, including antibodies, carbohydrates, peptides, glycopeptides, glycolipids, lectins, and nucleosides.

[0805] In addition to residues of hydrophilic polymers, the chemical used to derivative the polypeptides of the present invention can be a saccharide residue. Exemplary saccharides which can be derived include, for example, monosaccharides or sugar alcohols, such as erythrose, threose, ribose, arabinose, xylose, lyxose, fructose, sorbitol, mannitol and sedoheptulose, with preferred monosaccharides being fructose, mannose, xylose, arabinose, mannitol and sorbitol; and disaccharides, such as lactose, sucrose, maltose and cellobiose. Other saccharides include, for example, inositol and ganglioside head groups. Other suitable saccharides, in addition to those exemplified above, will be readily apparent to one skilled in the art based on the present disclosure. Generally, saccharides which may be used for derivitization include saccharides that can be attached to the polypeptides of the invention via alkylation or acylation reactions.

[0806] Moreover, the invention also encompasses derivitization of the polypeptides of the present invention, for example, with lipids (including cationic, anionic, polymerized, charged, synthetic, saturated, unsaturated, and any combination of the above, etc.). stabilizing agents.

[0807] The invention encompasses derivitization of the polypeptides of the present invention, for example, with compounds that may serve a stabilizing function (e.g., to increase the polypeptides half-life in solution, to make the polypeptides more water soluble, to increase the polypeptides hydrophilic or hydrophobic character, etc.). Polymers useful as stabilizing materials may be of natural, semi-synthetic (modified natural) or synthetic origin. Exemplary natural polymers include naturally occurring polysaccharides, such as, for example, arabinans, fructans, fucans, galactans, galacturonans, glucans, mannans, xylans (such as, for example, inulin), levan, fucoidan, carrageenan, galatocarolose, pectic acid, pectins, including amylose, pullulan, glycogen, amylopectin, cellulose, dextran, dextrin, dextrose, glucose, polyglucose, polydextrose, pustulan, chitin, agarose, keratin, chondroitin, dermatan, hyaluronic acid, alginic acid, xanthin gum, starch and various other natural homopolymer or heteropolymers, such as those containing one or more of the following aldoses, ketoses, acids or amines: erythose, threose, ribose, arabinose, xylose, lyxose, allose, altrose, glucose, dextrose, mannose, gulose, idose, galactose, talose, erythrulose, ribulose, xylulose, psicose, fructose, sorbose, tagatose, mannitol, sorbitol, lactose, sucrose, trehalose, maltose, cellobiose, glycine, serine, threonine, cysteine, tyrosine, asparagine, glutamine, aspartic acid, glutamic acid, lysine, arginine, histidine, glucuronic acid, gluconic acid, glucaric acid, galacturonic acid, mannuronic acid, glucosamine, galactosamine, and neuraminic acid, and naturally occurring derivatives thereof Accordingly, suitable polymers include, for example, proteins, such as albumin, polyalginates, and polylactide-coglycolide polymers. Exemplary semi-synthetic polymers include carboxymethylcellulose, hydroxymethylcellulose, hydroxypropylmethylcellulose, methylcellulose, and methoxycellulose. Exemplary synthetic polymers include polyphosphazenes, hydroxyapatites, fluoroapatite polymers, polyethylenes (such as, for example, polyethylene glycol (including for example, the class of compounds referred to as Pluronics.RTM., commercially available from BASF, Parsippany, N.J.), polyoxyethylene, and polyethylene terephthlate), polypropylenes (such as, for example, polypropylene glycol), polyurethanes (such as, for example, polyinyl alcohol (PVA), polyinyl chloride and polyinylpyrrolidone), polyamides including nylon, polystyrene, polylactic acids, fluorinated hydrocarbon polymers, fluorinated carbon polymers (such as, for example, polytetrafluoroethylene), acrylate, methacrylate, and polymethylmethacrylate, and derivatives thereof. Methods for the preparation of derivatized polypeptides of the invention which employ polymers as stabilizing compounds will be readily apparent to one skilled in the art, in view of the present disclosure, when coupled with information known in the art, such as that described and referred to in Unger, U.S. Pat. No. 5,205,290, the disclosure of which is hereby incorporated by reference herein in its entirety.

[0808] Moreover, the invention encompasses additional modifications of the polypeptides of the present invention. Such additional modifications are known in the art, and are specifically provided, in addition to methods of derivitization, etc., in U.S. Pat. No. 6,028,066, which is hereby incorporated in its entirety herein.

[0809] The polypeptides of the invention may be in monomers or multimers (i.e., dimers, trimers, tetramers and higher multimers). Accordingly, the present invention relates to monomers and multimers of the polypeptides of the invention, their preparation, and compositions (preferably, Therapeutics) containing them. In specific embodiments, the polypeptides of the invention are monomers, dimers, trimers or tetramers. In additional embodiments, the multimers of the invention are at least dimers, at least trimers, or at least tetramers.

[0810] Multimers encompassed by the invention may be homomers or heteromers. As used herein, the term homomer, refers to a multimer containing only polypeptides corresponding to the amino acid sequence of SEQ ID NO:2, 24, 54, and/or 56 or encoded by the cDNA contained in a deposited clone (including fragments, variants, splice variants, and fusion proteins, corresponding to these polypeptides as described herein). These homomers may contain polypeptides having identical or different amino acid sequences. In a specific embodiment, a homomer of the invention is a multimer containing only polypeptides having an identical amino acid sequence. In another specific embodiment, a homomer of the invention is a multimer containing polypeptides having different amino acid sequences. In specific embodiments, the multimer of the invention is a homodimer (e.g., containing polypeptides having identical or different amino acid sequences) or a homotrimer (e.g., containing polypeptides having identical and/or different amino acid sequences). In additional embodiments, the homomeric multimer of the invention is at least a homodimer, at least a homotrimer, or at least a homotetramer.

[0811] As used herein, the term heteromer refers to a multimer containing one or more heterologous polypeptides (i.e., polypeptides of different proteins) in addition to the polypeptides of the invention. In a specific embodiment, the multimer of the invention is a heterodimer, a heterotrimer, or a heterotetramer. In additional embodiments, the heteromeric multimer of the invention is at least a heterodimer, at least a heterotrimer, or at least a heterotetramer.

[0812] Multimers of the invention may be the result of hydrophobic, hydrophilic, ionic and/or covalent associations and/or may be indirectly linked, by for example, liposome formation. Thus, in one embodiment, multimers of the invention, such as, for example, homodimers or homotrimers, are formed when polypeptides of the invention contact one another in solution. In another embodiment, heteromultimers of the invention, such as, for example, heterotrimers or heterotetramers, are formed when polypeptides of the invention contact antibodies to the polypeptides of the invention (including antibodies to the heterologous polypeptide sequence in a fusion protein of the invention) in solution. In other embodiments, multimers of the invention are formed by covalent associations with and/or between the polypeptides of the invention. Such covalent associations may involve one or more amino acid residues contained in the polypeptide sequence (e.g., that recited in the sequence listing, or contained in the polypeptide encoded by a deposited clone). In one instance, the covalent associations are cross-linking between cysteine residues located within the polypeptide sequences which interact in the native (i.e., naturally occurring) polypeptide. In another instance, the covalent associations are the consequence of chemical or recombinant manipulation. Alternatively, such covalent associations may involve one or more amino acid residues contained in the heterologous polypeptide sequence in a fusion protein of the invention.

[0813] In one example, covalent associations are between the heterologous sequence contained in a fusion protein of the invention (see, e.g., U.S. Pat. No. 5,478,925). In a specific example, the covalent associations are between the heterologous sequence contained in an Fe fusion protein of the invention (as described herein). In another specific example, covalent associations of fusion proteins of the invention are between heterologous polypeptide sequence from another protein that is capable of forming covalently associated multimers, such as for example, osteoprotegerin (see, e.g., International Publication NO: WO 98/49305, the contents of which are herein incorporated by reference in its entirety). In another embodiment, two or more polypeptides of the invention are joined through peptide linkers. Examples include those peptide linkers described in U.S. Pat. No. 5,073,627 (hereby incorporated by reference). Proteins comprising multiple polypeptides of the invention separated by peptide linkers may be produced using conventional recombinant DNA technology.

[0814] Another method for preparing multimer polypeptides of the invention involves use of polypeptides of the invention fused to a leucine zipper or isoleucine zipper polypeptide sequence. Leucine zipper and isoleucine zipper domains are polypeptides that promote multimerization of the proteins in which they are found. Leucine zippers were originally identified in several DNA-binding proteins (Landschulz et al., Science 240:1759, (1988)), and have since been found in a variety of different proteins. Among the known leucine zippers are naturally occurring peptides and derivatives thereof that dimerize or trimerize. Examples of leucine zipper domains suitable for producing soluble multimeric proteins of the invention are those described in PCT application WO 94/10308, hereby incorporated by reference. Recombinant fusion proteins comprising a polypeptide of the invention fused to a polypeptide sequence that dimerizes or trimerizes in solution are expressed in suitable host cells, and the resulting soluble multimeric fusion protein is recovered from the culture supernatant using techniques known in the art.

[0815] Trimeric polypeptides of the invention may offer the advantage of enhanced biological activity. Preferred leucine zipper moieties and isoleucine moieties are those that preferentially form trimers. One example is a leucine zipper derived from lung surfactant protein D (SPD), as described in Hoppe et al. (FEBS Letters 344:191, (1994)) and in U.S. patent application Ser. No. 08/446,922, hereby incorporated by reference. Other peptides derived from naturally occurring trimeric proteins may be employed in preparing trimeric polypeptides of the invention.

[0816] In another example, proteins of the invention are associated by interactions between Flag® polypeptide sequence contained in fusion proteins of the invention containing Flag® polypeptide sequence. In a further embodiment, associations proteins of the invention are associated by interactions between heterologous polypeptide sequence contained in Flag® fusion proteins of the invention and anti-Flag® antibody.

[0817] The multimers of the invention may be generated using chemical techniques known in the art. For example, polypeptides desired to be contained in the multimers of the invention may be chemically cross-linked using linker molecules and linker molecule length optimization techniques known in the art (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Additionally, multimers of the invention may be generated using techniques known in the art to form one or more inter-molecule cross-links between the cysteine residues located within the sequence of the polypeptides desired to be contained in the multimer (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Further, polypeptides of the invention may be routinely modified by the addition of cysteine or biotin to the C terminus or N-terminus of the polypeptide and techniques known in the art may be applied to generate multimers containing one or more of these modified polypeptides (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Additionally, techniques known in the art may be applied to generate liposomes containing the polypeptide components desired to be contained in the multimer of the invention (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety).

[0818] Alternatively, multimers of the invention may be generated using genetic engineering techniques known in the art. In one embodiment, polypeptides contained in multimers of the invention are produced recombinantly using fusion protein technology described herein or otherwise known in the art (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). In a specific embodiment, polynucleotides coding for a homodimer of the invention are generated by ligating a polynucleotide sequence encoding a polypeptide of the invention to a sequence encoding a linker polypeptide and then further to a synthetic polynucleotide encoding the translated product of the polypeptide in the reverse orientation from the original C-terminus to the N-terminus (lacking the leader sequence) (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). In another embodiment, recombinant techniques described herein or otherwise known in the art are applied to generate recombinant polypeptides of the invention which contain a transmembrane domain (or hydrophobic or signal peptide) and which can be incorporated by membrane reconstitution techniques into liposomes (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety).

[0819] In addition, the polynucleotide insert of the present invention could be operatively linked to “artificial” or chimeric promoters and transcription factors. Specifically, the artificial promoter could comprise, or alternatively consist, of any combination of cis-acting DNA sequence elements that are recognized by trans-acting transcription factors. Preferably, the cis acting DNA sequence elements and trans-acting transcription factors are operable in mammals. Further, the trans-acting transcription factors of such “artificial” promoters could also be “artificial” or chimeric in design themselves and could act as activators or repressors to said “artificial” promoter.

[0820] Uses of the Polynucleotides

[0821] Each of the polynucleotides identified herein can be used in numerous ways as reagents. The following description should be considered exemplary and utilizes known techniques.

[0822] The polynucleotides of the present invention are useful for chromosome identification. There exists an ongoing need to identify new chromosome markers, since few chromosome marking reagents, based on actual sequence data (repeat polymorphisms), are presently available. Each polynucleotide of the present invention can be used as a chromosome marker.

[0823] Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp) from the sequences shown in SEQ ID NO:1, 23, 53, and/or 55. Primers can be selected using computer analysis so that primers do not span more than one predicted exon in the genomic DNA. These primers are then used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the SEQ ID NO:1, 23, 53, and/or 55 will yield an amplified fragment.

[0824] Similarly, somatic hybrids provide a rapid method of PCR mapping the polynucleotides to particular chromosomes. Three or more clones can be assigned per day using a single thermal cycler. Moreover, sublocalization of the polynucleotides can be achieved with panels of specific chromosome fragments. Other gene mapping strategies that can be used include in situ hybridization, prescreening with labeled flow-sorted chromosomes, and preselection by hybridization to construct chromosome specific-cDNA libraries.

[0825] Precise chromosomal location of the polynucleotides can also be achieved using fluorescence in situ hybridization (FISH) of a metaphase chromosomal spread. This technique uses polynucleotides as short as 500 or 600 bases; however, polynucleotides 2,000-4,000 bp are preferred. For a review of this technique, see Verma et al., “Human Chromosomes: a Manual of Basic Techniques,” Pergamon Press, New York (1988).

[0826] For chromosome mapping, the polynucleotides can be used individually (to mark a single chromosome or a single site on that chromosome) or in panels (for marking multiple sites and/or multiple chromosomes). Preferred polynucleotides correspond to the noncoding regions of the cDNAs because the coding sequences are more likely conserved within gene families, thus increasing the chance of cross hybridization during chromosomal mapping.

[0827] Once a polynucleotide has been mapped to a precise chromosomal location, the physical position of the polynucleotide can be used in linkage analysis. Linkage analysis establishes coinheritance between a chromosomal location and presentation of a particular disease. Disease mapping data are known in the art. Assuming 1 megabase mapping resolution and one gene per 20 kb, a cDNA precisely localized to a chromosomal region associated with the disease could be one of 50-500 potential causative genes.

[0828] Thus, once coinheritance is established, differences in the polynucleotide and the corresponding gene between affected and unaffected organisms can be examined. First, visible structural alterations in the chromosomes, such as deletions or translocations, are examined in chromosome spreads or by PCR. If no structural alterations exist, the presence of point mutations are ascertained. Mutations observed in some or all affected organisms, but not in normal organisms, indicates that the mutation may cause the disease. However, complete sequencing of the polypeptide and the corresponding gene from several normal organisms is required to distinguish the mutation from a polymorphism. If a new polymorphism is identified, this polymorphic polypeptide can be used for further linkage analysis.

[0829] Furthermore, increased or decreased expression of the gene in affected organisms as compared to unaffected organisms can be assessed using polynucleotides of the present invention. Any of these alterations (altered expression, chromosomal rearrangement, or mutation) can be used as a diagnostic or prognostic marker.

[0830] Thus, the invention also provides a diagnostic method useful during diagnosis of a disorder, involving measuring the expression level of polynucleotides of the present invention in cells or body fluid from an organism and comparing the measured gene expression level with a standard level of polynucleotide expression level, whereby an increase or decrease in the gene expression level compared to the standard is indicative of a disorder.

[0831] By “measuring the expression level of a polynucleotide of the present invention” is intended qualitatively or quantitatively measuring or estimating the level of the polypeptide of the present invention or the level of the mRNA encoding the polypeptide in a first biological sample either directly (e.g., by determining or estimating absolute protein level or mRNA level) or relatively (e.g., by comparing to the polypeptide level or mRNA level in a second biological sample). Preferably, the polypeptide level or mRNA level in the first biological sample is measured or estimated and compared to a standard polypeptide level or mRNA level, the standard being taken from a second biological sample obtained from an individual not having the disorder or being determined by averaging levels from a population of organisms not having a disorder. As will be appreciated in the art, once a standard polypeptide level or mRNA level is known, it can be used repeatedly as a standard for comparison.

[0832] By “biological sample” is intended any biological sample obtained from an organism, body fluids, cell line, tissue culture, or other source which contains the polypeptide of the present invention or mRNA. As indicated, biological samples include body fluids (such as the following non-limiting examples, sputum, amniotic fluid, urine, saliva, breast milk, secretions, interstitial fluid, blood, serum, spinal fluid, etc.) which contain the polypeptide of the present invention, and other tissue sources found to express the polypeptide of the present invention. Methods for obtaining tissue biopsies and body fluids from organisms are well known in the art. Where the biological sample is to include mRNA, a tissue biopsy is the preferred source.

[0833] The method(s) provided above may Preferably be applied in a diagnostic method and/or kits in which polynucleotides and/or polypeptides are attached to a solid support. In one exemplary method, the support may be a “gene chip” or a “biological chip” as described in U.S. Pat. Nos. 5,837,832, 5,874,219, and 5,856,174. Further, such a gene chip with polynucleotides of the present invention attached may be used to identify polymorphisms between the polynucleotide sequences, with polynucleotides isolated from a test subject. The knowledge of such polymorphisms (i.e. their location, as well as, their existence) would be beneficial in identifying disease loci for many disorders, including proliferative diseases and conditions. Such a method is described in U.S. Pat. Nos. 5,858,659 and 5,856,104. The US Patents referenced supra are hereby incorporated by reference in their entirety herein.

[0834] The present invention encompasses polynucleotides of the present invention that are chemically synthesized, or reproduced as peptide nucleic acids (PNA), or according to other methods known in the art. The use of PNAs would serve as the preferred form if the polynucleotides are incorporated onto a solid support, or gene chip. For the purposes of the present invention, a peptide nucleic acid (PNA) is a polyamide type of DNA analog and the monomeric units for adenine, guanine, thymine and cytosine are available commercially (Perceptive Biosystems). Certain components of DNA, such as phosphorus, phosphorus oxides, or deoxyribose derivatives, are not present in PNAs. As disclosed by P. E. Nielsen, M. Egholm, R. H. Berg and O. Buchardt, Science 254, 1497 (1991); and M. Egholm, O. Buchardt, L. Christensen, C. Behrens, S. M. Freier, D. A. Driver, R. H. Berg, S. K. Kim, B. Norden, and P. E. Nielsen, Nature 365, 666 (1993), PNAs bind specifically and tightly to complementary DNA strands and are not degraded by nucleases. In fact, PNA binds more strongly to DNA than DNA itself does. This is probably because there is no electrostatic repulsion between the two strands, and also the polyamide backbone is more flexible. Because of this, PNA/DNA duplexes bind under a wider range of stringency conditions than DNA/DNA duplexes, making it easier to perform multiplex hybridization. Smaller probes can be used than with DNA due to the stronger binding characteristics of PNA:DNA hybrids. In addition, it is more likely that single base mismatches can be determined with PNA/DNA hybridization because a single mismatch in a PNA/DNA 15-mer lowers the melting point (T.sub.m) by 8°-20° C., vs. 4°-16° C. for the DNA/DNA 15-mer duplex. Also, the absence of charge groups in PNA means that hybridization can be done at low ionic strengths and reduce possible interference by salt during the analysis.

[0835] In addition to the foregoing, a polynucleotide can be used to control gene expression through triple helix formation or antisense DNA or RNA. Antisense techniques are discussed, for example, in Okano, J. Neurochem. 56: 560 (1991); “Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple helix formation is discussed in, for instance Lee et al., Nucleic Acids Research 6: 3073 (1979); Cooney et al., Science 241: 456 (1988); and Dervan et al., Science 251: 1360 (1991). Both methods rely on binding of the polynucleotide to a complementary DNA or RNA. For these techniques, preferred polynucleotides are usually oligonucleotides 20 to 40 bases in length and complementary to either the region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxy-nucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988).) Triple helix formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques are effective in model systems, and the information disclosed herein can be used to design antisense or triple helix polynucleotides in an effort to treat or prevent disease.

[0836] The present invention encompasses the addition of a nuclear localization signal, operably linked to the 5′ end, 3′ end, or any location therein, to any of the oligonucleotides, antisense oligonucleotides, triple helix oligonucleotides, ribozymes, PNA oligonucleotides, and/or polynucleotides, of the present invention. See, for example, G. Cutrona, et al., Nat. Biotech., 18:300-303, (2000); which is hereby incorporated herein by reference.

[0837] Polynucleotides of the present invention are also useful in gene therapy. One goal of gene therapy is to insert a normal gene into an organism having a defective gene, in an effort to correct the genetic defect. The polynucleotides disclosed in the present invention offer a means of targeting such genetic defects in a highly accurate manner. Another goal is to insert a new gene that was not present in the host genome, thereby producing a new trait in the host cell. In one example, polynucleotide sequences of the present invention may be used to construct chimeric RNA/DNA oligonucleotides corresponding to said sequences, specifically designed to induce host cell mismatch repair mechanisms in an organism upon systemic injection, for example (Bartlett, R. J., et al., Nat. Biotech, 18:615-622 (2000), which is hereby incorporated by reference herein in its entirety). Such RNA/DNA oligonucleotides could be designed to correct genetic defects in certain host strains, and/or to introduce desired phenotypes in the host (e.g., introduction of a specific polymorphism within an endogenous gene corresponding to a polynucleotide of the present invention that may ameliorate and/or prevent a disease symptom and/or disorder, etc.). Alternatively, the polynucleotide sequence of the present invention may be used to construct duplex oligonucleotides corresponding to said sequence, specifically designed to correct genetic defects in certain host strains, and/or to introduce desired phenotypes into the host (e.g., introduction of a specific polymorphism within an endogenous gene corresponding to a polynucleotide of the present invention that may ameliorate and/or prevent a disease symptom and/or disorder, etc). Such methods of using duplex oligonucleotides are known in the art and are encompassed by the present invention (see EP1007712, which is hereby incorporated by reference herein in its entirety).

[0838] The polynucleotides are also useful for identifying organisms from minute biological samples. The United States military, for example, is considering the use of restriction fragment length polymorphism (RFLP) for identification of its personnel. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identifying personnel. This method does not suffer from the current limitations of “Dog Tags” which can be lost, switched, or stolen, making positive identification difficult. The polynucleotides of the present invention can be used as additional DNA markers for RFLP.

[0839] The polynucleotides of the present invention can also be used as an alternative to RFLP, by determining the actual base-by-base DNA sequence of selected portions of an organisms genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, organisms can be identified because each organism will have a unique set of DNA sequences. Once an unique ID database is established for an organism, positive identification of that organism, living or dead, can be made from extremely small tissue samples. Similarly, polynucleotides of the present invention can be used as polymorphic markers, in addition to, the identification of transformed or non-transformed cells and/or tissues.

[0840] There is also a need for reagents capable of identifying the source of a particular tissue. Such need arises, for example, when presented with tissue of unknown origin. Appropriate reagents can comprise, for example, DNA probes or primers specific to particular tissue prepared from the sequences of the present invention. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination. Moreover, as mentioned above, such reagents can be used to screen and/or identify transformed and non-transformed cells and/or tissues.

[0841] In the very least, the polynucleotides of the present invention can be used as molecular weight markers on Southern gels, as diagnostic probes for the presence of a specific mRNA in a particular cell type, as a probe to “subtract-out” known sequences in the process of discovering novel polynucleotides, for selecting and making oligomers for attachment to a “gene chip” or other support, to raise anti-DNA antibodies using DNA immunization techniques, and as an antigen to elicit an immune response.

[0842] Uses of the Polypeptides

[0843] Each of the polypeptides identified herein can be used in numerous ways. The following description should be considered exemplary and utilizes known techniques.

[0844] A polypeptide of the present invention can be used to assay protein levels in a biological sample using antibody-based techniques. For example, protein expression in tissues can be studied with classical immunohistological methods. (Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096 (1987).) Other antibody-based methods useful for detecting protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels are known in the art and include enzyme labels, such as, glucose oxidase, and radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99mTc), and fluorescent labels, such as fluorescein and rhodamine, and biotin.

[0845] In addition to assaying protein levels in a biological sample, proteins can also be detected in vivo by imaging. Antibody labels or markers for in vivo imaging of protein include those detectable by X-radiography, NMR or ESR. For X-radiography, suitable labels include radioisotopes such as barium or cesium, which emit detectable radiation but are not overtly harmful to the subject. Suitable markers for NMR and ESR include those with a detectable characteristic spin, such as deuterium, which may be incorporated into the antibody by labeling of nutrients for the relevant hybridoma.

[0846] A protein-specific antibody or antibody fragment which has been labeled with an appropriate detectable imaging moiety, such as a radioisotope (for example, 131I, 112In, 99mTc), a radio-opaque substance, or a material detectable by nuclear magnetic resonance, is introduced (for example, parenterally, subcutaneously, or intraperitoneally) into the mammal. It will be understood in the art that the size of the subject and the imaging system used will determine the quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope moiety, for a human subject, the quantity of radioactivity injected will normally range from about 5 to 20 millicuries of 99mTc. The labeled antibody or antibody fragment will then preferentially accumulate at the location of cells which contain the specific protein. In vivo tumor imaging is described in S. W. Burchiel et al., “Immunopharmacokinetics of Radiolabeled Antibodies and Their Fragments.” (Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, S. W. Burchiel and B. A. Rhodes, eds., Masson Publishing Inc. (1982).)

[0847] Thus, the invention provides a diagnostic method of a disorder, which involves (a) assaying the expression of a polypeptide of the present invention in cells or body fluid of an individual; (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of a disorder. With respect to cancer, the presence of a relatively high amount of transcript in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.

[0848] Moreover, polypeptides of the present invention can be used to treat, prevent, and/or diagnose disease. For example, patients can be administered a polypeptide of the present invention in an effort to replace absent or decreased levels of the polypeptide (e.g., insulin), to supplement absent or decreased levels of a different polypeptide (e.g., hemoglobin S for hemoglobin B, SOD, catalase, DNA repair proteins), to inhibit the activity of a polypeptide (e.g., an oncogene or tumor suppressor), to activate the activity of a polypeptide (e.g., by binding to a receptor), to reduce the activity of a membrane bound receptor by competing with it for free ligand (e.g., soluble TNF receptors used in reducing inflammation), or to bring about a desired response (e.g., blood vessel growth inhibition, enhancement of the immune response to proliferative cells or tissues).

[0849] Similarly, antibodies directed to a polypeptide of the present invention can also be used to treat, prevent, and/or diagnose disease. For example, administration of an antibody directed to a polypeptide of the present invention can bind and reduce overproduction of the polypeptide. Similarly, administration of an antibody can activate the polypeptide, such as by binding to a polypeptide bound to a membrane (receptor).

[0850] At the very least, the polypeptides of the present invention can be used as molecular weight markers on SDS-PAGE gels or on molecular sieve gel filtration columns using methods well known to those of skill in the art. Polypeptides can also be used to raise antibodies, which in turn are used to measure protein expression from a recombinant cell, as a way of assessing transformation of the host cell. Moreover, the polypeptides of the present invention can be used to test the following biological activities.

[0851] Gene Therapy Methods

[0852] Another aspect of the present invention is to gene therapy methods for treating or preventing disorders, diseases and conditions. The gene therapy methods relate to the introduction of nucleic acid (DNA, RNA and antisense DNA or RNA) sequences into an animal to achieve expression of a polypeptide of the present invention. This method requires a polynucleotide which codes for a polypeptide of the invention that operatively linked to a promoter and any other genetic elements necessary for the expression of the polypeptide by the target tissue. Such gene therapy and delivery techniques are known in the art, see, for example, WO90/11092, which is herein incorporated by reference.

[0853] Thus, for example, cells from a patient may be engineered with a polynucleotide (DNA or RNA) comprising a promoter operably linked to a polynucleotide of the invention ex vivo, with the engineered cells then being provided to a patient to be treated with the polypeptide. Such methods are well-known in the art. For example, see Belldegrun et al., J. Natl. Cancer Inst., 85:207-216 (1993); Ferrantini et al., Cancer Research, 53:107-1112 (1993); Ferrantini et al., J. Immunology 153: 4604-4615 (1994); Kaido, T., et al., Int. J. Cancer 60: 221-229 (1995); Ogura et al., Cancer Research 50: 5102-5106 (1990); Santodonato, et al., Human Gene Therapy 7:1-10 (1996); Santodonato, et al., Gene Therapy 4:1246-1255 (1997); and Zhang, et al., Cancer Gene Therapy 3: 31-38 (1996)), which are herein incorporated by reference. In one embodiment, the cells which are engineered are arterial cells. The arterial cells may be reintroduced into the patient through direct injection to the artery, the tissues surrounding the artery, or through catheter injection.

[0854] As discussed in more detail below, the polynucleotide constructs can be delivered by any method that delivers injectable materials to the cells of an animal, such as, injection into the interstitial space of tissues (heart, muscle, skin, lung, liver, and the like). The polynucleotide constructs may be delivered in a pharmaceutically acceptable liquid or aqueous carrier.

[0855] In one embodiment, the polynucleotide of the invention is delivered as a naked polynucleotide. The term “naked” polynucleotide, DNA or RNA refers to sequences that are free from any delivery vehicle that acts to assist, promote or facilitate entry into the cell, including viral sequences, viral particles, liposome formulations, lipofectin or precipitating agents and the like. However, the polynucleotides of the invention can also be delivered in liposome forimulations and lipofectin formulations and the like can be prepared by methods well known to those skilled in the art. Such methods are described, for example, in U.S. Pat. Nos. 5,593,972, 5,589,466, and 5,580,859, which are herein incorporated by reference.

[0856] The polynucleotide vector constructs of the invention used in the gene therapy method are preferably constructs that will not integrate into the host genome nor will they contain sequences that allow for replication. Appropriate vectors include pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; pSVK3, pBPV, pMSG and pSVL available from Pharmacia; and pEF1/V5, pcDNA3.1, and pRc/CMV2 available from Invitrogen. Other suitable vectors will be readily apparent to the skilled artisan.

[0857] Any strong promoter known to those skilled in the art can be used for driving the expression of polynucleotide sequence of the invention. Suitable promoters include adenoviral promoters, such as the adenoviral major late promoter; or heterologous promoters, such as the cytomegalovirus (CMV) promoter; the respiratory syncytial virus (RSV) promoter; inducible promoters, such as the MMT promoter, the metallothionein promoter; heat shock promoters; the albumin promoter; the ApoAI promoter; human globin promoters; viral thymidine kinase promoters, such as the Herpes Simplex thymidine kinase promoter; retroviral LTRs; the b-actin promoter; and human growth hormone promoters. The promoter also may be the native promoter for the polynucleotides of the invention.

[0858] Unlike other gene therapy techniques, one major advantage of introducing naked nucleic acid sequences into target cells is the transitory nature of the polynucleotide synthesis in the cells. Studies have shown that non-replicating DNA sequences can be introduced into cells to provide production of the desired polypeptide for periods of up to six months.

[0859] The polynucleotide construct of the invention can be delivered to the interstitial space of tissues within the an animal, including of muscle, skin, brain, lung, liver, spleen, bone marrow, thymus, heart, lymph, blood, bone, cartilage, pancreas, kidney, gall bladder, stomach, intestine, testis, ovary, uterus, rectum, nervous system, eye, gland, and connective tissue. Interstitial space of the tissues comprises the intercellular, fluid, mucopolysaccharide matrix among the reticular fibers of organ tissues, elastic fibers in the walls of vessels or chambers, collagen fibers of fibrous tissues, or that same matrix within connective tissue ensheathing muscle cells or in the lacunae of bone. It is similarly the space occupied by the plasma of the circulation and the lymph fluid of the lymphatic channels. Delivery to the interstitial space of muscle tissue is preferred for the reasons discussed below. They may be conveniently delivered by injection into the tissues comprising these cells. They are preferably delivered to and expressed in persistent, non-dividing cells which are differentiated, although delivery and expression may be achieved in non-differentiated or less completely differentiated cells, such as, for example, stem cells of blood or skin fibroblasts. In vivo muscle cells are particularly competent in their ability to take up and express polynucleotides.

[0860] For the naked nucleic acid sequence injection, an effective dosage amount of DNA or RNA will be in the range of from about 0.05 mg/kg body weight to about 50 mg/kg body weight. Preferably the dosage will be from about 0.005 mg/kg to about 20 mg/kg and more preferably from about 0.05 mg/kg to about 5 mg/kg. Of course, as the artisan of ordinary skill will appreciate, this dosage will vary according to the tissue site of injection. The appropriate and effective dosage of nucleic acid sequence can readily be determined by those of ordinary skill in the art and may depend on the condition being treated and the route of administration.

[0861] The preferred route of administration is by the parenteral route of injection into the interstitial space of tissues. However, other parenteral routes may also be used, such as, inhalation of an aerosol formulation particularly for delivery to lungs or bronchial tissues, throat or mucous membranes of the nose. In addition, naked DNA constructs can be delivered to arteries during angioplasty by the catheter used in the procedure.

[0862] The naked polynucleotides are delivered by any method known in the art, including, but not limited to, direct needle injection at the delivery site, intravenous injection, topical administration, catheter infusion, and so-called “gene guns”. These delivery methods are known in the art.

[0863] The constructs may also be delivered with delivery vehicles such as viral sequences, viral particles, liposome formulations, lipofectin, precipitating agents, etc. Such methods of delivery are known in the art.

[0864] In certain embodiments, the polynucleotide constructs of the invention are complexed in a liposome preparation. Liposomal preparations for use in the instant invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. However, cationic liposomes are particularly preferred because a tight charge complex can be formed between the cationic liposome and the polyanionic nucleic acid. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Felgner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7416 (1987), which is herein incorporated by reference); mRNA (Malone et al., Proc. Natl. Acad. Sci. USA, 86:6077-6081 (1989), which is herein incorporated by reference); and purified transcription factors (Debs et al., J. Biol. Chem., 265:10189-10192 (1990), which is herein incorporated by reference), in functional form.

[0865] Cationic liposomes are readily available. For example, N-[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes are particularly useful and are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Felgner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7416 (1987), which is herein incorporated by reference). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boehringer).

[0866] Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, e.g. PCT Publication NO: WO 90/11092 (which is herein incorporated by reference) for a description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes. Preparation of DOTMA liposomes is explained in the literature, see, e.g., Feigner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7417, which is herein incorporated by reference. Similar methods can be used to prepare liposomes from other cationic lipid materials.

[0867] Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl, choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.

[0868] For example, commercially dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), and dioleoylphosphatidyl ethanolamine (DOPE) can be used in various combinations to make conventional liposomes, with or without the addition of cholesterol. Thus, for example, DOPG/DOPC vesicles can be prepared by drying 50 mg each of DOPG and DOPC under a stream of nitrogen gas into a sonication vial. The sample is placed under a vacuum pump overnight and is hydrated the following day with deionized water. The sample is then sonicated for 2 hours in a capped vial, using a Heat Systems model 350 sonicator equipped with an inverted cup (bath type) probe at the maximum setting while the bath is circulated at 15EC. Alternatively, negatively charged vesicles can be prepared without sonication to produce multilamellar vesicles or by extrusion through nucleopore membranes to produce unilamellar vesicles of discrete size. Other methods are known and available to those of skill in the art.

[0869] The liposomes can comprise multilamellar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs), with SUVs being preferred. The various liposome-nucleic acid complexes are prepared using methods well known in the art. See, e.g., Straubinger et al., Methods of Immunology, 101:512-527 (1983), which is herein incorporated by reference. For example, MLVs containing nucleic acid can be prepared by depositing a thin film of phospholipid on the walls of a glass tube and subsequently hydrating with a solution of the material to be encapsulated. SUVs are prepared by extended sonication of MLVs to produce a homogeneous population of unilamellar liposomes. The material to be entrapped is added to a suspension of preformed MLVs and then sonicated. When using liposomes containing cationic lipids, the dried lipid film is resuspended in an appropriate solution such as sterile water or an isotonic buffer solution such as 10 mM Tris/NaCl, sonicated, and then the preformed liposomes are mixed directly with the DNA. The liposome and DNA form a very stable complex due to binding of the positively charged liposomes to the cationic DNA. SUVs find use with small nucleic acid fragments. LUVs are prepared by a number of methods, well known in the art. Commonly used methods include Ca2+-EDTA chelation (Papahadjopoulos et al., Biochim. Biophys. Acta, 394:483 (1975); Wilson et al., Cell, 17:77 (1979)); ether injection (Deamer et al., Biochim. Biophys. Acta, 443:629 (1976); Ostro et al., Biochem. Biophys. Res. Commun., 76:836 (1977); Fraley et al., Proc. Natl. Acad. Sci. USA, 76:3348 (1979)); detergent dialysis (Enoch et al., Proc. Natl. Acad. Sci. USA, 76:145 (1979)); and reverse-phase evaporation (REV) (Fraley et al., J. Biol. Chem., 255:10431 (1980); Szoka et al., Proc. Natl. Acad. Sci. USA, 75:145 (1978); Schaefer-Ridder et al., Science, 215:166 (1982)), which are herein incorporated by reference.

[0870] Generally, the ratio of DNA to liposomes will be from about 10:1 to about 1:10. Preferably, the ration will be from about 5:1 to about 1:5. More preferably, the ration will be about 3:1 to about 1:3. Still more preferably, the ratio will be about 1:1.

[0871] U.S. Pat. No. 5,676,954 (which is herein incorporated by reference) reports on the injection of genetic material, complexed with cationic liposomes carriers, into mice. U.S. Pat. Nos. 4,897,355, 4,946,787, 5,049,386, 5,459,127, 5,589,466, 5,693,622, 5,580,859, 5,703,055, and international publication NO: WO 94/9469 (which are herein incorporated by reference) provide cationic lipids for use in transfecting DNA into cells and mammals. U.S. Pat. Nos. 5,589,466, 5,693,622, 5,580,859, 5,703,055, and international publication NO: WO 94/9469 (which are herein incorporated by reference) provide methods for delivering DNA-cationic lipid complexes to mammals.

[0872] In certain embodiments, cells are engineered, ex vivo or in vivo, using a retroviral particle containing RNA which comprises a sequence encoding polypeptides of the invention. Retroviruses from which the retroviral plasmid vectors may be derived include, but are not limited to, Moloney Murine Leukemia Virus, spleen necrosis virus, Rous sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, gibbon ape leukemia virus, human immunodeficiency virus, Myeloproliferative Sarcoma Virus, and mammary tumor virus.

[0873] The retroviral plasmid vector is employed to transduce packaging cell lines to form producer cell lines. Examples of packaging cells which may be transfected include, but are not limited to, the PE501, PA317, R-2, R-AM, PA12, T19-14×, VT-19-17-H2, RCRE, RCRIP, GP+E-86, GP+envAm12, and DAN cell lines as described in Miller, Human Gene Therapy, 1:5-14 (1990), which is incorporated herein by reference in its entirety. The vector may transduce the packaging cells through any means known in the art. Such means include, but are not limited to, electroporation, the use of liposomes, and CaPO4 precipitation. In one alternative, the retroviral plasmid vector may be encapsulated into a liposome, or coupled to a lipid, and then administered to a host.

[0874] The producer cell line generates infectious retroviral vector particles which include polynucleotide encoding polypeptides of the invention. Such retroviral vector particles then may be employed, to transduce eukaryotic cells, either in vitro or in vivo. The transduced eukaryotic cells will express polypeptides of the invention.

[0875] In certain other embodiments, cells are engineered, ex vivo or in vivo, with polynucleotides of the invention contained in an adenovirus vector. Adenovirus can be manipulated such that it encodes and expresses polypeptides of the invention, and at the same time is inactivated in terms of its ability to replicate in a normal lytic viral life cycle. Adenovirus expression is achieved without integration of the viral DNA into the host cell chromosome, thereby alleviating concerns about insertional mutagenesis. Furthermore, adenoviruses have been used as live enteric vaccines for many years with an excellent safety profile (Schwartzet al., Am. Rev. Respir. Dis., 109:233-238 (1974)). Finally, adenovirus mediated gene transfer has been demonstrated in a number of instances including transfer of alpha-1-antitrypsin and CFTR to the lungs of cotton rats (Rosenfeld et al., Science, 252:431-434 (1991); Rosenfeld et al., Cell, 68:143-155 (1992)). Furthermore, extensive studies to attempt to establish adenovirus as a causative agent in human cancer were uniformly negative (Green et al. Proc. Natl. Acad. Sci. USA, 76:6606 (1979)).

[0876] Suitable adenoviral vectors useful in the present invention are described, for example, in Kozarsky and Wilson, Curr. Opin. Genet. Devel., 3:499-503 (1993); Rosenfeld et al., Cell, 68:143-155 (1992); Engelhardt et al., Human Genet. Ther., 4:759-769 (1993); Yang et al., Nature Genet., 7:362-369 (1994); Wilson et al., Nature , 365:691-692 (1993); and U.S. Pat. No. 5,652,224, which are herein incorporated by reference. For example, the adenovirus vector Ad2 is useful and can be grown in human 293 cells. These cells contain the E1 region of adenovirus and constitutively express E1a and E1b, which complement the defective adenoviruses by providing the products of the genes deleted from the vector. In addition to Ad2, other varieties of adenovirus (e.g., Ad3, Ad5, and Ad7) are also useful in the present invention.

[0877] Preferably, the adenoviruses used in the present invention are replication deficient. Replication deficient adenoviruses require the aid of a helper virus and/or packaging cell line to form infectious particles. The resulting virus is capable of infecting cells and can express a polynucleotide of interest which is operably linked to a promoter, but cannot replicate in most cells. Replication deficient adenoviruses may be deleted in one or more of all or a portion of the following genes: E1a, E1b, E3, E4, E2a, or L1 through L5.

[0878] In certain other embodiments, the cells are engineered, ex vivo or in vivo, using an adeno-associated virus (AAV). AAVs are naturally occurring defective viruses that require helper viruses to produce infectious particles (Muzyczka, Curr. Topics in Microbiol. Immunol., 158:97 (1992)). It is also one of the few viruses that may integrate its DNA into non-dividing cells. Vectors containing as little as 300 base pairs of AAV can be packaged and can integrate, but space for exogenous DNA is limited to about 4.5 kb. Methods for producing and using such AAVs are known in the art. See, for example, U.S. Pat. Nos. 5,139,941, 5,173,414, 5,354,678, 5,436,146, 5,474,935, 5,478,745, and 5,589,377.

[0879] For example, an appropriate AAV vector for use in the present invention will include all the sequences necessary for DNA replication, encapsidation, and host-cell integration. The polynucleotide construct containing polynucleotides of the invention is inserted into the AAV vector using standard cloning methods, such as those found in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press (1989). The recombinant AAV vector is then transfected into packaging cells which are infected with a helper virus, using any standard technique, including lipofection, electroporation, calcium phosphate precipitation, etc. Appropriate helper viruses include adenoviruses, cytomegaloviruses, vaccinia viruses, or herpes viruses. Once the packaging cells are transfected and infected, they will produce infectious AAV viral particles which contain the polynucleotide construct of the invention. These viral particles are then used to transduce eukaryotic cells, either ex vivo or in vivo. The transduced cells will contain the polynucleotide construct integrated into its genome, and will express the desired gene product.

[0880] Another method of gene therapy involves operably associating heterologous control regions and endogenous polynucleotide, sequences (e.g. encoding the polypeptide sequence of interest) via homologous recombination (see, e.g., U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; International Publication NO: WO 96/29411, published Sep. 26, 1996; International Publication NO: WO 94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci. USA, 86:8932-8935 (1989); and Zijlstra et al., Nature, 342:435-438 (1989). This method involves the activation of a gene which is present in the target cells, but which is not normally expressed in the cells, or is expressed at a lower level than desired.

[0881] Polynucleotide constructs are made, using standard techniques known in the art, which contain the promoter with targeting sequences flanking the promoter. Suitable promoters are described herein. The targeting sequence is sufficiently complementary to an endogenous sequence to permit homologous recombination of the promoter-targeting sequence with the endogenous sequence. The targeting sequence will be sufficiently near the 5′ end of the desired endogenous polynucleotide sequence so the promoter will be operably linked to the endogenous sequence upon homologous recombination.

[0882] The promoter and the targeting sequences can be amplified using PCR. Preferably, the amplified promoter contains distinct restriction enzyme sites on the 5′ and 3′ ends. Preferably, the 3′ end of the first targeting sequence contains the same restriction enzyme site as the 5′ end of the amplified promoter and the 5′ end of the second targeting sequence contains the same restriction site as the 3′ end of the amplified promoter. The amplified promoter and targeting sequences are digested and ligated together.

[0883] The promoter-targeting sequence construct is delivered to the cells, either as naked polynucleotide, or in conjunction with transfection-facilitating agents, such as liposomes, viral sequences, viral particles, whole viruses, lipofection, precipitating agents, etc., described in more detail above. The P promoter-targeting sequence can be delivered by any method, included direct needle injection, intravenous injection, topical administration, catheter infusion, particle accelerators, etc. The methods are described in more detail below.

[0884] The promoter-targeting sequence construct is taken up by cells. Homologous recombination between the construct and the endogenous sequence takes place, such that an endogenous sequence is placed under the control of the promoter. The promoter then drives the expression of the endogenous sequence.

[0885] The polynucleotides encoding polypeptides of the present invention may be administered along with other polynucleotides encoding angiogenic proteins. Angiogenic proteins include, but are not limited to, acidic and basic fibroblast growth factors, VEGF-1, VEGF-2 (VEGF-C), VEGF-3 (VEGF-B), epidermal growth factor alpha and beta, platelet-derived endothelial cell growth factor, platelet-derived growth factor, tumor necrosis factor alpha, hepatocyte growth factor, insulin like growth factor, colony stimulating factor, macrophage colony stimulating factor, granulocyte/macrophage colony stimulating factor, and nitric oxide synthase.

[0886] Preferably, the polynucleotide encoding a polypeptide of the invention contains a secretory signal sequence that facilitates secretion of the protein. Typically, the signal sequence is positioned in the coding region of the polynucleotide to be expressed towards or at the 5′ end of the coding region. The signal sequence may be homologous or heterologous to the polynucleotide of interest and may be homologous or heterologous to the cells to be transfected. Additionally, the signal sequence may be chemically synthesized using methods known in the art.

[0887] Any mode of administration of any of the above-described polynucleotides constructs can be used so long as the mode results in the expression of one or more molecules in an amount sufficient to provide a therapeutic effect. This includes direct needle injection, systemic injection, catheter infusion, biolistic injectors, particle accelerators (i.e., “gene guns”), gelfoam sponge depots, other commercially available depot materials, osmotic pumps (e.g., Alza minipumps), oral or suppositorial solid (tablet or pill) pharmaceutical formulations, and decanting or topical applications during surgery. For example, direct injection of naked calcium phosphate-precipitated plasmid into rat liver and rat spleen or a protein-coated plasmid into the portal vein has resulted in gene expression of the foreign gene in the rat livers. (Kaneda et al., Science, 243:375 (1989)).

[0888] A preferred method of local administration is by direct injection. Preferably, a recombinant molecule of the present invention complexed with a delivery vehicle is administered by direct injection into or locally within the area of arteries. Administration of a composition locally within the area of arteries refers to injecting the composition centimeters and preferably, millimeters within arteries.

[0889] Another method of local administration is to contact a polynucleotide construct of the present invention in or around a surgical wound. For example, a patient can undergo surgery and the polynucleotide construct can be coated on the surface of tissue inside the wound or the construct can be injected into areas of tissue inside the wound.

[0890] Therapeutic compositions useful in systemic administration, include recombinant molecules of the present invention complexed to a targeted delivery vehicle of the present invention. Suitable delivery vehicles for use with systemic administration comprise liposomes comprising ligands for targeting the vehicle to a particular site.

[0891] Preferred methods of systemic administration, include intravenous injection, aerosol, oral and percutaneous (topical) delivery. Intravenous injections can be performed using methods standard in the art. Aerosol delivery can also be performed using methods standard in the art (see, for example, Stribling et al., Proc. Natl. Acad. Sci. USA, 189:11277-11281 (1992), which is incorporated herein by reference). Oral delivery can be performed by complexing a polynucleotide construct of the present invention to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers, include plastic capsules or tablets, such as those known in the art. Topical delivery can be performed by mixing a polynucleotide construct of the present invention with a lipophilic reagent (e.g., DMSO) that is capable of passing into the skin.

[0892] Determining an effective amount of substance to be delivered can depend upon a number of factors including, for example, the chemical structure and biological activity of the substance, the age and weight of the animal, the precise condition requiring treatment and its severity, and the route of administration. The frequency of treatments depends upon a number of factors, such as the amount of polynucleotide constructs administered per dose, as well as the health and history of the subject. The precise amount, number of doses, and timing of doses will be determined by the attending physician or veterinarian. Therapeutic compositions of the present invention can be administered to any animal, preferably to mammals and birds. Preferred mammals include humans, dogs, cats, mice, rats, rabbits sheep, cattle, horses and pigs, with humans being particularly preferred.

[0893] Biological Activities

[0894] The polynucleotides or polypeptides, or agonists or antagonists of the present invention can be used in assays to test for one or more biological activities. If these polynucleotides and polypeptides do exhibit activity in a particular assay, it is likely that these molecules may be involved in the diseases associated with the biological activity. Thus, the polynucleotides or polypeptides, or agonists or antagonists could be used to treat the associated disease.

[0895] Immune Activity

[0896] The polynucleotides or polypeptides, or agonists or antagonists of the present invention may be useful in treating, preventing, and/or diagnosing diseases, disorders, and/or conditions of the immune system, by activating or inhibiting the proliferation, differentiation, or mobilization (chemotaxis) of immune cells. Immune cells develop through a process called hematopoiesis, producing myeloid (platelets, red blood cells, neutrophils, and macrophages) and lymphoid (B and T lymphocytes) cells from pluripotent stem cells. The etiology of these immune diseases, disorders, and/or conditions may be genetic, somatic, such as cancer or some autoimmune diseases, disorders, and/or conditions, acquired (e.g., by chemotherapy or toxins), or infectious. Moreover, a polynucleotides or polypeptides, or agonists or antagonists of the present invention can be used as a marker or detector of a particular immune system disease or disorder.

[0897] A polynucleotides or polypeptides, or agonists or antagonists of the present invention may be useful in treating, preventing, and/or diagnosing diseases, disorders, and/or conditions of hematopoietic cells. A polynucleotides or polypeptides, or agonists or antagonists of the present invention could be used to increase differentiation and proliferation of hematopoietic cells, including the pluripotent stem cells, in an effort to treat or prevent those diseases, disorders, and/or conditions associated with a decrease in certain (or many) types hematopoietic cells. Examples of immunologic deficiency syndromes include, but are not limited to: blood protein diseases, disorders, and/or conditions (e.g. agammaglobulinemia, dysgammaglobulinemia), ataxia telangiectasia, common variable immunodeficiency, Digeorge Syndrome, HIV infection, HTLV-BLV infection, leukocyte adhesion deficiency syndrome, lymphopenia, phagocyte bactericidal dysfunction, severe combined immunodeficiency (SCIDs), Wiskott-Aldrich Disorder, anemia, thrombocytopenia, or hemoglobinuria.

[0898] Moreover, a polynucleotides or polypeptides, or agonists or antagonists of the present invention could also be used to modulate hemostatic (the stopping of bleeding) or thrombolytic activity (clot formation). For example, by increasing hemostatic or thrombolytic activity, a polynucleotides or polypeptides, or agonists or antagonists of the present invention could be used to treat or prevent blood coagulation diseases, disorders, and/or conditions (e.g., afibrinogenemia, factor deficiencies, arterial thrombosis, venous thrombosis, etc.), blood platelet diseases, disorders, and/or conditions (e.g. thrombocytopenia), or wounds resulting from trauma, surgery, or other causes. Alternatively, a polynucleotides or polypeptides, or agonists or antagonists of the present invention that can decrease hemostatic or thrombolytic activity could be used to inhibit or dissolve clotting. Polynucleotides or polypeptides, or agonists or antagonists of the present invention are may also be useful for the detection, prognosis, treatment, and/or prevention of heart attacks (infarction), strokes, scarring, fibrinolysis, uncontrolled bleeding, uncontrolled coagulation, uncontrolled complement fixation, and/or inflammation.

[0899] A polynucleotides or polypeptides, or agonists or antagonists of the present invention may also be useful in treating, preventing, and/or diagnosing autoimmune diseases, disorders, and/or conditions. Many autoimmune diseases, disorders, and/or conditions result from inappropriate recognition of self as foreign material by immune cells. This inappropriate recognition results in an immune response leading to the destruction of the host tissue. Therefore, the administration of a polynucleotides or polypeptides, or agonists or antagonists of the present invention that inhibits an immune response, particularly the proliferation, differentiation, or chemotaxis of T-cells, may be an effective therapy in preventing autoimmune diseases, disorders, and/or conditions.

[0900] Examples of autoimmune diseases, disorders, and/or conditions that can be treated, prevented, and/or diagnosed or detected by the present invention include, but are not limited to: Addison's Disease, hemolytic anemia, antiphospholipid syndrome, rheumatoid arthritis, dermatitis, allergic encephalomyelitis, glomerulonephritis, Goodpasture's Syndrome, Graves' Disease, Multiple Sclerosis, Myasthenia Gravis, Neuritis, Ophthalmia, Bullous Pemphigoid, Pemphigus, Polyendocrinopathies, Purpura, Reiter's Disease, Stiff-Man Syndrome, Autoimmune Thyroiditis, Systemic Lupus Erythematosus, Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulin dependent diabetes mellitis, and autoimmune inflammatory eye disease.

[0901] Similarly, allergic reactions and conditions, such as asthma (particularly allergic asthma) or other respiratory problems, may also be treated, prevented, and/or diagnosed by polynucleotides or polypeptides, or agonists or antagonists of the present invention. Moreover, these molecules can be used to treat anaphylaxis, hypersensitivity to an antigenic molecule, or blood group incompatibility.

[0902] A polynucleotides or polypeptides, or agonists or antagonists of the present invention may also be used to treat, prevent, and/or diagnose organ rejection or graft-versus-host disease (GVHD). Organ rejection occurs by host immune cell destruction of the transplanted tissue through an immune response. Similarly, an immune response is also involved in GVHD, but, in this case, the foreign transplanted immune cells destroy the host tissues. The administration of a polynucleotides or polypeptides, or agonists or antagonists of the present invention that inhibits an immune response, particularly the proliferation, differentiation, or chemotaxis of T-cells, may be an effective therapy in preventing organ rejection or GVHD.

[0903] Similarly, a polynucleotides or polypeptides, or agonists or antagonists of the present invention may also be used to modulate inflammation. For example, the polypeptide or polynucleotide or agonists or antagonist may inhibit the proliferation and differentiation of cells involved in an inflammatory response. These molecules can be used to treat, prevent, and/or diagnose inflammatory conditions, both chronic and acute conditions, including chronic prostatitis, granulomatous prostatitis and malacoplakia, inflammation associated with infection (e.g., septic shock, sepsis, or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine induced lung injury, inflammatory bowel disease, Crohn's disease, or resulting from over production of cytokines (e.g., TNF or IL-1.)

[0904] Hyperproliferative Disorders

[0905] A polynucleotides or polypeptides, or agonists or antagonists of the invention can be used to treat, prevent, and/or diagnose hyperproliferative diseases, disorders, and/or conditions, including neoplasms. A polynucleotides or polypeptides, or agonists or antagonists of the present invention may inhibit the proliferation of the disorder through direct or indirect interactions. Alternatively, a polynucleotides or polypeptides, or agonists or antagonists of the present invention may proliferate other cells which can inhibit the hyperproliferative disorder.

[0906] For example, by increasing an immune response, particularly increasing antigenic qualities of the hyperproliferative disorder or by proliferating, differentiating, or mobilizing T-cells, hyperproliferative diseases, disorders, and/or conditions can be treated, prevented, and/or diagnosed. This immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, decreasing an immune response may also be a method of treating, preventing, and/or diagnosing hyperproliferative diseases, disorders, and/or conditions, such as a chemotherapeutic agent.

[0907] Examples of hyperproliferative diseases, disorders, and/or conditions that can be treated, prevented, and/or diagnosed by polynucleotides or polypeptides, or agonists or antagonists of the present invention include, but are not limited to neoplasms located in the: colon, abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, and urogenital.

[0908] Similarly, other hyperproliferative diseases, disorders, and/or conditions can also be treated, prevented, and/or diagnosed by a polynucleotides or polypeptides, or agonists or antagonists of the present invention. Examples of such hyperproliferative diseases, disorders, and/or conditions include, but are not limited to: hypergammaglobulinemia, lymphoproliferative diseases, disorders, and/or conditions, paraproteinemias, purpura, sarcoidosis, Sezary Syndrome, Waldenstron's Macroglobulinemia, Gaucher's Disease, histiocytosis, and any other hyperproliferative disease, besides neoplasia, located in an organ system listed above.

[0909] One preferred embodiment utilizes polynucleotides of the present invention to inhibit aberrant cellular division, by gene therapy using the present invention, and/or protein fusions or fragments thereof.

[0910] Thus, the present invention provides a method for treating or preventing cell proliferative diseases, disorders, and/or conditions by inserting into an abnormally proliferating cell a polynucleotide of the present invention, wherein said polynucleotide represses said expression.

[0911] Another embodiment of the present invention provides a method of treating or preventing cell-proliferative diseases, disorders, and/or conditions in individuals comprising administration of one or more active gene copies of the present invention to an abnormally proliferating cell or cells. In a preferred embodiment, polynucleotides of the present invention is a DNA construct comprising a recombinant expression vector effective in expressing a DNA sequence encoding said polynucleotides. In another preferred embodiment of the present invention, the DNA construct encoding the polynucleotides of the present invention is inserted into cells to be treated utilizing a retrovirus, or more Preferably an adenoviral vector (See G J. Nabel, et. al., PNAS 1999 96: 324-326, which is hereby incorporated by reference). In a most preferred embodiment, the viral vector is defective and will not transform non-proliferating cells, only proliferating cells. Moreover, in a preferred embodiment, the polynucleotides of the present invention inserted into proliferating cells either alone, or in combination with or fused to other polynucleotides, can then be modulated via an external stimulus (i.e. magnetic, specific small molecule, chemical, or drug administration, etc.), which acts upon the promoter upstream of said polynucleotides to induce expression of the encoded protein product. As such the beneficial therapeutic affect of the present invention may be expressly modulated (i.e. to increase, decrease, or inhibit expression of the present invention) based upon said external stimulus.

[0912] Polynucleotides of the present invention may be useful in repressing expression of oncogenic genes or antigens. By “repressing expression of the oncogenic genes” is intended the suppression of the transcription of the gene, the degradation of the gene transcript (pre-message RNA), the inhibition of splicing, the destruction of the messenger RNA, the prevention of the post-translational modifications of the protein, the destruction of the protein, or the inhibition of the normal function of the protein.

[0913] For local administration to abnormally proliferating cells, polynucleotides of the present invention may be administered by any method known to those of skill in the art including, but not limited to transfection, electroporation, microinjection of cells, or in vehicles such as liposomes, lipofectin, or as naked polynucleotides, or any other method described throughout the specification. The polynucleotide of the present invention may be delivered by known gene delivery systems such as, but not limited to, retroviral vectors (Gilboa, J. Virology 44:845 (1982); Hocke, Nature 320:275 (1986); Wilson, et al., Proc. Natl. Acad. Sci. U.S.A. 85:3014), vaccinia virus system (Chakrabarty et al., Mol. Cell Biol. 5:3403 (1985) or other efficient DNA delivery systems (Yates et al., Nature 313:812 (1985)) known to those skilled in the art. These references are exemplary only and are hereby incorporated by reference. In order to specifically deliver or transfect cells which are abnormally proliferating and spare non-dividing cells, it is preferable to utilize a retrovirus, or adenoviral (as described in the art and elsewhere herein) delivery system known to those of skill in the art. Since host DNA replication is required for retroviral DNA to integrate and the retrovirus will be unable to self replicate due to the lack of the retrovirus genes needed for its life cycle. Utilizing such a retroviral delivery system for polynucleotides of the present invention will target said gene and constructs to abnormally proliferating cells and will spare the non-dividing normal cells.

[0914] The polynucleotides of the present invention may be delivered directly to cell proliferative disorder/disease sites in internal organs, body cavities and the like by use of imaging devices used to guide an injecting needle directly to the disease site. The polynucleotides of the present invention may also be administered to disease sites at the time of surgical intervention.

[0915] By “cell proliferative disease” is meant any human or animal disease or disorder, affecting any one or any combination of organs, cavities, or body parts, which is characterized by single or multiple local abnormal proliferations of cells, groups of cells, or tissues, whether benign or malignant.

[0916] Any amount of the polynucleotides of the present invention may be administered as long as it has a biologically inhibiting effect on the proliferation of the treated cells. Moreover, it is possible to administer more than one of the polynucleotide of the present invention simultaneously to the same site. By “biologically inhibiting” is meant partial or total growth inhibition as well as decreases in the rate of proliferation or growth of the cells. The biologically inhibitory dose may be determined by assessing the effects of the polynucleotides of the present invention on target malignant or abnormally proliferating cell growth in tissue culture, tumor growth in animals and cell cultures, or any other method known to one of ordinary skill in the art.

[0917] The present invention is further directed to antibody-based therapies which involve administering of anti-polypeptides and anti-polynucleotide antibodies to a mammalian, preferably human, patient for treating, preventing, and/or diagnosing one or more of the described diseases, disorders, and/or conditions. Methods for producing anti-polypeptides and anti-polynucleotide antibodies polyclonal and monoclonal antibodies are described in detail elsewhere herein. Such antibodies may be provided in pharmaceutically acceptable compositions as known in the art or as described herein.

[0918] A summary of the ways in which the antibodies of the present invention may be used therapeutically includes binding polynucleotides or polypeptides of the present invention locally or systemically in the body or by direct cytotoxicity of the antibody, e.g. as mediated by complement (CDC) or by effector cells (ADCC). Some of these approaches are described in more detail below. Armed with the teachings provided herein, one of ordinary skill in the art will know how to use the antibodies of the present invention for diagnostic, monitoring or therapeutic purposes without undue experimentation.

[0919] In particular, the antibodies, fragments and derivatives of the present invention are useful for treating, preventing, and/or diagnosing a subject having or developing cell proliferative and/or differentiation diseases, disorders, and/or conditions as described herein. Such treatment comprises administering a single or multiple doses of the antibody, or a fragment, derivative, or a conjugate thereof.

[0920] The antibodies of this invention may be advantageously utilized in combination with other monoclonal or chimeric antibodies, or with lymphokines or hematopoietic growth factors, for example, which serve to increase the number or activity of effector cells which interact with the antibodies.

[0921] It is preferred to use high affinity and/or potent in vivo inhibiting and/or neutralizing antibodies against polypeptides or polynucleotides of the present invention, fragments or regions thereof, for both immunoassays directed to and therapy of diseases, disorders, and/or conditions related to polynucleotides or polypeptides, including fragments thereof, of the present invention. Such antibodies, fragments, or regions, will preferably have an affinity for polynucleotides or polypeptides, including fragments thereof. Preferred binding affinities include those with a dissociation constant or Kd less than 5×10-6M, 10-6M, 5×10-7M, 10-7M, 5×10-8M, 10-8M, 5×10-9M, 10-9M, 5×10-10M, 10-10M, 5×10-11M, 10-11M, 5×10-12M, 10-12M, 5×10-13M, 10-13M, 5×10-14M, 10-14M, 5×10-15M, and 10-15M.

[0922] Moreover, polypeptides of the present invention may be useful in inhibiting the angiogenesis of proliferative cells or tissues, either alone, as a protein fusion, or in combination with other polypeptides directly or indirectly, as described elsewhere herein. In a most preferred embodiment, said anti-angiogenesis effect may be achieved indirectly, for example, through the inhibition of hematopoietic, tumor-specific cells, such as tumor-associated macrophages (See Joseph I B, et al. J Natl Cancer Inst, 90(21):1648-53 (1998), which is hereby incorporated by reference). Antibodies directed to polypeptides or polynucleotides of the present invention may also result in inhibition of angiogenesis directly, or indirectly (See Witte L, et al., Cancer Metastasis Rev. 17(2):155-61 (1998), which is hereby incorporated by reference)).

[0923] Polypeptides, including protein fusions, of the present invention, or fragments thereof may be useful in inhibiting proliferative cells or tissues through the induction of apoptosis. Said polypeptides may act either directly, or indirectly to induce apoptosis of proliferative cells and tissues, for example in the activation of a death-domain receptor, such as tumor necrosis factor (TNF) receptor-1, CD95 (Fas/APO-1), TNF-receptor-related apoptosis-mediated protein (TRAMP) and TNF-related apoptosis-inducing ligand (TRAIL) receptor-1 and -2 (See Schulze-Osthoff K, et al., Eur J Biochem 254(3):439-59 (1998), which is hereby incorporated by reference). Moreover, in another preferred embodiment of the present invention, said polypeptides may induce apoptosis through other mechanisms, such as in the activation of other proteins which will activate apoptosis, or through stimulating the expression of said proteins, either alone or in combination with small molecule drugs or adjuvants, such as apoptonin, galectins, thioredoxins, antiinflammatory proteins (See for example, Mutat. Res. 400(1-2):447-55 (1998), Med Hypotheses.50(5):423-33 (1998), Chem. Biol. Interact. Apr 24;111-112:23-34 (1998), J Mol Med.76(6):402-12 (1998), Int. J. Tissue React. 20(1):3-15 (1998), which are all hereby incorporated by reference).

[0924] Polypeptides, including protein fusions to, or fragments thereof, of the present invention are useful in inhibiting the metastasis of proliferative cells or tissues. Inhibition may occur as a direct result of administering polypeptides, or antibodies directed to said polypeptides as described elsewhere herein, or indirectly, such as activating the expression of proteins known to inhibit metastasis, for example alpha 4 integrins, (See, e.g., Curr Top Microbiol Inmunol 1998;231:125-41, which is hereby incorporated by reference). Such therapeutic affects of the present invention may be achieved either alone, or in combination with small molecule drugs or adjuvants.

[0925] In another embodiment, the invention provides a method of delivering compositions containing the polypeptides of the invention (e.g., compositions containing polypeptides or polypeptide antibodies associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs) to targeted cells expressing the polypeptide of the present invention. Polypeptides or polypeptide antibodies of the invention may be associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs via hydrophobic, hydrophilic, ionic and/or covalent interactions.

[0926] Polypeptides, protein fusions to, or fragments thereof, of the present invention are useful in enhancing the immunogenicity and/or antigenicity of proliferating cells or tissues, either directly, such as would occur if the polypeptides of the present invention ‘vaccinated’ the immune response to respond to proliferative antigens and immunogens, or indirectly, such as in activating the expression of proteins known to enhance the immune response (e.g. chemokines), to said antigens and immunogens.

[0927] Cardiovascular Disorders

[0928] Polynucleotides or polypeptides, or agonists or antagonists of the invention may be used to treat, prevent, and/or diagnose cardiovascular diseases, disorders, and/or conditions, including peripheral artery disease, such as limb ischemia.

[0929] Cardiovascular diseases, disorders, and/or conditions include cardiovascular abnormalities, such as arterio-arterial fistula, arteriovenous fistula, cerebral arteriovenous malformations, congenital heart defects, pulmonary atresia, and Scimitar Syndrome. Congenital heart defects include aortic coarctation, cor triatriatum, coronary vessel anomalies, crisscross heart, dextrocardia, patent ductus arteriosus, Ebstein's anomaly, Eisenmenger complex, hypoplastic left heart syndrome, levocardia, tetralogy of fallot, transposition of great vessels, double outlet right ventricle, tricuspid atresia, persistent truncus arteriosus, and heart septal defects, such as aortopulmonary septal defect, endocardial cushion defects, Lutembacher's Syndrome, trilogy of Fallot, ventricular heart septal defects.

[0930] Cardiovascular diseases, disorders, and/or conditions also include heart disease, such as arrhythmias, carcinoid heart disease, high cardiac output, low cardiac output, cardiac tamponade, endocarditis (including bacterial), heart aneurysm, cardiac arrest, congestive heart failure, congestive cardiomyopathy, paroxysmal dyspnea, cardiac edema, heart hypertrophy, congestive cardiomyopathy, left ventricular hypertrophy, right ventricular hypertrophy, post-infarction heart rupture, ventricular septal rupture, heart valve diseases, myocardial diseases, myocardial ischemia, pericardial effusion, pericarditis (including constrictive and tuberculous), pneumopericardium, postpericardiotomy syndrome, pulmonary heart disease, rheumatic heart disease, ventricular dysfunction, hyperemia, cardiovascular pregnancy complications, Scimitar Syndrome, cardiovascular syphilis, and cardiovascular tuberculosis.

[0931] Arrhythmias include sinus arrhythmia, atrial fibrillation, atrial flutter, bradycardia, extrasystole, Adams-Stokes Syndrome, bundle-branch block, sinoatrial block, long QT syndrome, parasystole, Lown-Ganong-Levine Syndrome, Mahaim-type pre-excitation syndrome, Wolff-Parkinson-White syndrome, sick sinus syndrome, tachycardias, and ventricular fibrillation. Tachycardias include paroxysmal tachycardia, supraventricular tachycardia, accelerated idioventricular rhythm, atrioventricular nodal reentry tachycardia, ectopic atrial tachycardia, ectopic junctional tachycardia, sinoatrial nodal reentry tachycardia, sinus tachycardia, Torsades de Pointes, and ventricular tachycardia.

[0932] Heart valve disease include aortic valve insufficiency, aortic valve stenosis, hear murmurs, aortic valve prolapse, mitral valve prolapse, tricuspid valve prolapse, mitral valve insufficiency, mitral valve stenosis, pulmonary atresia, pulmonary valve insufficiency, pulmonary valve stenosis, tricuspid atresia, tricuspid valve insufficiency, and tricuspid valve stenosis.

[0933] Myocardial diseases include alcoholic cardiomyopathy, congestive cardiomyopathy, hypertrophic cardiomyopathy, aortic subvalvular stenosis, pulmonary subvalvular stenosis, restrictive cardiomyopathy, Chagas cardiomyopathy, endocardial fibroelastosis, endomyocardial fibrosis, Kearns Syndrome, myocardial reperfusion injury, and myocarditis.

[0934] Myocardial ischemias include coronary disease, such as angina pectoris, coronary aneurysm, coronary arteriosclerosis, coronary thrombosis, coronary vasospasm, myocardial infarction and myocardial stunning.

[0935] Cardiovascular diseases also include vascular diseases such as aneurysms, angiodysplasia, angiomatosis, bacillary angiomatosis, Hippel-Lindau Disease, Klippel-Trenaunay-Weber Syndrome, Sturge-Weber Syndrome, angioneurotic edema, aortic diseases, Takayasu's Arteritis, aortitis, Leriche's Syndrome, arterial occlusive diseases, arteritis, enarteritis, polyarteritis nodosa, cerebrovascular diseases, disorders, and/or conditions, diabetic angiopathies, diabetic retinopathy, embolisms, thrombosis, erythromelalgia, hemorrhoids, hepatic veno-occlusive disease, hypertension, hypotension, ischemia, peripheral vascular diseases, phlebitis, pulmonary veno-occlusive disease, Raynaud's disease, CREST syndrome, retinal vein occlusion, Scimitar syndrome, superior vena cava syndrome, telangiectasia, atacia telangiectasia, hereditary hemorrhagic telangiectasia, varicocele, varicose veins, varicose ulcer, vasculitis, and venous insufficiency.

[0936] Aneurysms include dissecting aneurysms, false aneurysms, infected aneurysms, ruptured aneurysms, aortic aneurysms, cerebral aneurysms, coronary aneurysms, heart aneurysms, and iliac aneurysms.

[0937] Arterial occlusive diseases include arteriosclerosis, intermittent claudication, carotid stenosis, fibromuscular dysplasias, mesenteric vascular occlusion, Moyamoya disease, renal artery obstruction, retinal artery occlusion, and thromboangiitis obliterans.

[0938] Cerebrovascular diseases, disorders, and/or conditions include carotid artery diseases, cerebral amyloid angiopathy, cerebral aneurysm, cerebral anoxia, cerebral arteriosclerosis, cerebral arteriovenous malformation, cerebral artery diseases, cerebral embolism and thrombosis, carotid artery thrombosis, sinus thrombosis, Wallenberg's syndrome, cerebral hemorrhage, epidural hematoma, subdural hematoma, subaraxhnoid hemorrhage, cerebral infarction, cerebral ischemia (including transient), subclavian steal syndrome, periventricular leukomalacia, vascular headache, cluster headache, migraine, and vertebrobasilar insufficiency.

[0939] Embolisms include air embolisms, amniotic fluid embolisms, cholesterol embolisms, blue toe syndrome, fat embolisms, pulmonary embolisms, and thromoboembolisms. Thrombosis include coronary thrombosis, hepatic vein thrombosis, retinal vein occlusion, carotid artery thrombosis, sinus thrombosis, Wallenberg's syndrome, and thrombophlebitis.

[0940] Ischemia includes cerebral ischemia, ischemic colitis, compartment syndromes, anterior compartment syndrome, myocardial ischemia, reperfusion injuries, and peripheral limb ischemia. Vasculitis includes aortitis, arteritis, Behcet's Syndrome, Churg-Strauss Syndrome, mucocutaneous lymph node syndrome, thromboangiitis obliterans, hypersensitivity vasculitis, Schoenlein-Henoch purpura, allergic cutaneous vasculitis, and Wegener's granulomatosis.

[0941] Polynucleotides or polypeptides, or agonists or antagonists of the invention, are especially effective for the treatment of critical limb ischemia and coronary disease.

[0942] Polypeptides may be administered using any method known in the art, including, but not limited to, direct needle injection at the delivery site, intravenous injection, topical administration, catheter infusion, biolistic injectors, particle accelerators, gelfoam sponge depots, other commercially available depot materials, osmotic pumps, oral or suppositorial solid pharmaceutical formulations, decanting or topical applications during surgery, aerosol delivery. Such methods are known in the art. Polypeptides of the invention may be administered as part of a Therapeutic, described in more detail below. Methods of delivering polynucleotides of the invention are described in more detail herein.

[0943] Diseases at the Cellular Level

[0944] Diseases associated with increased cell survival or the inhibition of apoptosis that could be treated, prevented, and/or diagnosed by the polynucleotides or polypeptides and/or antagonists or agonists of the invention, include cancers (such as follicular lymphomas, carcinomas with p53 mutations, and hormone-dependent tumors, including, but not limited to colon cancer, cardiac tumors, pancreatic cancer, melanoma, retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicular cancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma, endothelioma, osteoblastoma, osteoclastoma, osteosarcoma, chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi's sarcoma and ovarian cancer); autoimmune diseases, disorders, and/or conditions (such as, multiple sclerosis, Sjogren's syndrome, Hashimoto's thyroiditis, biliary cirrhosis, Behcet's disease, Crohn's disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) and viral infections (such as herpes viruses, pox viruses and adenoviruses), inflammation, graft v. host disease, acute graft rejection, and chronic graft rejection. In preferred embodiments, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention are used to inhibit growth, progression, and/or metastasis of cancers, in particular those listed above.

[0945] Additional diseases or conditions associated with increased cell survival that could be treated, prevented or diagnosed by the polynucleotides or polypeptides, or agonists or antagonists of the invention, include, but are not limited to, progression, and/or metastases of malignancies and related disorders such as leukemia (including acute leukemias (e.g., acute lymphocytic leukemia, acute myelocytic leukemia (including myeloblastic, promyelocytic, myelomonocytic, monocytic, and erythroleukemia)) and chronic leukemias (e.g., chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia)), polycythemia vera, lymphomas (e.g., Hodgkin's disease and non-Hodgkin's disease), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors including, but not limited to, sarcomas and carcinomas such as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, and retinoblastoma.

[0946] Diseases associated with increased apoptosis that could be treated, prevented, and/or diagnosed by the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, include AIDS; neurodegenerative diseases, disorders, and/or conditions (such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Retinitis pigmentosa, Cerebellar degeneration and brain tumor or prior associated disease); autoimmune diseases, disorders, and/or conditions (such as, multiple sclerosis, Sjogren's syndrome, Hashimoto's thyroiditis, biliary cirrhosis, Behcet's disease, Crohn's disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) myelodysplastic syndromes (such as aplastic anemia), graft v. host disease, ischemic injury (such as that caused by myocardial infarction, stroke and reperfusion injury), liver injury (e.g., hepatitis related liver injury, ischemia/reperfusion injury, cholestosis (bile duct injury) and liver cancer); toxin-induced liver disease (such as that caused by alcohol), septic shock, cachexia and anorexia.

[0947] Wound Healing and Epithelial Cell Proliferation

[0948] In accordance with yet a further aspect of the present invention, there is provided a process for utilizing the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, for therapeutic purposes, for example, to stimulate epithelial cell proliferation and basal keratinocytes for the purpose of wound healing, and to stimulate hair follicle production and healing of dermal wounds. Polynucleotides or polypeptides, as well as agonists or antagonists of the invention, may be clinically useful in stimulating wound healing including surgical wounds, excisional wounds, deep wounds involving damage of the dermis and epidermis, eye tissue wounds, dental tissue wounds, oral cavity wounds, diabetic ulcers, dermal ulcers, cubitus ulcers, arterial ulcers, venous stasis ulcers, burns resulting from heat exposure or chemicals, and other abnormal wound healing conditions such as uremia, malnutrition, vitamin deficiencies and complications associated with systemic treatment with steroids, radiation therapy and antineoplastic drugs and antimetabolites. Polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to promote dermal reestablishment subsequent to dermal loss.

[0949] The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to increase the adherence of skin grafts to a wound bed and to stimulate re-epithelialization from the wound bed. The following are a non-exhaustive list of grafts that polynucleotides or polypeptides, agonists or antagonists of the invention, could be used to increase adherence to a wound bed: autografts, artificial skin, allografts, autodermic graft, autoepidermic grafts, avacular grafts, Blair-Brown grafts, bone graft, brephoplastic grafts, cutis graft, delayed graft, dermic graft, epidermic graft, fascia graft, full thickness graft, heterologous graft, xenograft, homologous graft, hyperplastic graft, lamellar graft, mesh graft, mucosal graft, Ollier-Thiersch graft, omenpal graft, patch graft, pedicle graft, penetrating graft, split skin graft, thick split graft. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, can be used to promote skin strength and to improve the appearance of aged skin.

[0950] It is believed that the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, will also produce changes in hepatocyte proliferation, and epithelial cell proliferation in the lung, breast, pancreas, stomach, small intestine, and large intestine. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could promote proliferation of epithelial cells such as sebocytes, hair follicles, hepatocytes, type II pneumocytes, mucin-producing goblet cells, and other epithelial cells and their progenitors contained within the skin, lung, liver, and gastrointestinal tract. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may promote proliferation of endothelial cells, keratinocytes, and basal keratinocytes.

[0951] The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could also be used to reduce the side effects of gut toxicity that result from radiation, chemotherapy treatments or viral infections. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may have a cytoprotective effect on the small intestine mucosa. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may also stimulate healing of mucositis (mouth ulcers) that result from chemotherapy and viral infections.

[0952] The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could further be used in full regeneration of skin in full and partial thickness skin defects, including burns, (i.e., repopulation of hair follicles, sweat glands, and sebaceous glands), treatment of other skin defects such as psoriasis. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to treat epidermolysis bullosa, a defect in adherence of the epidermis to the underlying dermis which results in frequent, open and painful blisters by accelerating reepithelialization of these lesions. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could also be used to treat gastric and doudenal ulcers and help heal by scar formation of the mucosal lining and regeneration of glandular mucosa and duodenal mucosal lining more rapidly. Inflamamatory bowel diseases, such as Crohn's disease and ulcerative colitis, are diseases which result in destruction of the mucosal surface of the small or large intestine, respectively. Thus, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to promote the resurfacing of the mucosal surface to aid more rapid healing and to prevent progression of inflammatory bowel disease. Treatment with the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, is expected to have a significant effect on the production of mucus throughout the gastrointestinal tract and could be used to protect the intestinal mucosa from injurious substances that are ingested or following surgery. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to treat diseases associate with the under expression of the polynucleotides of the invention.

[0953] Moreover, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to prevent and heal damage to the lungs due to various pathological states. A growth factor such as the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, which could stimulate proliferation and differentiation and promote the repair of alveoli and brochiolar epithelium to prevent or treat acute or chronic lung damage. For example, emphysema, which results in the progressive loss of aveoli, and inhalation injuries, i.e., resulting from smoke inhalation and burns, that cause necrosis of the bronchiolar epithelium and alveoli could be effectively treated, prevented, and/or diagnosed using the polynucleotides or polypeptides, and/or agonists or antagonists of the invention. Also, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to stimulate the proliferation of and differentiation of type II pneumocytes, which may help treat or prevent disease such as hyaline membrane diseases, such as infant respiratory distress syndrome and bronchopulmonary displasia, in premature infants.

[0954] The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could stimulate the proliferation and differentiation of hepatocytes and, thus, could be used to alleviate or treat liver diseases and pathologies such as fulminant liver failure caused by cirrhosis, liver damage caused by viral hepatitis and toxic substances (i.e., acetaminophen, carbon tetraholoride and other hepatotoxins known in the art).

[0955] In addition, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used treat or prevent the onset of diabetes mellitus. In patients with newly diagnosed Types I and II diabetes, where some islet cell function remains, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to maintain the islet function so as to alleviate, delay or prevent permanent manifestation of the disease. Also, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used as an auxiliary in islet cell transplantation to improve or promote islet cell function.

[0956] Neurological Diseases

[0957] Nervous system diseases, disorders, and/or conditions, which can be treated, prevented, and/or diagnosed with the compositions of the invention (e.g., polypeptides, polynucleotides, and/or agonists or antagonists), include, but are not limited to, nervous system injuries, and diseases, disorders, and/or conditions which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated, prevented, and/or diagnosed in a patient (including human and non-human mammalian patients) according to the invention, include but are not limited to, the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems: (1) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia; (2) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries; (3) malignant lesions, in which a portion of the nervous system is destroyed or injured by malignant tissue which is either a nervous system associated malignancy or a malignancy derived from non-nervous system tissue; (4) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster, or herpes simplex virus or with Lyme disease, tuberculosis, syphilis; (5) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson's disease, Alzheimer's disease, Huntington's chorea, or amyotrophic lateral sclerosis (ALS); (6) lesions associated with nutritional diseases, disorders, and/or conditions, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration; (7) neurological lesions associated with systemic diseases including, but not limited to, diabetes (diabetic neuropathy, Bell's palsy), systemic lupus erythematosus, carcinoma, or sarcoidosis; (8) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and (9) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including, but not limited to, multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multifocal leukoencephalopathy, and central pontine myelinolysis.

[0958] In a preferred embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to protect neural cells from the damaging effects of cerebral hypoxia. According to this embodiment, the compositions of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral hypoxia. In one aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral ischemia. In another aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral infarction. In another aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose or prevent neural cell injury associated with a stroke. In a further aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with a heart attack.

[0959] The compositions of the invention which are useful for treating or preventing a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, compositions of the invention which elicit any of the following effects may be useful according to the invention: (1) increased survival time of neurons in culture; (2) increased sprouting of neurons in culture or in vivo; (3) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or (4) decreased symptoms of neuron dysfunction in vivo. Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may routinely be measured using a method set forth herein or otherwise known in the art, such as, for example, the method set forth in Arakawa et al. (J. Neurosci. 10:3507-3515 (1990)); increased sprouting of neurons may be detected by methods known in the art, such as, for example, the methods set forth in Pestronk et al. (Exp. Neurol. 70:65-82 (1980)) or Brown et al. (Ann. Rev. Neurosci. 4:17-42 (1981)); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., using techniques known in the art and depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.

[0960] In specific embodiments, motor neuron diseases, disorders, and/or conditions that may be treated, prevented, and/or diagnosed according to the invention include, but are not limited to, diseases, disorders, and/or conditions such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as diseases, disorders, and/or conditions that selectively affect neurons such as amyotrophic lateral sclerosis, and including, but not limited to, progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).

[0961] Infectious Disease

[0962] A polypeptide or polynucleotide and/or agonist or antagonist of the present invention can be used to treat, prevent, and/or diagnose infectious agents. For example, by increasing the immune response, particularly increasing the proliferation and differentiation of B and/or T cells, infectious diseases may be treated, prevented, and/or diagnosed. The immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, polypeptide or polynucleotide and/or agonist or antagonist of the present invention may also directly inhibit the infectious agent, without necessarily eliciting an immune response.

[0963] Viruses are one example of an infectious agent that can cause disease or symptoms that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention. Examples of viruses, include, but are not limited to Examples of viruses, include, but are not limited to the following DNA and RNA viruses and viral families: Arbovirus, Adenoviridae, Arenaviridae, Arterivirus, Birnaviridae, Bunyaviridae, Caliciviridae, Circoviridae, Coronaviridae, Dengue, EBV, HIV, Flaviviridae, Hepadnaviridae (Hepatitis), Herpesviridae (such as, Cytomegalovirus, Herpes Simplex, Herpes Zoster), Mononegavirus (e.g., Paramyxoviridae, Morbillivirus, Rhabdoviridae), Orthomyxoviridae (e.g., Influenza A, Influenza B, and parainfluenza), Papiloma virus, Papovaviridae, Parvoviridae, Picornaviridae, Poxyiridae (such as Smallpox or Vaccinia), Reoviridae (e.g., Rotavirus), Retroviridae (HTLV-I, HTLV-II, Lentivirus), and Togaviridae (e.g., Rubivirus). Viruses falling within these families can cause a variety of diseases or symptoms, including, but not limited to: arthritis, bronchiollitis, respiratory syncytial virus, encephalitis, eye infections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome, hepatitis (A, B, C, E, Chronic Active, Delta), Japanese B encephalitis, Junin, Chikungunya, Rift Valley fever, yellow fever, meningitis, opportunistic infections (e.g., AIDS), pneumonia, Burkitt's Lymphoma, chickenpox, hemorrhagic fever, Measles, Mumps, Parainfluenza, Rabies, the common cold, Polio, leukemia, Rubella, sexually transmitted diseases, skin diseases (e.g., Kaposi's, warts), and viremia. polynucleotides or polypeptides, or agonists or antagonists of the invention, can be used to treat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose: meningitis, Dengue, EBV, and/or hepatitis (e.g., hepatitis B). In an additional specific embodiment polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat patients nonresponsive to one or more other commercially available hepatitis vaccines. In a further specific embodiment polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose AIDS.

[0964] Similarly, bacterial or fungal agents that can cause disease or symptoms and that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention include, but not limited to, include, but not limited to, the following Gram-Negative and Gram-positive bacteria and bacterial families and fungi: Actinomycetales (e.g., Corynebacterium, Mycobacterium, Norcardia), Cryptococcus neoformans, Aspergillosis, Bacillaceae (e.g., Anthrax, Clostridium), Bacteroidaceae, Blastomycosis, Bordetella, Borrelia (e.g., Borrelia burgdorferi), Brucellosis, Candidiasis, Campylobacter, Coccidioidomycosis, Cryptococcosis, Dermatocycoses, E. coli (e.g., Enterotoxigenic E. coli and Enterohemorrhagic E. coli), Enterobacteriaceae (Klebsiella, Salmonella (e.g., Salmonella typhi, and Salmonella paratyphi), Serratia, Yersinia), Erysipelothrix, Helicobacter, Legionellosis, Leptospirosis, Listeria, Mycoplasmatales, Mycobacterium leprae, Vibrio cholerae, Neisseriaceae (e.g., Acinetobacter, Gonorrhea, Menigococcal), Meisseria meningitidis, Pasteurellacea Infections (e.g., Actinobacillus, Heamophilus (e.g., Heamophilus influenza type B), Pasteurella), Pseudomonas, Rickettsiaceae, Chlamydiaceae, Syphilis, Shigella spp., Staphylococcal, Meningiococcal, Pneumococcal and Streptococcal (e.g., Streptococcus pneumoniae and Group B Streptococcus). These bacterial or fungal families can cause the following diseases or symptoms, including, but not limited to: bacteremia, endocarditis, eye infections (conjunctivitis, tuberculosis, uveitis), gingivitis, opportunistic infections (e.g., AIDS related infections), paronychia, prosthesis-related infections, Reiter's Disease, respiratory tract infections, such as Whooping Cough or Empyema, sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery, Paratyphoid Fever, food poisoning, Typhoid, pneumonia, Gonorrhea, meningitis (e.g., mengitis types A and B), Chlamydia, Syphilis, Diphtheria, Leprosy, Paratuberculosis, Tuberculosis, Lupus, Botulism, gangrene, tetanus, impetigo, Rheumatic Fever, Scarlet Fever, sexually transmitted diseases, skin diseases (e.g., cellulitis, dermatocycoses), toxemia, urinary tract infections, wound infections. Polynucleotides or polypeptides, agonists or antagonists of the invention, can be used to treat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, agonists or antagonists of the invention are used to treat, prevent, and/or diagnose: tetanus, Diptheria, botulism, and/or meningitis type B.

[0965] Moreover, parasitic agents causing disease or symptoms that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention include, but not limited to, the following families or class: Amebiasis, Babesiosis, Coccidiosis, Cryptosporidiosis, Dientamoebiasis, Dourine, Ectoparasitic, Giardiasis, Helminthiasis, Leishmaniasis, Theileriasis, Toxoplasmosis, Trypanosomiasis, and Trichomonas and Sporozoans (e.g., Plasmodium virax, Plasmodium falciparium, Plasmodium malariae and Plasmodium ovale). These parasites can cause a variety of diseases or symptoms, including, but not limited to: Scabies, Trombiculiasis, eye infections, intestinal disease (e.g., dysentery, giardiasis), liver disease, lung disease, opportunistic infections (e.g., AIDS related), malaria, pregnancy complications, and toxoplasmosis. polynucleotides or polypeptides, or agonists or antagonists of the invention, can be used totreat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose malaria.

[0966] Preferably, treatment or prevention using a polypeptide or polynucleotide and/or agonist or antagonist of the present invention could either be by administering an effective amount of a polypeptide to the patient, or by removing cells from the patient, supplying the cells with a polynucleotide of the present invention, and returning the engineered cells to the patient (ex vivo therapy). Moreover, the polypeptide or polynucleotide of the present invention can be used as an antigen in a vaccine to raise an immune response against infectious disease.

[0967] Regeneration

[0968] A polynucleotide or polypeptide and/or agonist or antagonist of the present invention can be used to differentiate, proliferate, and attract cells, leading to the regeneration of tissues. (See, Science 276:59-87 (1997).) The regeneration of tissues could be used to repair, replace, or protect tissue damaged by congenital defects, trauma (wounds, burns, incisions, or ulcers), age, disease (e.g. osteoporosis, osteocarthritis, periodontal disease, liver failure), surgery, including cosmetic plastic surgery, fibrosis, reperfusion injury, or systemic cytokine damage.

[0969] Tissues that could be regenerated using the present invention include organs (e.g., pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac), vasculature (including vascular and lymphatics), nervous, hematopoietic, and skeletal (bone, cartilage, tendon, and ligament) tissue. Preferably, regeneration occurs without or decreased scarring. Regeneration also may include angiogenesis.

[0970] Moreover, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase regeneration of tissues difficult to heal. For example, increased tendon/ligament regeneration would quicken recovery time after damage. A polynucleotide or polypeptide and/or agonist or antagonist of the present invention could also be used prophylactically in an effort to avoid damage. Specific diseases that could be treated, prevented, and/or diagnosed include of tendinitis, carpal tunnel syndrome, and other tendon or ligament defects. A further example of tissue regeneration of non-healing wounds includes pressure ulcers, ulcers associated with vascular insufficiency, surgical, and traumatic wounds.

[0971] Similarly, nerve and brain tissue could also be regenerated by using a polynucleotide or polypeptide and/or agonist or antagonist of the present invention to proliferate and differentiate nerve cells. Diseases that could be treated, prevented, and/or diagnosed using this method include central and peripheral nervous system diseases, neuropathies, or mechanical and traumatic diseases, disorders, and/or conditions (e.g., spinal cord disorders, head trauma, cerebrovascular disease, and stoke). Specifically, diseases associated with peripheral nerve injuries, peripheral neuropathy (e.g., resulting from chemotherapy or other medical therapies), localized neuropathies, and central nervous system diseases (e.g., Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome), could all be treated, prevented, and/or diagnosed using the polynucleotide or polypeptide and/or agonist or antagonist of the present invention.

[0972] Binding Activity

[0973] A polypeptide of the present invention may be used to screen for molecules that bind to the polypeptide or for molecules to which the polypeptide binds. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the molecule bound. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors),or small molecules.

[0974] Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a fragment of the ligand, or a natural substrate, a ligand, a structural or functional mimetic. (See, Coligan et al., Current Protocols in Immunology 1(2):Chapter 5 (1991).) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or at least, a fragment of the receptor capable of being bound by the polypeptide (e.g., active site). In either case, the molecule can be rationally designed using known techniques.

[0975] Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide (or cell membrane containing the expressed polypeptide) are then preferably contacted with a test compound potentially containing the molecule to observe binding, stimulation, or inhibition of activity of either the polypeptide or the molecule.

[0976] The assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a label, or in an assay involving competition with a labeled competitor. Further, the assay may test whether the candidate compound results in a signal generated by binding to the polypeptide.

[0977] Alternatively, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.

[0978] Preferably, an ELISA assay can measure polypeptide level or activity in a sample (e.g., biological sample) using a monoclonal or polyclonal antibody. The antibody can measure polypeptide level or activity by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.

[0979] Additionally, the receptor to which a polypeptide of the invention binds can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting (Coligan, et al., Current Protocols in Immun., 1(2), Chapter 5, (1991)). For example, expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the polypeptides, for example, NIH3T3 cells which are known to contain multiple receptors for the FGF family proteins, and SC-3 cells, and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the polypeptides. Transfected cells which are grown on glass slides are exposed to the polypeptide of the present invention, after they have been labeled. The polypeptides can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase.

[0980] Following fixation and incubation, the slides are subjected to auto-radiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an iterative sub-pooling and re-screening process, eventually yielding a single clones that encodes the putative receptor.

[0981] As an alternative approach for receptor identification, the labeled polypeptides can be photoaffinity linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE analysis and exposed to X-ray film. The labeled complex containing the receptors of the polypeptides can be excised, resolved into peptide fragments, and subjected to protein microsequencing. The amino acid sequence obtained from microsequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the genes encoding the putative receptors.

[0982] Moreover, the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as “DNA shuffling”) may be employed to modulate the activities of polypeptides of the invention thereby effectively generating agonists and antagonists of polypeptides of the invention. See generally, U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252, and 5,837,458, and Patten, P. A., et al., Curr. Opinion Biotechnol. 8:724-33 (1997); Harayama, S. Trends Biotechnol. 16(2):76-82 (1998); Hansson, L. O., et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo, M. M. and Blasco, R. Biotechniques 24(2):308-13 (1998) (each of these patents and publications are hereby incorporated by reference). In one embodiment, alteration of polynucleotides and corresponding polypeptides of the invention may be achieved by DNA shuffling. DNA shuffling involves the assembly of two or more DNA segments into a desired polynucleotide sequence of the invention molecule by homologous, or site-specific, recombination. In another embodiment, polynucleotides and corresponding polypeptides of the invention may be altered by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods prior to recombination. In another embodiment, one or more components, motifs, sections, parts, domains, fragments, etc., of the polypeptides of the invention may be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous molecules. In preferred embodiments, the heterologous molecules are family members. In further preferred embodiments, the heterologous molecule is a growth factor such as, for example, platelet-derived growth factor (PDGF), insulin-like growth factor (IGF-I), transforming growth factor (TGF)-alpha, epidermal growth factor (EGF), fibroblast growth factor (FGF), TGF-beta, bone morphogenetic protein (BMP)-2, BMP-4, BMP-5, BMP-6, BMP-7, activins A and B, decapentaplegic(dpp), 60A, OP-2, dorsalin, growth differentiation factors (GDFs), nodal, MIS, inhibin-alpha, TGF-beta1, TGF-beta2, TGF-beta3, TGF-beta5, and glial-derived neurotrophic factor (GDNF).

[0983] Other preferred fragments are biologically active fragments of the polypeptides of the invention. Biologically active fragments are those exhibiting activity similar, but not necessarily identical, to an activity of the polypeptide. The biological activity of the fragments may include an improved desired activity, or a decreased undesirable activity.

[0984] Additionally, this invention provides a method of screening compounds to identify those which modulate the action of the polypeptide of the present invention. An example of such an assay comprises combining a mammalian fibroblast cell, a the polypeptide of the present invention, the compound to be screened and 3 [H] thymidine under cell culture conditions where the fibroblast cell would normally proliferate. A control assay may be performed in the absence of the compound to be screened and compared to the amount of fibroblast proliferation in the presence of the compound to determine if the compound stimulates proliferation by determining the uptake of 3[H] thymidine in each case. The amount of fibroblast cell proliferation is measured by liquid scintillation chromatography which measures the incorporation of 3[H] thymidine. Both agonist and antagonist compounds may be identified by this procedure.

[0985] In another method, a mammalian cell or membrane preparation expressing a receptor for a polypeptide of the present invention is incubated with a labeled polypeptide of the present invention in the presence of the compound. The ability of the compound to enhance or block this interaction could then be measured. Alternatively, the response of a known second messenger system following interaction of a compound to be screened and the receptor is measured and the ability of the compound to bind to the receptor and elicit a second messenger response is measured to determine if the compound is a potential agonist or antagonist. Such second messenger systems include but are not limited to, cAMP guanylate cyclase, ion channels or phosphoinositide hydrolysis.

[0986] All of these above assays can be used as diagnostic or prognostic markers. The molecules discovered using these assays can be used to treat, prevent, and/or diagnose disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptides of the invention from suitably manipulated cells or tissues. Therefore, the invention includes a method of identifying compounds which bind to the polypeptides of the invention comprising the steps of: (a) incubating a candidate binding compound with the polypeptide; and (b) determining if binding has occurred. Moreover, the invention includes a method of identifying agonists/antagonists comprising the steps of: (a) incubating a candidate compound with the polypeptide, (b) assaying a biological activity, and (b) determining if a biological activity of the polypeptide has been altered.

[0987] Also, one could identify molecules bind a polypeptide of the invention experimentally by using the beta-pleated sheet regions contained in the polypeptide sequence of the protein. Accordingly, specific embodiments of the invention are directed to polynucleotides encoding polypeptides which comprise, or alternatively consist of, the amino acid sequence of each beta pleated sheet regions in a disclosed polypeptide sequence. Additional embodiments of the invention are directed to polynucleotides encoding polypeptides which comprise, or alternatively consist of, any combination or all of contained in the polypeptide sequences of the invention. Additional preferred embodiments of the invention are directed to polypeptides which comprise, or alternatively consist of, the amino acid sequence of each of the beta pleated sheet regions in one of the polypeptide sequences of the invention. Additional embodiments of the invention are directed to polypeptides which comprise, or alternatively consist of, any combination or all of the beta pleated sheet regions in one of the polypeptide sequences of the invention.

[0988] Targeted Delivery

[0989] In another embodiment, the invention provides a method of delivering compositions to targeted cells expressing a receptor for a polypeptide of the invention, or cells expressing a cell bound form of a polypeptide of the invention.

[0990] As discussed herein, polypeptides or antibodies of the invention may be associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs via hydrophobic, hydrophilic, ionic and/or covalent interactions. In one embodiment, the invention provides a method for the specific delivery of compositions of the invention to cells by administering polypeptides of the invention (including antibodies) that are associated with heterologous polypeptides or nucleic acids. In one example, the invention provides a method for delivering a therapeutic protein into the targeted cell. In another example, the invention provides a method for delivering a single stranded nucleic acid (e.g., antisense or ribozymes) or double stranded nucleic acid (e.g., DNA that can integrate into the cell's genome or replicate episomally and that can be transcribed) into the targeted cell.

[0991] In another embodiment, the invention provides a method for the specific destruction of cells (e.g., the destruction of tumor cells) by administering polypeptides of the invention (e.g., polypeptides of the invention or antibodies of the invention) in association with toxins or cytotoxic prodrugs.

[0992] By “toxin” is meant compounds that bind and activate endogenous cytotoxic effector systems, radioisotopes, holotoxins, modified toxins, catalytic subunits of toxins, or any molecules or enzymes not normally present in or on the surface of a cell that under defined conditions cause the cell's death. Toxins that may be used according to the methods of the invention include, but are not limited to, radioisotopes known in the art, compounds such as, for example, antibodies (or complement fixing containing portions thereof) that bind an inherent or induced endogenous cytotoxic effector system, thymidine kinase, endonuclease, RNAse, alpha toxin, ricin, abrin, Pseudomonas exotoxin A, diphtheria toxin, saporin, momordin, gelonin, pokeweed antiviral protein, alpha-sarcin and cholera toxin. By “cytotoxic prodrug” is meant a non-toxic compound that is converted by an enzyme, normally present in the cell, into a cytotoxic compound. Cytotoxic prodrugs that may be used according to the methods of the invention include, but are not limited to, glutamyl derivatives of benzoic acid mustard alkylating agent, phosphate derivatives of etoposide or mitomycin C, cytosine arabinoside, daunorubisin, and phenoxyacetamide derivatives of doxorubicin.

[0993] Drug Screening

[0994] Further contemplated is the use of the polypeptides of the present invention, or the polynucleotides encoding these polypeptides, to screen for molecules which modify the activities of the polypeptides of the present invention. Such a method would include contacting the polypeptide of the present invention with a selected compound(s) suspected of having antagonist or agonist activity, and assaying the activity of these polypeptides following binding.

[0995] This invention is particularly useful for screening therapeutic compounds by using the polypeptides of the present invention, or binding fragments thereof, in any of a variety of drug screening techniques. The polypeptide or fragment employed in such a test may be affixed to a solid support, expressed on a cell surface, free in solution, or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or fragment. Drugs are screened against such transformed cells in competitive binding assays. One may measure, for example, the formulation of complexes between the agent being tested and a polypeptide of the present invention.

[0996] Thus, the present invention provides methods of screening for drugs or any other agents which affect activities mediated by the polypeptides of the present invention. These methods comprise contacting such an agent with a polypeptide of the present invention or a fragment thereof and assaying for the presence of a complex between the agent and the polypeptide or a fragment thereof, by methods well known in the art. In such a competitive binding assay, the agents to screen are typically labeled. Following incubation, free agent is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of a particular agent to bind to the polypeptides of the present invention.

[0997] Another technique for drug screening provides high throughput screening for compounds having suitable binding affinity to the polypeptides of the present invention, and is described in great detail in European Patent Application 84/03564, published on Sep. 13, 1984, which is incorporated herein by reference herein. Briefly stated, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. The peptide test compounds are reacted with polypeptides of the present invention and washed. Bound polypeptides are then detected by methods well known in the art. Purified polypeptides are coated directly onto plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing antibodies may be used to capture the peptide and immobilize it on the solid support.

[0998] This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding polypeptides of the present invention specifically compete with a test compound for binding to the polypeptides or fragments thereof. In this manner, the antibodies are used to detect the presence of any peptide which shares one or more antigenic epitopes with a polypeptide of the invention.

[0999] The human CAN-12 polypeptides and/or peptides of the present invention, or immunogenic fragments or oligopeptides thereof, can be used for screening therapeutic drugs or compounds in a variety of drug screening techniques. The fragment employed in such a screening assay may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The reduction or abolition of activity of the formation of binding complexes between the ion channel protein and the agent being tested can be measured. Thus, the present invention provides a method for screening or assessing a plurality of compounds for their specific binding affinity with a CAN-12 polypeptide, or a bindable peptide fragment, of this invention, comprising providing a plurality of compounds, combining the CAN-12 polypeptide, or a bindable peptide fragment, with each of a plurality of compounds for a time sufficient to allow binding under suitable conditions and detecting binding of the CAN-12 polypeptide or peptide to each of the plurality of test compounds, thereby identifying the compounds that specifically bind to the CAN-12 polypeptide or peptide.

[1000] Methods of identifying compounds that modulate the activity of the novel human CAN-12 polypeptides and/or peptides are provided by the present invention and comprise combining a potential or candidate compound or drug modulator of calpain biological activity with an CAN-12 polypeptide or peptide, for example, the CAN-12 amino acid sequence as set forth in SEQ ID NOS:2, and measuring an effect of the candidate compound or drug modulator on the biological activity of the CAN-12 polypeptide or peptide. Such measurable effects include, for example, physical binding interaction; the ability to cleave a suitable calpain substrate; effects on native and cloned CAN-12-expressing cell line; and effects of modulators or other calpain-mediated physiological measures.

[1001] Another method of identifying compounds that modulate the biological activity of the novel CAN-12 polypeptides of the present invention comprises combining a potential or candidate compound or drug modulator of a calpain biological activity with a host cell that expresses the CAN-12 polypeptide and measuring an effect of the candidate compound or drug modulator on the biological activity of the CAN-12 polypeptide. The host cell can also be capable of being induced to express the CAN-12 polypeptide, e.g., via inducible expression. Physiological effects of a given modulator candidate on the CAN-12 polypeptide can also be measured. Thus, cellular assays for particular calpain modulators may be either direct measurement or quantification of the physical biological activity of the CAN-12 polypeptide, or they may be measurement or quantification of a physiological effect. Such methods preferably employ a CAN-12 polypeptide as described herein, or an overexpressed recombinant CAN-12 polypeptide in suitable host cells containing an expression vector as described herein, wherein the CAN-12 polypeptide is expressed, overexpressed, or undergoes upregulated expression.

[1002] Another aspect of the present invention embraces a method of screening for a compound that is capable of modulating the biological activity of a CAN-12 polypeptide, comprising providing a host cell containing an expression vector harboring a nucleic acid sequence encoding a CAN-12 polypeptide, or a functional peptide or portion thereof (e.g., SEQ ID NOS:2); determining the biological activity of the expressed CAN-12 polypeptide in the absence of a modulator compound; contacting the cell with the modulator compound and determining the biological activity of the expressed CAN-12 polypeptide in the presence of the modulator compound. In such a method, a difference between the activity of the CAN-12 polypeptide in the presence of the modulator compound and in the absence of the modulator compound indicates a modulating effect of the compound.

[1003] Essentially any chemical compound can be employed as a potential modulator or ligand in the assays according to the present invention. Compounds tested as calpain modulators can be any small chemical compound, or biological entity (e.g., protein, sugar, nucleic acid, lipid). Test compounds will typically be small chemical molecules and peptides. Generally, the compounds used as potential modulators can be dissolved in aqueous or organic (e.g., DMSO-based) solutions. The assays are designed to screen large chemical libraries by automating the assay steps and providing compounds from any convenient source. Assays are typically run in parallel, for example, in microtiter formats on microtiter plates in robotic assays. There are many suppliers of chemical compounds, including Sigma (St. Louis, Mo.), Aldrich (St. Louis, Mo.), Sigma-Aldrich (St. Louis, Mo.), Fluka Chemika-Biochemica Analytika (Buchs, Switzerland), for example. Also, compounds may be synthesized by methods known in the art.

[1004] High throughput screening methodologies are particularly envisioned for the detection of modulators of the novel CAN-12 polynucleotides and polypeptides described herein. Such high throughput screening methods typically involve providing a combinatorial chemical or peptide library containing a large number of potential therapeutic compounds (e.g., ligand or modulator compounds). Such combinatorial chemical libraries or ligand libraries are then screened in one or more assays to identify those library members (e.g., particular chemical species or subclasses) that display a desired characteristic activity. The compounds so identified can serve as conventional lead compounds, or can themselves be used as potential or actual therapeutics.

[1005] A combinatorial chemical library is a collection of diverse chemical compounds generated either by chemical synthesis or biological synthesis, by combining a number of chemical building blocks (i.e., reagents such as amino acids). As an example, a linear combinatorial library, e.g., a polypeptide or peptide library, is formed by combining a set of chemical building blocks in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide or peptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks.

[1006] The preparation and screening of combinatorial chemical libraries is well known to those having skill in the pertinent art. Combinatorial libraries include, without limitation, peptide libraries (e.g. U.S. Pat. No. 5,010,175; Furka, 1991, Int. J. Pept. Prot. Res., 37:487-493; and Houghton et al., 1991, Nature, 354:84-88). Other chemistries for generating chemical diversity libraries can also be used. Nonlimiting examples of chemical diversity library chemistries include, peptides (PCT Publication No. WO 91/019735), encoded peptides (PCT Publication No. WO 93/20242), random bio-oligomers (PCT Publication No. WO 92/00091), benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., 1993, Proc. Natl. Acad. Sci. USA, 90:6909-6913), vinylogous polypeptides (Hagihara et al., 1992, J. Amer. Chem. Soc., 114:6568), nonpeptidal peptidomimetics with glucose scaffolding (Hirschmann et al., 1992, J. Amer. Chem. Soc., 114:9217-9218), analogous organic synthesis of small compound libraries (Chen et al., 1994, J. Amer. Chem. Soc., 116:2661), oligocarbamates (Cho et al., 1993, Science, 261:1303), and/or peptidyl phosphonates (Campbell et al., 1994, J. Org. Chem., 59:658), nucleic acid libraries (see Ausubel, Berger and Sambrook, all supra), peptide nucleic acid libraries (U.S. Pat. No. 5,539,083), antibody libraries (e.g., Vaughn et al., 1996, Nature Biotechnology, 14(3):309-314) and PCT/US96/10287), carbohydrate libraries (e.g., Liang et al., 1996, Science, 274-1520-1522) and U.S. Pat. No. 5,593,853), small organic molecule libraries (e.g., benzodiazepines, Baum C&EN, Jan. 18, 1993, page 33; and U.S. Pat. No. 5,288,514; isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506,337; and the like).

[1007] Devices for the preparation of combinatorial libraries are commercially available (e.g., 357 MPS, 390 MPS, Advanced Chem Tech, Louisville KY; Symphony, Rainin, Woburn, Mass.; 433A Applied Biosystems, Foster City, Calif.; 9050 Plus, Millipore, Bedford, Mass.). In addition, a large number of combinatorial libraries are commercially available (e.g., ComGenex, Princeton, N.J.; Asinex, Moscow, Russia; Tripos, Inc., St. Louis, Mo.; ChemStar, Ltd., Moscow, Russia; 3D Pharmaceuticals, Exton, Pa.; Martek Biosciences, Columbia, Md., and the like).

[1008] In one embodiment, the invention provides solid phase based in vitro assays in a high throughput format, where the cell or tissue expressing an ion channel is attached to a solid phase substrate. In such high throughput assays, it is possible to screen up to several thousand different modulators or ligands in a single day. In particular, each well of a microtiter plate can be used to perform a separate assay against a selected potential modulator, or, if concentration or incubation time effects are to be observed, every 5-10 wells can test a single modulator. Thus, a single standard microtiter plate can assay about 96 modulators. If 1536 well plates are used, then a single plate can easily assay from about 100 to about 1500 different compounds. It is possible to assay several different plates per day; thus, for example, assay screens for up to about 6,000-20,000 different compounds are possible using the described integrated systems.

[1009] In another of its aspects, the present invention encompasses screening and small molecule (e.g., drug) detection assays which involve the detection or identification of small molecules that can bind to a given protein, i.e., a CAN-12 polypeptide or peptide. Particularly preferred are assays suitable for high throughput screening methodologies.

[1010] In such binding-based detection, identification, or screening assays, a functional assay is not typically required. All that is needed is a target protein, preferably substantially purified, and a library or panel of compounds (e.g., ligands, drugs, small molecules) or biological entities to be screened or assayed for binding to the protein target. Preferably, most small molecules that bind to the target protein will modulate activity in some manner, due to preferential, higher affinity binding to functional areas or sites on the protein.

[1011] An example of such an assay is the fluorescence based thermal shift assay (3-Dimensional Pharmaceuticals, Inc., 3DP, Exton, Pa.) as described in U.S. Pat. Nos. 6,020,141 and 6,036,920 to Pantoliano et al.; see also, J. Zimmerman, 2000, Gen. Eng. News, 20(8)). The assay allows the detection of small molecules (e.g., drugs, ligands) that bind to expressed, and preferably purified, ion channel polypeptide based on affinity of binding determinations by analyzing thermal unfolding curves of protein-drug or ligand complexes. The drugs or binding molecules determined by this technique can be further assayed, if desired, by methods, such as those described herein, to determine if the molecules affect or modulate function or activity of the target protein.

[1012] To purify a CAN-12 polypeptide or peptide to measure a biological binding or ligand binding activity, the source may be a whole cell lysate that can be prepared by successive freeze-thaw cycles (e.g., one to three) in the presence of standard protease inhibitors. The CAN-12 polypeptide may be partially or completely purified by standard protein purification methods, e.g., affinity chromatography using specific antibody described infra, or by ligands specific for an epitope tag engineered into the recombinant CAN-12 polypeptide molecule, also as described herein. Binding activity can then be measured as described.

[1013] Compounds which are identified according to the methods provided herein, and which modulate or regulate the biological activity or physiology of the CAN-12 polypeptides according to the present invention are a preferred embodiment of this invention. It is contemplated that such modulatory compounds may be employed in treatment and therapeutic methods for treating a condition that is mediated by the novel CAN-12 polypeptides by administering to an individual in need of such treatment a therapeutically effective amount of the compound identified by the methods described herein.

[1014] In addition, the present invention provides methods for treating an individual in need of such treatment for a disease, disorder, or condition that is mediated by the CAN-12 polypeptides of the invention, comprising administering to the individual a therapeutically effective amount of the CAN-12-modulating compound identified by a method provided herein.

[1015] Antisense and Ribozyme (Antagonists)

[1016] In specific embodiments, antagonists according to the present invention are nucleic acids corresponding to the sequences contained in SEQ ID NO:1, 23, 53, and/or 55, or the complementary strand thereof, and/or to nucleotide sequences contained a deposited clone. In one embodiment, antisense sequence is generated internally by the organism, in another embodiment, the antisense sequence is separately administered (see, for example, O'Connor, Neurochem., 56:560 (1991). Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Antisense technology can be used to control gene expression through antisense DNA or RNA, or through triple-helix formation. Antisense techniques are discussed for example, in Okano, Neurochem., 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple helix formation is discussed in, for instance, Lee et al., Nucleic Acids Research, 6:3073 (1979); Cooney et al., Science, 241:456 (1988); and Dervan et al., Science, 251:1300 (1991). The methods are based on binding of a polynucleotide to a complementary DNA or RNA.

[1017] For example, the use of c-myc and c-myb antisense RNA constructs to inhibit the growth of the non-lymphocytic leukemia cell line HL-60 and other cell lines was previously described. (Wickstrom et al. (1988); Anfossi et al. (1989)). These experiments were performed in vitro by incubating cells with the oligoribonucleotide. A similar procedure for in vivo use is described in WO 91/15580. Briefly, a pair of oligonucleotides for a given antisense RNA is produced as follows: A sequence complimentary to the first 15 bases of the open reading frame is flanked by an EcoR1 site on the 5 end and a HindIII site on the 3 end. Next, the pair of oligonucleotides is heated at 90° C. for one minute and then annealed in 2× ligation buffer (20 mM TRIS HCl pH 7.5, 10 mM MgCl2, 10MM dithiothreitol (DTT) and 0.2 mM ATP) and then ligated to the EcoR1/Hind III site of the retroviral vector PMV7 (WO 91/15580).

[1018] For example, the 5′ coding portion of a polynucleotide that encodes the mature polypeptide of the present invention may be used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription thereby preventing transcription and the production of the receptor. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into receptor polypeptide.

[1019] In one embodiment, the antisense nucleic acid of the invention is produced intracellularly by transcription from an exogenous sequence. For example, a vector or a portion thereof, is transcribed, producing an antisense nucleic acid (RNA) of the invention. Such a vector would contain a sequence encoding the antisense nucleic acid of the invention. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in vertebrate cells. Expression of the sequence encoding a polypeptide of the invention, or fragments thereof, can be by any promoter known in the art to act in vertebrate, preferably human cells. Such promoters can be inducible or constitutive. Such promoters include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, Nature, 29:304-310 (1981), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., Cell, 22:787-797 (1980), the herpes thymidine promoter (Wagner et al., Proc. Natl. Acad. Sci. U.S.A., 78:1441-1445 (1981), the regulatory sequences of the metallothionein gene (Brinster et al., Nature, 296:39-42 (1982)), etc.

[1020] The antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of an RNA transcript of a gene of interest. However, absolute complementarity, although preferred, is not required. A sequence “complementary to at least a portion of an RNA,” referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double stranded antisense nucleic acids of the invention, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid Generally, the larger the hybridizing nucleic acid, the more base mismatches with a RNA sequence of the invention it may contain and still form a stable duplex (or triplex as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

[1021] Oligonucleotides that are complementary to the 5′ end of the message, e.g., the 5′ untranslated sequence up to and including the AUG initiation codon, should work most efficiently at inhibiting translation. However, sequences complementary to the 3′ untranslated sequences of mRNAs have been shown to be effective at inhibiting translation of mRNAs as well. See generally, Wagner, R., Nature, 372:333-335 (1994). Thus, oligonucleotides complementary to either the 5′- or 3′-non-translated, non-coding regions of a polynucleotide sequence of the invention could be used in an antisense approach to inhibit translation of endogenous mRNA. Oligonucleotides complementary to the 5′ untranslated region of the mRNA should include the complement of the AUG start codon. Antisense oligonucleotides complementary to mRNA coding regions are less efficient inhibitors of translation but could be used in accordance with the invention. Whether designed to hybridize to the 5′-, 3′- or coding region of mRNA, antisense nucleic acids should be at least six nucleotides in length, and are preferably oligonucleotides ranging from 6 to about 50 nucleotides in length. In specific aspects the oligonucleotide is at least 10 nucleotides, at least 17 nucleotides, at least 25 nucleotides or at least 50 nucleotides.

[1022] The polynucleotides of the invention can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, hybridization, etc. The oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556 (1989); Lemaitre et al., Proc. Natl. Acad. Sci., 84:648-652 (1987); PCT Publication NO: WO88/09810, published Dec. 15, 1988) or the blood-brain barrier (see, e.g., PCT Publication NO: WO89/10134, published Apr. 25, 1988), hybridization-triggered cleavage agents. (See, e.g., Krol et al., BioTechniques, 6:958-976 (1988)) or intercalating agents. (See, e.g., Zon, Pharm. Res., 5:539-549 (1988)). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent, etc.

[1023] The antisense oligonucleotide may comprise at least one modified base moiety which is selected from the group including, but not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine; 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine.

[1024] The antisense oligonucleotide may also comprise at least one modified sugar moiety selected from the group including, but not limited to, arabinose, 2-fluoroarabinose, xylulose, and hexose.

[1025] In yet another embodiment, the antisense oligonucleotide comprises at least one modified phosphate backbone selected from the group including, but not limited to, a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof In yet another embodiment, the antisense oligonucleotide is an a-anomeric oligonucleotide. An a-anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gautier et al., Nucl. Acids Res., 15:6625-6641 (1987)). The oligonucleotide is a 2-0-methylribonucleotide (Inoue et al., Nucl. Acids Res., 15:6131-6148 (1987)), or a chimeric RNA-DNA analogue (Inoue et al., FEBS Lett. 215:327-330 (1987)).

[1026] Polynucleotides of the invention may be synthesized by standard methods known in the art, e.g. by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc.). As examples, phosphorothioate oligonucleotides may be synthesized by the method of Stein et al. (Nucl. Acids Res., 16:3209 (1988)), methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports (Sarin et al., Proc. Natl. Acad. Sci. U.S.A., 85:7448-7451 (1988)), etc.

[1027] While antisense nucleotides complementary to the coding region sequence of the invention could be used, those complementary to the transcribed untranslated region are most preferred.

[1028] Potential antagonists according to the invention also include catalytic RNA, or a ribozyme (See, e.g., PCT International Publication WO 90/11364, published Oct. 4, 1990; Sarver et al, Science, 247:1222-1225 (1990). While ribozymes that cleave mRNA at site specific recognition sequences can be used to destroy mRNAs corresponding to the polynucleotides of the invention, the use of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target mRNA have the following sequence of two bases: 5′-UG-3′. The construction and production of hammerhead ribozymes is well known in the art and is described more fully in Haseloff and Gerlach, Nature, 334:585-591 (1988). There are numerous potential hammerhead ribozyme cleavage sites within each nucleotide sequence disclosed in the sequence listing. Preferably, the ribozyme is engineered so that the cleavage recognition site is located near the 5′ end of the mRNA corresponding to the polynucleotides of the invention; i.e., to increase efficiency and minimize the intracellular accumulation of non-functional mRNA transcripts.

[1029] As in the antisense approach, the ribozymes of the invention can be composed of modified oligonucleotides (e.g. for improved stability, targeting, etc.) and should be delivered to cells which express the polynucleotides of the invention in vivo. DNA constructs encoding the ribozyme may be introduced into the cell in the same manner as described above for the introduction of antisense encoding DNA. A preferred method of delivery involves using a DNA construct “encoding” the ribozyme under the control of a strong constitutive promoter, such as, for example, pol III or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to destroy endogenous messages and inhibit translation. Since ribozymes unlike antisense molecules, are catalytic, a lower intracellular concentration is required for efficiency.

[1030] Antagonist/agonist compounds may be employed to inhibit the cell growth and proliferation effects of the polypeptides of the present invention on neoplastic cells and tissues, i.e. stimulation of angiogenesis of tumors, and, therefore, retard or prevent abnormal cellular growth and proliferation, for example, in tumor formation or growth.

[1031] The antagonist/agonist may also be employed to prevent hyper-vascular diseases, and prevent the proliferation of epithelial lens cells after extracapsular cataract surgery. Prevention of the mitogenic activity of the polypeptides of the present invention may also be desirous in cases such as restenosis after balloon angioplasty.

[1032] The antagonist/agonist may also be employed to prevent the growth of scar tissue during wound healing.

[1033] The antagonist/agonist may also be employed to treat, prevent, and/or diagnose the diseases described herein.

[1034] Thus, the invention provides a method of treating or preventing diseases, disorders, and/or conditions, including but not limited to the diseases, disorders, and/or conditions listed throughout this application, associated with overexpression of a polynucleotide of the present invention by administering to a patient (a) an antisense molecule directed to the polynucleotide of the present invention, and/or (b) a ribozyme directed to the polynucleotide of the present invention.

[1035] invention, and/or (b) a ribozyme directed to the polynucleotide of the present invention.

[1036] Biotic Associations

[1037] A polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase the organisms ability, either directly or indirectly, to initiate and/or maintain biotic associations with other organisms. Such associations may be symbiotic, nonsymbiotic, endosymbiotic, macrosymbiotic, and/or microsymbiotic in nature. In general, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase the organisms ability to form biotic associations with any member of the fungal, bacterial, lichen, mycorrhizal, cyanobacterial, dinoflaggellate, and/or algal, kingdom, phylums, families, classes, genuses, and/or species.

[1038] The mechanism by which a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase the host organisms ability, either directly or indirectly, to initiate and/or maintain biotic associations is variable, though may include, modulating osmolarity to desirable levels for the symbiont, modulating pH to desirable levels for the symbiont, modulating secretions of organic acids, modulating the secretion of specific proteins, phenolic compounds, nutrients, or the increased expression of a protein required for host-biotic organisms interactions (e.g., a receptor, ligand, etc.). Additional mechanisms are known in the art and are encompassed by the invention (see, for example, “Microbial Signalling and Communication”, eds., R. England, G. Hobbs, N. Bainton, and D. McL. Roberts, Cambridge University Press, Cambridge, (1999); which is hereby incorporated herein by reference).

[1039] In an alternative embodiment, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may decrease the host organisms ability to form biotic associations with another organism, either directly or indirectly. The mechanism by which a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may decrease the host organisms ability, either directly or indirectly, to initiate and/or maintain biotic associations with another organism is variable, though may include, modulating osmolarity to undesirable levels, modulating pH to undesirable levels, modulating secretions of organic acids, modulating the secretion of specific proteins, phenolic compounds, nutrients, or the decreased expression of a protein required for host-biotic organisms interactions (e.g., a receptor, ligand, etc.). Additional mechanisms are known in the art and are encompassed by the invention (see, for example, “Microbial Signalling and Communication”, eds., R. England, G. Hobbs, N. Bainton, and D. McL. Roberts, Cambridge University Press, Cambridge, (1999); which is hereby incorporated herein by reference).

[1040] The hosts ability to maintain biotic associations with a particular pathogen has significant implications for the overall health and fitness of the host. For example, human hosts have symbiosis with enteric bacteria in their gastrointestinal tracts, particularly in the small and large intestine. In fact, bacteria counts in feces of the distal colon often approach 1012 per milliliter of feces. Examples of bowel flora in the gastrointestinal tract are members of the Enterobacteriaceae, Bacteriodes, in addition to a-hemolytic streptococci, E. coli, Bifobacteria, Anaerobic cocci, Eubacteria, Costridia, lactobacilli, and yeasts. Such bacteria, among other things, assist the host in the assimilation of nutrients by breaking down food stuffs not typically broken down by the hosts digestive system, particularly in the hosts bowel. Therefore, increasing the hosts ability to maintain such a biotic association would help assure proper nutrition for the host.

[1041] Aberrations in the enteric bacterial population of mammals, particularly humans, has been associated with the following disorders: diarrhea, ileus, chronic inflammatory disease, bowel obstruction, duodenal diverticula, biliary calculous disease, and malnutrition. A polynucleotide or polypeptide and/or agonist or antagonist of the present invention are useful for treating, detecting, diagnosing, prognosing, and/or ameliorating, either directly or indirectly, and of the above mentioned diseases and/or disorders associated with aberrant enteric flora population.

[1042] The composition of the intestinal flora, for example, is based upon a variety of factors, which include, but are not limited to, the age, race, diet, malnutrition, gastric acidity, bile salt excretion, gut motility, and immune mechanisms. As a result, the polynucleotides and polypeptides, including agonists, antagonists, and fragments thereof, may modulate the ability of a host to form biotic associations by affecting, directly or indirectly, at least one or more of these factors.

[1043] Although the predominate intestinal flora comprises anaerobic organisms, an underlying percentage represents aerobes (e.g., E. coli). This is significant as such aerobes rapidly become the predominate organisms in intraabdominal infections—effectively becoming opportunistic early in infection pathogenesis. As a result, there is an intrinsic need to control aerobe populations, particularly for immune compromised individuals.

[1044] In a preferred embodiment, a polynucleotides and polypeptides, including agonists, antagonists, and fragments thereof, are useful for inhibiting biotic associations with specific enteric symbiont organisms in an effort to control the population of such organisms.

[1045] Biotic associations occur not only in the gastrointestinal tract, but also on an in the integument. As opposed to the gastrointestinal flora, the cutaneous flora is comprised almost equally with aerobic and anaerobic organisms. Examples of cutaneous flora are members of the gram-positive cocci (e.g., S. aureus, coagulase-negative staphylococci, micrococcus, M. sedentarius), gram-positive bacilli (e.g., Corynebacterium species, C. minutissimum, Brevibacterium species, Propoionibacterium species, P. acnes), gram-negative bacilli (e.g., Acinebacter species), and fungi (Pityrosporum orbiculare). The relatively low number of flora associated with the integument is based upon the inability of many organisms to adhere to the skin. The organisms referenced above have acquired this unique ability. Therefore, the polynucleotides and polypeptides of the present invention may have uses which include modulating the population of the cutaneous flora, either directly or indirectly.

[1046] Aberrations in the cutaneous flora are associated with a number of significant diseases and/or disorders, which include, but are not limited to the following: impetigo, ecthyma, blistering distal dactulitis, pustules, folliculitis, cutaneous abscesses, pitted keratolysis, trichomycosis axcillaris, dermatophytosis complex, axillary odor, erthyrasma, cheesy foot odor, acne, tinea versicolor, seborrheic dermititis, and Pityrosporum folliculitis, to name a few. A polynucleotide or polypeptide and/or agonist or antagonist of the present invention are useful for treating, detecting, diagnosing, prognosing, and/or ameliorating, either directly or indirectly, and of the above mentioned diseases and/or disorders associated with aberrant cutaneous flora population.

[1047] Additional biotic associations, including diseases and disorders associated with the aberrant growth of such associations, are known in the art and are encompassed by the invention. See, for example, “Infectious Disease”, Second Edition, Eds., S. L., Gorbach, J. G., Bartlett, and N. R., Blacklow, W. B. Saunders Company, Philadelphia, (1998); which is hereby incorporated herein by reference).

[1048] Pheromones

[1049] In another embodiment, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase the organisms ability to synthesize and/or release a pheromone. Such a pheromone may, for example, alter the organisms behavior and/or metabolism.

[1050] A polynucleotide or polypeptide and/or agonist or antagonist of the present invention may modulate the biosynthesis and/or release of pheromones, the organisms ability to respond to pheromones (e.g., behaviorally, and/or metabolically), and/or the organisms ability to detect pheromones. Preferably, any of the pheromones, and/or volatiles released from the organism, or induced, by a polynucleotide or polypeptide and/or agonist or antagonist of the invention have behavioral effects the organism.

[1051] Other Activities

[1052] The polypeptide of the present invention, as a result of the ability to stimulate vascular endothelial cell growth, may be employed in treatment for stimulating re-vascularization of ischemic tissues due to various disease conditions such as thrombosis, arteriosclerosis, and other cardiovascular conditions. These polypeptide may also be employed to stimulate angiogenesis and limb regeneration, as discussed above.

[1053] The polypeptide may also be employed for treating wounds due to injuries, burns, post-operative tissue repair, and ulcers since they are mitogenic to various cells of different origins, such as fibroblast cells and skeletal muscle cells, and therefore, facilitate the repair or replacement of damaged or diseased tissue.

[1054] The polypeptide of the present invention may also be employed stimulate neuronal growth and to treat, prevent, and/or diagnose neuronal damage which occurs in certain neuronal disorders or neuro-degenerative conditions such as Alzheimer's disease, Parkinson's disease, and AIDS-related complex. The polypeptide of the invention may have the ability to stimulate chondrocyte growth, therefore, they may be employed to enhance bone and periodontal regeneration and aid in tissue transplants or bone grafts.

[1055] The polypeptide of the present invention may be also be employed to prevent skin aging due to sunburn by stimulating keratinocyte growth.

[1056] The polypeptide of the invention may also be employed for preventing hair loss, since FGF family members activate hair-forming cells and promotes melanocyte growth. Along the same lines, the polypeptides of the present invention may be employed to stimulate growth and differentiation of hematopoietic cells and bone marrow cells when used in combination with other cytokines.

[1057] The polypeptide of the invention may also be employed to maintain organs before transplantation or for supporting cell culture of primary tissues.

[1058] The polypeptide of the present invention may also be employed for inducing tissue of mesodermal origin to differentiate in early embryos.

[1059] The polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also increase or decrease the differentiation or proliferation of embryonic stem cells, besides, as discussed above, hematopoietic lineage.

[1060] The polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used to modulate mammalian characteristics, such as body height, weight, hair color, eye color, skin, percentage of adipose tissue, pigmentation, size, and shape (e.g., cosmetic surgery). Similarly, polypeptides or polynucleotides and/or agonist or antagonists of the present invention may be used to modulate mammalian metabolism affecting catabolism, anabolism, processing, utilization, and storage of energy.

[1061] Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may be used to change a mammal's mental state or physical state by influencing biorhythms, caricadic rhythms, depression (including depressive diseases, disorders, and/or conditions), tendency for violence, tolerance for pain, reproductive capabilities (preferably by Activin or Inhibin-like activity), hormonal or endocrine levels, appetite, libido, memory, stress, or other cognitive qualities.

[1062] Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used to increase the efficacy of a pharmaceutical composition, either directly or indirectly. Such a use may be administered in simultaneous conjunction with said pharmaceutical, or separately through either the same or different route of administration (e.g., intravenous for the polynucleotide or polypeptide of the present invention, and orally for the pharmaceutical, among others described herein.).

[1063] Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used to prepare individuals for extraterrestrial travel, low gravity environments, prolonged exposure to extraterrestrial radiation levels, low oxygen levels, reduction of metabolic activity, exposure to extraterrestrial pathogens, etc. Such a use may be administered either prior to an extraterrestrial event, during an extraterrestrial event, or both. Moreover, such a use may result in a number of beneficial changes in the recipient, such as, for example, any one of the following, non-limiting, effects: an increased level of hematopoietic cells, particularly red blood cells which would aid the recipient in coping with low oxygen levels; an increased level of B-cells, T-cells, antigen presenting cells, and/or macrophages, which would aid the recipient in coping with exposure to extraterrestrial pathogens, for example; a temporary (i.e., reversible) inhibition of hematopoietic cell production which would aid the recipient in coping with exposure to extraterrestrial radiation levels; increase and/or stability of bone mass which would aid the recipient in coping with low gravity environments; and/or decreased metabolism which would effectively facilitate the recipients ability to prolong their extraterrestrial travel by any one of the following, non-limiting means: (i) aid the recipient by decreasing their basal daily energy requirements; (ii) effectively lower the level of oxidative and/or metabolic stress in recipient (i.e., to enable recipient to cope with increased extraterrestial radiation levels by decreasing the level of internal oxidative/metabolic damage acquired during normal basal energy requirements; and/or (iii) enabling recipient to subsist at a lower metabolic temperature (i.e., cryogenic, and/or sub-cryogenic environment).

[1064] Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used as a food additive or preservative, such as to increase or decrease storage capabilities, fat content, lipid, protein, carbohydrate, vitamins, minerals, cofactors or other nutritional components.

[1065] Other Preferred Embodiments

[1066] Further preferred is a method of making a recombinant vector comprising inserting any of the above isolated nucleic acid molecule(s) into a vector. Also preferred is the recombinant vector produced by this method. Also preferred is a method of making a recombinant host cell comprising introducing the vector into a host cell, as well as the recombinant host cell produced by this method.

[1067] Also preferred is a method of making an isolated polypeptide comprising culturing this recombinant host cell under conditions such that said polypeptide is expressed and recovering said polypeptide. Also preferred is this method of making an isolated polypeptide, wherein said recombinant host cell is a eukaryotic cell and said polypeptide is a protein comprising an amino acid sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:2, 24, 54, and/or 56 wherein Y is an integer set forth in Table I and said position of the “Total AA of ORF” of SEQ ID NO:2, 24, 54, and/or 56 is defined in Table I; and an amino acid sequence of a protein encoded by a cDNA clone identified by a cDNA Clone Identifier in Table I and contained in the deposit with the ATCC Deposit Number shown for said cDNA clone in Table I. The isolated polypeptide produced by this method is also preferred.

[1068] Also preferred is a method of treatment of an individual in need of an increased level of a protein activity, which method comprises administering to such an individual a pharmaceutical composition comprising an amount of an isolated polypeptide, polynucleotide, or antibody of the claimed invention effective to increase the level of said protein activity in said individual.

[1069] Having generally described the invention, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting.

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EXAMPLES

Description of the Preferred Embodiments

Example 1

Bioinformatics Analysis

[1085] To search for novel protease inhibitors, a Hidden-Markov Model (HMM) of cysteine proteases (obtained from the Pfam database in Sanger center) was used to search against the human genomic sequence database using a computer program called GENEWISEDB. Genomic sequences that were found to have a GENEWISEDB matching score of more than 15 were selected for further analysis. The genomic sequence contained in BAC (bacteria artificial chromosome) AC015980 (Genbank Accession No. AC015980) was found to contain a putative exon sequence. The portion of the sequence from AC015980 that matched was extracted and back-searched against the Genbank non-redundant protein database using the BLASTX program (SEQ ID NO:26). The most similar protein sequence, the human CAN5 protein (SEQ ID NO:4), was used as a template to predict more exons from AC015980 using the GENEWISEDB program (see FIG. 7). The final predicted exons were assembled and a full length clone of the gene was obtained using the predicted exon sequences. The protein sequence was found to have significant sequence homology with a family of known proteases. Based on the sequence, structure and known calpain signature sequences, the novel gene was determined to represent a novel human calpain protease and have provisionally named the gene CAN-12 (calcium activated neutral protease 12) and the protease itself as calpain 12.

Example 2

Method for Constructing a Size Fractionated Brain and Testis cDNA Library

[1086] Brain and testis poly A+RNA was purchased from Clontech and converted into double stranded cDNA using the SuperScript™ Plasmid System for cDNA Synthesis and Plasmid Cloning (Life Technologies) except that no radioisotope was incorporated in either of the cDNA synthesis steps and that the cDNA was fractionated by HPLC. This was accomplished on a TransGenomics HPLC system equipped with a size exclusion column (TosoHass) with dimensions of 7.8 mm×30 cm and a particle size of 10 um. Tris buffered saline was used as the mobile phase and the column was run at a flow rate of 0.5 mL/min.

[1087] The resulting chromatograms were analyzed to determine which fractions should be pooled to obtain the largest cDNA's; generally fractions that eluted in the range of 12 to 15 minutes were pooled. The cDNA was precipitated prior to ligation into the Sal I/Not I sites in the pSport vector supplied with the kit. Using a combination of PCR with primers to the ends of the vector and Sal I/Not I restriction enzyme digestion of mini-prep DNA, it was determined that the average insert size of the library was greater the 3.5 Kb. The overall complexity of the library was greater that 107 independent clones. The library was amplified in semi-solid agar for 2 days at 30° C. An aliquot (200 microliters) of the amplified library was inoculated into a 200 ml culture for single-stranded DNA isolation by super-infection with a f1 helper phage. After overnight growth, the released phage particles with precipitated with PEG and the DNA isolated with proteinase K, SDS and phenol extractions. The single stranded circular DNA was concentrated by ethanol precipitation and used for the cDNA capture experiments.

Example 3

Method of Cloning the Novel Human CAN-12 Calpain

[1088] Using the predicted exon genomic sequence from bac AC015980 (FIG. 7; SEQ ID NO:13, 14, 15, 16, 17, and 26) an antisense 80 bp oligonucleotide with biotin on the 5′ end was designed with the following sequence;

75′bAGGGAGCCACTGCCGATGGAGCTCAGGGTGGCCGGGAAGCTGGTGTCTTCAAAGAGGCAGCCATTCCTCAGGCACTC-3′(SEQ ID NO:18)

[1089] One microliter (one hundred and fifty nanograms) of the biotinylated oligonucleotide was added to six microliters (six micrograms) of a mixture of single-stranded covalently closed circular liver, brain, testis, and spleen cDNA libraries and seven microliters of 100% formamide in a 0.5 ml PCR tube. The library was a mixture of the brain and testis cDNA library referenced in Example 2, in addition to, commercially available liver and spleen cDNA libraries from Life Technologies (Rockville, Md.). The mixture was heated in a thermal cycler to 95° C. for 2 mins. Fourteen microliters of 2× hybridization buffer (50% formamide, 1.5 M NaCl, 0.04 M NaPO4, pH 7.2, 5 mM EDTA, 0.2% SDS) was added to the heated probe/cDNA library mixture and incubated at 42° C. for 26 hours. Hybrids between the biotinylated oligonucleotide and the circular cDNA were isolated by diluting the hybridization mixture to 220 microliters in a solution containing 1 M NaCl, 10 mM Tris-HCl pH 7.5, 1 mM EDTA, pH 8.0 and adding 125 microliters of streptavidin magnetic beads. This solution was incubated at 42° C. for 60 mins, mixing every 5 mins to resuspend the beads. The beads were separated from the solution with a magnet and the beads washed three times in 200 microliters of 0.1× SSPE, 0.1% SDS at 45° C.

[1090] The single stranded cDNAs were released from the biotinlyated oligonucleotide/streptavidin magnetic bead complex by adding 50 microliters of 0.1 N NaOH and incubating at room temperature for 10 mins. Six microliters of 3 M Sodium Acetate was added along with 15 micrograms of glycogen and the solution ethanol precipitated with 120 microliters of 100% ethanol. The DNA was resuspended in 12 microliters of TE (10 mM Tris-HCl, pH 8.0), 1 mM EDTA, pH 8.0). The single stranded cDNA was converted into double strands in a thermal cycler by mixing 5 microliters of the captured DNA with 1.5 microliters 10 micromolar standard SP6 primer (homologous to a sequence on the cDNA cloning vector) and 1.5 microliters of 10× PCR buffer. The mixture was heated to 95° C. for 20 seconds then ramped down to 59° C. At this time 15 microliters of a repair mix, that was preheated to 70° C. (Repair mix contains 4 microliters of 5 mM dNTPs (1.25 mM each), 1.5 microliters of 10× PCR buffer, 9.25 microliters of water, and 0.25 microliters of Taq polymerase). The solution was ramped back to 73° C. and incubated for 23 mins. The repaired DNA was ethanol precipitate and resuspended in 10 microliters of TE. Two microliters were electroporated in E. coli DH12S cells and resulting colonies were screen by PCR, using a primer pair designed from the genomic exonic sequence to identify the proper cDNAs.

[1091] Oligonucleotides used to identity the cDNA by PCR.

[1092] AC015980-L1 GACTTTGAGGCCCTGCTG (SEQ ID NO:19)

[1093] AC015980-R1 ACAGGAACCCAGTTCCCATA (SEQ ID NO:20)

[1094] A single cDNA clone was positive by PCR. The insert was sized and the clone was sequenced. The sequence of the cDNA clone revealed an unspliced intron, in addition to a three base-pair deletion (SEQ ID NO:1). Further attempts to obtain more clones with this method were unsuccessful, so an RT-PCR cloning approach was applied.

[1095] The nucleotide sequence and the encoded polypeptide for CAN-12 containing the unspliced intron and three base-pair deletion is shown in FIGS. 1A-E (SEQ ID NO:1).

Example 4

Method of Cloning the Novel Human CAN-12 Calpain via RT-PCR

[1096] The cDNA was amplified from testis stranded cDNA and spinal cord first strand cDNA using the following RT-PCR primer pair in a standard PCR reaction (25 ng of DNA template were added to the reaction mixture along with each oligonucleotide primer at a final concentration of 0.2 μM each. The total volume of the reactions was 50 μL).

8(SEQ ID NO:21)RT-PCR Sense PRIMERCACCTGCCATGTCTCTGTG(SEQ ID NO:22)RT-PCR Antisense PRIMERGATTATAACAAGGTGGTGTTGAAGA

[1097] The thermal cycling conditions for the PCR were as follows:

996° C. 2 minutesThen 45 cycles of:94° C.30 seconds55° C.30 seconds72° C. 3 minutesThen one cycle of:72° C.10 minutes 4° C.hold

[1098] The PCR was then subjected to electrophoresis on a 1% agarose gel. Bands on the gel were visualized of the predicted size. The bands were excised from the gel with a razor blade.

[1099] The PCR products were then extracted from the agarose gel slice using the Qiagen QIAquick™ Gel Extraction kit. Briefly, 3 volumes of buffer QG are added to the gel slice. The mixture is incubated at 50° C. until the agarose is melted. Then one volume of isopropanol is added. The sample is applied to a QIAquick spin column and centrifuged for 1 minute at high speed. The DNA binds to the column. The column is washed by applying 750 μL of buffer PE to and centrifuging for 1 minute. The column is then dried by spinning for an additional minute at high speed. The DNA is eluted from the column by applying 30 μL of elution buffer (buffer EB), letting the column stand for 1 minute, then centrifuging the column at high speed for 1 minute. The eluate is collected in a microcentrifuge tube.

[1100] Next, a ‘TA’ cloning procedure was used to insert the amplified fragment into a plasmid vector. In order to use the ‘TA’ cloning strategy, the PCR amplicon must have a 3′ ‘A’ overhang which is generated by Taq polymerase. Since a high fidelity, proofreading enzyme was used for the PCR amplification, the proofreading properties of the enzyme mix cause the ‘A’ overhang to be removed. Therefore, before the ‘TA’ cloning could be done, ‘A’ overhangs had to be added to the PCR product. To do this, the PCR product was incubated for 15 minutes at 72° C. in a mixture containing 5 units of Taq polymerase, 1× PCR buffer and 0.2 mM dATP (all from Roche). The Taq polymerase is from Thermus aquaticus BM, recombinant E. coli. The 10× PCR buffer contains 100 mM Tris-HCl, 15 mM MgCl2, 500 mM KCl, pH 8.3.

[1101] The PCR products with added 3′ ‘A’ overhangs was then immediately used for ‘TA’ cloning. To do this, the TOPO TA Cloning® Kit for Sequencing from Invitrogen was used.

[1102] The following reaction mixture was set up:

[1103] 4 μL PCR product

[1104] 1 μL Salt Solution

[1105] 1 μL pCR® 4-TOPO® vector

[1106] This was incubated at room temperature for 5 minutes.

[1107] Then 2 μL of this reaction were added to a vial of TOP10 One Shot® chemically competent E. Coli. This was incubated on ice for 5 minutes. The cells were then heat shocked at 42° C. for 30 seconds. Cells were transferred to ice for another 5 minutes. 250 μL of room temperature S.O.C. medium was added to the cells. The cells were then incubated at 37° C. for 1 hour with shaking for aeration. 50 μL of cells were spread on selective plates containing 50 μg/μL carbenicillin and incubated at 37° C. overnight. A more detailed protocol for this kit from Invitrogen is available from their website (http://www.invitrogen.com).

[1108] The next step was to screen colonies that grew on the selective plates for positive clones. This was done by growing 7 colonies from the testis PCR and 7 from the spinal cord PCR overnight in 4 mL of LB broth containing 50 μg/μL carbenicillin. The plasmid DNA was then isolated from the bacteria using the Qiagen QIAquick Spin Miniprep Kit. Protocols for this are available from the Qiagen company web site (http://www.qiagen.com).

[1109] Once the plasmid DNA was purified, a restriction digest analysis was performed to determine if the clones were correct. A restriction enzyme digestion was performed with NotI and SpeI restriction endonucleases, using the suggested buffer and 5 μL of the purified plasmid, 5 units of enzyme in a total volume of 20 μL. The mixture was incubated at 37° C. for 2 hours. The digest was visualized by electrophoretic separation on a 1% agarose gel stained with ethidium bromide. From this analysis it was apparent the plasmids contained one size insert corresponding to the predicted insert size of the transcript. Two clones from each PCR reaction were sequenced using Applied Biosystems BigDye™ dideoxy terminator cycle sequencing on an Applied Biosystems 3700 capillary array DNA sequencer.

[1110] The above method resulted in several positive clones. After sequencing, it was determined that all of them had an unspliced intron that introduced a stop codon, with the exception of clone le (CAN-12v1; FIGS. 8A-C; SEQ ID NO:53). Clone 1e was correct, except for it was missing 3 amino acids in the middle of the protein (See FIG. 10A-B). It is thought that these three amino acids may represent an exon of the CAN-12v1 polynucleotide.

[1111] Although the other clones contained the unspliced intron, one of the clones, clone 1b, had the missing 3 amino acids. Thus, clone le and clone 1b were recombinately combined together effectively cutting out the region of clone 1e that was missing the terminal three amino acids, and replacing it with the same region from clone 1b which did have the three amino acids. The resulting recombinant clone is named clone 1e1b (CAN-12v2), and is provided in FIGS. 9A-C (SEQ ID NO:55).

[1112] The method of recombinately combining clone le and clone 1b are provided below. The part of clone le that had the missing exon was excised by restriction digestion with unique cutting enzymes BamHI and AvaI. The corresponding fragment with the small exon (three amino acids) from clone 1b was excised with the same enzymes and inserted into clone le. This yielded the complete correct coding sequence that was predicted. The clone was called 1e1b (CAN-12v2; FIGS. 9A-C; SEQ ID NO:55). CAN-12v2 is believed to represent the true physioligical form of CAN-12.

Example 5

Expression Profiling of the Novel Human CAN-12 Calpain

[1113] The same PCR primer pair that was used to identify the novel CAN-12 cDNA clones via RT-PCR (SEQ ID NO: 21 and 22) was used to measure the steady state levels of mRNA by quantitative PCR. Briefly, first strand cDNA was made from commercially available mRNA. The relative amount of cDNA used in each assay was determined by performing a parallel experiment using a primer pair for a gene expressed in equal amounts in all tissues, cyclophilin. The cyclophilin primer pair detected small variations in the amount of cDNA in each sample and these data were used for normalization of the data obtained with the primer pair for the novel CAN-12. The PCR data was converted into a relative assessment of the difference in transcript abundance amongst the tissues tested and the data is presented in FIG. 4. Transcripts corresponding to CAN-12 were expressed highly in the spinal cord; significantly in lymph node, thymus, and to a lesser extent, in spleen.

Example 6

Method of Assessing the Expression Profile of the Novel CAN-12 Polypeptides of the Present Invention Using Expanded mRNA Tissue and Cell Sources

[1114] Total RNA from tissues was isolated using the TriZol protocol (Invitrogen) and quantified by determining its absorbance at 260 nM. An assessment of the 18s and 28s ribosomal RNA bands was made by denaturing gel electrophoresis to determine RNA integrity.

[1115] The specific sequence to be measured was aligned with related genes found in GenBank to identity regions of significant sequence divergence to maximize primer and probe specificity. Gene-specific primers and probes were designed using the ABI primer express software to amplify small amplicons (150 base pairs or less) to maximize the likelihood that the primers function at 100% efficiency. All primer/probe sequences were searched against Public Genbank databases to ensure target specificity. Primers and probes were obtained from ABI.

[1116] For CAN-12, the primer probe sequences were as follows

[1117] Forward Primer 5′-TCGTGCCCTGCATATTGGA-3′ (SEQ ID NO:143)

[1118] Reverse Primer 5′-AAAAGATGTGCTTCCTGGAGAAGA-3′ (SEQ ID NO:144)

[1119] TaqMan Probe 5′-CCCACCAGAAGTCAGAGTTCGTCCTCAG-3′ (SEQ ID NO:145)

[1120] DNA Contamination

[1121] To access the level of contaminating genomic DNA in the RNA, the RNA was divided into 2 aliquots and one half was treated with Rnase-free Dnase (Invitrogen). Samples from both the Dnase-treated and non-treated were then subjected to reverse transcription reactions with (RT+) and without (RT−) the presence of reverse transcriptase. TaqMan assays were carried out with gene-specific primers (see above) and the contribution of genomic DNA to the signal detected was evaluated by comparing the threshold cycles obtained with the RT+/RT− non-Dnase treated RNA to that on the RT+/RT− Dnase treated RNA. The amount of signal contributed by genomic DNA in the Dnased RT− RNA must be less that 10% of that obtained with Dnased RT+ RNA. If not the RNA was not used in actual experiments.

[1122] Reverse Transcription reaction and Sequence Detection

[1123] 100 ng of Dnase-treated total RNA was annealed to 2.5 μM of the respective gene-specific reverse primer in the presence of 5.5 mM Magnesium Chloride by heating the sample to 72° C. for 2 min and then cooling to 55° C. for 30 min. 1.25 U/μl of MuLv reverse transcriptase and 500 μM of each dNTP was added to the reaction and the tube was incubated at 37° C. for 30 min. The sample was then heated to 90° C. for 5 min to denature enzyme.

[1124] Quantitative sequence detection was carried out on an ABI PRISM 7700 by adding to the reverse transcribed reaction 2.5 μM forward and reverse primers, 500 μM of each dNTP, buffer and 5U AmpliTaq Gold™. The PCR reaction was then held at 94° C. for 12 min, followed by 40 cycles of 94° C. for 15 sec and 60° C. for 30 sec.

[1125] Data Handling

[1126] The threshold cycle (Ct) of the lowest expressing tissue (the highest Ct value) was used as the baseline of expression and all other tissues were expressed as the relative abundance to that tissue by calculating the difference in Ct value between the baseline and the other tissues and using it as the exponent in 2(ΔCt)

[1127] The expanded expression profile of the CAN-12 polypeptide, is provided in FIG. 12 and described elsewhere herein.

Example 7

Method of Measuring the Protease Activity of CAN-12 Polypeptides

[1128] Protease activity of the CAN-12 polypeptide are measured by following the inhibition of proteolytic activity in cells, tissues, and/or in in vitro assays. Cysteine proteases of the calpain family (of which the present invention is a member) catalyze the hydrolysis of peptide, amide, ester, thiol ester and thiono ester bonds. Any assay that measures cleavage of these bonds can be used to quantitate enzymatic activity. In vitro assays for measuring protease activity using synthetic peptide fluorescent, spectrophotometric either through the use of single substrates (see below for examples), and fluorescence resonance transfer assays are well described in the art, as single substrates or as part of substrate libraries (Backes et al., 2000; Knight, C. G. Fluorimetric Assays of Proteolytic Enzymes. Meth. Enzymol. 248: 18-34 (1995)). In addition proteolytic activity is measured by following production of peptide products. Such approaches are well known to those familiar with the art (reviewed in McGeehan, G. M., Bickett, D. M., Wiseman, J. S., Green, M., Berman, Meth. Enzymol. 248: 35-46 (1995))

[1129] A complete set of protocols that have been used to evaluate calpain activity and are provided in Calpain Methods and Protocols John Elce ed. In Meth. Mol. Biol. Volume 144, 2000 (Humana Press, Totowa, N.J.).

[1130] Inhibitor Identification

[1131] Early work on calpain inhibitors produced nonselective enzyme inhibitors. Peptidyl aldehydes such as leupeptin and antipain inhibit calpain but also other proteases including serine proteases. Irreversible inhibitors such as the E64 family have also been studied, and peptidyl halomethanes and diazomethanes have long been used as protease inhibitors (Hayes et al., Drug News Perspect 11:215-222, 1998). Given the multiple therapeutic indications for the inhibition of calpain it appears that the achievement of selective modulators including specific inhibitors of this enzyme is an important goal.

[1132] The CAN-12 may be incubated with potential inhibitors (preferably small molecule inhibitors or antibodies provided elsewhere herein) for different times and with varying concentrations. Residual protease activity could then be measured according to any appropriate means known in the art. Enzyme activity in the presence of control may be expressed as fraction of control and curve fit to pre-incubation time and serpin concentration to determine inhibitory parameters including concentration that half maximally inhibits the enzyme activity.

[1133] Non-limiting examples of in vitro protease assays are well described in the art. Non-limiting examples of a spectrophotometric protease assays are the thrombin and tryptase assays measuring time-dependent optical density change followed at 405 nm using a kinetic microplate reader (Molecular Devices UVmax)(Balasubramanian, et al., Active site-directed synthetic thrombin inhibitors: synthesis, in vitro and in vivo activity profile of BMY 44621 and analogs. an examination of the role of the amino group in the D-Phe-Pro-Arg-H series. J. Med. Chem. 36:300-303 (1993); and Combrink et al., Novel 1,2-Benzisothiazol-3-one-1,1-dioxide Inhibitors of Human Mast Cell Tryptase. J. Med. Chem. 41:4854-4860 (1998)).

[1134] An example of a fluorescence assay which may be used for the present invention is the Factor VIIa assay. Briefly, the Factor VIIa assay is measured in the presence of human recombinant tissue factor (INNOVIN from Dade Behring Cat.# B4212-100). Human Factor VIIa may be obtained from Enzyme Research Labs (Cat.# HFVIIA 1640). Enzymatic activity could be measured in a buffer containing 150 mM NaCl, 5 mM CaCl2, 1 mM CHAPS and 1 mg/ml PEG 6000 (pH 7.4) with 1 nM FVIIa and 100 μM D-Ile-Pro-Arg-AFC (Enzyme Systems Products, Km >200 μM) 0.66% DMSO. The assay (302 μl total volume) may be incubated at room temperature for 2 hr prior to reading fluorometric signal (Ex 405/Em 535) using a Molecular Devices or Victor 2 (Wallac) fluorescent plate reader.

[1135] In addition to the methods described above, protease activity (and therefore serpin activity) can be measured using fluorescent resonance energy transfer (FRET with Quencher -Pn-P3-P2-P1- -P1′-P2′-Fluorophore), fluorescent peptide bound to beads (Fluorophore -Pn-P3-P2-P1- -P1′-P2′-Bead), dye-protein substrates and serpin-protease gel shifts. All of which are well known to those skilled in the art (see a non-limiting review in Knight, C. G. Fluorimetric Assays of Proteolytic Enzymes. Meth. Enzymol. 248: 18-34 (1995)).

[1136] Additional assay methods are known in the art and are encompassed by the present invention. See, for example, Backes B J, Harris J L, Leonetti F, Craik C S, Ellman J A. Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nat Biotechnol. 18:187-93 (2000); Balasubramanian, et al., Active site-directed synthetic thrombin inhibitors: synthesis, in vitro and in vivo activity profile of BMY 44621 and analogs. an examination of the role of the amino group in the D-Phe-Pro-Arg-H series. J. Med. Chem. 36:300-303 (1993); and Combrink et al., Novel 1,2-Benzisothiazol-3-one-1,1-dioxide Inhibitors of Human Mast Cell Tryptase. J. Med. Chem. 41:4854-4860 (1998) and those methods described in: Calpain Methods and Protocols (ed J. S. Elce) Meth. Mol. Biol. 144, 2000 and Calpain: Pharmacology and Toxicology of a calcium-dependent protease (K. Wang & P. -W. Yuen editors) Taylor & Francis Philadelphia, Pa, 1999; which are hereby incorporated herein by reference in their entirety.

Example 8

Determination of the Preferred Substrate Sequence of the CAN-12 Protease

[1137] The preferred substrate sequence specificity of the CAN-12 metalliprotease of the present invention may be determined using using two redundant peptide libraries and Edman peptide sequencing (1-2) as shown below.

[1138] The first peptide library is random, can vary in length and incorporates a modification at the N-terminus to block Edman sequencing. In the example provided, biotin is used as the blocking group. Proteolytic cleavage of the library is allowed to proceed long enough to turn over approximately 5-10% of the library. Edman sequencing of the peptide mixture provides the preferred substrate residues for the P′ sites on the protease. The second peptide library has fixed P′ residues to restrict the proteolytic cleavage site and an affinity tag for removing the C-terminal product of the proteolysis, leaving the N-terminal peptide product pool behind for Edman sequencing to determine the amino acid residues preferred in the P1, P2, P3 etc. . . . sites of the protease.

[1139] Reagents.

[1140] The endoproteases Factor Xa (New England BioLabs, Inc., Beverly, Mass.) and human kidney Renin (Calbiochem, San Diego, Calif.) were purchased for validation experiments. A hexapeptide library containing 4.7×107 peptide species was synthesized by the Molecular Redesign group (Natarajan & Riexinger) at Bristol-Myers Squibb Company (Princeton, N.J.). The library contained equivalent representation of 19 amino acid residues at each of the six degenerate positions and incorporated an N-terminal biotin group and a C-terminal amide. Cysteine residues were excluded from the peptide pool and Methionine residues were replaced with Norleucine.

[1141] Endoprotease Cleavage of the Peptide Library.

[1142] The following method may be used to determine the preferred substrate sequence downstream of the cleavage site. A 1.88 mM peptide library solution is prepared in phosphate buffer (10 mM Sodium Phosphate (pH 7.6), 0.1 M NaCl, and 10% DMSO) and is incubated with 2-30 μg endoprotease at 37° C. Using a fluorescamine assay to estimate the extent of peptide cleavage, the reaction is stopped at 5-10% completion with incubation at 100° C. for 2.0 minutes. Peptide pools are subjected to Edman sequencing. The data obtained is normalized and corrected for differences in efficiency of cleavage and recovery in the sequencer.

[1143] Fluorescamine Assay to Monitor Peptide Cleavage.

[1144] Primary amines generated during peptide cleavage is measured by reaction with fluorescamine (Aldrich, St. Louis, Mo.), as described in reference 3. The relative fluorescence is determined by measuring signals at □ex=355 nm and □em=460 nm on a PerkinElmer Wallac 1420 Spectrofluorometer. Reactions are sampled at multiple time points and assayed in triplicate. The amount of cleavage product formed is determined using the relative fluorescence produced by varying concentrations of a peptide standard of known concentration.

REFERENCES

[1145] (1) “Substrate Specificity of Cathepsins D and E Determined by N-Terminal and C-Terminal Sequencing of Peptide Pools” D. Arnold et al. (1997) Eur. J. Biochem. 249, 171.

[1146] (2) “Determination of Protease Cleavage Site Motifs Using Mixture-Based Oriented Peptide Libraries” B. E. Turk et al. (2001) Nature Biotech. 19, 661.

[1147] (3) “Fluorescamine: a Reagent for Assay of Amino Acids, Peptides, Proteins, and Primary Amines in the Picomole Range” S. Udenfirend, S. Stein, P. Bohlen, W. Dairman, W. Leimgruber, and M. Weigele (1972) Science 178, 87.

Example 9

Chromosomal Mapping of Calpain 12 and Linkage to Neurodegenerative Disorders

[1148] The calpain12 polynucleotides of the present invention were used to determine the chromosomal localization of the calpain12 gene. The comparison of the chromosomal location of the calpain 12 gene with the location of chromosomal regions which have been shown to be associated with specific diseases or conditions, e.g. by linkage analysis, can be indicative of diseases in which calpain12 may play a role.

[1149] A chromosomal localization of the calpain12 gene was performed by using the nucleic acid sequence (SEQ ID NO:1) of the invention in a database search of the recently completed draft of human genome sequence. Using the Basic Local Alignment Search Tool 2 (BLAST2), the first 200 bp of calpain12 cDNA sequence showed a perfect alignment of nucleotides 62 to 200 with the minus strand of Homo sapiens chromosome 2 clone RP11-541A15 nucleotide 177952 to 177814, and a perfect alignment of nucleotide 1 to 62 of calpain 12 cDNA (SEQ ID NO:1) with the nucleotide 94118 to 94179 of the same clone, suggesting the likelihood of an intron intervening this 200 cDNA fragment. To confirm the map of calpain 12 gene, another BLAST2 search was done with a 300pb fragment of calpain 12 cDNA sequence containing nucleotides 4251 up to poly A signal sequence at position 4550 (SEQ ID NO:1). An alignment with 97% identities (292/300) of this calpain 3′ sequence was found with nucleotide 125724 to 126023 of the same Homo sapiens chromosome 2 clone RP11-541A15. In order to get a refined map of this clone containing the locus of calpain12, a map search of NCBI genome database was performed. RP11-541A15 (Acc# AC015980.2) was found within a BAC contig adjacent to clone 852C13 (AL133246.2) mapping in 2p21-p22.

[1150] A whole-genome linkage scan in multiple sclerosis families (Ebers et al. A full genome search in multiple sclerosis. Nature Genet. 13: 472-476, 1996.) identified 5 susceptibility loci on chromosomes 2, 3, 5, 11, and X. In particular, an association was identified with marker D2S119 on chromosome 2 and MS. We further delineated the localization of this marker, D2S119, on 2p16-p21 based on a radiation hybrid linkage map retrieved from an online query at NCBI web site: http:/www.ncbi.nlm.nih.gov/genome/sts/. Since the map of calpain 12 and the susceptibility marker D2S119 overlaps, it is reasonable to postulate that calpain 12 may contribute to MS. Furthermore, the transcription profile of calpain12 indicated a prominent expression in spinal cord, and implication of calpains in MS has been suggested (Shields D C et al. A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc Natl Acad Sci U S A. 96:11486-91.1999).

Example 10

Method of Screening for Compounds that Interact With the CAN-12 Polypeptide

[1151] The following assays are designed to identify compounds that bind to the CAN-12 polypeptide, bind to other cellular proteins that interact with the CAN-12 polypeptide, and to compounds that interfere with the interaction of the CAN-12 polypeptide with other cellular proteins.

[1152] Such compounds can include, but are not limited to, other cellular proteins. Specifically, such compounds can include, but are not limited to, peptides, such as, for example, soluble peptides, including, but not limited to Ig-tailed fusion peptides, comprising extracellular portions of CAN-12 polypeptide transmembrane receptors, and members of random peptide libraries (see, e.g., Lam, K. S. et al., 1991, Nature 354:82-84; Houghton, R. et al., 1991, Nature 354:84-86), made of D-and/or L-configuration amino acids, phosphopeptides (including, but not limited to, members of random or partially degenerate phosphopeptide libraries; see, e.g., Songyang, Z., et al., 1993, Cell 72:767-778), antibodies (including, but not limited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab′).sub.2 and FAb expression libary fragments, and epitope-binding fragments thereof), and small organic or inorganic molecules.

[1153] Compounds identified via assays such as those described herein can be useful, for example, in elaborating the biological function of the CAN-12 polypeptide, and for ameliorating symptoms of tumor progression, for example. In instances, for example, whereby a tumor progression state or disorder results from a lower overall level of CAN-12 expression, CAN-12 polypeptide, and/or CAN-12 polypeptide activity in a cell involved in the tumor progression state or disorder, compounds that interact with the CAN-12 polypeptide can include ones which accentuate or amplify the activity of the bound CAN-12 polypeptide. Such compounds would bring about an effective increase in the level of CAN-12 polypeptide activity, thus ameliorating symptoms of the tumor progression disorder or state. In instances whereby mutations within the CAN-12 polypeptide cause aberrant CAN-12 polypeptides to be made which have a deleterious effect that leads to tumor progression, compounds that bind CAN-12 polypeptide can be identified that inhibit the activity of the bound CAN-12 polypeptide. Assays for testing the effectiveness of such compounds are known in the art and discussed, elsewhere herein.

Example 11

Method of Screening, in vitro, Compounds that Bind to the CAN-12 Polypeptide

[1154] In vitro systems can be designed to identify compounds capable of binding the CAN-12 polypeptide of the invention. Compounds identified can be useful, for example, in modulating the activity of wild type and/or mutant CAN-12 polypeptide, preferably mutant CAN-12 polypeptide, can be useful in elaborating the biological function of the CAN-12 polypeptide, can be utilized in screens for identifying compounds that disrupt normal CAN-12 polypeptide interactions, or can in themselves disrupt such interactions.

[1155] The principle of the assays used to identify compounds that bind to the CAN-12 polypeptide involves preparing a reaction mixture of the CAN-12 polypeptide and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex which can be removed and/or detected in the reaction mixture. These assays can be conducted in a variety of ways. For example, one method to conduct such an assay would involve anchoring CAN-12 polypeptide or the test substance onto a solid phase and detecting CAN-12 polypeptide/test compound complexes anchored on the solid phase at the end of the reaction. In one embodiment of such a method, the CAN-12 polypeptide can be anchored onto a solid surface, and the test compound, which is not anchored, can be labeled, either directly or indirectly.

[1156] In practice, microtitre plates can conveniently be utilized as the solid phase. The anchored component can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished by simply coating the solid surface with a solution of the protein and drying. Alternatively, an immobilized antibody, preferably a monoclonal antibody, specific for the protein to be immobilized can be used to anchor the protein to the solid surface. The surfaces can be prepared in advance and stored.

[1157] In order to conduct the assay, the nonimmobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the previously immobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the previously nonimmobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the immobilized component (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody).

[1158] Alternatively, a reaction can be conducted in a liquid phase, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for CAN-12 polypeptide or the test compound to anchor any complexes formed in solution, and a labeled antibody specific for the other component of the possible complex to detect anchored complexes.

Example 12

Method of Identifying Compounds that Interfere with CAN-12 Polypeptide/Cellular Product Interaction

[1159] The CAN-12 polypeptide of the invention can, in vivo, interact with one or more cellular or extracellular macromolecules, such as proteins. Such macromolecules include, but are not limited to, nucleic acid molecules and those products identified via methods such as those described, elsewhere herein. For the purposes of this discussion, such cellular and extracellular macromolecules are referred to herein as “binding partner(s)”. For the purpose of the present invention, “binding partner” may also encompass small molecule compounds, polysaccarides, lipids, and any other molecule or molecule type referenced herein. Compounds that disrupt such interactions can be useful in regulating the activity of the CAN-12 polypeptide, especially mutant CAN-12 polypeptide. Such compounds can include, but are not limited to molecules such as antibodies, peptides, and the like described in elsewhere herein.

[1160] The basic principle of the assay systems used to identify compounds that interfere with the interaction between the CAN-12 polypeptide and its cellular or extracellular binding partner or partners involves preparing a reaction mixture containing the CAN-12 polypeptide, and the binding partner under conditions and for a time sufficient to allow the two products to interact and bind, thus forming a complex. In order to test a compound for inhibitory activity, the reaction mixture is prepared in the presence and absence of the test compound. The test compound can be initially included in the reaction mixture, or can be added at a time subsequent to the addition of CAN-12 polypeptide and its cellular or extracellular binding partner. Control reaction mixtures are incubated without the test compound or with a placebo. The formation of any complexes between the CAN-12 polypeptide and the cellular or extracellular binding partner is then detected. The formation of a complex in the control reaction, but not in the reaction mixture containing the test compound, indicates that the compound interferes with the interaction of the CAN-12 polypeptide and the interactive binding partner. Additionally, complex formation within reaction mixtures containing the test compound and normal CAN-12 polypeptide can also be compared to complex formation within reaction mixtures containing the test compound and mutant CAN-12 polypeptide. This comparison can be important in those cases wherein it is desirable to identify compounds that disrupt interactions of mutant but not normal CAN-12 polypeptide.

[1161] The assay for compounds that interfere with the interaction of the CAN-12 polypeptide and binding partners can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring either the CAN-12 polypeptide or the binding partner onto a solid phase and detecting complexes anchored on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the compounds being tested. For example, test compounds that interfere with the interaction between the CAN-12 polypeptide and the binding partners, e.g., by competition, can be identified by conducting the reaction in the presence of the test substance; i.e., by adding the test substance to the reaction mixture prior to or simultaneously with the CAN-12 polypeptide and interactive cellular or extracellular binding partner. Alternatively, test compounds that disrupt preformed complexes, e.g. compounds with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed. The various formats are described briefly below.

[1162] In a heterogeneous assay system, either the CAN-12 polypeptide or the interactive cellular or extracellular binding partner, is anchored onto a solid surface, while the non-anchored species is labeled, either directly or indirectly. In practice, microtitre plates are conveniently utilized. The anchored species can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished simply by coating the solid surface with a solution of the CAN-12 polypeptide or binding partner and drying. Alternatively, an immobilized antibody specific for the species to be anchored can be used to anchor the species to the solid surface. The surfaces can be prepared in advance and stored.

[1163] In order to conduct the assay, the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody). Depending upon the order of addition of reaction components, test compounds, which inhibit complex formation or which disrupt preformed complexes can be detected.

[1164] Alternatively, the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes. Again, depending upon the order of addition of reactants to the liquid phase, test compounds which inhibit complex or which disrupt preformed complexes can be identified.

[1165] In an alternate embodiment of the invention, a homogeneous assay can be used. In this approach, a preformed complex of the CAN-12 polypeptide and the interactive cellular or extracellular binding partner product is prepared in which either the CAN-12 polypeptide or their binding partners are labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Pat. No. 4,109,496 by Rubenstein which utilizes this approach for immunoassays). The addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances which disrupt CAN-12 polypeptide-cellular or extracellular binding partner interaction can be identified.

[1166] In a particular embodiment, the CAN-12 polypeptide can be prepared for immobilization using recombinant DNA techniques known in the art. For example, the CAN-12 polypeptide coding region can be fused to a glutathione-S-transferase (GST) gene using a fusion vector such as pGEX-5X-1, in such a manner that its binding activity is maintained in the resulting fusion product. The interactive cellular or extracellular product can be purified and used to raise a monoclonal antibody, using methods routinely practiced in the art and described above. This antibody can be labeled with the radioactive isotope .sup.125 I, for example, by methods routinely practiced in the art. In a heterogeneous assay, e.g., the GST-CAN-12 polypeptide fusion product can be anchored to glutathione-agarose beads. The interactive cellular or extracellular binding partner product can then be added in the presence or absence of the test compound in a manner that allows interaction and binding to occur. At the end of the reaction period, unbound material can be washed away, and the labeled monoclonal antibody can be added to the system and allowed to bind to the complexed components. The interaction between the CAN-12 polypeptide and the interactive cellular or extracellular binding partner can be detected by measuring the amount of radioactivity that remains associated with the glutathione-agarose beads. A successful inhibition of the interaction by the test compound will result in a decrease in measured radioactivity.

[1167] Alternatively, the GST-CAN-12 polypeptide fusion product and the interactive cellular or extracellular binding partner product can be mixed together in liquid in the absence of the solid glutathione-agarose beads. The test compound can be added either during or after the binding partners are allowed to interact. This mixture can then be added to the glutathione-agarose beads and unbound material is washed away. Again the extent of inhibition of the binding partner interaction can be detected by adding the labeled antibody and measuring the radioactivity associated with the beads.

[1168] In another embodiment of the invention, these same techniques can be employed using peptide fragments that correspond to the binding domains of the CAN-12 polypeptide product and the interactive cellular or extracellular binding partner (in case where the binding partner is a product), in place of one or both of the full length products.

[1169] Any number of methods routinely practiced in the art can be used to identify and isolate the protein's binding site. These methods include, but are not limited to, mutagenesis of one of the genes encoding one of the products and screening for disruption of binding in a co-immunoprecipitation assay. Compensating mutations in the gene encoding the second species in the complex can be selected. Sequence analysis of the genes encoding the respective products will reveal the mutations that correspond to the region of the product involved in interactive binding. Alternatively, one product can be anchored to a solid surface using methods described in this Section above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide comprising the binding domain can remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the cellular or extracellular binding partner product is obtained, short gene segments can be engineered to express peptide fragments of the product, which can then be tested for binding activity and purified or synthesized.

Example 13

Isolation of a Specific Clone from the Deposited Sample

[1170] The deposited material in the sample assigned the ATCC Deposit Number cited in Table I for any given cDNA clone also may contain one or more additional plasmids, each comprising a cDNA clone different from that given clone. Thus, deposits sharing the same ATCC Deposit Number contain at least a plasmid for each cDNA clone identified in Table I. Typically, each ATCC deposit sample cited in Table I comprises a mixture of approximately equal amounts (by weight) of about 1-10 plasmid DNAs, each containing a different cDNA clone and/or partial cDNA clone; but such a deposit sample may include plasmids for more or less than 2 cDNA clones.

[1171] Two approaches can be used to isolate a particular clone from the deposited sample of plasmid DNA(s) cited for that clone in Table I. First, a plasmid is directly isolated by screening the clones using a polynucleotide probe corresponding to SEQ ID NO:1.

[1172] Particularly, a specific polynucleotide with 30-40 nucleotides is synthesized using an Applied Biosystems DNA synthesizer according to the sequence reported. The oligonucleotide is labeled, for instance, with 32P-(-ATP using T4 polynucleotide kinase and purified according to routine methods. (E.g., Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, N.Y. (1982).) The plasmid mixture is transformed into a suitable host, as indicated above (such as XL-1 Blue (Stratagene)) using techniques known to those of skill in the art, such as those provided by the vector supplier or in related publications or patents cited above. The transformants are plated on 1.5% agar plates (containing the appropriate selection agent, e.g., ampicillin) to a density of about 150 transformants (colonies) per plate. These plates are screened using Nylon membranes according to routine methods for bacterial colony screening (e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edit., (1989), Cold Spring Harbor Laboratory Press, pages 1.93 to 1.104), or other techniques known to those of skill in the art.

[1173] Alternatively, two primers of 17-20 nucleotides derived from both ends of the SEQ ID NO:1 (i.e., within the region of SEQ ID NO:1 bounded by the 5′ NT and the 3′ NT of the clone defined in Table I) are synthesized and used to amplify the desired cDNA using the deposited cDNA plasmid as a template. The polymerase chain reaction is carried out under routine conditions, for instance, in 25 ul of reaction mixture with 0.5 ug of the above cDNA template. A convenient reaction mixture is 1.5-5 mM MgCl2, 0.01% (w/v) gelatin, 20 uM each of dATP, dCTP, dGTP, dTTP, 25 pmol of each primer and 0.25 Unit of Taq polymerase. Thirty five cycles of PCR (denaturation at 94 degree C. for 1 min; annealing at 55 degree C. for 1 min; elongation at 72 degree C. for 1 min) are performed with a Perkin-Elmer Cetus automated thermal cycler. The amplified product is analyzed by agarose gel electrophoresis and the DNA band with expected molecular weight is excised and purified. The PCR product is verified to be the selected sequence by subcloning and sequencing the DNA product.

[1174] The polynucleotide(s) of the present invention, the polynucleotide encoding the polypeptide of the present invention, or the polypeptide encoded by the deposited clone may represent partial, or incomplete versions of the complete coding region (i.e., full-length gene). Several methods are known in the art for the identification of the 5′ or 3′ non-coding and/or coding portions of a gene which may not be present in the deposited clone. The methods that follow are exemplary and should not be construed as limiting the scope of the invention. These methods include but are not limited to, filter probing, clone enrichment using specific probes, and protocols similar or identical to 5′ and 3′ “RACE” protocols that are well known in the art. For instance, a method similar to 5′ RACE is available for generating the missing 5′ end of a desired full-length transcript. (Fromont-Racine et al., Nucleic Acids Res. 21(7):1683-1684 (1993)).

[1175] Briefly, a specific RNA oligonucleotide is ligated to the 5′ ends of a population of RNA presumably containing full-length gene RNA transcripts. A primer set containing a primer specific to the ligated RNA oligonucleotide and a primer specific to a known sequence of the gene of interest is used to PCR amplify the 5′ portion of the desired full-length gene. This amplified product may then be sequenced and used to generate the full-length gene.

[1176] This above method starts with total RNA isolated from the desired source, although poly-A+ RNA can be used. The RNA preparation can then be treated with phosphatase if necessary to eliminate 5′ phosphate groups on degraded or damaged RNA that may interfere with the later RNA ligase step. The phosphatase should then be inactivated and the RNA treated with tobacco acid pyrophosphatase in order to remove the cap structure present at the 5′ ends of messenger RNAs. This reaction leaves a 5′ phosphate group at the 5′ end of the cap cleaved RNA which can then be ligated to an RNA oligonucleotide using T4 RNA ligase.

[1177] This modified RNA preparation is used as a template for first strand cDNA synthesis using a gene specific oligonucleotide. The first strand synthesis reaction is used as a template for PCR amplification of the desired 5′ end using a primer specific to the ligated RNA oligonucleotide and a primer specific to the known sequence of the gene of interest. The resultant product is then sequenced and analyzed to confirm that the 5′ end sequence belongs to the desired gene. Moreover, it may be advantageous to optimize the RACE protocol to increase the probability of isolating additional 5′ or 3′ coding or non-coding sequences. Various methods of optimizing a RACE protocol are known in the art, though a detailed description summarizing these methods can be found in B. C. Schaefer, Anal. Biochem., 227:255-273, (1995).

[1178] An alternative method for carrying out 5′ or 3′ RACE for the identification of coding or non-coding sequences is provided by Frohman, M. A., et al., Proc.Nat'l.Acad.Sci.USA, 85:8998-9002 (1988). Briefly, a cDNA clone missing either the 5′ or 3′ end can be reconstructed to include the absent base pairs extending to the translational start or stop codon, respectively. In some cases, cDNAs are missing the start of translation, therefor. The following briefly describes a modification of this original 5′ RACE procedure. Poly A+ or total RNAs reverse transcribed with Superscript II (Gibco/BRL) and an antisense or I complementary primer specific to the cDNA sequence. The primer is removed from the reaction with a Microcon Concentrator (Amicon). The first-strand cDNA is then tailed with dATP and terminal deoxynucleotide transferase (Gibco/BRL). Thus, an anchor sequence is produced which is needed for PCR amplification. The second strand is synthesized from the dA-tail in PCR buffer, Taq DNA polymerase (Perkin-Elmer Cetus), an oligo-dT primer containing three adjacent restriction sites (XhoIJ Sail and ClaI) at the 5′ end and a primer containing just these restriction sites. This double-stranded cDNA is PCR amplified for 40 cycles with the same primers as well as a nested cDNA-specific antisense primer. The PCR products are size-separated on an ethidium bromide-agarose gel and the region of gel containing cDNA products the predicted size of missing protein-coding DNA is removed. cDNA is purified from the agarose with the Magic PCR Prep kit (Promega), restriction digested with XhoI or SalI, and ligated to a plasmid such as pBluescript SKII (Stratagene) at XhoI and EcoRV sites. This DNA is transformed into bacteria and the plasmid clones sequenced to identify the correct protein-coding inserts. Correct 5′ ends are confirmed by comparing this sequence with the putatively identified homologue and overlap with the partial cDNA clone. Similar methods known in the art and/or commercial kits are used to amplify and recover 3′ ends.

[1179] Several quality-controlled kits are commercially available for purchase. Similar reagents and methods to those above are supplied in kit form from Gibco/BRL for both 5′ and 3′ RACE for recovery of full length genes. A second kit is available from Clontech which is a modification of a related technique, SLIC (single-stranded ligation to single-stranded cDNA), developed by Dumas et al., Nucleic Acids Res., 19:5227-32(1991). The major differences in procedure are that the RNA is alkaline hydrolyzed after reverse transcription and RNA ligase is used to join a restriction site-containing anchor primer to the first-strand cDNA. This obviates the necessity for the dA-tailing reaction which results in a polyT stretch that is difficult to sequence past.

[1180] An alternative to generating 5′ or 3′ cDNA from RNA is to use cDNA library double-stranded DNA. An asymmetric PCR-amplified antisense cDNA strand is synthesized with an antisense cDNA-specific primer and a plasmid-anchored primer. These primers are removed and a symmetric PCR reaction is performed with a nested cDNA-specific antisense primer and the plasmid-anchored primer.

[1181] RNA Ligase Protocol for Generating the 5′ or 3′ End Sequences to Obtain full Length Genes

[1182] Once a gene of interest is identified, several methods are available for the identification of the 5′ or 3′ portions of the gene which may not be present in the original cDNA plasmid. These methods include, but are not limited to, filter probing, clone enrichment using specific probes and protocols similar and identical to 5′ and 3RACE. While the full-length gene may be present in the library and can be identified by probing, a useful method for generating the 5′ or 3′ end is to use the existing sequence information from the original cDNA to generate the missing information. A method similar to 5RACE is available for generating the missing 5′ end of a desired full-length gene. (This method was published by Fromont-Racine et al., Nucleic Acids Res., 21(7): 1683-1684 (1993)). Briefly, a specific RNA oligonucleotide is ligated to the 5′ ends of a population of RNA presumably 30 containing full-length gene RNA transcript and a primer set containing a primer specific to the ligated RNA oligonucleotide and a primer specific to a known sequence of the gene of interest, is used to PCR amplify the 5′ portion of the desired full length gene which may then be sequenced and used to generate the full length gene. This method starts with total RNA isolated from the desired source, poly A RNA may be used but is not a prerequisite for this procedure. The RNA preparation may then be treated with phosphatase if necessary to eliminate 5′ phosphate groups on degraded or damaged RNA which may interfere with the later RNA ligase step. The phosphatase if used is then inactivated and the RNA is treated with tobacco acid pyrophosphatase in order to remove the cap structure present at the 5′ ends of messenger RNAs. This reaction leaves a 5′ phosphate group at the 5′ end of the cap cleaved RNA which can then be ligated to an RNA oligonucleotide using T4 RNA ligase. This modified RNA preparation can then be used as a template for first strand cDNA synthesis using a gene specific oligonucleotide. The first strand synthesis reaction can then be used as a template for PCR amplification of the desired 5′ end using a primer specific to the ligated RNA oligonucleotide and a primer specific to the known sequence of the apoptosis related of interest. The resultant product is then sequenced and analyzed to confirm that the 5′ end sequence belongs to the relevant apoptosis related.

Example 14

Bacterial Expression of a Polypeptide

[1183] A polynucleotide encoding a polypeptide of the present invention is amplified using PCR oligonucleotide primers corresponding to the 5′ and 3′ ends of the DNA sequence, as outlined in Example 13, to synthesize insertion fragments. The primers used to amplify the cDNA insert should preferably contain restriction sites, such as BamHI and XbaI, at the 5′ end of the primers in order to clone the amplified product into the expression vector. For example, BamHI and XbaI correspond to the restriction enzyme sites on the bacterial expression vector pQE-9. (Qiagen, Inc., Chatsworth, Calif.). This plasmid vector encodes antibiotic resistance (Ampr), a bacterial origin of replication (ori), an IPTG-regulatable promoter/operator (P/O), a ribosome binding site (RBS), a 6-histidine tag (6-His), and restriction enzyme cloning sites.

[1184] The pQE-9 vector is digested with BamHI and XbaI and the amplified fragment is ligated into the pQE-9 vector maintaining the reading frame initiated at the bacterial RBS. The ligation mixture is then used to transform the E. coli strain M15/rep4 (Qiagen, Inc.) which contains multiple copies of the plasmid pREP4, that expresses the lacI repressor and also confers kanamycin resistance (Kanr). Transformants are identified by their ability to grow on LB plates and ampicillin/kanamycin resistant colonies are selected. Plasmid DNA is isolated and confirmed by restriction analysis.

[1185] Clones containing the desired constructs are grown overnight (O/N) in liquid culture in LB media supplemented with both Amp (100 ug/mil) and Kan (25 ug/ml). The O/N culture is used to inoculate a large culture at a ratio of 1:100 to 1:250. The cells are grown to an optical density 600 (O.D.600) of between 0.4 and 0.6. IPTG (Isopropyl-B-D-thiogalacto pyranoside) is then added to a final concentration of 1 mM. IPTG induces by inactivating the lacI repressor, clearing the P/O leading to increased gene expression.

[1186] Cells are grown for an extra 3 to 4 hours. Cells are then harvested by centrifugation (20 mins at 6000× g). The cell pellet is solubilized in the chaotropic agent 6 Molar Guanidine HCl by stirring for 3-4 hours at 4 degree C. The cell debris is removed by centrifugation, and the supernatant containing the polypeptide is loaded onto a nickel-nitrilo-tri-acetic acid (“Ni-NTA”) affinity resin column (available from QIAGEN, Inc., supra). Proteins with a 6× His tag bind to the Ni-NTA resin with high affinity and can be purified in a simple one-step procedure (for details see: The QIAexpressionist (1995) QIAGEN, Inc., supra).

[1187] Briefly, the supernatant is loaded onto the column in 6 M guanidine-HCl, pH 8, the column is first washed with 10 volumes of 6 M guanidine-HCl, pH 8, then washed with 10 volumes of 6 M guanidine-HCl pH 6, and finally the polypeptide is eluted with 6 M guanidine-HCl, pH 5.

[1188] The purified protein is then renatured by dialyzing it against phosphate-buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus 200 nM NaCl. Alternatively, the protein can be successfully refolded while immobilized on the Ni-NTA column. The recommended conditions are as follows: renature using a linear 6M-1M urea gradient in 500 mM NaCl, 20% glycerol, 20 mM Tris/HCl pH 7.4, containing protease inhibitors. The renaturation should be performed over a period of 1.5 hours or more. After renaturation the proteins are eluted by the addition of 250 mM imidazole. Imidazole is removed by a final dialyzing step against PBS or 50 mM sodium acetate pH 6 buffer plus 200 mM NaCl. The purified protein is stored at 4 degree C. or frozen at −80 degree C.

Example 15

Purification of a Polypeptide from an Inclusion Body

[1189] The following alternative method can be used to purify a polypeptide expressed in E coli when it is present in the form of inclusion bodies. Unless otherwise specified, all of the following steps are conducted at 4-10 degree C.

[1190] Upon completion of the production phase of the E. coli fermentation, the cell culture is cooled to 4-10 degree C. and the cells harvested by continuous centrifugation at 15,000 rpm (Heraeus Sepatech). On the basis of the expected yield of protein per unit weight of cell paste and the amount of purified protein required, an appropriate amount of cell paste, by weight, is suspended in a buffer solution containing 100 mM Tris, 50 mM EDTA, pH 7.4. The cells are dispersed to a homogeneous suspension using a high shear nuxer.

[1191] The cells are then lysed by passing the solution through a microfluidizer (Microfluidics, Corp. or APV Gaulin, Inc.) twice at 4000-6000 psi. The homogenate is then mixed with NaCl solution to a final concentration of 0.5 M NaCl, followed by centrifugation at 7000× g for 15 min. The resultant pellet is washed again using 0.5M NaCl, 100 mM Tris, 50 mM EDTA, pH 7.4.

[1192] The resulting washed inclusion bodies are solubilized with 1.5 M guanidine hydrochloride (GuHCl) for 2-4 hours. After 7000× g centrifugation for 15 min., the pellet is discarded and the polypeptide containing supernatant is incubated at 4 degree C. overnight to allow further GuHCl extraction.

[1193] Following high speed centrifugation (30,000× g) to remove insoluble particles, the GuHCl solubilized protein is refolded by quickly mixing the GuHCl extract with 20 volumes of buffer containing 50 mM sodium, pH 4.5, 150 mM NaCl, 2 mM EDTA by vigorous stirring. The refolded diluted protein solution is kept at 4 degree C. without mixing for 12 hours prior to further purification steps.

[1194] To clarify the refolded polypeptide solution, a previously prepared tangential filtration unit equipped with 0.16 um membrane filter with appropriate surface area (e.g., Filtron), equilibrated with 40 mM sodium acetate, pH 6.0 is employed. The filtered sample is loaded onto a cation exchange resin (e.g., Poros HS-50, Perceptive Biosystems). The column is washed with 40 mM sodium acetate, pH 6.0 and eluted with 250 mM, 500 mM, 1000 mM, and 1500 nM NaCl in the same buffer, in a stepwise manner. The absorbance at 280 nm of the effluent is continuously monitored. Fractions are collected and further analyzed by SDS-PAGE.

[1195] Fractions containing the polypeptide are then pooled and mixed with 4 volumes of water. The diluted sample is then loaded onto a previously prepared set of tandem columns of strong anion (Poros HQ-50, Perceptive Biosystems) and weak anion (Poros CM-20, Perceptive Biosystems) exchange resins. The columns are equilibrated with 40 mM sodium acetate, pH 6.0. Both columns are washed with 40 mM sodium acetate, pH 6.0, 200 mM NaCl. The CM-20 column is then eluted using a 10 column volume linear gradient ranging from 0.2 M NaCl, 50 mM sodium acetate, pH 6.0 to 1.0 M NaCl, 50 mM sodium acetate, pH 6.5. Fractions are collected under constant A280 monitoring of the effluent. Fractions containing the polypeptide (determined, for instance, by 16% SDS-PAGE) are then pooled.

[1196] The resultant polypeptide should exhibit greater than 95% purity after the above refolding and purification steps. No major contaminant bands should be observed from Coomassie blue stained 16% SDS-PAGE gel when 5 ug of purified protein is loaded. The purified protein can also be tested for endotoxin/LPS contamination, and typically the LPS content is less than 0.1 ng/ml according to LAL assays.

Example 16

Cloning and Expression of a Polypeptide in a Baculovirus Expression System

[1197] In this example, the plasmid shuttle vector pAc373 is used to insert a polynucleotide into a baculovirus to express a polypeptide. A typical baculovirus expression vector contains the strong polyhedrin promoter of the Autographa californica nuclear polyhedrosis virus (AcMNPV) followed by convenient restriction sites, which may include, for example BamHI, Xba I and Asp718. The polyadenylation site of the simian virus 40 (“SV40”) is often used for efficient polyadenylation. For easy selection of recombinant virus, the plasmid contains the beta-galactosidase gene from E. coli under control of a weak Drosophila promoter in the same orientation, followed by the polyadenylation signal of the polyhedrin gene. The inserted genes are flanked on both sides by viral sequences for cell-mediated homologous recombination with wild-type viral DNA to generate a viable virus that express the cloned polynucleotide.

[1198] Many other baculovirus vectors can be used in place of the vector above, such as pVL941 and pAcIM1, as one skilled in the art would readily appreciate, as long as the construct provides appropriately located signals for transcription, translation, secretion and the like, including a signal peptide and an in-frame AUG as required. Such vectors are described, for instance, in Luckow et al., Virology 170:31-39 (1989).

[1199] A polynucleotide encoding a polypeptide of the present invention is amplified using PCR oligonucleotide primers corresponding to the 5′ and 3′ ends of the DNA sequence, as outlined in Example 13, to synthesize insertion fragments. The primers used to amplify the cDNA insert should preferably contain restriction sites at the 5′ end of the primers in order to clone the amplified product into the expression vector. Specifically, the cDNA sequence contained in the deposited clone, including the AUG initiation codon and the naturally associated leader sequence identified elsewhere herein (if applicable), is amplified using the PCR protocol described in Example 13. If the naturally occurring signal sequence is used to produce the protein, the vector used does not need a second signal peptide. Alternatively, the vector can be modified to include a baculovirus leader sequence, using the standard methods described in Summers et al., “A Manual of Methods for Baculovirus Vectors and Insect Cell Culture Procedures,” Texas Agricultural Experimental Station Bulletin No. 1555 (1987).

[1200] The amplified fragment is isolated from a 1% agarose gel using a commercially available kit (“Geneclean,” BIO 101 Inc., La Jolla, Calif.). The fragment then is digested with appropriate restriction enzymes and again purified on a 1% agarose gel.

[1201] The plasmid is digested with the corresponding restriction enzymes and optionally, can be dephosphorylated using calf intestinal phosphatase, using routine procedures known in the art. The DNA is then isolated from a 1% agarose gel using a commercially available kit (“Geneclean” BIO 101 Inc., La Jolla, Calif.).

[1202] The fragment and the dephosphorylated plasmid are ligated together with T4 DNA ligase. E. coli HB101 or other suitable E. coli hosts such as XL-1 Blue (Stratagene Cloning Systems, La Jolla, Calif.) cells are transformed with the ligation mixture and spread on culture plates. Bacteria containing the plasmid are identified by digesting DNA from individual colonies and analyzing the digestion product by gel electrophoresis. The sequence of the cloned fragment is confirmed by DNA sequencing.

[1203] Five ug of a plasmid containing the polynucleotide is co-transformed with 1.0 ug of a commercially available linearized baculovirus DNA (“BaculoGoldtm baculovirus DNA”, Pharmingen, San Diego, Calif.), using the lipofection method described by Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413-7417 (1987). One ug of BaculoGoldtm virus DNA and 5ug of the plasmid are mixed in a sterile well of a microtiter plate containing 50ul of serum-free Grace's medium (Life Technologies Inc., Gaithersburg, Md.). Afterwards, 10 ul Lipofectin plus 90 ul Grace's medium are added, mixed and incubated for 15 minutes at room temperature. Then the transfection mixture is added drop-wise to Sf9 insect cells (ATCC CRL 1711) seeded in a 35 mm tissue culture plate with 1 ml Grace's medium without serum. The plate is then incubated for 5 hours at 27 degrees C. The transfection solution is then removed from the plate and 1 ml of Grace's insect medium supplemented with 10% fetal calf serum is added. Cultivation is then continued at 27 degrees C. for four days.

[1204] After four days the supernatant is collected and a plaque assay is performed, as described by Summers and Smith, supra. An agarose gel with “Blue Gal” (Life Technologies Inc., Gaithersburg) is used to allow easy identification and isolation of gal-expressing clones, which produce blue-stained plaques. (A detailed description of a “plaque assay” of this type can also be found in the user's guide for insect cell culture and baculovirology distributed by Life Technologies Inc., Gaithersburg, page 9-10.) After appropriate incubation, blue stained plaques are picked with the tip of a micropipettor (e.g., Eppendorf). The agar containing the recombinant viruses is then resuspended in a microcentrifuge tube containing 200 ul of Grace's medium and the suspension containing the recombinant baculovirus is used to infect Sf9 cells seeded in 35 mm dishes. Four days later the supernatants of these culture dishes are harvested and then they are stored at 4 degree C.

[1205] To verify the expression of the polypeptide, Sf9 cells are grown in Grace's medium supplemented with 10% heat-inactivated FBS. The cells are infected with the recombinant baculovirus containing the polynucleotide at a multiplicity of infection (“MOI”) of about 2. If radiolabeled proteins are desired, 6 hours later the medium is removed and is replaced with SF900 II medium minus methionine and cysteine (available from Life Technologies Inc., Rockville, Md.). After 42 hours, 5 uCi of 35S-methionine and 5 uCi 35S-cysteine (available from Amersham) are added. The cells are further incubated for 16 hours and then are harvested by centrifugation. The proteins in the supernatant as well as the intracellular proteins are analyzed by SDS-PAGE followed by autoradiography (if radiolabeled).

[1206] Microsequencing of the amino acid sequence of the amino terminus of purified protein may be used to determine the amino terminal sequence of the produced protein.

Example 17

Expression of a Polypeptide in Mammalian Cells

[1207] The polypeptide of the present invention can be expressed in a mammalian cell. A typical mammalian expression vector contains a promoter element, which mediates the initiation of transcription of mRNA, a protein coding sequence, and signals required for the termination of transcription and polyadenylation of the transcript. Additional elements include enhancers, Kozak sequences and intervening sequences flanked by donor and acceptor sites for RNA splicing. Highly efficient transcription is achieved with the early and late promoters from SV40, the long terminal repeats (LTRs) from Retroviruses, e.g., RSV, HTLVI, HIVI and the early promoter of the cytomegalovirus (CMV). However, cellular elements can also be used (e.g., the human actin promoter).

[1208] Suitable expression vectors for use in practicing the present invention include, for example, vectors such as pSVL and pMSG (Pharmacia, Uppsala, Sweden), pRSVcat (ATCC 37152), pSV2dhfr (ATCC 37146), pBC12MI (ATCC 67109), pCMVSport 2.0, and pCMVSport 3.0. Mammalian host cells that could be used include, human Hela, 293, H9 and Jurkat cells, mouse NIH3T3 and C127 cells, Cos 1, Cos 7 and CV1, quail QC1-3 cells, mouse L cells and Chinese hamster ovary (CHO) cells.

[1209] Alternatively, the polypeptide can be expressed in stable cell lines containing the polynucleotide integrated into a chromosome. The co-transformation with a selectable marker such as dhfr, gpt, neomycin, hygromycin allows the identification and isolation of the transformed cells.

[1210] The transformed gene can also be amplified to express large amounts of the encoded protein. The DHFR (dihydrofolate reductase) marker is useful in developing cell lines that carry several hundred or even several thousand copies of the gene of interest. (See, e.g., Alt, F. W., et al., J. Biol. Chem. . . . 253:1357-1370 (1978); Hamlin, J. L. and Ma, C., Biochem. et Biophys. Acta, 1097:107-143 (1990); Page, M. J. and Sydenham, M. A., Biotechnology 9:64-68 (1991).) Another useful selection marker is the enzyme glutamine synthase (GS) (Murphy et al., Biochem J. 227:277-279 (1991); Bebbington et al., Bio/Technology 10:169-175 (1992). Using these markers, the mammalian cells are grown in selective medium and the cells with the highest resistance are selected. These cell lines contain the amplified gene(s) integrated into a chromosome. Chinese hamster ovary (CHO) and NSO cells are often used for the production of proteins.

[1211] A polynucleotide of the present invention is amplified according to the protocol outlined in herein. If the naturally occurring signal sequence is used to produce the protein, the vector does not need a second signal peptide. Alternatively, if the naturally occurring signal sequence is not used, the vector can be modified to include a heterologous signal sequence. (See, e.g., WO 96/34891.) The amplified fragment is isolated from a 1% agarose gel using a commercially available kit (“Geneclean,” BIO 101 Inc., La Jolla, Calif.). The fragment then is digested with appropriate restriction enzymes and again purified on a 1% agarose gel.

[1212] The amplified fragment is then digested with the same restriction enzyme and purified on a 1% agarose gel. The isolated fragment and the dephosphorylated vector are then ligated with T4 DNA ligase. E. coli HB101 or XL-1 Blue cells are then transformed and bacteria are identified that contain the fragment inserted into plasmid pC6 using, for instance, restriction enzyme analysis.

[1213] Chinese hamster ovary cells lacking an active DHFR gene is used for transformation. Five μg of an expression plasmid is cotransformed with 0.5 ug of the 10. plasmid pSVneo using lipofectin (Felgner et al., supra). The plasmid pSV2-neo contains a dominant selectable marker, the neo gene from Tn5 encoding an enzyme that confers resistance to a group of antibiotics including G418. The cells are seeded in alpha minus MEM supplemented with 1 mg/ml G418. After 2 days, the cells are trypsinized and seeded in hybridoma cloning plates (Greiner, Germany) in alpha 15 minus MEM supplemented with 10, 25, or 50 ng/ml of methotrexate plus 1 mg/ml G418. After about 10-14 days single clones are trypsinized and then seeded in 6-well petri dishes or 10 ml flasks using different concentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM). Clones growing at the highest concentrations of methotrexate are then transferred to new 6-well plates containing even higher 20 concentrations of methotrexate (1 uM, 2 uM, 5 uM, 10 mM, 20 mM). The same procedure is repeated until clones are obtained which grow at a concentration of 100-200 uM. Expression of the desired gene product is analyzed, for instance, by SDS-PAGE and Western blot or by reversed phase HPLC analysis.

Example 18

Protein Fusions

[1214] The polypeptides of the present invention are preferably fused to other proteins. These fusion proteins can be used for a variety of applications. For example, fusion of the present polypeptides to His-tag, HA-tag, protein A, IgG domains, and maltose binding protein facilitates purification. (See Example described herein; see also EP A 394,827; Traunecker, et al., Nature 331:84-86 (1988).) Similarly, fusion to IgG-1, IgG-3, and albumin increases the half-life time in vivo. Nuclear localization signals fused to the polypeptides of the present invention can target the protein to a specific subcellular localization, while covalent heterodimer or homodimers can increase or decrease the activity of a fusion protein. Fusion proteins can also create chimeric molecules having more than one function. Finally, fusion proteins can increase solubility and/or stability of the fused protein compared to the non-fused protein. All of the types of fusion proteins described above can be made by modifying the following protocol, which outlines the fusion of a polypeptide to an IgG molecule.

[1215] Briefly, the human Fc portion of the IgG molecule can be PCR amplified, using primers that span the 5′ and 3′ ends of the sequence described below. These primers also should have convenient restriction enzyme sites that will facilitate cloning into an expression vector, preferably a mammalian expression vector. Note that the polynucleotide is cloned without a stop codon, otherwise a fusion protein will not be produced.

[1216] The naturally occurring signal sequence may be used to produce the protein (if applicable). Alternatively, if the naturally occurring signal sequence is not used, the vector can be modified to include a heterologous signal sequence. (See, e.g., WO 96/34891 and/or U.S. Pat. No. 6,066,781, supra.)

10Human IgG Fc region:(SEQ ID NO:48)GGGATCCGGAGCCCAAATCTTCTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAATTCGAGGGTGCACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACTCCTGAGGTCACATGCGTGGTGGTGGACGTAAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAACCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCAAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAATGAGTGCGACGGCCGCGACTCTAGAGGAT

Example 19

Method of Creating N- and C-terminal Deletion Mutants Corresponding to the CAN-12, CAN-12v1, and CAN-12v2 Polypeptides of the Present Invention

[1217] As described elsewhere herein, the present invention encompasses the creation of N- and C-terminal deletion mutants, in addition to any combination of N- and C-terminal deletions thereof, corresponding to the CAN-12, CAN-12v1, and CAN-12v2 polypeptides of the present invention. A number of methods are available to one skilled in the art for creating such mutants. Such methods may include a combination of PCR amplification and gene cloning methodology. Although one of skill in the art of molecular biology, through the use of the teachings provided or referenced herein, and/or otherwise known in the art as standard methods, could readily create each deletion mutant of the present invention, exemplary methods are described below.

[1218] Briefly, using the isolated cDNA clone encoding the full-length CAN-12, CAN-12v1, or CAN-12v2 polypeptide sequence (as described in Example 13, for example), appropriate primers of about 15-25 nucleotides derived from the desired 5′ and 3′ positions of SEQ ID NO:1, 53, or 55 may be designed to PCR amplify, and subsequently clone, the intended N- and/or C-terminal deletion mutant. Such primers could comprise, for example, an inititation and stop codon for the 5′ and 3′ primer, respectively. Such primers may also comprise restriction sites to facilitate cloning of the deletion mutant post amplification. Moreover, the primers may comprise additional sequences, such as, for example, flag-tag sequences, kozac sequences, or other sequences discussed and/or referenced herein.

[1219] For example, in the case of the P23 to L581 CAN-12 N-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

115′ Primer5′-GCAGCA GCGGCCGC CCACAGCAACCCCAACAGGACTTTG-3′(SEQ ID NO:49) NotI3′ Primer5′-GCAGCA GTCGAC TAACAAGGTGGTGTTGAAGATTAAA-3′(SEQ ID NO:50) SalI

[1220] For example, in the case of the M1 to L423 CAN-12 C-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

125′ Primer5′-GCAGCA GCGGCCGC ATGTCTCTGTGGCCACCTTTCCG-3′(SEQ ID NO:51) NotI3′ Primer5′-GCAGCA GTCGAC GAGGTAGAAGCCAATGGCGAGGAG-3′(SEQ ID NO:52) SalI

[1221] For example, in the case of the R90 to L694 CAN-12v1 N-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

135′ Primer5′-GCAGCA GCGGCCGC AGGCTGGATCTGTGCCAGGGGATAG-3′(SEQ ID NO:94) NotI3′ Primer5′-GCAGCA GTCGAC TAACAAGGTGGTGTTGAAG-3′(SEQ ID NO:95) SalI

[1222] For example, in the case of the M1 to G561 CAN-12v1 C-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

145′ Primer5′-GCAGCA GCGGCCGC ATGTCTCTGTGGCCACCTTTCCG-3′(SEQ ID NO:96) NotI3′ Primer5′- GCAGCA GTCGAC CCCCTGGCAGGCTTCCAGGCTAAAG-3′(SEQ ID NO:97) SalI

[1223] For example, in the case of the R90 to L697 CAN-12v2 N-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

155′ Primer5′-GCAGCA GCGGCCGC AGGCTGGATCTGTGCCAGGGGATAG-3′(SEQ ID NO:98) NotI3′ Primer5′-GCAGCA GTCGAC TAACAAGGTGGTGTTGAAG-3′(SEQ ID NO:99) SalI

[1224] For example, in the case of the M1 to G564 CAN-12v2 C-terminal deletion mutant, the following primers could be used to amplify a cDNA fragment corresponding to this deletion mutant:

165′ Primer5′-GCAGCA GCGGCCGC ATGTCTCTGTGGCCACCTTTCCG-3′(SEQ ID NO:100) NotI3′ Primer5′-GCAGCA GTCGAC CCCCTGGCAGGCTTCCAGGCTAAAG-3′(SEQ ID NO:101) SalI

[1225] Representative PCR amplification conditions are provided below, although the skilled artisan would appreciate that other conditions may be required for efficient amplification. A 100 ul PCR reaction mixture may be prepared using long of the template DNA (cDNA clone of CAN-12), 200 uM 4dNTPs, 1 uM primers, 0.25U Taq DNA polymerase (PE), and standard Taq DNA polymerase buffer. Typical PCR cycling condition are as follows:

1720-25 cycles:45 sec, 93 degrees 2 min, 50 degrees 2 min, 72 degrees1 cycle:10 min, 72 degrees

[1226] After the final extension step of PCR, 5U Klenow Fragment may be added and incubated for 15 min at 30 degrees.

[1227] Upon digestion of the fragment with the NotI and SalI restriction enzymes, the fragment could be cloned into an appropriate expression and/or cloning vector which has been similarly digested (e.g., pSport1, among others). The skilled artisan would appreciate that other plasmids could be equally substituted, and may be desirable in certain circumstances. The digested fragment and vector are then ligated using a DNA ligase, and then used to transform competent E.coli cells using methods provided herein and/or otherwise known in the art.

[1228] The 5′ primer sequence for amplifying any additional N-terminal deletion mutants may be determined by reference to the following formula:

[1229] (S+(X*3)) to ((S+(X*3))+25), wherein ‘S’ is equal to the nucleotide position of the initiating start codon of the CAN-12, CAN-12v1, or CAN12-v2 gene (SEQ ID NO:1, 53, or 55), and ‘X’ is equal to the most N-terminal amino acid of the intended N-terminal deletion mutant. The first term will provide the start 5′ nucleotide position of the 5′ primer, while the second term will provide the end 3′ nucleotide position of the 5′ primer corresponding to sense strand of SEQ ID NO:1, 53, or 55. Once the corresponding nucleotide positions of the primer are determined, the final nucleotide sequence may be created by the addition of applicable restriction site sequences to the 5′ end of the sequence, for example. As referenced herein, the addition of other sequences to the 5′ primer may be desired in certain circumstances (e.g., kozac sequences, etc.).

[1230] The 3′ primer sequence for amplifying any additional N-terminal deletion mutants may be determined by reference to the following formula:

[1231] (S+(X*3)) to ((S+(X*3))-25), wherein ‘S’ is equal to the nucleotide position of the initiating start codon of the CAN-12, CAN-12v1, or CAN12-v2 gene (SEQ ID NO:1, 53, or 55), and ‘X’ is equal to the most C-terminal amino acid of the intended N-terminal deletion mutant. The first term will provide the start 5′ nucleotide position of the 3′ primer, while the second term will provide the end 3′ nucleotide position of the 3′ primer corresponding to the anti-sense strand of SEQ ID NO:1, 53, or 55. Once the corresponding nucleotide positions of the primer are determined, the final nucleotide sequence may be created by the addition of applicable restriction site sequences to the 5′ end of the sequence, for example. As referenced herein, the addition of other sequences to the 3′ primer may be desired in certain circumstances (e.g., stop codon sequences, etc.). The skilled artisan would appreciate that modifications of the above nucleotide positions may be necessary for optimizing PCR amplification.

[1232] The same general formulas provided above may be used in identifying the 5′ and 3′ primer sequences for amplifying any C-terminal deletion mutant of the present invention. Moreover, the same general formulas provided above may be used in identifying the 5′ and 3′ primer sequences for amplifying any combination of N-terminal and C-terminal deletion mutant of the present invention. The skilled artisan would appreciate that modifications of the above nucleotide positions may be necessary for optimizing PCR amplification.

Example 20

Site Directed/Site-Specific Mutagenesis

[1233] In vitro site-directed mutagenesis is an invaluable technique for studying protein structure-function relationships and gene expression, for example, as well as for vector modification. Site-directed mutagenesis can also be used for creating any of one or more of the mutants of the present invention, particularly the conservative and/or non-conservative amino acid substitution mutants of the prsent invention. Approaches utilizing single stranded DNA (ssDNA) as the template have been reported (e.g., T. A. Kunkel et al., 1985, Proc. Natl. Acad. Sci. USA), 82:488-492; M. A. Vandeyar et al., 1988, Gene, 65(1):129-133; M. Sugimoto et al., 1989, Anal. Biochem., 179(2):309-311; and J. W. Taylor et al., 1985, Nuc. Acids. Res., 13(24):8765-8785).

[1234] The use of PCR in site-directed mutagenesis accomplishes strand separation by using a denaturing step to separate the complementary strands and to allow efficient polymerization of the PCR primers. PCR site-directed mutagenesis methods thus permit site specific mutations to be incorporated in virtually any double stranded plasmid, thus eliminating the need for re-subcloning into M13-based bacteriophage vectors or single-stranded rescue. (M. P. Weiner et al., 1995, Molecular Biology: Current Innovations and Future Trends, Eds. A. M. Griffin and H. G. Griffin, Horizon Scientific Press, Norfolk, UK; and C. Papworth et al., 1996, Strategies, 9(3):3-4).

[1235] A protocol for performing site-directed mutagenesis, particularly employing the QuikChange™ site-directed mutagenesis kit (Stratagene, La Jolla, Calif.; U.S. Pat. Nos. 5,789,166 and 5,923,419) is provided for making point mutations, to switch or substitute amino acids, and to delete or insert single or multiple amino acids in the RATL1d6 amino acid sequence of this invention.

[1236] Primer Design

[1237] For primer design using this protocol, the mutagenic oligonucleotide primers are designed individually according to the desired mutation. The following considerations should be made for designing mutagenic primers: 1) Both of the mutagenic primers must contain the desired mutation and anneal to the same sequence on opposite strands of the plasmid; 2) Primers should be between 25 and 45 bases in length, and the melting temperature (Tm) of the primers should be greater than, or equal to, 78° C. The following formula is commonly used for estimating the Tm of primers: T=81.5 +0.41 (%GC)−675/N-% mismatch. For calculating Tm, N is the primer length in bases; and values for % GC and % mismatch are whole numbers. For calculating Tm for primers intended to introduce insertions or deletions, a modified version of the above formula is employed: T=81.5+0.41 (%GC)−675/N, where N does not include the bases which are being inserted or deleted; 3) The desired mutation (deletion or insertion) should be in the middle of the primer with approximately 10-15 bases of correct sequence on both sides; 4) The primers optimally should have a minimum GC content of 40%, and should terminate in one or more C or G bases; 5) Primers need not be 5′-phosphorylated, but must be purified either by fast polynucleotide liquid chromatography (FPLC) or by polyacrylamide gel electrophoresis (PAGE). Failure to purify the primers results in a significant decrease in mutation efficiency; and 6). It is important that primer concentration is in excess. It is suggested to vary the amount of template while keeping the concentration of the primers constantly in excess (QuikChange™ Site-Directed Mutagenesis Kit, Stratagene, La Jolla, Calif.).

[1238] Protocol for Setting Up the Reactions

[1239] Using the above-described primer design, two complimentary oligonucleotides containing the desired mutation, flanked by unmodified nucleic acid sequence, are synthesized. The resulting oligonucleotide primers are purified.

[1240] A control reaction is prepared using 5 μl 10× reaction buffer (100 mM KCl; 100 mM (NH4)2SO4; 200 mM Tris-HCl, pH 8.8; 20 mM MgSO4; 1% Triton® X-100; 1 mg/ml nuclease-free bovine serum albumin, BSA); 2 μl (10 ng) of pWhitescript™, 4.5-kb control plasmid (5 ng/μl); 1.25 μl (125 ng) of oligonucleotide control primer #1 (34-mer, 100 ng/μl); 1.25 μl (125 ng) of oligonucleotide control primer #2 (34-mer, 100 ng/μl); 1 μl of dNTP mix; double distilled H2O; to a final volume of 50 μl. Thereafter, 1 μl of DNA polymerase (PfuTurbo® DNA Polymerase, Stratagene), (2.5U/μl) is added. PfuTurbo® DNA Polymerase is stated to have 6-fold higher fidelity in DNA synthesis than does Taq polymerase. To maximize temperature cycling performance, use of thin-walled test tubes is suggested to ensure optimum contact with the heating blocks of the temperature cycler.

[1241] The sample reaction is prepared by combining 5 μl of 10× reaction buffer; x μl (5-50 ng) of dsDNA template; x μl (125 ng) of oligonucleotide primer #1; x μl (5-50 ng) of dsDNA template; x μl (125 ng) of oligonucleotide primer #2; 1 μl of dNTP mix; and ddH2O to a final volume of 50 μl. Thereafter, 1 μl of DNA polymerase (PfuTurbo DNA Polymerase, Stratagene), (2.5U/μl) is added.

[1242] It is suggested that if the thermal cycler does not have a hot-top assembly, each reaction should be overlaid with approximately 30 μl of mineral oil.

[1243] Cycling the Reactions

[1244] Each reaction is cycled using the following cycling parameters:

18SegmentCyclesTemperatureTime1195° C.30 seconds212-1895° C.30 seconds55° C. 1 minute68° C. 2 minutes/kb ofplasmid length

[1245] For the control reaction, a 12-minute extension time is used and the reaction is run for 12 cycles. Segment 2 of the above cycling parameters is adjusted in accordance with the type of mutation desired. For example, for point mutations, 12 cycles are used; for single amino acid changes, 16 cycles are used; and for multiple amino acid deletions or insertions, 18 cycles are used. Following the temperature cycling, the reaction is placed on ice for 2 minutes to cool the reaction to <37° C.

[1246] Digesting the Products and Transforming Competent Cells

[1247] One μl of the DpnI restriction enzyme (10 U/μl) is added directly (below mineral oil overlay) to each amplification reaction using a small, pointed pipette tip. The reaction mixture is gently and thoroughly mixed by pipetting the solution up and down several times. The reaction mixture is then centrifuged for 1 minute in a microcentrifuge. Immediately thereafter, each reaction is incubated at 37° C. for 1 hour to digest the parental (i.e., the non-mutated) supercoiled dsDNA.

[1248] Competent cells (i.e., XL1-Blue supercompetent cells, Stratagene) are thawed gently on ice. For each control and sample reaction to be transformed, 50 μl of the supercompetent cells are aliquotted to a prechilled test tube (Falcon 2059 polypropylene). Next, 1 μl of the DpnI-digested DNA is transferred from the control and the sample reactions to separate aliquots of the supercompetent cells. The transformation reactions are gently swirled to mix and incubated for 30 minutes on ice. Thereafter, the transformation reactions are heat-pulsed for 45 seconds at 42° C. for 2 minutes.

[1249] 0.5 ml of NZY+ broth, preheated to 42° C. is added to the transformation reactions which are then incubated at 37° C. for 1 hour with shaking at 225-250 rpm. An aliquot of each transformation reaction is plated on agar plates containing the appropriate antibiotic for the vector. For the mutagenesis and transformation controls, cells are spread on LB-ampicillin agar plates containing 80 μg/ml of X-gal and 20 mM MIPTG. Transformation plates are incubated for >16 hours at 37° C.

Example 21

Regulation of Protein Expression Via Controlled Aggregation in the Endoplasmic Reticulum

[1250] As described more particularly herein, proteins regulate diverse cellular processes in higher organisms, ranging from rapid metabolic changes to growth and differentiation. Increased production of specific proteins could be used to prevent certain diseases and/or disease states. Thus, the ability to modulate the expression of specific proteins in an organism would provide significant benefits.

[1251] Numerous methods have been developed to date for introducing foreign genes, either under the control of an inducible, constitutively active, or endogenous promoter, into organisms. Of particular interest are the inducible promoters (see, M. Gossen, et al., Proc. Natl. Acad. Sci. USA., 89:5547 (1992); Y. Wang, et al., Proc. Natl. Acad. Sci. USA, 91:8180 (1994), D. No., et al., Proc. Natl. Acad. Sci. USA, 93:3346 (1996); and V. M. Rivera, et al., Nature Med, 2:1028 (1996); in addition to additional examples disclosed elsewhere herein). In one example, the gene for erthropoietin (Epo) was transferred into mice and primates under the control of a small molecule inducer for expression (e.g., tetracycline or rapamycin) (see, D. Bohl, et al., Blood, 92:1512, (1998); K. G. Rendahl, et al., Nat.,Biotech, 16:757, (1998); V. M. Rivera, et al., Proc. Natl. Acad. Sci. USA, 96:8657 (1999); and X. Ye et al., Science, 283:88 (1999). Although such systems enable efficient induction of the gene of interest in the organism upon addition of the inducing agent (i.e., tetracycline, rapamycin, etc,.), the levels of expression tend to peak at 24 hours and trail off to background levels after 4 to 14 days. Thus, controlled transient expression is virtually impossible using these systems, though such control would be desirable.

[1252] A new alternative method of controlling gene expression levels of a protein from a transgene (i.e., includes stable and transient transformants) has recently been elucidated (V. M. Rivera., et al., Science, 287:826-830, (2000)). This method does not control gene expression at the level of the mRNA like the aforementioned systems. Rather, the system controls the level of protein in an active secreted form. In the absence of the inducing agent, the protein aggregates in the ER and is not secreted. However, addition of the inducing agent results in dis-aggregation of the protein and the subsequent secretion from the ER. Such a system affords low basal secretion, rapid, high level secretion in the presence of the inducing agent, and rapid cessation of secretion upon removal of the inducing agent. In fact, protein secretion reached a maximum level within 30 minutes of induction, and a rapid cessation of secretion within 1 hour of removing the inducing agent. The method is also applicable for controlling the level of production for membrane proteins.

[1253] Detailed methods are presented in V. M. Rivera., et al., Science, 287:826-830, (2000)), briefly:

[1254] Fusion protein constructs are created using polynucleotide sequences of the present invention with one or more copies (preferably at least 2, 3, 4, or more) of a conditional aggregation domain (CAD) a domain that interacts with itself in a ligand-reversible manner (i.e., in the presence of an inducing agent) using molecular biology methods known in the art and discussed elsewhere herein. The CAD domain may be the mutant domain isolated from the human FKBP12 (Phe36 to Met) protein (as disclosed in V. M. Rivera., et al., Science, 287:826-830, (2000), or alternatively other proteins having domains with similar ligand-reversible, self-aggregation properties. As a principle of design the fusion protein vector would contain a furin cleavage sequence operably linked between the polynucleotides of the present invention and the CAD domains. Such a cleavage site would enable the proteolytic cleavage of the CAD domains from the polypeptide of the present invention subsequent to secretion from the ER and upon entry into the trans-Golgi (J. B. Denault, et al., FEBS Lett., 379:113, (1996)). Alternatively, the skilled artisan would recognize that any proteolytic cleavage sequence could be substituted for the furin sequence provided the substituted sequence is cleavable either endogenously (e.g., the furin sequence) or exogenously (e.g., post secretion, post purification, post production, etc.). The preferred sequence of each feature of the fusion protein construct, from the 5′ to 3′ direction with each feature being operably linked to the other, would be a promoter, signal sequence, “X” number of (CAD)x domains, the furin sequence (or other proteolytic sequence), and the coding sequence of the polypeptide of the present invention. The artisan would appreciate that the promotor and signal sequence, independent from the other, could be either the endogenous promotor or signal sequence of a polypeptide of the present invention, or alternatively, could be a heterologous signal sequence and promotor.

[1255] The specific methods described herein for controlling protein secretion levels through controlled ER aggregation are not meant to be limiting are would be generally applicable to any of the polynucleotides and polypeptides of the present invention, including variants, homologues, orthologs, and fragments therein.

Example 22

Alteration of Protein Glycosylation Sites to Enhance Characteristics of Polypeptides of the Invention

[1256] Many eukaryotic cell surface and proteins are post-translationally processed to incorporate N-linked and O-linked carbohydrates (Kornfeld and Kornfeld (1985) Annu. Rev. Biochem. 54:631-64; Rademacher et al., (1988) Annu. Rev. Biochem. 57:785-838). Protein glycosylation is thought to serve a variety of functions including: augmentation of protein folding, inhibition of protein aggregation, regulation of intracellular trafficking to organelles, increasing resistance to proteolysis, modulation of protein antigenicity, and mediation of intercellular adhesion (Fieldler and Simons (1995) Cell, 81:309-312; Helenius (1994) Mol. Biol. Of the Cell 5:253-265; Olden et al., (1978) Cell, 13:461-473; Caton et al., (1982) Cell, 37:417-427; Alexamnder and Elder (1984), Science, 226:1328-1330; and Flack et al., (1994), J. Biol. Chem., 269:14015-14020). In higher organisms, the nature and extent of glycosylation can markedly affect the circulating half-life and bio-availability of proteins by mechanisms involving receptor mediated uptake and clearance (Ashwell and Morrell, (1974), Adv. Enzymol., 41:99-128; Ashwell and Harford (1982), Ann. Rev. Biochem., 51:531-54). Receptor systems have been identified that are thought to play a major role in the clearance of serum proteins through recognition of various carbohydrate structures on the glycoproteins (Stockert (1995), Physiol. Rev., 75:591-609; Kery et al., (1992), Arch. Biochem. Biophys., 298:49-55). Thus, production strategies resulting in incomplete attachment of terminal sialic acid residues might provide a means of shortening the bioavailability and half-life of glycoproteins. Conversely, expression strategies resulting in saturation of terminal sialic acid attachment sites might lengthen protein bioavailability and half-life.

[1257] In the development of recombinant glycoproteins for use as pharmaceutical products, for example, it has been speculated that the pharmacodynamics of recombinant proteins can be modulated by the addition or deletion of glycosylation sites from a glycoproteins primary structure (Berman and Lasky (1985a) Trends in Biotechnol., 3:51-53). However, studies have reported that the deletion of N-linked glycosylation sites often impairs intracellular transport and results in the intracellular accumulation of glycosylation site variants (Machamer and Rose (1988), J. Biol Chem., 263:5955-5960; Gallagher et al., (1992), J. Virology., 66:7136-7145; Collier et al., (1993), Biochem., 32:7818-7823; Claffey et al., (1995) Biochemica et Biophysica Acta, 1246:1-9; Dube et al., (1988), J. Biol. Chem. 263:17516-17521). While glycosylation site variants of proteins can be expressed intracellularly, it has proved difficult to recover useful quantities from growth conditioned cell culture medium.

[1258] Moreover, it is unclear to what extent a glycosylation site in one species will be recognized by another species glycosylation machinery. Due to the importance of glycosylation in protein metabolism, particularly the secretion and/or expression of the protein, whether a glycosylation signal is recognized may profoundly determine a proteins ability to be expressed, either endogenously or recombinately, in another organism (i.e., expressing a human protein in E.coli, yeast, or viral organisms; or an E.coli, yeast, or viral protein in human, etc.). Thus, it may be desirable to add, delete, or modify a glycosylation site, and possibly add a glycosylation site of one species to a protein of another species to improve the proteins functional, bioprocess purification, and/or structural characteristics (e.g., a polypeptide of the present invention).

[1259] A number of methods may be employed to identify the location of glycosylation sites within a protein. One preferred method is to run the translated protein sequence through the PROSITE computer program (Swiss Institute of Bioinformatics). Once identified, the sites could be systematically deleted, or impaired, at the level of the DNA using mutagenesis methodology known in the art and available to the skilled artisan, Preferably using PCR-directed mutagenesis (See Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, N.Y. (1982)). Similarly, glycosylation sites could be added, or modified at the level of the DNA using similar methods, preferably PCR methods (See, Maniatis, supra). The results of modifying the glycosylation sites for a particular protein (e.g., solubility, secretion potential, activity, aggregation, proteolytic resistance, etc.) could then be analyzed using methods know in the art.

[1260] The skilled artisan would acknowledge the existence of other computer algorithms capable of predicting the location of glycosylation sites within a protein. For example, the Motif computer program (Genetics Computer Group suite of programs) provides this function, as well.

Example 23

Method of Enhancing the Biological Activity/Functional Characteristics of Invention through Molecular Evolution

[1261] Although many of the most biologically active proteins known are highly effective for their specified function in an organism, they often possess characteristics that make them undesirable for transgenic, therapeutic, and/or industrial applications. Among these traits, a short physiological half-life is the most prominent problem, and is present either at the level of the protein, or the level of the proteins mRNA. The ability to extend the half-life, for example, would be particularly important for a proteins use in gene therapy, transgenic animal production, the bioprocess production and purification of the protein, and use of the protein as a chemical modulator among others. Therefore, there is a need to identify novel variants of isolated proteins possessing characteristics which enhance their application as a therapeutic for treating diseases of animal origin, in addition to the proteins applicability to common industrial and pharmaceutical applications.

[1262] Thus, one aspect of the present invention relates to the ability to enhance specific characteristics of invention through directed molecular evolution. Such an enhancement may, in a non-limiting example, benefit the inventions utility as an essential component in a kit, the inventions physical attributes such as its solubility, structure, or codon optimization, the inventions specific biological activity, including any associated enzymatic activity, the proteins enzyme kinetics, the proteins Ki, Kcat, Km, Vmax, Kd, protein-protein activity, protein-DNA binding activity, antagonist/inhibitory activity (including direct or indirect interaction), agonist activity (including direct or indirect interaction), the proteins antigenicity (e.g., where it would be desirable to either increase or decrease the antigenic potential of the protein), the immunogenicity of the protein, the ability of the protein to form dimers, trimers, or multimers with either itself or other proteins, the antigenic efficacy of the invention, including its subsequent use a preventative treatment for disease or disease states, or as an effector for targeting diseased genes. Moreover, the ability to enhance specific characteristics of a protein may also be applicable to changing the characterized activity of an enzyme to an activity completely unrelated to its initially characterized activity. Other desirable enhancements of the invention would be specific to each individual protein, and would thus be well known in the art and contemplated by the present invention.

[1263] For example, an engineered calpain may be constitutively active upon binding of its cognate substrate. Alternatively, an engineered calpain may be constitutively active in the absence of substrate binding, and/or may exhibit increased efficacy in inhibiting cysteine proteases. In yet another example, an engineered calpain may be capable of being activated with less than all of the regulatory factors and/or conditions typically required for calpain activation (e.g., substrate binding, phosphorylation, cofactor binding, Ca+ binding, Ca+ activation, conformational changes, etc.). Such calpain would be useful in screens to identify calpain modulators, among other uses described herein.

[1264] Directed evolution is comprised of several steps. The first step is to establish a library of variants for the gene or protein of interest. The most important step is to then select for those variants that entail the activity you wish to identify. The design of the screen is essential since your screen should be selective enough to eliminate non-useful variants, but not so stringent as to eliminate all variants. The last step is then to repeat the above steps using the best variant from the previous screen. Each successive cycle, can then be tailored as necessary, such as increasing the stringency of the screen, for example.

[1265] Over the years, there have been a number of methods developed to introduce mutations into macromolecules. Some of these methods include, random mutagenesis, “error-prone” PCR, chemical mutagenesis, site-directed mutagenesis, and other methods well known in the art (for a comprehensive listing of current mutagenesis methods, see Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, N.Y. (1982)). Typically, such methods have been used, for example, as tools for identifying the core functional region(s) of a protein or the function of specific domains of a protein (if a multi-domain protein). However, such methods have more recently been applied to the identification of macromolecule variants with specific or enhanced characteristics.

[1266] Random mutagenesis has been the most widely recognized method to date. Typically, this has been carried out either through the use of “error-prone” PCR (as described in Moore, J., et al, Nature Biotechnology 14:458, (1996), or through the application of randomized synthetic oligonucleotides corresponding to specific regions of interest (as described by Derbyshire, K. M. et al, Gene, 46:145-152, (1986), and Hill, D E, et al, Methods Enzymol., 55:559-568, (1987). Both approaches have limits to the level of mutagenesis that can be obtained. However, either approach enables the investigator to effectively control the rate of mutagenesis. This is particularly important considering the fact that mutations beneficial to the activity of the enzyme are fairly rare. In fact, using too high a level of mutagenesis may counter or inhibit the desired benefit of a useful mutation.

[1267] While both of the aforementioned methods are effective for creating randomized pools of macromolecule variants, a third method, termed “DNA Shuffling”, or “sexual PCR” (WPC, Stemmer, PNAS, 91:10747, (1994)) has recently been elucidated. DNA shuffling has also been referred to as “directed molecular evolution”, “exon-shuffling”, “directed enzyme evolution”, “in vitro evolution”, and “artificial evolution”. Such reference terms are known in the art and are encompassed by the invention. This new, preferred, method apparently overcomes the limitations of the previous methods in that it not only propagates positive traits, but simultaneously eliminates negative traits in the resulting progeny.

[1268] DNA shuffling accomplishes this task by combining the principal of in vitro recombination, along with the method of “error-prone” PCR. In effect, you begin with a randomly digested pool of small fragments of your gene, created by Dnase I digestion, and then introduce said random fragments into an “error-prone” PCR assembly reaction. During the PCR reaction, the randomly sized DNA fragments not only hybridize to their cognate strand, but also may hybridize to other DNA fragments corresponding to different regions of the polynucleotide of interest—regions not typically accessible via hybridization of the entire polynucleotide. Moreover, since the PCR assembly reaction utilizes “error-prone” PCR reaction conditions, random mutations are introduced during the DNA synthesis step of the PCR reaction for all of the fragments—further diversifying the potential hybridization sites during the annealing step of the reaction.

[1269] A variety of reaction conditions could be utilized to carry-out the DNA shuffling reaction. However, specific reaction conditions for DNA shuffling are provided, for example, in PNAS, 91:10747, (1994). Briefly:

[1270] Prepare the DNA substrate to be subjected to the DNA shuffling reaction. Preparation may be in the form of simply purifying the DNA from contaminating cellular material, chemicals, buffers, oligonucleotide primers, deoxynucleotides, RNAs, etc., and may entail the use of DNA purification kits as those provided by Qiagen, Inc., or by the Promega, Corp., for example.

[1271] Once the DNA substrate has been purified, it would be subjected to Dnase I digestion. About 2-4ug of the DNA substrate(s) would be digested with 0.0015 units of Dnase I (Sigma) per ul in 100ul of 50 mM Tris-HCL, pH 7.4/1 mM MgCl2 for 10-20 min. at room temperature. The resulting fragments of 10-50 bp could then be purified by running them through a 2% low-melting point agarose gel by electrophoresis onto DE81 ion-exchange paper (Whatmann) or could be purified using Microcon concentrators (Amicon) of the appropriate molecular weight cutoff, or could use oligonucleotide purification columns (Qiagen), in addition to other methods known in the art. If using DE81 ion-exchange paper, the 10-50 bp fragments could be eluted from said paper using 1M NaCl, followed by ethanol precipitation.

[1272] The resulting purified fragments would then be subjected to a PCR assembly reaction by re-suspension in a PCR mixture containing: 2 mM of each dNTP, 2.2 mM MgCl2, 50 mM KCl, 10 mM Tris·HCL, pH 9.0, and 0.1% Triton X-100, at a final fragment concentration of 10-30ng/ul. No primers are added at this point. Taq DNA polymerase (Promega) would be used at 2.5 units per 100ul of reaction mixture. A PCR program of 94 C for 60 s; 94 C for 30 s, 50-55 C for 30 s, and 72 C for 30 s using 30-45 cycles, followed by 72 C for 5 min using an MJ Research (Cambridge, Mass.) PTC-150 thermocycler. After the assembly reaction is completed, a 1:40 dilution of the resulting primerless product would then be introduced into a PCR mixture (using the same buffer mixture used for the assembly reaction) containing 0.8um of each primer and subjecting this mixture to 15 cycles of PCR (using 94 C for 30 s, 50 C for 30 s, and 72 C for 30 s). The referred primers would be primers corresponding to the nucleic acid sequences of the polynucleotide(s) utilized in the shuffling reaction. Said primers could consist of modified nucleic acid base pairs using methods known in the art and referred to else where herein, or could contain additional sequences (i.e., for adding restriction sites, mutating specific base-pairs, etc.).

[1273] The resulting shuffled, assembled, and amplified product can be purified using methods well known in the art (e.g., Qiagen PCR purification kits) and then subsequently cloned using appropriate restriction enzymes.

[1274] Although a number of variations of DNA shuffling have been published to date, such variations would be obvious to the skilled artisan and are encompassed by the invention. The DNA shuffling method can also be tailored to the desired level of mutagenesis using the methods described by Zhao, et al. (Nucl Acid Res., 25(6): 1307-1308, (1997).

[1275] As described above, once the randomized pool has been created, it can then be subjected to a specific screen to identify the variant possessing the desired characteristic(s). Once the variant has been identified, DNA corresponding to the variant could then be used as the DNA substrate for initiating another round of DNA shuffling. This cycle of shuffling, selecting the optimized variant of interest, and then re-shuffling, can be repeated until the ultimate variant is obtained. Examples of model screens applied to identify variants created using DNA shuffling technology may be found in the following publications: J. C., Moore, et al., J. Mol. Biol., 272:336-347, (1997), F. R., Cross, et al., Mol. Cell. Biol., 18:2923-2931, (1998), and A. Crameri., et al., Nat. Biotech., 15:436-438, (1997).

[1276] DNA shuffling has several advantages. First, it makes use of beneficial mutations. When combined with screening, DNA shuffling allows the discovery of the best mutational combinations and does not assume that the best combination contains all the mutations in a population. Secondly, recombination occurs simultaneously with point mutagenesis. An effect of forcing DNA polymerase to synthesize full-length genes from the small fragment DNA pool is a background mutagenesis rate. In combination with a stringent selection method, enzymatic activity has been evolved up to 16000 fold increase over the wild-type form of the enzyme. In essence, the background mutagenesis yielded the genetic variability on which recombination acted to enhance the activity.

[1277] A third feature of recombination is that it can be used to remove deleterious mutations. As discussed above, during the process of the randomization, for every one beneficial mutation, there may be at least one or more neutral or inhibitory mutations. Such mutations can be removed by including in the assembly reaction an excess of the wild-type random-size fragments, in addition to the random-size fragments of the selected mutant from the previous selection. During the next selection, some of the most active variants of the polynucleotide/polypeptide/enzyme, should have lost the inhibitory mutations.

[1278] Finally, recombination enables parallel processing. This represents a significant advantage since there are likely multiple characteristics that would make a protein more desirable (e.g. solubility, activity, etc.). Since it is increasingly difficult to screen for more than one desirable trait at a time, other methods of molecular evolution tend to be inhibitory. However, using recombination, it would be possible to combine the randomized fragments of the best representative variants for the various traits, and then select for multiple properties at once.

[1279] DNA shuffling can also be applied to the polynucleotides and polypeptides of the present invention to decrease their immunogenicity in a specified host. For example, a particular variant of the present invention may be created and isolated using DNA shuffling technology. Such a variant may have all of the desired characteristics, though may be highly immunogenic in a host due to its novel intrinsic structure. Specifically, the desired characteristic may cause the polypeptide to have a non-native structure which could no longer be recognized as a “self” molecule, but rather as a “foreign”, and thus activate a host immune response directed against the novel variant. Such a limitation can be overcome, for example, by including a copy of the gene sequence for a xenobiotic ortholog of the native protein in with the gene sequence of the novel variant gene in one or more cycles of DNA shuffling. The molar ratio of the ortholog and novel variant DNAs could be varied accordingly. Ideally, the resulting hybrid variant identified would contain at least some of the coding sequence which enabled the xenobiotic protein to evade the host immune system, and additionally, the coding sequence of the original novel variant that provided the desired characteristics.

[1280] Likewise, the invention encompasses the application of DNA shuffling technology to the evolution of polynucleotides and polypeptides of the invention, wherein one or more cycles of DNA shuffling include, in addition to the gene template DNA, oligonucleotides coding for known allelic sequences, optimized codon sequences, known variant sequences, known polynucleotide polymorphism sequences, known ortholog sequences, known homologue sequences, additional homologous sequences, additional non-homologous sequences, sequences from another species, and any number and combination of the above.

[1281] In addition to the described methods above, there are a number of related methods that may also be applicable, or desirable in certain cases. Representative among these are the methods discussed in PCT applications WO 98/31700, and WO 98/32845, which are hereby incorporated by reference. Furthermore, related methods can also be applied to the polynucleotide sequences of the present invention in order to evolve invention for creating ideal variants for use in gene therapy, protein engineering, evolution of whole cells containing the variant, or in the evolution of entire enzyme pathways containing polynucleotides of the invention as described in PCT applications WO 98/13485, WO 98/13487, WO 98/27230, WO 98/31837, and Crameri, A., et al., Nat. Biotech., 15:436-438, (1997), respectively.

[1282] Additional methods of applying “DNA Shuffling” technology to the polynucleotides and polypeptides of the present invention, including their proposed applications, may be found in U.S. Pat. No. 5,605,793; PCT Application No. WO 95/22625; PCT Application No. WO 97/20078; PCT Application No. WO 97/35966; and PCT Application No. WO 98/42832; PCT Application No. WO 00/09727 specifically provides methods for applying DNA shuffling to the identification of herbicide selective crops which could be applied to the polynucleotides and polypeptides of the present invention; additionally, PCT Application No. WO 00/12680 provides methods and compositions for generating, modifying, adapting, and optimizing polynucleotide sequences that confer detectable phenotypic properties on plant species; each of the above are hereby incorporated in their entirety herein for all purposes.

Example 24

Method of Determining Alterations in a Gene Corresponding to a Polynucleotide

[1283] RNA isolated from entire families or individual patients presenting with a phenotype of interest (such as a disease) is be isolated. cDNA is then generated from these RNA samples using protocols known in the art. (See, Sambrook.) The cDNA is then used as a template for PCR, employing primers surrounding regions of interest in SEQ ID NO:1. Suggested PCR conditions consist of 35 cycles at 95 degrees C. for 30 seconds; 60-120 seconds at 52-58 degrees C.; and 60-120 seconds at 70 degrees C., using buffer solutions described in Sidransky et al., Science 252:706 (1991).

[1284] PCR products are then sequenced using primers labeled at their 5′ end with T4 polynucleotide kinase, employing SequiTherm Polymerase. (Epicentre Technologies). The intron-exon borders of selected exons is also determined and genomic PCR products analyzed to confirm the results. PCR products harboring suspected mutations is then cloned and sequenced to validate the results of the direct sequencing.

[1285] PCR products is cloned into T-tailed vectors as described in Holton et al., Nucleic Acids Research, 19:1156 (1991) and sequenced with T7 polymerase (United States Biochemical). Affected individuals are identified by mutations not present in unaffected individuals.

[1286] Genomic rearrangements are also observed as a method of determining alterations in a gene corresponding to a polynucleotide. Genomic clones isolated according to Example 2 are nick-translated with digoxigenindeoxy-uridine 5′-triphosphate (Boehringer Manheim), and FISH performed as described in Johnson et al., Methods Cell Biol. 35:73-99 (1991). Hybridization with the labeled probe is carried out using a vast excess of human cot-i DNA for specific hybridization to the corresponding genomic locus.

[1287] Chromosomes are counterstained with 4,6-diamino-2-phenylidole and propidium iodide, producing a combination of C- and R-bands. Aligned images for precise mapping are obtained using a triple-band filter set (Chroma Technology, Brattleboro, Vt.) in combination with a cooled charge-coupled device camera (Photometrics, Tucson, Ariz.) and variable excitation wavelength filters. (Johnson et al., Genet. Anal. Tech. Appl., 8:75 (1991).) Image collection, analysis and chromosomal fractional length measurements are performed using the ISee Graphical Program System. (Inovision Corporation, Durham, N.C.) Chromosome alterations of the genomic region hybridized by the probe are identified as insertions, deletions, and translocations. These alterations are used as a diagnostic marker for an associated disease.

Example 25

Method of Detecting Abnormal Levels of a Polypeptide in a Biological Sample

[1288] A polypeptide of the present invention can be detected in a biological sample, and if an increased or decreased level of the polypeptide is detected, this polypeptide is a marker for a particular phenotype. Methods of detection are numerous, and thus, it is understood that one skilled in the art can modify the following assay to fit their particular needs.

[1289] For example, antibody-sandwich ELISAs are used to detect polypeptides in a sample, preferably a biological sample. Wells of a microtiter plate are coated with specific antibodies, at a final concentration of 0.2 to 10 ug/ml. The antibodies are either monoclonal or polyclonal and are produced by the method described elsewhere herein. The wells are blocked so that non-specific binding of the polypeptide to the well is reduced.

[1290] The coated wells are then incubated for >2 hours at RT with a sample containing the polypeptide. Preferably, serial dilutions of the sample should be used to validate results. The plates are then washed three times with deionized or distilled water to remove unbounded polypeptide.

[1291] Next, 50 ul of specific antibody-alkaline phosphatase conjugate, at a concentration of 25-400 ng, is added and incubated for 2 hours at room temperature. The plates are again washed three times with deionized or distilled water to remove unbounded conjugate.

[1292] Add 75 ul of 4-methylumbelliferyl phosphate (MUP) or p-nitrophenyl phosphate (NPP) substrate solution to each well and incubate 1 hour at room temperature. Measure the reaction by a microtiter plate reader. Prepare a standard curve, using serial dilutions of a control sample, and plot polypeptide concentration on the X-axis (log scale) and fluorescence or absorbance of the Y-axis (linear scale). Interpolate the concentration of the polypeptide in the sample using the standard curve.

Example 26

Formulation

[1293] The invention also provides methods of treatment and/or prevention diseases, disorders, and/or conditions (such as, for example, any one or more of the diseases or disorders disclosed herein) by administration to a subject of an effective amount of a Therapeutic. By therapeutic is meant a polynucleotides or polypeptides of the invention (including fragments and variants), agonists or antagonists thereof, and/or antibodies thereto, in combination with a pharmaceutically acceptable carrier type (e.g., a sterile carrier).

[1294] The Therapeutic will be formulated and dosed in a fashion consistent with good medical practice, taking into account the clinical condition of the individual patient (especially the side effects of treatment with the Therapeutic alone), the site of delivery, the method of administration, the scheduling of administration, and other factors known to practitioners. The “effective amount” for purposes herein is thus determined by such considerations.

[1295] As a general proposition, the total pharmaceutically effective amount of the Therapeutic administered parenterally per dose will be in the range of about 1 ug/kg/day to 10 mg/kg/day of patient body weight, although, as noted above, this will be subject to therapeutic discretion. More preferably, this dose is at least 0.01 mg/kg/day, and most preferably for humans between about 0.01 and 1 mg/kg/day for the hormone. If given continuously, the Therapeutic is typically administered at a dose rate of about 1 ug/kg/hour to about 50 ug/kg/hour, either by 1-4 injections per day or by continuous subcutaneous infusions, for example, using a mini-pump. An intravenous bag solution may also be employed. The length of treatment needed to observe changes and the interval following treatment for responses to occur appears to vary depending on the desired effect.

[1296] Therapeutics can be administered orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, gels, drops or transdermal patch), bucally, or as an oral or nasal spray. “Pharmaceutically acceptable carrier” refers to a non-toxic solid, semisolid or liquid filler, diluent, encapsulating material or formulation auxiliary of any. The term “parenteral” as used herein refers to modes of administration which include intravenous, intramuscular, intraperitoneal, intrasternal, subcutaneous and intraarticular injection and infusion.

[1297] In yet an additional embodiment, the Therapeutics of the invention are delivered orally using the drug delivery technology described in U.S. Pat. No. 6,258,789, which is hereby incorporated by reference herein.

[1298] Therapeutics of the invention are also suitably administered by sustained-release systems. Suitable examples of sustained-release Therapeutics are administered orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, gels, drops or transdermal patch), bucally, or as an oral or nasal spray. “Pharmaceutically acceptable carrier” refers to a non-toxic solid, semisolid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. The term “parenteral” as used herein refers to modes of administration which include intravenous, intramuscular, intraperitoneal, intrasternal, subcutaneous and intraarticular injection and infusion.

[1299] Therapeutics of the invention may also be suitably administered by sustained-release systems. Suitable examples of sustained-release Therapeutics include suitable polymeric materials (such as, for example, semi-permeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules), suitable hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, and sparingly soluble derivatives (such as, for example, a sparingly soluble salt).

[1300] Sustained-release matrices include polylactides (U.S. Pat. No. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma-ethyl-L-glutamate (Sidman et al., Biopolymers 22:547-556 (1983)), poly (2-hydroxyethyl methacrylate) (Langer et al., J. Biomed. Mater. Res. 15:167-277 (1981), and Langer, Chem. Tech. 12:98-105 (1982)), ethylene vinyl acetate (Langer et al., Id.) or poly-D-(−)-3-hydroxybutyric acid (EP 133,988).

[1301] Sustained-release Therapeutics also include liposomally entrapped Therapeutics of the invention (see, generally, Langer, Science 249:1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 317-327 and 353-365 (1989)). Liposomes containing the Therapeutic are prepared by methods known per se: DE 3,218,121; Epstein et al., Proc. Natl. Acad. Sci. (USA) 82:3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci.(USA) 77:4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP 142,641; Japanese Pat. Appl. 83-118008; U.S. Pat. Nos. 4,485,045 and 4,544,545; and EP 102,324. Ordinarily, the liposomes are of the small (about 200-800 Angstroms) unilamellar type in which the lipid content is greater than about 30 mol. percent cholesterol, the selected proportion being adjusted for the optimal Therapeutic.

[1302] In yet an additional embodiment, the Therapeutics of the invention are delivered by way of a pump (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321:574 (1989)).

[1303] Other controlled release systems are discussed in the review by Langer (Science 249:1527-1533 (1990)).

[1304] For parenteral administration, in one embodiment, the Therapeutic is formulated generally by mixing it at the desired degree of purity, in a unit dosage injectable form (solution, suspension, or emulsion), with a pharmaceutically acceptable carrier, i.e., one that is non-toxic to recipients at the dosages and concentrations employed and is compatible with other ingredients of the formulation. For example, the formulation preferably does not include oxidizing agents and other compounds that are known to be deleterious to the Therapeutic.

[1305] Generally, the formulations are prepared by contacting the Therapeutic uniformly and intimately with liquid carriers or finely divided solid carriers or both. Then, if necessary, the product is shaped into the desired formulation. Preferably the carrier is a parenteral carrier, more preferably a solution that is isotonic with the blood of the recipient. Examples of such carrier vehicles include water, saline, Ringer's solution, and dextrose solution. Non-aqueous vehicles such as fixed oils and ethyl oleate are also useful herein, as well as liposomes.

[1306] The carrier suitably contains minor amounts of additives such as substances that enhance isotonicity and chemical stability. Such materials are non-toxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, succinate, acetic acid, and other organic acids or their salts; antioxidants such as ascorbic acid; low molecular weight (less than about ten residues) polypeptides, e.g., polyarginine or tripeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyinylpyrrolidone; amino acids, such as glycine, glutamic acid, aspartic acid, or arginine; monosaccharides, disaccharides, and other carbohydrates including cellulose or its derivatives, glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; counterions such as sodium; and/or nonionic surfactants such as polysorbates, poloxamers, or PEG.

[1307] The Therapeutic will typically be formulated in such vehicles at a concentration of about 0.1 mg/ml to 100 mg/ml, preferably 1-10 mg/ml, at a pH of about 3 to 8. It will be understood that the use of certain of the foregoing excipients, carriers, or stabilizers will result in the formation of polypeptide salts.

[1308] Any pharmaceutical used for therapeutic administration can be sterile. Sterility is readily accomplished by filtration through sterile filtration membranes (e.g., 0.2 micron membranes). Therapeutics generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.

[1309] Therapeutics ordinarily will be stored in unit or multi-dose containers, for example, sealed ampoules or vials, as an aqueous solution or as a lyophilized formulation for reconstitution. As an example of a lyophilized formulation, 10-ml vials are filled with 5 ml of sterile-filtered 1% (w/v) aqueous Therapeutic solution, and the resulting mixture is lyophilized. The infusion solution is prepared by reconstituting the lyophilized Therapeutic using bacteriostatic Water-for-Injection.

[1310] The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the Therapeutics of the invention. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. In addition, the Therapeutics may be employed in conjunction with other therapeutic compounds.

[1311] The Therapeutics of the invention may be administered alone or in combination with adjuvants. Adjuvants that may be administered with the Therapeutics of the invention include, but are not limited to, alum, alum plus deoxycholate (ImmunoAg), MTP-PE (Biocine Corp.), QS21 (Genentech, Inc.), BCG, and MPL. In a specific embodiment, Therapeutics of the invention are administered in combination with alum. In another specific embodiment, Therapeutics of the invention are administered in combination with QS-21. Further adjuvants that may be administered with the Therapeutics of the invention include, but are not limited to, Monophosphoryl lipid immunomodulator, AdjuVax 100a, QS-21, QS-18, CRL1005, Aluminum salts, MF-59, and Virosomal adjuvant technology. Vaccines that may be administered with the Therapeutics of the invention include, but are not limited to, vaccines directed toward protection against MMR (measles, mumps, rubella), polio, varicella, tetanus/diptheria, hepatitis A, hepatitis B, haemophilus influenzae B, whooping cough, pneumonia, influenza, Lyme's Disease, rotavirus, cholera, yellow fever, Japanese encephalitis, poliomyelitis, rabies, typhoid fever, and pertussis. Combinations may be administered either concomitantly, e.g., as an admixture, separately but simultaneously or concurrently; or sequentially. This includes presentations in which the combined agents are administered together as a therapeutic mixture, and also procedures in which the combined agents are administered separately but simultaneously, e.g., as through separate intravenous lines into the same individual. Administration “in combination” further includes the separate administration of one of the compounds or agents given first, followed by the second.

[1312] The Therapeutics of the invention may be administered alone or in combination with other therapeutic agents. Therapeutic agents that may be administered in combination with the Therapeutics of the invention, include but not limited to, other members of the TNF family, chemotherapeutic agents, antibiotics, steroidal and non-steroidal anti-inflammatories, conventional immunotherapeutic agents, cytokines and/or growth factors. Combinations may be administered either concomitantly, e.g., as an admixture, separately but simultaneously or concurrently; or sequentially. This includes presentations in which the combined agents are administered together as a therapeutic mixture, and also procedures in which the combined agents are administered separately but simultaneously, e.g., as through separate intravenous lines into the same individual. Administration “in combination” further includes the separate administration of one of the compounds or agents given first, followed by the second.

[1313] In one embodiment, the Therapeutics of the invention are administered in combination with members of the TNF family. TNF, TNF-related or TNF-like molecules that may be administered with the Therapeutics of the invention include, but are not limited to, soluble forms of TNF-alpha, lymphotoxin-alpha (LT-alpha, also known as TNF-beta), LT-beta (found in complex heterotrimer LT-alpha2-beta), OPGL, FasL, CD27L, CD30L, CD40L, 4-1BBL, DcR3, OX40L, TNF-gamma (International Publication No. WO 96/14328), AIM-I (International Publication No. WO 97/33899), endokine-alpha (International Publication No. WO 98/07880), TR6 (International Publication No. WO 98/30694), OPG, and neutrokine-alpha (International Publication No. WO 98/18921, OX40, and nerve growth factor (NGF), and soluble forms of Fas, CD30, CD27, CD40 and 4-IBB, TR2 (International Publication No. WO 96/34095), DR3 (International Publication No. WO 97/33904), DR4 (International Publication No. WO 98/32856), TR5 (International Publication No. WO 98/30693), TR6 (International Publication No. WO 98/30694), TR7 (International Publication No. WO 98/41629), TRANK, TR9 (International Publication No. WO 98/56892),TR10 (International Publication No. WO 98/54202), 312C2 (International Publication No. WO 98/06842), and TR12, and soluble forms CD154, CD70, and CD153.

[1314] In certain embodiments, Therapeutics of the invention are administered in combination with antiretroviral agents, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and/or protease inhibitors. Nucleoside reverse transcriptase inhibitors that may be administered in combination with the Therapeutics of the invention, include, but are not limited to, RETROVIR (zidovudine/AZT), VIDEX (didanosine/ddI), HIVID (zalcitabine/ddC), ZERIT (stavudine/d4T), EPIVIR (lamivudine/3TC), and COMBIVIR (zidovudine/lamivudine). Non-nucleoside reverse transcriptase inhibitors that may be administered in combination with the Therapeutics of the invention, include, but are not limited to, VIRAMUNE (nevirapine), RESCRIPTOR (delavirdine), and SUSTIVA (efavirenz). Protease inhibitors that may be administered in combination with the Therapeutics of the invention, include, but are not limited to, CRIXIVAN (indinavir), NORVIR (ritonavir), INVIRASE (saquinavir), and VIRACEPT (nelfinavir). In a specific embodiment, antiretroviral agents, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and/or protease inhibitors may be used in any combination with Therapeutics of the invention to treat AIDS and/or to prevent or treat HIV infection.

[1315] In other embodiments, Therapeutics of the invention may be administered in combination with anti-opportunistic infection agents. Anti-opportunistic agents that may be administered in combination with the Therapeutics of the invention, include, but are not limited to, TRIMETHOPRIM-SULFAMETHOXAZOLE, DAPSONE, PENTAMIDINE, ATOVAQUONE, ISONIAZID, RIFAMPIN, PYRAZINAMIDE, ETHAMBUTOL, RIFABUTIN, CLARITHROMYCIN, AZITHROMYCIN, GANCICLOVIR, FOSCARNET, CIDOFOVIR, FLUCONAZOLE, ITRACONAZOLE, KETOCONAZOLE, ACYCLOVIR, FAMCICOLVIR, PYRIMETHAMINE, LEUCOVORIN, NEUPOGEN (filgrastim/G-CSF), and LEUKINE (sargramostim/GM-CSF). In a specific embodiment, Therapeutics of the invention are used in any combination with TRIMETHOPRIM-SULFAMETHOXAZOLE, DAPSONE, PENTAMIDINE, and/or ATOVAQUONE to prophylactically treat or prevent an opportunistic Pneumocystis carinii pneumonia infection. In another specific embodiment, Therapeutics of the invention are used in any combination with ISONIAZID, RIFAMPIN, PYRAZINAMIDE, and/or ETHAMBUTOL to prophylactically treat or prevent an opportunistic Mycobacterium avium complex infection. In another specific embodiment, Therapeutics of the invention are used in any combination with RIFABUTIN, CLARITHROMYCIN, and/or AZITHROMYCIN to prophylactically treat or prevent an opportunistic Mycobacterium tuberculosis infection. In another specific embodiment, Therapeutics of the invention are used in any combination with GANCICLOVIR, FOSCARNET, and/or CIDOFOVIR to prophylactically treat or prevent an opportunistic cytomegalovirus infection. In another specific embodiment, Therapeutics of the invention are used in any combination with FLUCONAZOLE, ITRACONAZOLE, and/or KETOCONAZOLE to prophylactically treat or prevent an opportunistic fungal infection. In another specific embodiment, Therapeutics of the invention are used in any combination with ACYCLOVIR and/or FAMCICOLVIR to prophylactically treat or prevent an opportunistic herpes simplex virus type I and/or type II infection. In another specific embodiment, Therapeutics of the invention are used in any combination with PYRIMETHAMINE and/or LEUCOVORIN to prophylactically treat or prevent an opportunistic Toxoplasma gondii infection. In another specific embodiment, Therapeutics of the invention are used in any combination with LEUCOVORIN and/or NEUPOGEN to prophylactically treat or prevent an opportunistic bacterial infection.

[1316] In a further embodiment, the Therapeutics of the invention are administered in combination with an antiviral agent. Antiviral agents that may be administered with the Therapeutics of the invention include, but are not limited to, acyclovir, ribavirin, amantadine, and remantidine.

[1317] In a further embodiment, the Therapeutics of the invention are administered in combination with an antibiotic agent. Antibiotic agents that may be administered with the Therapeutics of the invention include, but are not limited to, amoxicillin, beta-lactamases, aminoglycosides, beta-lactam (glycopeptide), beta-lactamases, Clindamycin, chloramphenicol, cephalosporins, ciprofloxacin, ciprofloxacin, erythromycin, fluoroquinolones, macrolides, metronidazole, penicillins, quinolones, rifampin, streptomycin, sulfonamide, tetracyclines, trimethoprim, trimethoprim-sulfamthoxazole, and vancomycin.

[1318] Conventional nonspecific immunosuppressive agents, that may be administered in combination with the Therapeutics of the invention include, but are not limited to, steroids, cyclosporine, cyclosporine analogs, cyclophosphamide methylprednisone, prednisone, azathioprine, FK-506, 15-deoxyspergualin, and other immunosuppressive agents that act by suppressing the function of responding T cells.

[1319] In specific embodiments, Therapeutics of the invention are administered in combination with immunosuppressants. Immunosuppressants preparations that may be administered with the Therapeutics of the invention include, but are not limited to, ORTHOCLONE (OKT3), SANDIMMUNE/NEORAL/SANGDYA (cyclosporin), PROGRAF (tacrolimus), CELLCEPT (mycophenolate), Azathioprine, glucorticosteroids, and RAPAMUNE (sirolimus). In a specific embodiment, immunosuppressants may be used to prevent rejection of organ or bone marrow transplantation.

[1320] In an additional embodiment, Therapeutics of the invention are administered alone or in combination with one or more intravenous immune globulin preparations. Intravenous immune globulin preparations that may be administered with the Therapeutics of the invention include, but not limited to, GAMMAR, IVEEGAM, SANDOGLOBULIN, GAMMAGARD S/D, and GAMIMUNE. In a specific embodiment, Therapeutics of the invention are administered in combination with intravenous immune globulin preparations in transplantation therapy (e.g., bone marrow transplant).

[1321] In an additional embodiment, the Therapeutics of the invention are administered alone or in combination with an anti-inflammatory agent. Anti-inflammatory agents that may be administered with the Therapeutics of the invention include, but are not limited to, glucocorticoids and the nonsteroidal anti-inflammatories, aminoarylcarboxylic acid derivatives, arylacetic acid derivatives, arylbutyric acid derivatives, arylcarboxylic acids, arylpropionic acid derivatives, pyrazoles, pyrazolones, salicylic acid derivatives, thiazinecarboxamides, e-acetamidocaproic acid, S-adenosylmethionine, 3-amino-4-hydroxybutyric acid, amixetrine, bendazac, benzydamine, bucolome, difenpiramide, ditazol, emorfazone, guaiazulene, nabumetone, nimesulide, orgotein, oxaceprol, paranyline, perisoxal, pifoxime, proquazone, proxazole, and tenidap.

[1322] In another embodiment, compositions of the invention are administered in combination with a chemotherapeutic agent. Chemotherapeutic agents that may be administered with the Therapeutics of the invention include, but are not limited to, antibiotic derivatives (e.g., doxorubicin, bleomycin, daunorubicin, and dactinomycin); antiestrogens (e.g., tamoxifen); antimetabolites (e.g., fluorouracil, 5-FU, methotrexate, floxuridine, interferon alpha-2b, glutamic acid, plicamycin, mercaptopurine, and 6-thioguanine); cytotoxic agents (e.g., carmustine, BCNU, lomustine, CCNU, cytosine arabinoside, cyclophosphamide, estramustine, hydroxyurea, procarbazine, mitomycin, busulfan, cis-platin, and vincristine sulfate); hormones (e.g., medroxyprogesterone, estramustine phosphate sodium, ethinyl estradiol, estradiol, megestrol acetate, methyltestosterone, diethylstilbestrol diphosphate, chlorotrianisene, and testolactone); nitrogen mustard derivatives (e.g., mephalen, chorambucil, mechlorethamine (nitrogen mustard) and thiotepa); steroids and combinations (e.g., bethamethasone sodium phosphate); and others (e.g., dicarbazine, asparaginase, mitotane, vincristine sulfate, vinblastine sulfate, and etoposide).

[1323] In a specific embodiment, Therapeutics of the invention are administered in combination with CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone) or any combination of the components of CHOP. In another embodiment, Therapeutics of the invention are administered in combination with Rituximab. In a further embodiment, Therapeutics of the invention are administered with Rituxmab and CHOP, or Rituxmab and any combination of the components of CHOP.

[1324] In an additional embodiment, the Therapeutics of the invention are administered in combination with cytokines. Cytokines that may be administered with the Therapeutics of the invention include, but are not limited to, IL2, IL3, IL4, IL5, IL6, IL7, IL10, IL12, IL13, IL15, anti-CD40, CD40L, IFN-gamma and TNF-alpha. In another embodiment, Therapeutics of the invention may be administered with any interleukin, including, but not limited to, IL-1alpha, IL-1beta, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20, and IL-21.

[1325] In an additional embodiment, the Therapeutics of the invention are administered in combination with angiogenic proteins. Angiogenic proteins that may be administered with the Therapeutics of the invention include, but are not limited to, Glioma Derived Growth Factor (GDGF), as disclosed in European Patent Number EP-399816; Platelet Derived Growth Factor-A (PDGF-A), as disclosed in European Patent Number EP-682110; Platelet Derived Growth Factor-B (PDGF-B), as disclosed in European Patent Number EP-282317; Placental Growth Factor (PIGF), as disclosed in International Publication Number WO 92/06194; Placental Growth Factor-2 (PIGF-2), as disclosed in Hauser et al., Gorwth Factors, 4:259-268 (1993); Vascular Endothelial Growth Factor (VEGF), as disclosed in International Publication Number WO 90/13649; Vascular Endothelial Growth Factor-A (VEGF-A), as disclosed in European Patent Number EP-506477; Vascular Endothelial Growth Factor-2 (VEGF-2), as disclosed in International Publication Number WO 96/39515; Vascular Endothelial Growth Factor B (VEGF-3); Vascular Endothelial Growth Factor B-186 (VEGF-B186), as disclosed in International Publication Number WO 96/26736; Vascular Endothelial Growth Factor-D (VEGF-D), as disclosed in International Publication Number WO 98/02543; Vascular Endothelial Growth Factor-D (VEGF-D), as disclosed in International Publication Number WO 98/07832; and Vascular Endothelial Growth Factor-E (VEGF-E), as disclosed in German Patent Number DE19639601. The above mentioned references are incorporated herein by reference herein.

[1326] In an additional embodiment, the Therapeutics of the invention are administered in combination with hematopoietic growth factors. Hematopoietic growth factors that may be administered with the Therapeutics of the invention include, but are not limited to, LEUKINE (SARGRAMOSTIM) and NEUPOGEN (FILGRASTIM).

[1327] In an additional embodiment, the Therapeutics of the invention are administered in combination with Fibroblast Growth Factors. Fibroblast Growth Factors that may be administered with the Therapeutics of the invention include, but are not limited to, FGF-1, FGF-2, FGF-3, FGF-4, FGF-5, FGF-6, FGF-7, FGF-8, FGF-9, FGF-10, FGF-11, FGF-12, FGF-13, FGF-14, and FGF-15.

[1328] In a specific embodiment, formulations of the present invention may further comprise antagonists of P-glycoprotein (also referred to as the multiresistance protein, or PGP), including antagonists of its encoding polynucleotides (e.g., antisense oligonucleotides, ribozymes, zinc-finger proteins, etc.). P-glycoprotein is well known for decreasing the efficacy of various drug administrations due to its ability to export intracellular levels of absorbed drug to the cell exterior. While this activity has been particularly pronounced in cancer cells in response to the administration of chemotherapy regimens, a variety of other cell types and the administration of other drug classes have been noted (e.g., T-cells and anti-HIV drugs). In fact, certain mutations in the PGP gene significantly reduces PGP function, making it less able to force drugs out of cells. People who have two versions of the mutated gene—one inherited from each parent—have more than four times less PGP than those with two normal versions of the gene. People may also have one normal gene and one mutated one. Certain ethnic populations have increased incidence of such PGP mutations. Among individuals from Ghana, Kenya, the Sudan, as well as African Americans, frequency of the normal gene ranged from 73% to 84%. In contrast, the frequency was 34% to 59% among British whites, Portuguese, Southwest Asian, Chinese, Filipino and Saudi populations. As a result, certain ethnic populations may require increased administration of PGP antagonist in the formulation of the present invention to arrive at the an efficacious dose of the therapeutic (e.g., those from African descent). Conversely, certain ethnic populations, particularly those having increased frequency of the mutated PGP (e.g., of Caucasian descent, or non-African descent) may require less pharmaceutical compositions in the formulation due to an effective increase in efficacy of such compositions as a result of the increased effective absorption (e.g., less PGP activity) of said composition.

[1329] Moreover, in another specific embodiment, formulations of the present invention may further comprise antagonists of OATP2 (also referred to as the multiresistance protein, or MRP2), including antagonists of its encoding polynucleotides (e.g., antisense oligonucleotides, ribozymes, zinc-finger proteins, etc.). The invention also further comprises any additional antagonists known to inhibit proteins thought to be attributable to a multidrug resistant phenotype in proliferating cells.

[1330] Preferred antagonists that formulations of the present may comprise include the potent P-glycoprotein inhibitor elacridar, and/or LY-335979. Other P-glycoprotein known in the art are also encompassed by the present invention.

[1331] In additional embodiments, the Therapeutics of the invention are administered in combination with other therapeutic or prophylactic regimens, such as, for example, radiation therapy.

Example 27

Method of Treating Decreased Levels of the Polypeptide

[1332] The present invention relates to a method for treating an individual in need of an increased level of a polypeptide of the invention in the body comprising administering to such an individual a composition comprising a therapeutically effective amount of an agonist of the invention (including polypeptides of the invention). Moreover, it will be appreciated that conditions caused by a decrease in the standard or normal expression level of a secreted protein in an individual can be treated by administering the polypeptide of the present invention, preferably in the secreted form. Thus, the invention also provides a method of treatment of an individual in need of an increased level of the polypeptide comprising administering to such an individual a Therapeutic comprising an amount of the polypeptide to increase the activity level of the polypeptide in such an individual.

[1333] For example, a patient with decreased levels of a polypeptide receives a daily dose 0.1-100 ug/kg of the polypeptide for six consecutive days. Preferably, the polypeptide is in the secreted form. The exact details of the dosing scheme, based on administration and formulation, are provided herein.

Example 28

Method of Treating Increased Levels of the Polypeptide

[1334] The present invention also relates to a method of treating an individual in need of a decreased level of a polypeptide of the invention in the body comprising administering to such an individual a composition comprising a therapeutically effective amount of an antagonist of the invention (including polypeptides and antibodies of the invention).

[1335] In one example, antisense technology is used to inhibit production of a polypeptide of the present invention. This technology is one example of a method of decreasing levels of a polypeptide, preferably a secreted form, due to a variety of etiologies, such as cancer. For example, a patient diagnosed with abnormally increased levels of a polypeptide is administered intravenously antisense polynucleotides at 0.5, 1.0, 1.5, 2.0 and 3.0 mg/kg day for 21 days. This treatment is repeated after a 7-day rest period if the treatment was well tolerated. The formulation of the antisense polynucleotide is provided herein.

Example 29

Method of Treatment Using Gene Therapy-ex vivo

[1336] One method of gene therapy transplants fibroblasts, which are capable of expressing a polypeptide, onto a patient. Generally, fibroblasts are obtained from a subject by skin biopsy. The resulting tissue is placed in tissue-culture medium and separated into small pieces. Small chunks of the tissue are placed on a wet surface of a tissue culture flask, approximately ten pieces are placed in each flask. The flask is turned upside down, closed tight and left at room temperature over night. After 24 hours at room temperature, the flask is inverted and the chunks of tissue remain fixed to the bottom of the flask and fresh media (e.g., Ham's F12 media, with 10% FBS, penicillin and streptomycin) is added. The flasks are then incubated at 37 degree C. for approximately one week.

[1337] At this time, fresh media is added and subsequently changed every several days. After an additional two weeks in culture, a monolayer of fibroblasts emerge. The monolayer is trypsinized and scaled into larger flasks.

[1338] pMV-7 (Kirschmeier, P. T. et al., DNA, 7:219-25 (1988)), flanked by the long terminal repeats of the Moloney murine sarcoma virus, is digested with EcoRI and HindIII and subsequently treated with calf intestinal phosphatase. The linear vector is fractionated on agarose gel and purified, using glass beads.

[1339] The cDNA encoding a polypeptide of the present invention can be amplified using PCR primers which correspond to the 5′ and 3′ end sequences respectively as set forth in Example 13 using primers and having appropriate restriction sites and initiation/stop codons, if necessary. Preferably, the 5′ primer contains an EcoRI site and the 3′ primer includes a HindIII site. Equal quantities of the Moloney murine sarcoma virus linear backbone and the amplified EcoRI and HindIII fragment are added together, in the presence of T4 DNA ligase. The resulting mixture is maintained under conditions appropriate for ligation of the two fragments. The ligation mixture is then used to transform bacteria HB101, which are then plated onto agar containing kanamycin for the purpose of confirming that the vector has the gene of interest properly inserted.

[1340] The amphotropic pA317 or GP+am12 packaging cells are grown in tissue culture to confluent density in Dulbecco's Modified Eagles Medium (DMEM) with 10% calf serum (CS), penicillin and streptomycin. The MSV vector containing the gene is then added to the media and the packaging cells transduced with the vector. The packaging cells now produce infectious viral particles containing the gene (the packaging cells are now referred to as producer cells).

[1341] Fresh media is added to the transduced producer cells, and subsequently, the media is harvested from a 10 cm plate of confluent producer cells. The spent media, containing the infectious viral particles, is filtered through a millipore filter to remove detached producer cells and this media is then used to infect fibroblast cells. Media is removed from a sub-confluent plate of fibroblasts and quickly replaced with the media from the producer cells. This media is removed and replaced with fresh media. If the titer of virus is high, then virtually all fibroblasts will be infected and no selection is required. If the titer is very low, then it is necessary to use a retroviral vector that has a selectable marker, such as neo or his. Once the fibroblasts have been efficiently infected, the fibroblasts are analyzed to determine whether protein is produced.

[1342] The engineered fibroblasts are then transplanted onto the host, either alone or after having been grown to confluence on cytodex 3 microcarrier beads.

Example 30

Gene Therapy Using Endogenous Genes Corresponding to Polynucleotides of the Invention

[1343] Another method of gene therapy according to the present invention involves operably associating the endogenous polynucleotide sequence of the invention with a promoter via homologous recombination as described, for example, in U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; International Publication NO: WO 96/29411, published Sep. 26, 1996; International Publication NO: WO 94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci. USA, 86:8932-8935 (1989); and Zijlstra et al., Nature, 342:435-438 (1989). This method involves the activation of a gene which is present in the target cells, but which is not expressed in the cells, or is expressed at a lower level than desired.

[1344] Polynucleotide constructs are made which contain a promoter and targeting sequences, which are homologous to the 5′ non-coding sequence of endogenous polynucleotide sequence, flanking the promoter. The targeting sequence will be sufficiently near the 5′ end of the polynucleotide sequence so the promoter will be operably linked to the endogenous sequence upon homologous recombination. The promoter and the targeting sequences can be amplified using PCR. Preferably, the amplified promoter contains distinct restriction enzyme sites on the 5′ and 3′ ends. Preferably, the 3′ end of the first targeting sequence contains the same restriction enzyme site as the 5′ end of the amplified promoter and the 5′ end of the second targeting sequence contains the same restriction site as the 3′ end of the amplified promoter.

[1345] The amplified promoter and the amplified targeting sequences are digested with the appropriate restriction enzymes and subsequently treated with calf intestinal phosphatase. The digested promoter and digested targeting sequences are added together in the presence of T4 DNA ligase. The resulting mixture is maintained under conditions appropriate for ligation of the two fragments. The construct is size fractionated on an agarose gel then purified by phenol extraction and ethanol precipitation.

[1346] In this Example, the polynucleotide constructs are administered as naked polynucleotides via electroporation. However, the polynucleotide constructs may also be administered with transfection-facilitating agents, such as liposomes, viral sequences, viral particles, precipitating agents, etc. Such methods of delivery are known in the art.

[1347] Once the cells are transfected, homologous recombination will take place which results in the promoter being operably linked to the endogenous polynucleotide sequence. This results in the expression of polynucleotide corresponding to the polynucleotide in the cell. Expression may be detected by immunological staining, or any other method known in the art.

[1348] Fibroblasts are obtained from a subject by skin biopsy. The resulting tissue is placed in DMEM+10% fetal calf serum. Exponentially growing or early stationary phase fibroblasts are trypsinized and rinsed from the plastic surface with nutrient medium. An aliquot of the cell suspension is removed for counting, and the remaining cells are subjected to centrifugation. The supernatant is aspirated and the pellet is resuspended in 5 ml of electroporation buffer (20 mM HEPES pH 7.3, 137 mM NaCl, 5 mM KCl, 0.7 mM Na2 HPO4, 6 mM dextrose). The cells are recentrifuged, the supernatant aspirated, and the cells resuspended in electroporation buffer containing 1 mg/ml acetylated bovine serum albumin. The final cell suspension contains approximately 3×106 cells/ml. Electroporation should be performed immediately following resuspension.

[1349] Plasmid DNA is prepared according to standard techniques. For example, to construct a plasmid for targeting to the locus corresponding to the polynucleotide of the invention, plasmid pUC 18 (MBI Fermentas, Amherst, N.Y.) is digested with HindIII. The CMV promoter is amplified by PCR with an XbaI site on the 5′ end and a BamHI site on the 3′end. Two non-coding sequences are amplified via PCR: one non-coding sequence (fragment 1) is amplified with a HindIII site at the 5′ end and an Xba site at the 3end; the other non-coding sequence (fragment 2) is amplified with a BamHI site at the 5end and a HindIII site at the 3′end. The CMV promoter and the fragments (1 and 2) are digested with the appropriate enzymes (CMV promoter—XbaI and BamHI; fragment 1—XbaI; fragment 2—BamHI) and ligated together. The resulting ligation product is digested with HindIII, and ligated with the HindIII-digested pUC18 plasmid.

[1350] Plasmid DNA is added to a sterile cuvette with a 0.4 cm electrode gap (Bio-Rad). The final DNA concentration is generally at least 120 μg/ml. 0.5 ml of the cell suspension (containing approximately 1.5×106 cells) is then added to the cuvette, and the cell suspension and DNA solutions are gently mixed. Electroporation is performed with a Gene-Pulser apparatus (Bio-Rad). Capacitance and voltage are set at 960 μF and 250-300 V, respectively. As voltage increases, cell survival decreases, but the percentage of surviving cells that stably incorporate the introduced DNA into their genome increases dramatically. Given these parameters, a pulse time of approximately 14-20 mSec should be observed.

[1351] Electroporated cells are maintained at room temperature for approximately 5 min, and the contents of the cuvette are then gently removed with a sterile transfer pipette. The cells are added directly to 10 ml of prewarmed nutrient media (DMEM with 15% calf serum) in a 10 cm dish and incubated at 37 degree C. The following day, the media is aspirated and replaced with 10 ml of fresh media and incubated for a further 16-24 hours.

[1352] The engineered fibroblasts are then injected into the host, either alone or after having been grown to confluence on cytodex 3 microcarrier beads. The fibroblasts now produce the protein product. The fibroblasts can then be introduced into a patient as described above.

Example 31

Method of Treatment Using Gene Therapy—in vivo

[1353] Another aspect of the present invention is using in vivo gene therapy methods to treat disorders, diseases and conditions. The gene therapy method relates to the introduction of naked nucleic acid (DNA, RNA, and antisense DNA or RNA) sequences into an animal to increase or decrease the expression of the polypeptide. The polynucleotide of the present invention may be operatively linked to a promoter or any other genetic elements necessary for the expression of the polypeptide by the target tissue. Such gene therapy and delivery techniques and methods are known in the art, see, for example, WO90/11092, WO98/11779; U.S. Pat. No. 5,693,622, 5,705,151, 5,580,859; Tabata et al., Cardiovasc. Res. 35(3):470-479 (1997); Chao et al., Pharmacol. Res. 35(6):517-522 (1997); Wolff, Neuromuscul. Disord. 7(5):314-318 (1997); Schwartz et al., Gene Ther. 3(5):405-411 (1996); Tsurumi et al., Circulation 94(12):3281-3290 (1996) (incorporated herein by reference).

[1354] The polynucleotide constructs may be delivered by any method that delivers injectable materials to the cells of an animal, such as, injection into the interstitial space of tissues (heart, muscle, skin, lung, liver, intestine and the like). The polynucleotide constructs can be delivered in a pharmaceutically acceptable liquid or aqueous carrier.

[1355] The term “naked” polynucleotide, DNA or RNA, refers to sequences that are free from any delivery vehicle that acts to assist, promote, or facilitate entry into the cell, including viral sequences, viral particles, liposome formulations, lipofectin or precipitating agents and the like. However, the polynucleotides of the present invention may also be delivered in liposome formulations (such as those taught in Felgner P. L. et al. (1995) Ann. NY Acad. Sci. 772:126-139 and Abdallah B. et al. (1995) Biol. Cell 85(1):1-7) which can be prepared by methods well known to those skilled in the art.

[1356] The polynucleotide vector constructs used in the gene therapy method are preferably constructs that will not integrate into the host genome nor will they contain sequences that allow for replication. Any strong promoter known to those skilled in the art can be used for driving the expression of DNA. Unlike other gene therapies techniques, one major advantage of introducing naked nucleic acid sequences into target cells is the transitory nature of the polynucleotide synthesis in the cells. Studies have shown that non-replicating DNA sequences can be introduced into cells to provide production of the desired polypeptide for periods of up to six months.

[1357] The polynucleotide construct can be delivered to the interstitial space of tissues within the an animal, including of muscle, skin, brain, lung, liver, spleen, bone marrow, thymus, heart, lymph, blood, bone, cartilage, pancreas, kidney, gall bladder, stomach, intestine, testis, ovary, uterus, rectum, nervous system, eye, gland, and connective tissue. Interstitial space of the tissues comprises the intercellular fluid, mucopolysaccharide matrix among the reticular fibers of organ tissues, elastic fibers in the walls of vessels or chambers, collagen fibers of fibrous tissues, or that same matrix within connective tissue ensheathing muscle cells or in the lacunae of bone. It is similarly the space occupied by the plasma of the circulation and the lymph fluid of the lymphatic channels. Delivery to the interstitial space of muscle tissue is preferred for the reasons discussed below. They may be conveniently delivered by injection into the tissues comprising these cells. They are preferably delivered to and expressed in persistent, non-dividing cells which are differentiated, although delivery and expression may be achieved in non-differentiated or less completely differentiated cells, such as, for example, stem cells of blood or skin fibroblasts. In vivo muscle cells are particularly competent in their ability to take up and express polynucleotides.

[1358] For the naked polynucleotide injection, an effective dosage amount of DNA or RNA will be in the range of from about 0.05 g/kg body weight to about 50 mg/kg body weight. Preferably the dosage will be from about 0.005 mg/kg to about 20 mg/kg and more preferably from about 0.05 mg/kg to about 5 mg/kg. Of course, as the artisan of ordinary skill will appreciate, this dosage will vary according to the tissue site of injection. The appropriate and effective dosage of nucleic acid sequence can readily be determined by those of ordinary skill in the art and may depend on the condition being treated and the route of administration. The preferred route of administration is by the parenteral route of injection into the interstitial space of tissues. However, other parenteral routes may also be used, such as, inhalation of an aerosol formulation particularly for delivery to lungs or bronchial tissues, throat or mucous membranes of the nose. In addition, naked polynucleotide constructs can be delivered to arteries during angioplasty by the catheter used in the procedure.

[1359] The dose response effects of injected polynucleotide in muscle in vivo is determined as follows. Suitable template DNA for production of “mRNA coding for polypeptide of the present invention is prepared in accordance with a standard recombinant DNA methodology. The template DNA, which may be either circular or linear, is either used as naked DNA or complexed with liposomes. The quadriceps muscles of mice are then injected with various amounts of the template DNA.

[1360] Five to six week old female and male Balb/C mice are anesthetized by intraperitoneal injection with 0.3 ml of 2.5% Avertin. A 1.5 cm incision is made on the anterior thigh, and the quadriceps muscle is directly visualized. The template DNA is injected in 0.1 ml of carrier in a 1 cc syringe through a 27 gauge needle over one minute, approximately 0.5 cm from the distal insertion site of the muscle into the knee and about 0.2 cm deep. A suture is placed over the injection site for future localization, and the skin is closed with stainless steel clips.

[1361] After an appropriate incubation time (e.g., 7 days) muscle extracts are prepared by excising the entire quadriceps. Every fifth 15 um cross-section of the individual quadriceps muscles is histochemically stained for protein expression. A time course for protein expression may be done in a similar fashion except that quadriceps from different mice are harvested at different times. Persistence of DNA in muscle following injection may be determined by Southern blot analysis after preparing total cellular DNA and HIRT supernatants from injected and control mice. The results of the above experimentation in mice can be use to extrapolate proper dosages and other treatment parameters in humans and other animals using naked DNA.

Example 32

Transgenic Animals

[1362] The polypeptides of the invention can also be expressed in transgenic animals. Animals of any species, including, but not limited to, mice, rats, rabbits, hamsters, guinea pigs, pigs, micro-pigs, goats, sheep, cows and non-human primates, e.g., baboons, monkeys, and chimpanzees may be used to generate transgenic animals. In a specific embodiment, techniques described herein or otherwise known in the art, are used to express polypeptides of the invention in humans, as part of a gene therapy protocol.

[1363] Any technique known in the art may be used to introduce the transgene (i.e., polynucleotides of the invention) into animals to produce the founder lines of transgenic animals. Such techniques include, but are not limited to, pronuclear microinjection (Paterson et al., Appl. Microbiol. Biotechnol. 40:691-698 (1994); Carver et al., Biotechnology (NY) 11:1263-1270 (1993); Wright et al., Biotechnology (NY) 9:830-834 (1991); and Hoppe et al., U.S. Pat. No. 4,873,191 (1989)); retrovirus mediated gene transfer into germ lines (Van der Putten et al., Proc. Natl. Acad. Sci., USA 82:6148-6152 (1985)), blastocysts or embryos; gene targeting in embryonic stem cells (Thompson et al., Cell 56:313-321 (1989)); electroporation of cells or embryos (Lo, 1983, Mol Cell. Biol. 3:1803-1814 (1983)); introduction of the polynucleotides of the invention using a gene gun (see, e.g., Ulmer et al., Science 259:1745 (1993); introducing nucleic acid constructs into embryonic pleuripotent stem cells and transferring the stem cells back into the blastocyst; and sperm-mediated gene transfer (Lavitrano et al., Cell 57:717-723 (1989); etc. For a review of such techniques, see Gordon, “Transgenic Animals,” Intl. Rev. Cytol. 115:171-229 (1989), which is incorporated by reference herein in its entirety.

[1364] Any technique known in the art may be used to produce transgenic clones containing polynucleotides of the invention, for example, nuclear transfer into enucleated oocytes of nuclei from cultured embryonic, fetal, or adult cells induced to quiescence (Campell et al., Nature 380:64-66 (1996); Wilmut et al., Nature 385:810-813 (1997)).

[1365] The present invention provides for transgenic animals that carry the transgene in all their cells, as well as animals which carry the transgene in some, but not all their cells, i.e., mosaic animals or chimeric. The transgene may be integrated as a single transgene or as multiple copies such as in concatamers, e.g., head-to-head tandems or head-to-tail tandems. The transgene may also be selectively introduced into and activated in a particular cell type by following, for example, the teaching of Lasko et al. (Lasko et al., Proc. Natl. Acad. Sci. USA 89:6232-6236 (1992)). The regulatory sequences required for such a cell-type specific activation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art. When it is desired that the polynucleotide transgene be integrated into the chromosomal site of the endogenous gene, gene targeting is preferred. Briefly, when such a technique is to be utilized, vectors containing some nucleotide sequences homologous to the endogenous gene are designed for the purpose of integrating, via homologous recombination with chromosomal sequences, into and disrupting the function of the nucleotide sequence of the endogenous gene. The transgene may also be selectively introduced into a particular cell type, thus inactivating the endogenous gene in only that cell type, by following, for example, the teaching of Gu et al. (Gu et al., Science 265:103-106 (1994)). The regulatory sequences required for such a cell-type specific inactivation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art.

[1366] Once transgenic animals have been generated, the expression of the recombinant gene may be assayed utilizing standard techniques. Initial screening may be accomplished by Southern blot analysis or PCR techniques to analyze animal tissues to verify that integration of the transgene has taken place. The level of mRNA expression of the transgene in the tissues of the transgenic animals may also be assessed using techniques which include, but are not limited to, Northern blot analysis of tissue samples obtained from the animal, in situ hybridization analysis, and reverse transcriptase-PCR(RT-PCR). Samples of transgenic gene-expressing tissue may also be evaluated immunocytochemically or immunohistochemically using antibodies specific for the transgene product.

[1367] Once the founder animals are produced, they may be bred, inbred, outbred, or crossbred to produce colonies of the particular animal. Examples of such breeding strategies include, but are not limited to: outbreeding of founder animals with more than one integration site in order to establish separate lines; inbreeding of separate lines in order to produce compound transgenics that express the transgene at higher levels because of the effects of additive expression of each transgene; crossing of heterozygous transgenic animals to produce animals homozygous for a given integration site in order to both augment expression and eliminate the need for screening of animals by DNA analysis; crossing of separate homozygous lines to produce compound heterozygous or homozygous lines; and breeding to place the transgene on a distinct background that is appropriate for an experimental model of interest.

[1368] Transgenic animals of the invention have uses which include, but are not limited to, animal model systems useful in elaborating the biological function of polypeptides of the present invention, studying diseases, disorders, and/or conditions associated with aberrant expression, and in screening for compounds effective in ameliorating such diseases, disorders, and/or conditions.

Example 33

Knock-Out Animals

[1369] Endogenous gene expression can also be reduced by inactivating or “knocking out” the gene and/or its promoter using targeted homologous recombination. (E.g., see Smithies et al., Nature 317:230-234 (1985); Thomas & Capecchi, Cell 51:503-512 (1987); Thompson et al., Cell 5:313-321 (1989); each of which is incorporated by reference herein in its entirety). For example, a mutant, non-functional polynucleotide of the invention (or a completely unrelated DNA sequence) flanked by DNA homologous to the endogenous polynucleotide sequence (either the coding regions or regulatory regions of the gene) can be used, with or without a selectable marker and/or a negative selectable marker, to transfect cells that express polypeptides of the invention in vivo. In another embodiment, techniques known in the art are used to generate knockouts in cells that contain, but do not express the gene of interest. Insertion of the DNA construct, via targeted homologous recombination, results in inactivation of the targeted gene. Such approaches are particularly suited in research and agricultural fields where modifications to embryonic stem cells can be used to generate animal offspring with an inactive targeted gene (e.g., see Thomas & Capecchi 1987 and Thompson 1989, supra). However this approach can be routinely adapted for use in humans provided the recombinant DNA constructs are directly administered or targeted to the required site in vivo using appropriate viral vectors that will be apparent to those of skill in the art.

[1370] In further embodiments of the invention, cells that are genetically engineered to express the polypeptides of the invention, or alternatively, that are genetically engineered not to express the polypeptides of the invention (e.g., knockouts) are administered to a patient in vivo. Such cells may be obtained from the patient (i.e., animal, including human) or an MHC compatible donor and can include, but are not limited to fibroblasts, bone marrow cells, blood cells (e.g., lymphocytes), adipocytes, muscle cells, endothelial cells etc. The cells are genetically engineered in vitro using recombinant DNA techniques to introduce the coding sequence of polypeptides of the invention into the cells, or alternatively, to disrupt the coding sequence and/or endogenous regulatory sequence associated with the polypeptides of the invention, e.g., by transduction (using viral vectors, and preferably vectors that integrate the transgene into the cell genome) or transfection procedures, including, but not limited to, the use of plasmids, cosmids, YACs, naked DNA, electroporation, liposomes, etc. The coding sequence of the polypeptides of the invention can be placed under the control of a strong constitutive or inducible promoter or promoter/enhancer to achieve expression, and preferably secretion, of the polypeptides of the invention. The engineered cells which express and preferably secrete the polypeptides of the invention can be introduced into the patient systemically, e.g., in the circulation, or intraperitoneally.

[1371] Alternatively, the cells can be incorporated into a matrix and implanted in the body, e.g., genetically engineered fibroblasts can be implanted as part of a skin graft; genetically engineered endothelial cells can be implanted as part of a lymphatic or vascular graft. (See, for example, Anderson et al. U.S. Pat. No. 5,399,349; and Mulligan & Wilson, U.S. Pat. No. 5,460,959 each of which is incorporated by reference herein in its entirety).

[1372] When the cells to be administered are non-autologous or non-MHC compatible cells, they can be administered using well known techniques which prevent the development of a host immune response against the introduced cells. For example, the cells may be introduced in an encapsulated form which, while allowing for an exchange of components with the immediate extracellular environment, does not allow the introduced cells to be recognized by the host immune system.

[1373] Transgenic and “knock-out” animals of the invention have uses which include, but are not limited to, animal model systems useful in elaborating the biological function of polypeptides of the present invention, studying diseases, disorders, and/or conditions associated with aberrant expression, and in screening for compounds effective in ameliorating such diseases, disorders, and/or conditions.

Example 34

Method of Isolating Antibody Fragments Directed Against CAN-12 From a Library of scFvs

[1374] Naturally occurring V-genes isolated from human PBLs are constructed into a library of antibody fragments which contain reactivities against CAN-12 to which the donor may or may not have been exposed (see e.g., U.S. Pat. No. 5,885,793 incorporated herein by reference in its entirety).

[1375] Rescue of the Library. A library of scFvs is constructed from the RNA of human PBLs as described in PCT publication WO 92/01047. To rescue phage displaying antibody fragments, approximately 109 E. coli harboring the phagemid are used to inoculate 50 ml of 2× TY containing 1% glucose and 100 μg/ml of ampicillin (2× TY-AMP-GLU) and grown to an O.D. of 0.8 with shaking. Five ml of this culture is used to inoculate 50 ml of 2× TY-AMP-GLU, 2×108 TU of delta gene 3 helper (M13 delta gene III, see PCT publication WO 92/01047) are added and the culture incubated at 37° C. for 45 minutes without shaking and then at 37° C. for 45 minutes with shaking. The culture is centrifuged at 4000 r.p.m. for 10 min. and the pellet resuspended in 2 liters of 2× TY containing 100 μg/ml ampicillin and 50 ug/ml kanamycin and grown overnight. Phage are prepared as described in PCT publication WO 92/01047.

[1376] M13 delta gene III is prepared as follows: M13 delta gene III helper phage does not encode gene III protein, hence, the phage(mid) displaying antibody fragments have a greater avidity of binding to antigen. Infectious M13 delta gene III particles are made by growing the helper phage in cells harboring a pUC19 derivative supplying the wild type gene III protein during phage morphogenesis. The culture is incubated for 1 hour at 37° C. without shaking and then for a further hour at 37° C. with shaking. Cells are spun down (IEC-Centra 8,400 r.p.m. for 10 min), resuspended in 300 ml 2× TY broth containing 100 μg ampicillin/ml and 25 μg kanamycin/ml (2× TY-AMP-KAN) and grown overnight, shaking at 37° C. Phage particles are purified and concentrated from the culture medium by two PEG-precipitations (Sambrook et al., 1990), resuspended in 2 ml PBS and passed through a 0.45 μm filter (Minisart NML; Sartorius) to give a final concentration of approximately 1013 transducing units/mil (ampicillin-resistant clones).

[1377] Panning of the Library.

[1378] Immunotubes (Nunc) are coated overnight in PBS with 4 ml of either 100 pg/ml or 10 pg/ml of a polypeptide of the present invention. Tubes are blocked with 2% Marvel-PBS for 2 hours at 37° C. and then washed 3 times in PBS. Approximately 1013 TU of phage is applied to the tube and incubated for 30 minutes at room temperature tumbling on an over and under turntable and then left to stand for another 1.5 hours. Tubes are washed 10 times with PBS 0.1% Tween-20 and 10 times with PBS. Phage are eluted by adding 1 mil of 100 mM triethylamine and rotating 15 minutes on an under and over turntable after which the solution is immediately neutralized with 0.5 ml of 1.0M Tris-HCl, pH 7.4. Phage are then used to infect 10 ml of mid-log E. coli TG1 by incubating eluted phage with bacteria for 30 minutes at 37° C. The E. coli are then plated on TYE plates containing 1% glucose and 100 pg/ml ampicillin. The resulting bacterial library is then rescued with delta gene 3 helper phage as described above to prepare phage for a subsequent round of selection. This process is then repeated for a total of 4 rounds of affinity purification with tube-washing increased to 20 times with PBS, 0.1% Tween-20 and 20 times with PBS for rounds 3 and 4.

[1379] Characterization of Binders.

[1380] Eluted phage from the 3rd and 4th rounds of selection are used to infect E. coli HB 2151 and soluble scFv is produced (Marks, et al., 1991) from single colonies for assay. ELISAs are performed with microtitre plates coated with either 10 pg/ml of the polypeptide of the present invention in 50 mM bicarbonate pH 9.6. Clones positive in ELISA are further characterized by PCR fingerprinting (see, e.g., PCT publication WO 92/01047) and then by sequencing. These ELISA positive clones may also be further characterized by techniques known in the art, such as, for example, epitope mapping, binding affinity, receptor signal transduction, ability to block or competitively inhibit antibody/antigen binding, and competitive agonistic or antagonistic activity.

[1381] Moreover, in another preferred method, the antibodies directed against the polypeptides of the present invention may be produced in plants. Specific methods are disclosed in U.S. Pat. Nos. 5,959,177, and 6,080,560, which are hereby incorporated in their entirety herein. The methods not only describe methods of expressing antibodies, but also the means of assembling foreign multimeric proteins in plants (i.e., antibodies, etc,), and the subsequent secretion of such antibodies from the plant.

Example 35

Identification and Cloning of VH and VL Domains of Antibodies Directed Against the CAN-12 Polypeptide

[1382] VH and VL domains may be identified and cloned from cell lines expressing an antibody directed against a CAN-12 epitope by performing PCR with VH and VL specific primers on cDNA made from the antibody expressing cell lines. Briefly, RNA is isolated from the cell lines and used as a template for RT-PCR designed to amplify the VH and VL domains of the antibodies expressed by the EBV cell lines. Cells may be lysed using the TRIzol reagent (Life Technologies, Rockville, Md.) and extracted with one fifth volume of chloroform. After addition of chloroform, the solution is allowed to incubate at room temperature for 10 minutes, and then centrifuged at 14,000 rpm for 15 minutes at 4 C in a tabletop centrifuge. The supernatant is collected and RNA is precipitated using an equal volume of isopropanol. Precipitated RNA is pelleted by centrifuging at 14,000 rpm for 15 minutes at 4 C in a tabletop centrifuge.

[1383] Following centrifugation, the supernatant is discarded and washed with 75% ethanol. Follwing the wash step, the RNA is centrifuged again at 800 rpm for 5 minutes at 4 C. The supernatant is discarded and the pellet allowed to air dry. RNA is the dissolved in DEPC water and heated to 60 C for 10 minutes. Quantities of RNA can be determined using optical density measurements. cDNA may be synthesized, according to methods well-known in the art and/or described herein, from 1.5-2.5 micrograms of RNA using reverse transciptase and random hexamer primers. cDNA is then used as a template for PCR amplification of VH and VL domains.

[1384] Primers used to amplify VH and VL genes are shown below. Typically a PCR reaction makes use of a single 5′primer and a single 3′primer. Sometimes, when the amount of available RNA template is limiting, or for greater efficiency, groups of 5′ and/or 3′primers may be used. For example, sometimes all five VH-5′primers and all JH3′primers are used in a single PCR reaction. The PCR reaction is carried out in a 50 microliter volume containing 1× PCR buffer, 2 mM of each dNTP, 0.7 units of High Fidelity Taq polymerse, 5′primer mix, 3′primer mix and 7.5 microliters of cDNA. The 5′and 3′primer mix of both VH and VL can be made by pooling together 22 pmole and 28 pmole, respectively, of each of the individual primers. PCR conditions are: 96 C for 5 minutes; followed by 25 cycles of 94 C for 1 minute, 50 C for 1 minute, and 72 C for 1 minute; followed by an extension cycle of 72 C for 10 minutes. After the reaction has been completed, sample tubes may be stored at 4 C.

19SEQ IDPrimer namePrimer SequenceNO:Primer Sequences Used to Amplify VH domains.Hu VH1-5′CAGGTGCAGCTGGTGCAGTCTGG105Hu VH2-5′CAGGTCAACTTAAGGGAGTCTGG106Hu VH3-5′GAGGTGCAGCTGGTGGAGTCTGG107Hu VH4-5′CAGGTGCAGCTGCAGGAGTCGGG108Hu VH5-5′GAGGTGCAGCTGTTGCAGTCTGC109Hu VH6-5′CAGGTACAGCTGCAGCAGTCAGG110Hu JH1-5′TGAGGAGACGGTGACCAGGGTGCC111Hu JH3-5′TGAAGAGACGGTGACCATTGTCCC112Hu JH4-5′TGAGGAGACGGTGACCAGGGTTCC113Hu JH6-5′TGAGGAGACGGTGACCGTGGTCCC114Primer Sequences Used to Amplify VL domainsHu Vkappa1-5′GACATCCAGATGACCCAGTCTCC115Hu Vkappa2a-GATGTTGTGATGACTCAGTCTCC1165′Hu Vkappa2b-GATATTGTGATGACTCAGTCTCC1175′Hu Vkappa3-5′GAAATTGTGTTGACGCAGTCTCC118Hu Vkappa4-5′GACATCGTGATGACCCAGTCTCC119Hu Vkappa5-5′GAAACGACACTCACGCAGTCTCC120Hu Vkappa6-5′GAAATTGTGCTGACTCAGTCTCC121Hu Vlambda1-CAGTCTGTGTTGACGCAGCCGCC1225′Hu Vlambda2-CAGTCTGCCCTGACTCAGCCTGC1235′Hu Vlambda3-TCCTATGTGCTGACTCAGCCACC1245′Hu Vlambda3b-TCTTCTGAGCTGACTCAGGACCC1255′Hu Vlambda4-CACGTTATACTGACTCAACCGCC1265′Hu Vlambda5-CAGGCTGTGCTCACTCAGCCGTC1275′Hu Vlambda6-AATTTTATGCTGACTCAGCCCCA1285′Hu Jkappa1-3′ACGTTTGATTTCCACCTTGGTCCC129Hu Jkappa2-3′ACGTTTGATCTCCAGCTTGGTCCC130Hu Jkappa3-3′ACGTTTGATATCCACTTTGGTCCC131Hu Jkappa4-3′ACGTTTGATCTCCACCTTGGTCCC132Hu Jkappa5-3′ACGTTTAATCTCCAGTCGTGTCCC133Hu Vlambda1-CAGTCTGTGTTGACGCAGCCGCC1343′Hu Vlambda2-CAGTCTGCCCTGACTCAGCCTGC1353′Hu Vlambda3-TCCTATGTGCTGACTCAGCCACC1363′Hu Vlambda3b-TCTTCTGAGCTGACTCAGGACCC1373′Hu Vlambda4-CACGTTATACTGACTCAACCGCC1383′Hu Vlambda5-CAGGCTGTGCTCACTCAGCCGTC1393′Hu Vlambda6-AATTTTATGCTGACTCAGCCCCA1403′

[1385] PCR samples are then electrophoresed on a 1.3% agarose gel. DNA bands of the expected sizes (−506 base pairs for VH domains, and 344 base pairs for VL domains) can be cut out of the gel and purified using methods well known in the art and/or described herein.

[1386] Purified PCR products can be ligated into a PCR cloning vector (TA vector from Invitrogen Inc., Carlsbad, Calif.). Individual cloned PCR products can be isolated after transfection of E. coli and blue/white color selection. Cloned PCR products may then be sequenced using methods commonly known in the art and/or described herein.

[1387] The PCR bands containing the VH domain and the VL domains can also be used to create full-length Ig expression vectors. VH and VL domains can be cloned into vectors containing the nucleotide sequences of a heavy (e.g., human IgG1 or human IgG4) or light chain (human kappa or human ambda) constant regions such that a complete heavy or light chain molecule could be expressed from these vectors when transfected into an appropriate host cell. Further, when cloned heavy and light chains are both expressed in one cell line (from either one or two vectors), they can assemble into a complete functional antibody molecule that is secreted into the cell culture medium. Methods using polynucleotides encoding VH and VL antibody domain to generate expression vectors that encode complete antibody molecules are well known within the art.

Example 36

Assays Detecting Stimulation or Inhibition of B cell Proliferation and Differentiation

[1388] Generation of functional humoral immune responses requires both soluble and cognate signaling between B-lineage cells and their microenvironment. Signals may impart a positive stimulus that allows a B-lineage cell to continue its programmed development, or a negative stimulus that instructs the cell to arrest its current developmental pathway. To date, numerous stimulatory and inhibitory signals have been found to influence B cell responsiveness including IL-2, IL-4, IL-5, IL-6, IL-7, IL10, IL-13, IL-14 and IL-15. Interestingly, these signals are by themselves weak effectors but can, in combination with various co-stimulatory proteins, induce activation, proliferation, differentiation, homing, tolerance and death among B cell populations.

[1389] One of the best studied classes of B-cell co-stimulatory proteins is the TNF-superfamily. Within this family CD40, CD27, and CD30 along with their respective ligands CD154, CD70, and CD153 have been found to regulate a variety of immune responses. Assays which allow for the detection and/or observation of the proliferation and differentiation of these B-cell populations and their precursors are valuable tools in determining the effects various proteins may have on these B-cell populations in terms of proliferation and differentiation. Listed below are two assays designed to allow for the detection of the differentiation, proliferation, or inhibition of B-cell populations and their precursors.

[1390] In Vitro Assay—Purified polypeptides of the invention, or truncated forms thereof, is assessed for its ability to induce activation, proliferation, differentiation or inhibition and/or death in B-cell populations and their precursors. The activity of the polypeptides of the invention on purified human tonsillar B cells, measured qualitatively over the dose range from 0.1 to 10,000 ng/mL, is assessed in a standard B-lymphocyte co-stimulation assay in which purified tonsillar B cells are cultured in the presence of either formalin-fixed Staphylococcus aureus Cowan I (SAC) or immobilized anti-human IgM antibody as the priming agent. Second signals such as IL-2 and IL-15 synergize with SAC and IgM crosslinking to elicit B cell proliferation as measured by tritiated-thymidine incorporation. Novel synergizing agents can be readily identified using this assay. The assay involves isolating human tonsillar B cells by magnetic bead (MACS) depletion of CD3-positive cells. The resulting cell population is greater than 95% B cells as assessed by expression of CD45R(B220).

[1391] Various dilutions of each sample are placed into individual wells of a 96-well plate to which are added 105 B-cells suspended in culture medium (RPMI 1640 containing 10% FBS, 5×10-5M2ME, 100 U/ml penicillin, 10 ug/ml streptomycin, and 10-5 dilution of SAC) in a total volume of 150ul. Proliferation or inhibition is quantitated by a 20 h pulse (1 uCi/well) with 3H-thymidine (6.7 Ci/mM) beginning 72 h post factor addition. The positive and negative controls are IL2 and medium respectively.

[1392] In Vivo Assay—BALB/c mice are injected (i.p.) twice per day with buffer only, or 2 mg/Kg of a polypeptide of the invention, or truncated forms thereof. Mice receive this treatment for 4 consecutive days, at which time they are sacrificed and various tissues and serum collected for analyses. Comparison of H&E sections from normal spleens and spleens treated with polypeptides of the invention identify the results of the activity of the polypeptides on spleen cells, such as the diffusion of peri-arterial lymphatic sheaths, and/or significant increases in the nucleated cellularity of the red pulp regions, which may indicate the activation of the differentiation and proliferation of B-cell populations. Immunohistochemical studies using a B cell marker, anti-CD45R(B220), are used to determine whether any physiological changes to splenic cells, such as splenic disorganization, are due to increased B-cell representation within loosely defined B-cell zones that infiltrate established T-cell regions.

[1393] Flow cytometric analyses of the spleens from mice treated with polypeptide is used to indicate whether the polypeptide specifically increases the proportion of ThB+, CD45R(B220)dull B cells over that which is observed in control mice.

[1394] Likewise, a predicted consequence of increased mature B-cell representation in vivo is a relative increase in serum Ig titers. Accordingly, serum IgM and IgA levels are compared between buffer and polypeptide-treated mice.

[1395] One skilled in the art could easily modify the exemplified-studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 37

T Cell Proliferation Assay

[1396] A CD3-induced proliferation assay is performed on PBMCs and is measured by the uptake of 3H-thymidine. The assay is performed as follows. Ninety-six well plates are coated with 100 (l/well of mAb to CD3 (HIT3a, Pharmingen) or isotype-matched control mAb (B33.1) overnight at 4 degrees C. (1 (g/ml in 0.05M bicarbonate buffer, pH 9.5), then washed three times with PBS. PBMC are isolated by F/H gradient centrifugation from human peripheral blood and added to quadruplicate wells (5×104/well) of mAb coated plates in RPMI containing 10% FCS and P/S in the presence of varying concentrations of polypeptides of the invention (total volume 200 ul). Relevant protein buffer and medium alone are controls. After 48 hr. culture at 37 degrees C., plates are spun for 2 min. at 1000 rpm and 100 (1 of supernatant is removed and stored −20 degrees C. for measurement of IL-2 (or other cytokines) if effect on proliferation is observed. Wells are supplemented with 100 ul of medium containing 0.5 uCi of 3H-thymidine and cultured at 37 degrees C. for 18-24 hr. Wells are harvested and incorporation of 3H-thymidine used as a measure of proliferation. Anti-CD3 alone is the positive control for proliferation. IL-2 (100 U/ml) is also used as a control which enhances proliferation. Control antibody which does not induce proliferation of T cells is used as the negative controls for the effects of polypeptides of the invention.

[1397] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 38

Effect of Polypeptides of the Invention on the Expression of MHC Class II, Costimulatory and Adhesion Molecules and Cell Differentiation of Monocytes and Monocyte-Derived Human Dendritic Cells

[1398] Dendritic cells are generated by the expansion of proliferating precursors found in the peripheral blood: adherent PBMC or elutriated monocytic fractions are cultured for 7-10 days with GM-CSF (50 ng/ml) and IL-4 (20 ng/ml). These dendritic cells have the characteristic phenotype of immature cells (expression of CD1, CD80, CD86, CD40 and MHC class II antigens). Treatment with activating factors, such as TNF-, causes a rapid change in surface phenotype (increased expression of MHC class I and II, costimulatory and adhesion molecules, downregulation of FC(RII, upregulation of CD83). These changes correlate with increased antigen-presenting capacity and with functional maturation of the dendritic cells.

[1399] FACS analysis of surface antigens is performed as follows. Cells are treated 1-3 days with increasing concentrations of polypeptides of the invention or LPS (positive control), washed with PBS containing 1% BSA and 0.02 mM sodium azide, and then incubated with 1:20 dilution of appropriate FITC- or PE-labeled monoclonal antibodies for 30 minutes at 4 degrees C. After an additional wash, the labeled cells are analyzed by flow cytometry on a FACScan (Becton Dickinson).

[1400] Effect on the production of cytokines. Cytokines generated by dendritic cells, in particular IL-12, are important in the initiation of T-cell dependent immune responses. IL-12 strongly influences the development of Th1 helper T-cell immune response, and induces cytotoxic T and NK cell function. An ELISA is used to measure the IL-12 release as follows. Dendritic cells (106/ml) are treated with increasing concentrations of polypeptides of the invention for 24 hours. LPS (100 ng/ml) is added to the cell culture as positive control. Supernatants from the cell cultures are then collected and analyzed for IL-12 content using commercial ELISA kit(e.g., R & D Systems (Minneapolis, Minn.)). The standard protocols provided with the kits are used.

[1401] Effect on the expression of MHC Class II, costimulatory and adhesion molecules. Three major families of cell surface antigens can be identified on monocytes: adhesion molecules, molecules involved in antigen presentation, and Fc receptor. Modulation of the expression of MHC class II antigens and other costimulatory molecules, such as B7 and ICAM-1, may result in changes in the antigen presenting capacity of monocytes and ability to induce T cell activation. Increase expression of Fc receptors may correlate with improved monocyte cytotoxic activity, cytokine release and phagocytosis.

[1402] FACS analysis is used to examine the surface antigens as follows. Monocytes are treated 1-5 days with increasing concentrations of polypeptides of the invention or LPS (positive control), washed with PBS containing 1% BSA and 0.02 mM sodium azide, and then incubated with 1:20 dilution of appropriate FITC- or PE-labeled monoclonal antibodies for 30 minutes at 4 degrees C. After an additional wash, the labeled cells are analyzed by flow cytometry on a FACScan (Becton Dickinson).

[1403] Monocyte activation and/or increased survival. Assays for molecules that activate (or alternatively, inactivate) monocytes and/or increase monocyte survival (or alternatively, decrease monocyte survival) are known in the art and may routinely be applied to determine whether a molecule of the invention functions as an inhibitor or activator of monocytes. Polypeptides, agonists, or antagonists of the invention can be screened using the three assays described below. For each of these assays, Peripheral blood mononuclear cells (PBMC) are purified from single donor leukopacks (American Red Cross, Baltimore, Md.) by centrifugation through a Histopaque gradient (Sigma). Monocytes are isolated from PBMC by counterflow centrifugal elutriation.

[1404] Monocyte Survival Assay.

[1405] Human peripheral blood monocytes progressively lose viability when cultured in absence of serum or other stimuli. Their death results from internally regulated process (apoptosis). Addition to the culture of activating factors, such as TNF-alpha dramatically improves cell survival and prevents DNA fragmentation. Propidium iodide (PI) staining is used to measure apoptosis as follows. Monocytes are cultured for 48 hours in polypropylene tubes in serum-free medium (positive control), in the presence of 100 ng/ml TNF-alpha (negative control), and in the presence of varying concentrations of the compound to be tested. Cells are suspended at a concentration of 2×106/ml in PBS containing PI at a final concentration of 5 (g/ml, and then incubated at room temperature for 5 minutes before FACScan analysis. PI uptake has been demonstrated to correlate with DNA fragmentation in this experimental paradigm.

[1406] Effect on Cytokine Release.

[1407] An important function of monocytes/macrophages is their regulatory activity on other cellular populations of the immune system through the release of cytokines after stimulation. An ELISA to measure cytokine release is performed as follows. Human monocytes are incubated at a density of 5×105 cells/ml with increasing concentrations of the a polypeptide of the invention and under the same conditions, but in the absence of the polypeptide. For IL-12 production, the cells are primed overnight with IFN (100 U/ml) in presence of a polypeptide of the invention. LPS (10 ng/ml) is then added. Conditioned media are collected after 24 h and kept frozen until use. Measurement of TNF-alpha, IL-10, MCP-1 and IL-8 is then performed using a commercially available ELISA kit(e.g., R & D Systems (Minneapolis, Minn.)) and applying the standard protocols provided with the kit.

[1408] Oxidative Burst.

[1409] Purified monocytes are plated in 96-w plate at 2-1×105 cell/well. Increasing concentrations of polypeptides of the invention are added to the wells in a total volume of 0.2 ml culture medium (RPMI 1640+10% FCS, glutamine and antibiotics). After 3 days incubation, the plates are centrifuged and the medium is removed from the wells. To the macrophage monolayers, 0.2 ml per well of phenol red solution (140 mM NaCl, 10 mM potassium phosphate buffer pH 7.0, 5.5 mM dextrose, 0.56 mM phenol red and 19 U/ml of HRPO) is added, together with the stimulant (200 nM PMA). The plates are incubated at 37(C for 2 hours and the reaction is stopped by adding 20 μl 1N NaOH per well. The absorbance is read at 610 nm. To calculate the amount of H2O2 produced by the macrophages, a standard curve of a H2O2 solution of known molarity is performed for each experiment.

[1410] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 39

Biological Effects of Polypeptides of the Invention Astrocyte and Neuronal Assays

[1411] Recombinant polypeptides of the invention, expressed in Escherichia coli and purified as described above, can be tested for activity in promoting the survival, neurite outgrowth, or phenotypic differentiation of cortical neuronal cells and for inducing the proliferation of glial fibrillary acidic protein immunopositive cells, astrocytes. The selection of cortical cells for the bioassay is based on the prevalent expression of FGF-1 and FGF-2 in cortical structures and on the previously reported enhancement of cortical neuronal survival resulting from FGF-2 treatment. A thymidine incorporation assay, for example, can be used to elucidate a polypeptide of the invention's activity on these cells.

[1412] Moreover, previous reports describing the biological effects of FGF-2 (basic FGF) on cortical or hippocampal neurons in vitro have demonstrated increases in both neuron survival and neurite outgrowth (Walicke et al., “Fibroblast growth factor promotes survival of dissociated hippocampal neurons and enhances neurite extension.” Proc. Natl. Acad. Sci. USA 83:3012-3016. (1986), assay herein incorporated by reference in its entirety). However, reports from experiments done on PC-12 cells suggest that these two responses are not necessarily synonymous and may depend on not only which FGF is being tested but also on which receptor(s) are expressed on the target cells. Using the primary cortical neuronal culture paradigm, the ability of a polypeptide of the invention to induce neurite outgrowth can be compared to the response achieved with FGF-2 using, for example, a thymidine incorporation assay.

[1413] Fibroblast and Endothelial Cell Assays.

[1414] Human lung fibroblasts are obtained from Clonetics (San Diego, Calif.) and maintained in growth media from Clonetics. Dermal microvascular endothelial cells are obtained from Cell Applications (San Diego, Calif.). For proliferation assays, the human lung fibroblasts and dermal microvascular endothelial cells can be cultured at 5,000 cells/well in a 96-well plate for one day in growth medium. The cells are then incubated for one day in 0.1% BSA basal medium. After replacing the medium with fresh 0.1% BSA medium, the cells are incubated with the test proteins for 3 days. Alamar Blue (Alamar Biosciences, Sacramento, Calif.) is added to each well to a final concentration of 10%. The cells are incubated for 4 hr. Cell viability is measured by reading in a CytoFluor fluorescence reader. For the PGE2 assays, the human lung fibroblasts are cultured at 5,000 cells/well in a 96-well plate for one day. After a medium change to 0.1% BSA basal medium, the cells are incubated with FGF-2 or polypeptides of the invention with or without IL-1(for 24 hours. The supernatants are collected and assayed for PGE2 by EIA kit (Cayman, Ann Arbor, Mich.). For the IL-6 assays, the human lung fibroblasts are cultured at 5,000 cells/well in a 96-well plate for one day. After a medium change to 0.1% BSA basal medium, the cells are incubated with FGF-2 or with or without polypeptides of the invention IL-1(for 24 hours. The supernatants are collected and assayed for IL-6 by ELISA kit (Endogen, Cambridge, Mass.).

[1415] Human lung fibroblasts are cultured with FGF-2 or polypeptides of the invention for 3 days in basal medium before the addition of Alamar Blue to assess effects on growth of the fibroblasts. FGF-2 should show a stimulation at 10-2500 ng/ml which can be used to compare stimulation with polypeptides of the invention.

[1416] Parkinson Models.

[1417] The loss of motor function in Parkinson's disease is attributed to a deficiency of striatal dopamine resulting from the degeneration of the nigrostriatal dopaminergic projection neurons. An animal model for Parkinson's that has been extensively characterized involves the systemic administration of 1-methyl-4 phenyl 1,2,3,6-tetrahydropyridine (MPTP). In the CNS, MPTP is taken-up by astrocytes and catabolized by monoamine oxidase B to 1-methyl-4-phenyl pyridine (MPP+) and released. Subsequently, MPP+ is actively accumulated in dopaminergic neurons by the high-affinity reuptake transporter for dopamine. MPP+ is then concentrated in mitochondria by the electrochemical gradient and selectively inhibits nicotidamide adenine disphosphate: ubiquinone oxidoreductionase (complex I), thereby interfering with electron transport and eventually generating oxygen radicals.

[1418] It has been demonstrated in tissue culture paradigms that FGF-2 (basic FGF) has trophic activity towards nigral dopaminergic neurons (Ferrari et al., Dev. Biol. 1989). Recently, Dr. Unsicker's group has demonstrated that administering FGF-2 in gel foam implants in the striatum results in the near complete protection of nigral dopaminergic neurons from the toxicity associated with MPTP exposure (Otto and Unsicker, J. Neuroscience, 1990).

[1419] Based on the data with FGF-2, polypeptides of the invention can be evaluated to determine whether it has an action similar to that of FGF-2 in enhancing dopaminergic neuronal survival in vitro and it can also be tested in vivo for protection of dopaminergic neurons in the striatum from the damage associated with MPTP treatment. The potential effect of a polypeptide of the invention is first examined in vitro in a dopaminergic neuronal cell culture paradigm. The cultures are prepared by dissecting the midbrain floor plate from gestation day 14 Wistar rat embryos. The tissue is dissociated with trypsin and seeded at a density of 200,000 cells/cm2 on polyorthinine-laminin coated glass coverslips. The cells are maintained in Dulbecco's Modified Eagle's medium and F12 medium containing hormonal supplements (Ni). The cultures are fixed with paraformaldehyde after 8 days in vitro and are processed for tyrosine hydroxylase, a specific marker for dopaminergic neurons, immunohistochemical staining. Dissociated cell cultures are prepared from embryonic rats. The culture medium is changed every third day and the factors are also added at that time.

[1420] Since the dopaminergic neurons are isolated from animals at gestation day 14, a developmental time which is past the stage when the dopaminergic precursor cells are proliferating, an increase in the number of tyrosine hydroxylase immunopositive neurons would represent an increase in the number of dopaminergic neurons surviving in vitro. Therefore, if a polypeptide of the invention acts to prolong the survival of dopaminergic neurons, it would suggest that the polypeptide may be involved in Parkinson's Disease.

[1421] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 40

The Effect of Polypeptides of the Invention on the Growth of Vascular Endothelial Cells

[1422] On day 1, human umbilical vein endothelial cells (HUVEC) are seeded at 2-5×104 cells/35 mm dish density in M199 medium containing 4% fetal bovine serum (FBS), 16 units/ml heparin, and 50 units/ml endothelial cell growth supplements (ECGS, Biotechnique, Inc.). On day 2, the medium is replaced with M199 containing 10% FBS, 8 units/ml heparin. A polypeptide having the amino acid sequence of SEQ ID NO:2, and positive controls, such as VEGF and basic FGF (bFGF) are added, at varying concentrations. On days 4 and 6, the medium is replaced. On day 8, cell number is determined with a Coulter Counter.

[1423] An increase in the number of HUVEC cells indicates that the polypeptide of the invention may proliferate vascular endothelial cells.

[1424] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 41

Stimulatory Effect of Polypeptides of the Invention on the Proliferation of Vascular Endothelial Cells

[1425] For evaluation of mitogenic activity of growth factors, the calorimetric MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)2H-tetrazolium) assay with the electron coupling reagent PMS (phenazine methosulfate) was performed (CellTiter 96 AQ, Promega). Cells are seeded in a 96-well plate (5,000 cells/well) in 0.1 mL serum-supplemented medium and are allowed to attach overnight. After serum-starvation for 12 hours in 0.5% FBS, conditions (bFGF, VEGF165 or a polypeptide of the invention in 0.5% FBS) with or without Heparin (8 U/ml) are added to wells for 48 hours. 20 mg of MTS/PMS mixture (1:0.05) are added per well and allowed to incubate for 1 hour at 37° C. before measuring the absorbance at 490 nm in an ELISA plate reader. Background absorbance from control wells (some media, no cells) is subtracted, and seven wells are performed in parallel for each condition. See, Leak et al. In Vitro Cell. Dev. Biol. 30A:512-518 (1994).

[1426] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 42

Inhibition of PDGF-induced Vascular Smooth Muscle Cell Proliferation Stimulatory Effect

[1427] HAoSMC proliferation can be measured, for example, by BrdUrd incorporation. Briefly, subconfluent, quiescent cells grown on the 4-chamber slides are transfected with CRP or FITC-labeled AT2-3LP. Then, the cells are pulsed with 10% calf serum and 6 mg/mil BrdUrd. After 24 h, immunocytochemistry is performed by using BrdUrd Staining Kit (Zymed Laboratories). In brief, the cells are incubated with the biotinylated mouse anti-BrdUrd antibody at 4 degrees C. for 2 h after being exposed to denaturing solution and then incubated with the streptavidin-peroxidase and diaminobenzidine. After counterstaining with hematoxylin, the cells are mounted for microscopic examination, and the BrdUrd-positive cells are counted. The BrdUrd index is calculated as a percent of the BrdUrd-positive cells to the total cell number. In addition, the simultaneous detection of the BrdUrd staining (nucleus) and the FITC uptake (cytoplasm) is performed for individual cells by the concomitant use of bright field illumination and dark field-UV fluorescent illumination. See, Hayashida et al., J. Biol. Chem. 6:271(36):21985-21992 (1996).

[1428] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 43

Stimulation of Nitric Oxide Production by Endothelial Cells

[1429] Nitric oxide released by the vascular endothelium is believed to be a mediator of vascular endothelium relaxation. Thus, activity of a polypeptide of the invention can be assayed by determining nitric oxide production by endothelial cells in response to the polypeptide.

[1430] Nitric oxide is measured in 96-well plates of confluent microvascular endothelial cells after 24 hours starvation and a subsequent 4 hr exposure to various levels of a positive control (such as VEGF-1) and the polypeptide of the invention. Nitric oxide in the medium is determined by use of the Griess reagent to measure total nitrite after reduction of nitric oxide-derived nitrate by nitrate reductase. The effect of the polypeptide of the invention on nitric oxide release is examined on HUVEC.

[1431] Briefly, NO release from cultured HUVEC monolayer is measured with a NO-specific polarographic electrode connected to a NO meter (Iso-NO, World Precision Instruments Inc.) (1049). Calibration of the NO elements is performed according to the following equation:

2KNO2+2KI+2H2SO4 6 2NO+I2+2H2O+2K2SO4

[1432] The standard calibration curve is obtained by adding graded concentrations of KNO2 (0, 5, 10, 25, 50, 100, 250, and 500 mmol/L) into the calibration solution containing KI and H2SO4. The specificity of the Iso-NO electrode to NO is previously determined by measurement of NO from authentic NO gas (1Q50). The culture medium is removed and HUVECs are washed twice with Dulbecco's phosphate buffered saline. The cells are then bathed in 5 ml of filtered Krebs-Henseleit solution in 6-well plates, and the cell plates are kept on a slide warmer (Lab Line Instruments Inc.) To maintain the temperature at 37° C. The NO sensor probe is inserted vertically into the wells, keeping the tip of the electrode 2 mm under the surface of the solution, before addition of the different conditions. S-nitroso acetyl penicillamin (SNAP) is used as a positive control. The amount of released NO is expressed as picomoles per 1×106 endothelial cells. All values reported are means of four to six measurements in each group (number of cell culture wells). See, Leak et al. Biochem. and Biophys. Res. Comm. 217:96-105 (1995).

[1433] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 44

Rescue of Ischemia in Rabbit Lower Limb Model

[1434] To study the in vivo effects of polynucleotides and polypeptides of the invention on ischemia, a rabbit hindlimb ischemia model is created by surgical removal of one femoral arteries as described previously (Takeshita et al., Am J. Pathol 147:1649-1660 (1995)). The excision of the femoral artery results in retrograde propagation of thrombus and occlusion of the external iliac artery. Consequently, blood flow to the ischemic limb is dependent upon collateral vessels originating from the internal iliac artery (Takeshitaet al. Am J. Pathol 147:1649-1660 (1995)). An interval of 10 days is allowed for post-operative recovery of rabbits and development of endogenous collateral vessels. At 10 day post-operatively (day 0), after performing a baseline angiogram, the internal iliac artery of the ischemic limb is transfected with 500 mg naked expression plasmid containing a polynucleotide of the invention by arterial gene transfer technology using a hydrogel-coated balloon catheter as described (Riessen et al. Hum Gene Ther. 4:749-758 (1993); Leclerc et al. J. Clin. Invest. 90: 936-944 (1992)). When a polypeptide of the invention is used in the treatment, a single bolus of 500 mg polypeptide of the invention or control is delivered into the internal iliac artery of the ischemic limb over a period of 1 min. through an infusion catheter. On day 30, various parameters are measured in these rabbits: (a) BP ratio—The blood pressure ratio of systolic pressure of the ischemic limb to that of normal limb; (b) Blood Flow and Flow Reserve—Resting FL: the blood flow during undilated condition and Max FL: the blood flow during fully dilated condition (also an indirect measure of the blood vessel amount) and Flow Reserve is reflected by the ratio of max FL: resting FL; (c) Angiographic Score—This is measured by the angiogram of collateral vessels. A score is determined by the percentage of circles in an overlaying grid that with crossing opacified arteries divided by the total number m the rabbit thigh; (d) Capillary density—The number of collateral capillaries determined in light microscopic sections taken from hindlimbs.

[1435] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 45

Effect of Polypeptides of the Invention on Vasodilation

[1436] Since dilation of vascular endothelium is important in reducing blood pressure, the ability of polypeptides of the invention to affect the blood pressure in spontaneously hypertensive rats (SHR) is examined. Increasing doses (0, 10, 30, 100, 300, and 900 mg/kg) of the polypeptides of the invention are administered to 13-14 week old spontaneously hypertensive rats (SHR). Data are expressed as the mean +/−SEM. Statistical analysis are performed with a paired t-test and statistical significance is defined as p<0.05 vs. the response to buffer alone.

[1437] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 46

Rat Ischemic Skin Flap Model

[1438] The evaluation parameters include skin blood flow, skin temperature, and factor VIII immunohistochemistry or endothelial alkaline phosphatase reaction. Expression of polypeptides of the invention, during the skin ischemia, is studied using in situ hybridization.

[1439] The study in this model is divided into three parts as follows:

[1440] a) Ischemic skin

[1441] b) Ischemic skin wounds

[1442] c) Normal wounds

[1443] The experimental protocol includes:

[1444] a) Raising a 3×4 cm, single pedicle full-thickness random skin flap (myocutaneous flap over the lower back of the animal).

[1445] b) An excisional wounding (4-6 mm in diameter) in the ischemic skin (skin-flap).

[1446] c) Topical treatment with a polypeptide of the invention of the excisional wounds (day 0, 1, 2, 3, 4 post-wounding) at the following various dosage ranges: 1 mg to 100 mg.

[1447] d) Harvesting the wound tissues at day 3, 5, 7, 10, 14 and 21 post-wounding for histological, immunohistochemical, and in situ studies.

[1448] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 47

Peripheral Arterial Disease Model

[1449] Angiogenic therapy using a polypeptide of the invention is a novel therapeutic strategy to obtain restoration of blood flow around the ischemia in case of peripheral arterial diseases. The experimental protocol includes:

[1450] a) One side of the femoral artery is ligated to create ischemic muscle of the hindlimb, the other side of hindlimb serves as a control.

[1451] b) a polypeptide of the invention, in a dosage range of 20 mg -500 mg, is delivered intravenously and/or intramuscularly 3 times (perhaps more) per week for 2-3 weeks.

[1452] c) The ischemic muscle tissue is collected after ligation of the femoral artery at 1, 2, and 3 weeks for the analysis of expression of a polypeptide of the invention and histology. Biopsy is also performed on the other side of normal muscle of the contralateral hindlimb.

[1453] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 48

Ischemic Myocardial Disease Model

[1454] A polypeptide of the invention is evaluated as a potent mitogen capable of stimulating the development of collateral vessels, and restructuring new vessels after coronary artery occlusion. Alteration of expression of the polypeptide is investigated in situ. The experimental protocol includes:

[1455] a) The heart is exposed through a left-side thoracotomy in the rat. Immediately, the left coronary artery is occluded with a thin suture (6-0) and the thorax is closed.

[1456] b) a polypeptide of the invention, in a dosage range of 20 mg -500 mg, is delivered intravenously and/or intramuscularly 3 times (perhaps more) per week for 2-4 weeks.

[1457] c) Thirty days after the surgery, the heart is removed and cross-sectioned for morphometric and in situ analyzes.

[1458] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 49

Rat Corneal Wound Healing Model

[1459] This animal model shows the effect of a polypeptide of the invention on neovascularization. The experimental protocol includes:

[1460] a) Making a 1-1.5 mm long incision from the center of cornea into the stromal layer.

[1461] b) Inserting a spatula below the lip of the incision facing the outer corner of the eye.

[1462] c) Making a pocket (its base is 1-1.5 mm form the edge of the eye).

[1463] d) Positioning a pellet, containing 50ng-5ug of a polypeptide of the invention, within the pocket.

[1464] e) Treatment with a polypeptide of the invention can also be applied topically to the corneal wounds in a dosage range of 20 mg-500 mg (daily treatment for five days).

[1465] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

Example 50

Diabetic Mouse and Glucocorticoid-Impaired Wound Healing Models

[1466] A. Diabetic db+/db+ Mouse Model.

[1467] To demonstrate that a polypeptide of the invention accelerates the healing process, the genetically diabetic mouse model of wound healing is used. The full thickness wound healing model in the db+/db+mouse is a well characterized, clinically relevant and reproducible model of impaired wound healing. Healing of the diabetic wound is dependent on formation of granulation tissue and re-epithelialization rather than contraction (Gartner, M. H. et al., J. Surg. Res. 52:389 (1992); Greenhalgh, D. G. et al., Am. J. Pathol. 136:1235 (1990)).

[1468] The diabetic animals have many of the characteristic features observed in Type II diabetes mellitus. Homozygous (db+/db+) mice are obese in comparison to their normal heterozygous (db+/+m) littermates. Mutant diabetic (db+/db+) mice have a single autosomal recessive mutation on chromosome 4 (db+) (Coleman et al. Proc. Natl. Acad. Sci. USA 77:283-293 (1982)). Animals show polyphagia, polydipsia and polyuria. Mutant diabetic mice (db+/db+) have elevated blood glucose, increased or normal insulin levels, and suppressed cell-mediated immunity (Mandel et al., J. Immunol. 120:1375 (1978); Debray-Sachs, M. et al., Clin. Exp. Immunol. 51(1):1-7 (1983); Leiter et al., Am. J. of Pathol. 114:46-55 (1985)). Peripheral neuropathy, myocardial complications, and microvascular lesions, basement membrane thickening and glomerular filtration abnormalities have been described in these animals (Norido, F. et al., Exp. Neurol. 83(2):221-232 (1984); Robertson et al., Diabetes 29(1):60-67 (1980); Giacomelli et al., Lab Invest. 40(4):460-473 (1979); Coleman, D. L., Diabetes 31 (Suppl): 1-6 (1982)). These homozygous diabetic mice develop hyperglycemia that is resistant to insulin analogous to human type II diabetes (Mandel et al., J. Immunol. 120:1375-1377 (1978)).

[1469] The characteristics observed in these animals suggests that healing in this model may be similar to the healing observed in human diabetes (Greenhalgh, et al., Am. J. of Pathol. 136:1235-1246 (1990)).

[1470] Genetically diabetic female C57BL/KsJ (db+/db+) mice and their non-diabetic (db+/+m) heterozygous littermates are used in this study (Jackson Laboratories). The animals are purchased at 6 weeks of age and are 8 weeks old at the beginning of the study. Animals are individually housed and received food and water ad libitum. All manipulations are performed using aseptic techniques. The experiments are conducted according to the rules and guidelines of Bristol-Myers Squibb Company's Institutional Animal Care and Use Committee and the Guidelines for the Care and Use of Laboratory Animals.

[1471] Wounding protocol is performed according to previously reported methods (Tsuboi, R. and Rifkin, D. B., J. Exp. Med. 172:245-251 (1990)). Briefly, on the day of wounding, animals are anesthetized with an intraperitoneal injection of Avertin (0.01 mg/mL), 2,2,2-tribromoethanol and 2-methyl-2-butanol dissolved in deionized water. The dorsal region of the animal is shaved and the skin washed with 70% ethanol solution and iodine. The surgical area is dried with sterile gauze prior to wounding. An 8 mm full-thickness wound is then created using a Keyes tissue punch. Immediately following wounding, the surrounding skin is gently stretched to eliminate wound expansion. The wounds are left open for the duration of the experiment. Application of the treatment is given topically for 5 consecutive days commencing on the day of wounding. Prior to treatment, wounds are gently cleansed with sterile saline and gauze sponges.

[1472] Wounds are visually examined and photographed at a fixed distance at the day of surgery and at two day intervals thereafter. Wound closure is determined by daily measurement on days 1-5 and on day 8. Wounds are measured horizontally and vertically using a calibrated Jameson caliper. Wounds are considered healed if granulation tissue is no longer visible and the wound is covered by a continuous epithelium.

[1473] A polypeptide of the invention is administered using at a range different doses, from 4 mg to 500 mg per wound per day for 8 days in vehicle. Vehicle control groups received 50 mL of vehicle solution.

[1474] Animals are euthanized on day 8 with an intraperitoneal injection of sodium pentobarbital (300 mg/kg). The wounds and surrounding skin are then harvested for histology and immunohistochemistry. Tissue specimens are placed in 10% neutral buffered formalin in tissue cassettes between biopsy sponges for further processing.

[1475] Three groups of 10 animals each (5 diabetic and 5 non-diabetic controls) are evaluated: 1) Vehicle placebo control, 2) untreated group, and 3) treated group.

[1476] Wound closure is analyzed by measuring the area in the vertical and horizontal axis and obtaining the total square area of the wound. Contraction is then estimated by establishing the differences between the initial wound area (day 0) and that of post treatment (day 8). The wound area on day 1 is 64 mm2, the corresponding size of the dermal punch. Calculations are made using the following formula:

[Open area on day 8]−[Open area on day 1]/[Open area on day 1]

[1477] Specimens are fixed in 10% buffered formalin and paraffin embedded blocks are sectioned perpendicular to the wound surface (5 mm) and cut using a Reichert-Jung microtome. Routine hematoxylin-eosin (H&E) staining is performed on cross-sections of bisected wounds. Histologic examination of the wounds are used to assess whether the healing process and the morphologic appearance of the repaired skin is altered by treatment with a polypeptide of the invention. This assessment included verification of the presence of cell accumulation, inflammatory cells, capillaries, fibroblasts, re-epithelialization and epidermal maturity (Greenhalgh, D. G. et al., Am. J. Pathol. 136:1235 (1990)). A calibrated lens micrometer is used by a blinded observer.

[1478] Tissue sections are also stained immunohistochemically with a polyclonal rabbit anti-human keratin antibody using ABC Elite detection system. Human skin is used as a positive tissue control while non-immune IgG is used as a negative control. Keratinocyte growth is determined by evaluating the extent of reepithelialization of the wound using a calibrated lens micrometer.

[1479] Proliferating cell nuclear antigen/cyclin (PCNA) in skin specimens is demonstrated by using anti-PCNA antibody (1:50) with an ABC Elite detection system. Human colon cancer can serve as a positive tissue control and human brain tissue can be used as a negative tissue control. Each specimen includes a section with omission of the primary antibody and substitution with non-immune mouse IgG. Ranking of these sections is based on the extent of proliferation on a scale of 0-8, the lower side of the scale reflecting slight proliferation to the higher side reflecting intense proliferation.

[1480] Experimental data are analyzed using an unpaired t test. A p value of <0.05 is considered significant.

[1481] B. Steroid Impaired Rat Model

[1482] The inhibition of wound healing by steroids has been well documented in various in vitro and in vivo systems (Wahl, Glucocorticoids and Wound healing. In: Anti-Inflammatory Steroid Action: Basic and Clinical Aspects. 280-302 (1989); Wahl et al., J. Immunol. 115: 476-481 (1975); Werb et al., J. Exp. Med. 147:1684-1694 (1978)). Glucocorticoids retard wound healing by inhibiting angiogenesis, decreasing vascular permeability (Ebert et al., An. Intern. Med. 37:701-705 (1952)), fibroblast proliferation, and collagen synthesis (Beck et al., Growth Factors. 5: 295-304 (1991); Haynes et al., J. Clin. Invest. 61: 703-797 (1978)) and producing a transient reduction of circulating monocytes (Haynes et al., J. Clin. Invest. 61: 703-797 (1978); Wahl, “Glucocorticoids and wound healing”, In: Antiinflammatory Steroid Action: Basic and Clinical Aspects, Academic Press, New York, pp. 280-302 (1989)). The systemic administration of steroids to impaired wound healing is a well establish phenomenon in rats (Beck et al., Growth Factors. 5: 295-304 (1991); Haynes et al., J. Clin. Invest. 61: 703-797 (1978); Wahl, “Glucocorticoids and wound healing”, In: Antiinflammatory Steroid Action: Basic and Clinical Aspects, Academic Press, New York, pp. 280-302 (1989); Pierce et al., Proc. Natl. Acad. Sci. USA 86: 2229-2233 (1989)).

[1483] To demonstrate that a polypeptide of the invention can accelerate the healing process, the effects of multiple topical applications of the polypeptide on full thickness excisional skin wounds in rats in which healing has been impaired by the systemic administration of methylprednisolone is assessed.

[1484] Young adult male Sprague Dawley rats weighing 250-300 g (Charles River Laboratories) are used in this example. The animals are purchased at 8 weeks of age and are 9 weeks old at the beginning of the study. The healing response of rats is impaired by the systemic administration of methylprednisolone (17 mg/kg/rat intramuscularly) at the time of wounding. Animals are individually housed and received food and water ad libitum. All manipulations are performed using aseptic techniques. This study would be conducted according to the rules and guidelines of Bristol-Myers Squibb Corporations Guidelines for the Care and Use of Laboratory Animals.

[1485] The wounding protocol is followed according to section A, above. On the day of wounding, animals are anesthetized with an intramuscular injection of ketamine (50 mg/kg) and xylazine (5 mg/kg). The dorsal region of the animal is shaved and the skin washed with 70% ethanol and iodine solutions. The surgical area is dried with sterile gauze prior to wounding. An 8 mm full-thickness wound is created using a Keyes tissue punch. The wounds are left open for the duration of the experiment. Applications of the testing materials are given topically once a day for 7 consecutive days commencing on the day of wounding and subsequent to methylprednisolone administration. Prior to treatment, wounds are gently cleansed with sterile saline and gauze sponges.

[1486] Wounds are visually examined and photographed at a fixed distance at the day of wounding and at the end of treatment. Wound closure is determined by daily measurement on days 1-5 and on day 8. Wounds are measured horizontally and vertically using a calibrated Jameson caliper. Wounds are considered healed if granulation tissue is no longer visible and the wound is covered by a continuous epithelium.

[1487] The polypeptide of the invention is administered using at a range different doses, from 4 mg to 500 mg per wound per day for 8 days in vehicle. Vehicle control groups received 50 mL of vehicle solution.

[1488] Animals are euthanized on day 8 with an intraperitoneal injection of sodium pentobarbital (300 mg/kg). The wounds and surrounding skin are then harvested for histology. Tissue specimens are placed in 10% neutral buffered formalin in tissue cassettes between biopsy sponges for further processing.

[1489] Four groups of 10 animals each (5 with methylprednisolone and 5 without glucocorticoid) are evaluated: 1) Untreated group 2) Vehicle placebo control 3) treated groups.

[1490] Wound closure is analyzed by measuring the area in the vertical and horizontal axis and obtaining the total area of the wound. Closure is then estimated by establishing the differences between the initial wound area (day 0) and that of post treatment (day 8). The wound area on day 1 is 64 mm2, the corresponding size of the dermal punch. Calculations are made using the following formula:

[Open area on day 8]−[Open area on day 1]/[Open area on day 1]

[1491] Specimens are fixed in 10% buffered formalin and paraffin embedded blocks are sectioned perpendicular to the wound surface (5 mm) and cut using an Olympus microtome. Routine hematoxylin-eosin (H&E) staining is performed on cross-sections of bisected wounds. Histologic examination of the wounds allows assessment of whether the healing process and the morphologic appearance of the repaired skin is improved by treatment with a polypeptide of the invention. A calibrated lens micrometer is used by a blinded observer to determine the distance of the wound gap.

[1492] Experimental data are analyzed using an unpaired t test. A p value of <0.05 is considered significant.

[1493] One skilled in the art could easily modify the exemplified studies to test the activity of polynucleotides of the invention (e.g., gene therapy), agonists, and/or antagonists of polynucleotides or polypeptides of the invention.

[1494] It will be clear that the invention may be practiced otherwise than as particularly described in the foregoing description and examples. Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, are within the scope of the appended claims.

[1495] The entire disclosure of each document cited (including patents, patent applications, journal articles, abstracts, laboratory manuals, books, or other disclosures) in the Background of the Invention, Detailed Description, and Examples is hereby incorporated herein by reference. Further, the hard copy of the sequence listing submitted herewith and the corresponding computer readable form are both incorporated herein by reference in their entireties.

20TABLE IVAtom NoResidueAtom namex coordy coordz coord1LYS12N−27.215919.7201−6.28242LYS12CA−26.697118.4591−5.77443LYS12C−27.734917.3482−5.73854LYS12O−27.410916.2063−6.03525LYS12CB−26.126618.6653−4.35946LYS12CG−24.733218.0137−4.27147LYS12CD−24.848316.4855−4.4338LYS12CE−23.443915.8647−4.54769LYS12NZ−22.701116.0707−3.295910LEU13N−28.980917.682−5.412711LEU13CA−30.06416.6951−5.404712LEU13C−30.253716.2158−6.840513LEU13O−30.386115.0234−7.098514LEU13CB−31.356317.3552−4.890715LEU13CG−31.172117.7804−3.42116LEU13CD1−32.454318.4737−2.924917LEU13CD2−30.883516.5465−2.544118ALA14N−30.241617.1744−7.767619ALA14CA−30.382516.9101−9.19520ALA14C−29.286615.9587−9.661321ALA14O−29.555314.9807−10.362822ALA14CB−30.331318.232−9.983523PRO15N−28.056916.2571−9.241924PRO15CA−26.877215.4556−9.56325PRO15C−27.02914.0783−8.923126PRO15O−26.676513.0642−9.527327PRO15CB−25.723116.2219−8.892228PRO15CG−26.262317.6337−8.593629PRO15CD−27.798717.5229−8.582130ARG16N−27.5814.0482−7.710231ARG16CA−27.790812.7957−6.995832ARG16C−28.785211.9184−7.733633ARG16O−28.719210.6897−7.657834ARG16CB−28.432813.1445−5.639835ARG16CG−27.390413.7645−4.691736ARG16CD−28.122414.4083−3.499637ARG16NE−27.489315.6684−3.155238ARG16CZ−26.872115.823−2.019639ARG16NH1−26.319616.9665−1.742640ARG16NH2−26.79714.8537−1.155341TYR17N−29.982212.8509−8.583242TYR17CA−30.426711.5765−9.111843TYR17C−29.969711.2849−10.538544TYR17O−30.255310.2132−11.072745TYR17CB−31.97111.5383−9.066646TYR17CG−32.52912.9543−8.937547TYR17CD1−32.530113.8102−10.041948TYR17CD2−33.015813.3997−7.70649TYR17CE1−32.894415.1493−9.881350TYR17CE2−33.380314.7389−7.545651TYR17CZ−33.28715.6204−8.625652TYR17OH−33.584416.9663−8.450753GLN28N−17.316719.6634−20.957754GLN28CA−16.671719.1545−22.176155GLN28C−17.639918.3959−23.100456GLN28O−17.69118.6208−24.308757GLN28CB−15.902420.2732−22.905958GLN28CG−16.857121.4214−23.283859GLN28CD−16.063122.5632−23.848160GLN28OE1−16.252822.9259−24.997161GLN28NE2−15.160623.145−23.037562ASP29N−17.81218.2585−24.232963ASP29CA−18.293717.1126−24.995564ASP29C−17.308116.7493−26.090565ASP29O−17.122517.4942−27.05266ASP29CB−19.709517.3082−25.576167ASP29CG−20.266415.967−25.957768ASP29OD1−21.081915.42−25.168969ASP29OD2−19.898315.4607−27.050870PHE30N−16.668615.5986−25.9271PHE30CA−15.688315.1073−26.87672PHE30C−16.237415.0541−28.291773PHE30O−15.584815.4889−29.221574PHE30CB−15.091313.7425−26.486575PHE30CG−13.931213.4564−27.436376PHE30CD1−12.818914.302−27.455377PHE30CD2−13.983612.3569−28.296378PHE30CE1−11.785614.0734−28.36779PHE30CE2−12.919212.0914−29.161580PHE30CZ−11.822212.9557−29.204181GLU31N−17.422714.4765−28.439182GLU31CA−18.069514.3384−29.7483GLU31C−18.496115.6958−30.297884GLU31O−18.174616.0281−31.436685GLU31CB−19.324813.4596−29.570786GLU31CG−18.996912.1952−28.751287GLU31CD−19.192912.4724−27.287688GLU31OE1−20.372812.5627−26.854789GLU31OE2−18.168412.5927−26.563690ALA32N−19.172416.4914−29.472891ALA32CA−19.625617.817−29.876792ALA32C−18.479218.7175−30.348793ALA32O−18.577119.3496−31.405194ALA32CB−20.307618.4749−28.663195LEU33N−17.395418.7607−29.575196LEU33CA−16.223119.5772−29.903197LEU33C−15.433119.0228−31.088498LEU33O−14.889719.7818−31.89199LEU33CB−15.301119.5611−28.6684100LEU33CG−16.015420.2097−27.4667101LEU33CD1−15.18219.9944−26.1896102LEU33CD2−16.195321.7178−27.7216103LEU34N−15.357117.6969−31.1802104LEU34CA−14.667817.0334−32.2855105LEU34C−15.472317.3381−33.5408106LEU34O−14.927117.7085−34.5669107LEU34CB−14.738115.5166−32.0247108LEU34CG−13.430814.8282−32.4594109LEU34CD1−13.480213.3423−32.0608110LEU34CD2−13.245314.9435−33.9839111ALA35N−16.785417.2046−33.4234112ALA35CA−17.707417.4638−34.5157113ALA35C−17.589418.9123−34.9803114ALA35O−17.516519.1899−36.1781115ALA35CB−19.140717.2174−34.0109116GLU36N−17.581919.8209−34.0104117GLU36CA−17.461621.2591−34.2319118GLU36C−16.217121.5709−35.0692119GLU36O−16.285722.2732−36.0777120GLU36CB−17.336621.903−32.8349121GLU36CG−16.829123.3574−32.9143122GLU36CD−15.326523.3815−32.8896123GLU36OE1−14.735222.8224−31.927124GLU36OE2−14.731623.9552−33.8408125CYS37N−15.085121.0145−34.6518126CYS37CA−13.822821.2122−35.3467127CYS37C−13.826520.4262−36.6526128CYS37O−13.208220.8268−37.6325129CYS37CB−12.703120.6447−34.4549130CYS37SG−11.798822.0477−33.7396131LEU38N−14.513719.2872−36.6354132LEU38CA−14.636518.4176−37.7991133LEU38C−15.242719.2608−38.8935134LEU38O−14.729419.3257−40.0108135LEU38CB−15.558317.2359−37.4444136LEU38CG−14.835315.9028−37.7188137LEU38CD1−13.522615.8275−36.9155138LEU38CD2−15.750314.7352−37.3062139ARG39N−16.305619.9654−38.5243140ARG39CA−17.029720.8292−39.4381141ARG39C−16.24422.0579−39.8902142ARG39O−15.904922.1629−41.0629143ARG39CB−18.318621.316−38.7483144ARG39CG−19.186820.1166−38.3268145ARG39CD−20.10320.5459−37.1664146ARG39NE−20.361819.4053−36.3068147ARG39CZ−21.571618.9628−36.1218148ARG39NH1−21.765217.9388−35.3449149ARG39NH2−22.591319.5263−36.7005150ASN40N−15.897322.9463−38.9598151ASN40CA−15.15824.169−39.2938152ASN40C−13.775923.9349−39.8974153ASN40O−13.08224.8845−40.2596154ASN40CB−14.987325.0138−38.0155155ASN40CG−16.316925.3188−37.3873156ASN40OD1−16.525225.0099−36.2256157ASN40ND2−17.234125.9335−38.1556158GLY41N−13.389322.667−40.0176159GLY41CA−12.096722.3184−40.5824160GLY41C−10.945222.9275−39.8082161GLY41O−10.096723.6122−40.3791162CYS42N−10.916722.6693−38.5057163CYS42CA−9.880323.2064−37.6375164CYS42C−9.461622.2276−36.5439165CYS42O−9.969221.1126−36.4619166CYS42CB−10.426524.4707−36.9437167CYS42SG−10.75325.7585−38.1837168LEU43N−8.519322.6577−35.7118169LEU43CA−8.013221.8337−34.6213170LEU43C−8.470322.3473−33.2651171LEU43O−8.577823.5611−33.0479172LEU43CB−6.477321.7117−34.6571173LEU43CG−5.957621.4349−36.0819174LEU43CD1−4.419921.3664−36.0489175LEU43CD2−6.509220.0994−36.615176PHE44N−8.695521.4162−32.3455177PHE44CA−9.146421.7627−31.0043178PHE44C−8.088322.4337−30.1214179PHE44O−6.949521.9754−29.9899180PHE44CB−9.820220.5294−30.3676181PHE44CG−9.88220.6174−28.8472182PHE44CD1−10.747821.5258−28.233183PHE44CD2−9.072519.7821−28.073184PHE44CE1−10.837121.5679−26.8396185PHE44CE2−9.160819.8264−26.6796186PHE44CZ−10.059820.7022−26.0661187GLU45N−8.481123.5795−29.5902188GLU45CA−7.663424.3474−28.6926189GLU45C−8.517424.3954−27.4403190GLU45O−9.553725.0596−27.3985191GLU45CB−7.446225.7576−29.2734192GLU45CG−6.792625.6599−30.6663193GLU45CD−5.403125.1005−30.5591194GLU45OE1−4.500525.842−30.0872195GLU45OE2−5.208323.9213−30.9566196ASP46N−8.127923.5759−26.4713197ASP46CA−8.827123.4565−25.2064198ASP46C−8.974524.79−24.4679199ASP46O−7.979225.4257−24.1015200ASP46CB−7.997322.5011−24.3257201ASP46CG−8.858721.8017−23.3145202ASP46OD1−9.440522.4985−22.4406203ASP46OD2−8.949920.5471−23.39204THR47N−10.231925.236−24.2636205THR47CA−10.578826.4827−23.5731206THR47C−10.544826.3291−22.0414207THR47O−10.670227.3036−21.297208THR47CB−11.99126.9051−24.0256209THR47OG1−12.068526.8763−25.4538210THR47CG2−12.299328.3333−23.5373211SER48N−10.356225.0947−21.5841212SER48CA−10.320224.7963−20.1625213SER48C−8.932724.3765−19.7007214SER48O−8.704424.1661−18.5061215SER48CB−11.305423.6448−19.8871216SER48OG−12.621324.0291−20.2945217PHE49N−8.012324.2454−20.6548218PHE49CA−6.643523.8505−20.3588219PHE49C−5.708924.3915−21.4418220PHE49O−5.115423.6305−22.2142221PHE49CB−6.580122.3116−20.2651222PHE49CG−5.329821.8633−19.5126223PHE49CD1−5.331221.8194−18.1156224PHE49CD2−4.183321.4888−20.2187225PHE49CE1−4.195621.3837−17.4269226PHE49CE2−3.04721.0549−19.5305227PHE49CZ−3.054120.9974−18.1343228PRO50N−5.564325.7267−21.5041229PRO50CA−4.729326.4558−22.4561230PRO50C−3.268726.0165−22.478231PRO50O−2.743925.4808−21.4869232PRO50CB−4.831327.9279−22.0172233PRO50CG−5.816527.9803−20.831234PRO50CD−6.282126.5397−20.5405235ALA51N−2.612126.2739−23.6058236ALA51CA−1.209825.9377−23.7851237ALA51C−0.349726.9614−23.0391238ALA51O0.722327.3612−23.5021239ALA51CB−0.848125.8622−25.281240THR52N−0.840527.3848−21.8767241THR52CA−0.155928.3625−21.0525242THR52C0.695827.7065−19.9669243THR52O0.70926.4813−19.8398244THR52CB−1.213629.2515−20.369245THR52OG1−2.078428.4487−19.5588246THR52CG2−2.046729.9875−21.4353247LEU53N1.516328.5131−19.2586248LEU53CA2.386328.037−18.1786249LEU53C1.575827.5585−16.9718250LEU53O2.068126.7947−16.1515251LEU53CB3.333629.1723−17.7501252LEU53CG4.609929.1306−18.6121253LEU53CD15.513730.3224−18.247254LEU53CD25.373427.8177−18.3543255SER54N0.331928.0127−16.8819256SER54CA−0.56927.6427−15.7938257SER54C−0.949626.1564−15.8412258SER54O−1.290525.5583−14.8192259SER54CB−1.857528.4696−15.9596260SER54OG−1.549129.864−15.8839261SER55N−0.916425.584−17.0444262SER55CA−1.220424.1714−17.2571263SER55C−0.041423.3364−16.7588264SER55O−0.209222.2061−16.2832265SER55CB−1.46923.9085−18.7566266SER55OG−0.242923.9254−19.4941267ILE56N1.156323.8991−16.9025268ILE56CA2.390523.2585−16.4678269ILE56C2.532223.3656−14.9373270ILE56O2.88622.3901−14.2855271ILE56CB3.557523.9946−17.1549272ILE56CG13.351423.9704−18.6829273ILE56CG24.891923.3115−16.798274ILE56CD14.371624.8964−19.3715275GLY57N2.264124.5079−14.3713276GLY57CA2.359824.7298−12.9266277GLY57C3.799624.4235−12.4989278GLY57O4.227423.2821−12.5859279LEU65N12.311525.9569−15.7051280LEU65CA12.131424.6761−16.4042281LEU65C11.091624.8704−17.538282LEU65O11.279424.3854−18.6495283LEU65CB11.524823.6404−15.4356284LEU65CG12.554723.1647−14.3945285LEU65CD111.852122.277−13.351286LEU65CD213.666422.3566−15.0896287PRO66N10.069625.653−17.3149288PRO66CA9.028225.8331−18.322289PRO66C9.228627.0866−19.1893290PRO66O8.260927.7518−19.5641291PRO66CB7.783426.0207−17.4333292PRO66CG8.294126.5192−16.0641293PRO66CD9.803326.2118−16.0068294PRO67N10.484227.3788−19.5276295PRO67CA10.824528.5473−20.3404296PRO67C11.292928.1703−21.7447297PRO67O12.16127.3217−21.9075298PRO67CB12.030229.1474−19.5952299PRO67CG12.672627.9643−18.8471300PRO67CD11.681226.7941−18.9858301ARG68N10.70128.7991−22.754302ARG68CA11.079328.5286−24.135303ARG68C10.725327.1529−24.6599304ARG68O11.460926.5524−25.4496305ARG68CB12.557828.8764−24.4017306ARG68CG12.818130.3504−24.0425307ARG68CD14.323730.6448−24.1658308ARG68NE14.585431.9972−23.709309ARG68CZ15.26432.2199−22.6207310ARG68NH115.479833.445−22.2438311ARG68NH215.729331.2393−21.9035312LEU69N9.592426.6432−24.2168313LEU69CA9.150525.3393−24.6592314LEU69C7.852625.4596−25.456315LEU69O6.905826.1202−25.0331316LEU69CB8.908424.3992−23.457317LEU69CG8.763225.1657−22.1248318LEU69CD17.4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1640VAL121CA−8.11385.031−23.1509641VAL121C−9.14084.4303−24.128642VAL121O−9.03173.276−24.5517643VAL121CB−6.67054.6559−23.5399644VAL121CG1−6.32615.265−24.9123645VAL121CG2−5.69945.2154−22.4827646PRO122N−10.18765.2355−24.526647PRO122CA−11.12324.7921−25.5543648PRO122C−10.33694.6489−26.8664649PRO122O−9.76745.5885−27.4207650PRO122CB−12.07326.0025−25.6621651PRO122CG−11.46387.1599−24.8396652PRO122CD−10.31636.5757−23.9929653LEU123N−10.29323.3366−27.3276654LEU123CA−9.33862.9467−28.3737655LEU123C−9.7283.5064−29.7541656LEU123O−8.92973.5627−30.6897657LEU123CB−9.26191.4084−28.4148658LEU123CG−8.94890.858−27.008659LEU123CD1−8.9634−0.6812−27.0383660LEU123CD2−7.56711.3497−26.5353661ASN124N−11.05563.8432−29.8956662ASN124CA−11.62594.3803−31.1327663ASN124C−11.18895.8395−31.3775664ASN124O−11.98116.7626−31.546665ASN124CB−13.16344.2757−31.0468666ASN124CG−13.70085.0409−29.8683667ASN124OD1−14.41256.0144−30.0524668ASN124ND2−13.36644.6068−28.6394669GLN125N−9.8226.007−31.4634670GLN125CA−9.18147.3052−31.6147671GLN125C−7.94667.1256−32.5074672GLN125O−7.33046.0632−32.5861673GLN125CB−8.75847.8764−30.2481674GLN125CG−10.00078.1186−29.3703675GLN125CD−9.62738.9664−28.1894676GLN125OE1−10.108610.0807−28.068677GLN125NE2−8.76168.4413−27.3035678SER126N−7.57778.2638−33.2006679SER126CA−6.57958.2017−34.263680SER126C−6.119.618−34.6132681SER126O−6.757810.6218−34.3314682SER126CB−7.15757.5132−35.5138683SER126OG−6.10457.2436−36.4424684PHE127N−4.91129.6319−35.3035685PHE127CA−4.412810.8268−35.9869686PHE127C−4.774510.8026−37.4801687PHE127O−4.680211.8116−38.1782688PHE127CB−2.878210.8614−35.8505689PHE127CG−2.486711.0463−34.3877690PHE127CD1−1.89669.9921−33.6854691PHE127CD2−2.716912.2688−33.7507692PHE127CE1−1.5410.1607−32.345693PHE127CE2−2.361212.4355−32.4099694PHE127CZ−1.775211.3805−31.7056695TYR131N−9.259513.5067−37.4336696TYR131CA−8.246113.9236−36.4549697TYR131C−8.686815.1692−35.6672698TYR131O−8.57115.2393−34.441699TYR131CB−6.884514.1573−37.1456700TYR131CG−6.012315.0932−36.3094701TYR131CD1−5.385414.636−35.1466702TYR131CD2−5.856716.4228−36.7094703TYR131CE1−4.67115.5291−34.3426704TYR131CE2−5.13817.3139−35.9092705TYR131CZ−4.560916.8715−34.7166706TYR131OH−3.87917.7694−33.9043707ALA132N−9.016816.2679−36.4355708ALA132CA−9.532817.5262−35.8823709ALA132C−8.592418.3499−34.9607710ALA132O−8.70919.5738−34.8854711ALA132CB−10.853217.2515−35.1364712GLY133N−7.75217.6291−34.1455713GLY133CA−6.935418.218−33.0956714GLY133C−7.607218.1022−31.7283715GLY133O−7.563919.0118−30.9002716ILE134N−8.159916.8637−31.4524717ILE134CA−8.917316.6142−30.2263718ILE134C−8.818215.1192−29.8913719ILE134O−8.881314.2514−30.7603720ILE134CB−10.359317.1524−30.3084721ILE134CG1−11.059217.0133−28.9422722ILE134CG2−11.142616.4052−31.4039723ILE134CD1−12.455917.662−28.9913724PHE135N−8.724714.8401−28.5422725PHE135CA−8.686313.4695−28.0316726PHE135C−9.450813.4417−26.7029727PHE135O−9.631514.454−26.0215728PHE135CB−7.242812.9517−27.8844729PHE135CG−6.584412.915−29.2601730PHE135CD1−5.527513.7812−29.5524731PHE135CD2−7.042712.0197−30.2306732PHE135CE1−4.9513.7723−30.8247733PHE135CE2−6.470212.0164−31.5053734PHE135CZ−5.428212.898−31.8044735ARG136N−9.869812.1836−26.3098736ARG136CA−10.614811.9692−25.0723737ARG136C−10.140810.7089−24.3312738ARG136O−9.63749.7405−24.9031739ARG136CB−12.133711.9063−25.3183740ARG136CG−12.469910.6748−26.1801741ARG136CD−13.942410.2825−25.9652742ARG136NE−14.34999.3766−27.0232743ARG136CZ−15.43769.5841−27.7076744ARG136NH1−15.7628.7525−28.6524745ARG136NH2−16.205910.6056−27.4648746PHE137N−10.344910.7858−22.9627747PHE137CA−9.80439.8128−22.011748PHE137C−10.77229.7426−20.8275749PHE137O−11.496710.6948−20.5245750PHE137CB−8.430610.2588−21.4726751PHE137CG−7.365610.217−22.5633752PHE137CD1−6.737111.3995−22.9629753PHE137CD2−7.01189.0021−23.1568754PHE137CE1−5.724711.363−23.9254755PHE137CE2−6.00128.966−24.1212756PHE137CZ−5.350210.1442−24.4974757TRP138N−10.73458.5614−20.1081758TRP138CA−11.55448.3889−18.9132759TRP138C−10.66828.1648−17.6812760TRP138O−9.58917.5783−17.7445761TRP138CB−12.57337.2508−19.0873762TRP138CG−13.87377.8635−19.5123763TRP138CD1−14.19258.302−20.7399764TRP138CD2−15.06728.1022−18.628765TRP138NE1−15.41388.7761−20.7391766TRP138CE2−15.96228.6761−19.5107767TRP138CE3−15.36437.8732−17.2856768TRP138CZ2−17.23759.072−19.1083769TRP138CZ3−16.64358.2685−16.8761770TRP138CH2−17.55338.8666−17.7597771PHE139N−11.25258.5736−16.4965772PHE139CA−10.60478.4027−15.1966773PHE139C−11.67848.0116−14.1835774PHE139O−12.83848.4183−14.2702775PHE139CB−9.7649.6274−14.7891776PHE139CG−8.938310.0973−15.9836777PHE139CD1−9.349811.2112−16.7203778PHE139CD2−7.77639.4121−16.3481779PHE139CE1−8.615111.6229−17.8355780PHE139CE2−7.0439.8219−17.4648781PHE139CZ−7.462710.9269−18.2099782TRP140N−11.21817.2355−13.1403783TRP140CA−12.01247.0661−11.921784TRP140C−11.65568.2532−11.0208785TRP140O−10.52998.754−11.0265786TRP140CB−11.60665.7386−11.2498787TRP140CG−12.075.687−9.8235788TRP140CD1−13.20495.1441−9.3567789TRP140CD2−11.32536.2514−8.6444790TRP140NE1−13.26395.2892−8.0555791TRP140CE2−12.16945.9322−7.598792TRP140CE3−10.12096.9325−8.4733793TRP140CZ2−11.85626.2641−6.2802794TRP140CZ3−9.81067.2898−7.1556795TRP140CH2−10.65456.9571−6.0853796HIS141N−12.67228.7017−10.2057797HIS141CA−12.50739.8245−9.2918798HIS141C−13.41919.5704−8.0813799HIS141O−14.62469.8188−8.0798800HIS141CB−12.93411.1155−10.0147801HIS141CG−12.053211.287−11.2152802HIS141ND1−10.812711.7037−11.1111803HIS141CD2−12.421311.027−12.4836804HIS141CE1−10.318311.7319−12.3074805HIS141NE2−11.185111.36−13.1359806TYR142N−12.7958.9359−7.0187807TYR142CA−13.34339.0058−5.6555808TYR142C−14.73148.3527−5.5148809TYR142O−15.48988.5952−4.5781810TYR142CB−13.39710.4616−5.1484811TYR142CG−12.007311.0876−5.0786812TYR142CD1−11.248211.2589−6.2396813TYR142CD2−11.496411.4996−3.8452814TYR142CE1−9.994311.8714−6.1724815TYR142CE2−10.247312.1222−3.7792816TYR142CZ−9.501412.319−4.9439817TYR142OH−8.270312.9606−4.8804818GLY143N−14.97957.3789−6.4539819GLY143CA−16.20536.619−6.5102820GLY143C−16.76646.5699−7.9246821GLY143O−17.25175.5321−8.3758822ASN144N−16.80157.7865−8.5793823ASN144CA−17.37437.914−9.9166824ASN144C−16.28267.8175−10.9978825ASN144O−15.08737.9838−10.7567826ASN144CB−18.10959.2584−10.0685827ASN144CG−19.28719.3093−9.1396828ASN144OD1−19.342110.171−8.2779829ASN144ND2−20.24548.3803−9.3069830TRP145N−16.7757.5382−12.2662831TRP145CA−15.92317.6557−13.4515832TRP145C−16.19069.0373−14.058833TRP145O−17.3119.5466−14.0413834TRP145CB−15.94756.4578−14.4157835TRP145CG−14.75515.6159−14.0635836TRP145CD1−14.60174.8703−12.9577837TRP145CD2−13.50015.4609−14.88838TRP145NE1−13.42974.2851−12.9715839TRP145CE2−12.74494.6195−14.0844840TRP145CE3−13.05135.9493−16.1065841TRP145CZ2−11.45954.2199−14.4501842TRP145CZ3−11.76775.5395−16.4885843TRP145CH2−10.98424.7093−15.6732844VAL146N−15.09439.6111−14.6657845VAL146CA−15.132310.9329−15.288846VAL146C−14.403910.7866−16.6377847VAL146O−13.348110.1608−16.7543848VAL146CB−14.506212.0252−14.4016849VAL146CG1−14.562713.3836−15.1259850VAL146CG2−15.293312.1222−13.0812851PRO147N−15.040711.4243−17.688852PRO147CA−14.442111.5445−19.0197853PRO147C−13.761112.9212−19.0753854PRO147O−14.257413.9182−18.5488855PRO147CB−15.713511.6846−19.8787856PRO147CG−16.829612.2116−18.9477857PRO147CD−16.353912.0027−17.496858VAL148N−12.584912.9549−19.7972859VAL148CA−11.851414.1932−20.0352860VAL148C−11.465614.2299−21.5245861VAL148O−11.024913.2515−22.1259862VAL148CB−10.571314.2143−19.1768863VAL148CG1−9.897715.597−19.2662864VAL148CG2−10.92213.9061−17.7098865VAL149N−11.633615.4826−22.0884866VAL149CA−11.310715.8132−23.4772867VAL149C−10.041616.689−23.4257868VAL149O−9.86317.5286−22.5332869VAL149CB−12.466616.541−24.1919870VAL149CG1−12.067916.8561−25.6467871VAL149CG2−13.717615.6425−24.1975872ILE150N−9.158416.5193−24.4747873ILE150CA−7.839717.1654−24.4977874ILE150C−7.370817.3781−25.9591875ILE150O−7.772816.6718−26.8855876ILE150CB−6.826816.3699−23.645877ILE150CG1−6.735914.8871−24.0676878ILE150CG2−5.438417.0398−23.6387879ILE150CD1−6.036914.7232−25.4318880ASP151N−6.456218.4073−26.1257881ASP151CA−5.766718.6717−27.3943882ASP151C−4.347318.0589−27.3541883ASP151O−3.801817.6815−26.3105884ASP151CB−5.656220.196−27.5904885ASP151CG−4.828820.8034−26.4927886ASP151OD1−3.584320.8953−26.6713887ASP151OD2−5.424121.2042−25.4574888ASP152N−3.691318.0528−28.5621889ASP152CA−2.424717.3595−28.815890ASP152C−1.228618.3059−28.9933891ASP152O−0.147617.9427−29.4503892ASP152CB−2.507516.1388−29.7539893ASP152CG−3.153716.4648−31.0697894ASP152OD1−2.471116.2908−32.1139895ASP152OD2−4.341316.8882−31.068896ARG153N−1.418119.5454−28.4233897ARG153CA−0.312420.46−28.1713898ARG153C0.26920.0286−26.8111899ARG153O−0.441919.9335−25.8052900ARG153CB−0.826721.9081−28.0912901ARG153CG−1.410322.3167−29.457902ARG153CD−2.917822.6007−29.3184903ARG153NE−3.115523.7076−28.3995904ARG153CZ−4.257423.8944−27.8041905ARG153NH1−5.265423.1038−28.0233906ARG153NH2−4.395924.8896−26.9796907LEU154N1.604519.6786−26.8477908LEU154CA2.341519.1173−25.7092909LEU154C3.541820.0371−25.3873910LEU154O3.99320.806−26.2439911LEU154CB2.814917.6876−26.038912LEU154CG1.690416.8972−26.7388913LEU154CD12.211315.5079−27.1503914LEU154CD20.479116.7385−25.7994915PRO155N4.131719.919−24.1374916PRO155CA5.257220.7795−23.7535917PRO155C6.586220.1545−24.2212918PRO155O7.09219.1556−23.7017919PRO155CB5.171320.6814−22.217920PRO155CG4.315319.4413−21.8727921PRO155CD3.597218.9944−23.1615922LEU162N9.103617.1652−22.7622923LEU162CA9.565317.3634−21.3825924LEU162C8.945316.3509−20.3944925LEU162O9.373816.2255−19.2479926LEU162CB9.171818.7986−20.9763927LEU162CG9.565919.7972−22.085928LEU162CD18.946921.1771−21.7988929LEU162CD211.098619.9205−22.171930VAL163N7.805915.7359−20.8548931VAL163CA6.900114.9282−20.0167932VAL163C6.859213.4935−20.5742933VAL163O7.629113.1371−21.4753934VAL163CB5.535415.6534−20.0225935VAL163CG14.440514.9111−20.8157936VAL163CG25.072315.9333−18.5813937PHE164N5.991912.5981−19.9705938PHE164CA6.059411.1646−20.2933939PHE164C5.691410.9875−21.7803940PHE164O4.858111.6769−22.3624941PHE164CB5.03310.3666−19.4641942PHE164CG5.416910.3322−17.9883943PHE164CD14.502510.7562−17.0208944PHE164CD26.67799.8748−17.5988945PHE164CE14.858510.7499−15.6698946PHE164CE27.03919.8751−16.2491947PHE164CZ6.131810.3218−15.2852948VAL165N6.39039.9741−22.4123949VAL165CA6.33539.7874−23.8582950VAL165C6.80568.3647−24.1952951VAL165O7.42177.6684−23.3901952VAL165CB7.205210.8184−24.6081953VAL165CG16.545812.2098−24.5778954VAL165CG28.611910.8981−23.9844955SER166N6.47857.9386−25.4751956SER166CA7.13286.7639−26.0454957SER166C6.8386.5724−27.5437958SER166O5.6866.5221−27.96959SER166CB6.76835.4809−25.2727960SER166OG7.70744.4486−25.5853961PHE173N2.24618.4031−28.877962PHE173CA1.33149.4965−28.6476963PHE173C0.3369.3901−27.514964PHE173O−0.497510.2913−27.372965PHE173CB0.685810.0229−29.9456966PHE173CG1.726710.7609−30.7817967PHE173CD11.829310.5041−32.1511968PHE173CD22.579711.6915−30.1812969PHE173CE12.820211.1379−32.9053970PHE173CE23.561412.3352−30.9387971PHE173CZ3.686512.0519−32.3009972TRP174N−0.24648.1445−27.29973TRP174CA−1.38328.0441−26.3625974TRP174C−0.96958.3698−24.9116975TRP174O−1.76298.8377−24.0928976TRP174CB−2.06156.6656−26.4833977TRP174CG−1.2515.612−25.7898978TRP174CD1−0.00535.2237−26.1002979TRP174CD2−1.69454.7987−24.6045980TRP174NE10.38064.2861−25.2719981TRP174CE2−0.59193.9966−24.3848982TRP174CE3−2.8474.736−23.8226983TRP174CZ2−0.56793.042−23.3686984TRP174CZ3−2.82113.7981−22.7832985TRP174CH2−1.71462.9625−22.5695986GLY175N0.3198.0074−24.5881987GLY175CA0.85488.0482−23.229988GLY175C0.9249.5013−22.7453989GLY175O0.47449.8591−21.6563990ALA176N1.552710.3575−23.6355991ALA176CA1.816211.7463−23.2667992ALA176C0.477812.4832−23.1036993ALA176O0.308713.3923−22.2917994ALA176CB2.608112.4016−24.4134995LEU177N−0.486212.0977−24.0175996LEU177CA−1.807212.7043−24.039997LEU177C−2.602612.2801−22.7889998LEU177O−3.364513.0632−22.2149999LEU177CB−2.559112.1878−25.28111000LEU177CG−2.182413.0175−26.52421001LEU177CD1−2.850312.4028−27.76891002LEU177CD2−2.665814.4711−26.35571003LEU178N−2.444510.9664−22.38841004LEU178CA−3.113210.4544−21.19061005LEU178C−2.525111.1643−19.95131006LEU178O−3.23411.5138−19.00341007LEU178CB−2.91778.9296−21.08911008LEU178CG−3.85638.3476−20.01231009LEU178CD1−5.32648.6533−20.35961010LEU178CD2−3.66376.822−19.93321011GLU179N−1.152411.3234−19.95721012GLU179CA−0.447511.9849−18.85421013GLU179C−0.930613.4538−18.78131014GLU179O−1.21713.995−17.70921015GLU179CB1.060311.9436−19.15761016GLU179CG1.83612.3442−17.89031017GLU179CD2.705613.5265−18.19761018GLU179OE13.950613.3429−18.22971019GLU179OE22.148414.6392−18.3991020LYS180N−1.061114.1019−20.00011021LYS180CA−1.529415.4849−20.0581022LYS180C−2.986315.5584−19.55961023LYS180O−3.406216.527−18.91951024LYS180CB−1.486615.9011−21.54161025LYS180CG−1.921717.3697−21.70581026LYS180CD−1.715717.8037−23.16931027LYS180CE−2.08619.2905−23.3261028LYS180NZ−3.451919.4078−23.85661029ALA181N−3.823614.534−19.95891030ALA181CA−5.22714.5397−19.56331031ALA181C−5.350414.3395−18.03771032ALA181O−6.272614.8376−17.38821033ALA181CB−5.914213.3553−20.26851034TYR182N−4.396813.5147−17.46741035TYR182CA−4.337813.3084−16.0141036TYR182C−3.91114.6397−15.36041037TYR182O−4.428615.0613−14.32331038TYR182CB−3.242812.2534−15.76041039TYR182CG−3.767211.0667−14.95341040TYR182CD1−2.882610.3532−14.14011041TYR182CD2−5.110210.6836−15.01691042TYR182CE1−3.33039.249−13.41011043TYR182CE2−5.56169.5844−14.28111044TYR182CZ−4.66818.8552−13.49231045TYR182OH−5.10837.7388−12.7921046ALA183N−2.908415.3364−16.01581047ALA183CA−2.498316.6457−15.52381048ALA183C−3.690117.6177−15.58661049ALA183O−3.864318.4841−14.72641050ALA183CB−1.38417.1672−16.44691051LYS184N−4.508717.4934−16.69771052LYS184CA−5.61118.422−16.91431053LYS184C−6.667918.2596−15.80711054LYS184O−7.277619.2443−15.3831055LYS184CB−6.229418.0837−18.28321056LYS184CG−7.20119.2001−18.70661057LYS184CD−7.641418.9677−20.16331058LYS184CE−8.736119.9852−20.53241059LYS184NZ−10.041919.4944−20.06941060LEU185N−6.976216.9651−15.42031061LEU185CA−7.975516.7511−14.37011062LEU185C−7.420217.1729−12.9971063LEU185O−8.165617.635−12.13121064LEU185CB−8.353515.2591−14.38171065LEU185CG−9.88715.1102−14.42441066LEU185CD1−10.485115.9782−15.54881067LEU185CD2−10.240813.6361−14.68841068SER186N−6.069616.9426−12.77481069SER186CA−5.496117.2909−11.47171070SER186C−5.399218.8264−11.36621071SER186O−5.529419.4181−10.2961072SER186CB−4.091816.6661−11.34421073SER186OG−3.214517.1663−12.35771074GLY187N−5.022319.4634−12.53241075GLY187CA−5.265220.8786−12.75561076GLY187C−4.085721.5354−13.45971077GLY187O−4.225822.4645−14.25111078SER188N−2.865821.077−13.01291079SER188CA−1.588221.562−13.51211080SER188C−0.652520.3481−13.55191081SER188O−0.769719.4057−12.76661082SER188CB−0.996722.6529−12.60051083SER188OG−1.884823.7722−12.55761084TYR189N0.430920.4751−14.41031085TYR189CA1.39419.3635−14.53451086TYR189C2.102819.1407−13.18751087TYR189O2.556418.0528−12.84231088TYR189CB2.420519.6809−15.63921089TYR189CG1.735919.639−17.00261090TYR189CD11.696620.7877−17.79581091TYR189CD21.143918.4599−17.46311092TYR189CE10.969720.7938−18.98821093TYR189CE20.443418.4535−18.67261094TYR189CZ0.337219.627−19.42381095TYR189OH−0.395819.6344−20.60381096GLU190N2.235320.2856−12.42711097GLU190CA2.916520.2945−11.13711098GLU190C2.088819.4928−10.11681099GLU190O2.611718.9198−9.16141100GLU190CB2.957621.7516−10.6421101GLU190CG3.884921.8584−9.4171102GLU190CD5.042222.7653−9.72011103GLU190OE15.882522.393−10.58261104GLU190OE25.117323.8523−9.08821105ASP191N0.719819.4753−10.32091106ASP191CA−0.172418.7469−9.42371107ASP191C−0.245617.2321−9.71981108ASP191O−1.127316.5148−9.2431109ASP191CB−1.598819.335−9.4551110ASP191CG−1.604320.8365−9.51471111ASP191OD1−2.498321.3884−10.20951112ASP191OD2−0.715921.4698−8.88271113LEU192N0.81916.7221−10.43651114LEU192CA1.180215.3111−10.42411115LEU192C2.364515.0764−9.45781116LEU192O2.605113.967−8.97561117LEU192CB1.60614.9339−11.85841118LEU192CG0.643315.546−12.8991119LEU192CD11.159115.2637−14.32221120LEU192CD2−0.773114.9614−12.73671121GLN193N3.222516.1521−9.29841122GLN193CA4.487416.0024−8.58361123GLN193C4.184715.9215−7.08881124GLN193O3.701616.8552−6.45311125GLN193CB5.424517.2036−8.82851126GLN193CG5.125317.9062−10.1681127GLN193CD6.007419.112−10.32151128GLN193OE16.584919.3114−11.37721129GLN193NE26.12619.9311−9.26121130SER194N4.458414.6824−6.54041131SER194CA4.140414.3758−5.15981132SER194C2.86613.5587−4.96661133SER194O2.522213.2064−3.83811134SER194CB4.356715.493−4.11721135SER194OG3.137716.2063−3.88641136GLY195N2.17613.2208−6.11411137GLY195CA1.135812.206−6.06581138GLY195C1.788210.822−6.09211139GLY195O2.887310.6093−6.60651140GLU199N−2.51216.1465−5.88061141GLU199CA−3.57737.0891−6.22521142GLU199C−3.85666.9376−7.73031143GLU199O−4.99936.8618−8.18121144GLU199CB−3.0468.5117−5.97941145GLU199CG−2.87628.7261−4.46541146GLU199CD−1.83419.7648−4.16541147GLU199OE1−1.6310.6852−5.00241148GLU199OE2−1.20589.6511−3.08091149ALA200N−2.72136.902−8.52781150ALA200CA−2.8426.7555−9.96051151ALA200C−3.455.3988−10.30971152ALA200O−4.32985.2754−11.16331153ALA200CB−1.43576.8497−10.58051154LEU201N−2.9224.3129−9.6351155LEU201CA−3.37512.957−9.94271156LEU201C−4.90752.8846−9.75471157LEU201O−5.61292.2233−10.52461158LEU201CB−2.73452.0008−8.91791159LEU201CG−2.26960.7033−9.60831160LEU201CD1−1.7303−0.2762−8.54911161LEU201CD2−3.43830.0413−10.36251162VAL202N−5.41273.5437−8.64551163VAL202CA−6.84973.6253−8.41771164VAL202C−7.50734.5069−9.48621165VAL202O−8.49474.0924−10.10741166VAL202CB−7.12394.2445−7.03231167VAL202CG1−8.64144.274−6.76491168VAL202CG2−6.43843.4126−5.93241169ASP203N−6.95765.7508−9.71911170ASP203CA−7.6626.72−10.5681171ASP203C−7.76436.2123−12.02671172ASP203O−8.64956.6136−12.78971173ASP203CB−6.93128.0729−10.50741174ASP203CG−7.51828.8924−9.39461175ASP203OD1−7.18338.6159−8.21171176ASP203OD2−8.30929.8239−9.70071177PHE204N−6.77455.3288−12.41811178PHE204CA−6.77874.6718−13.72091179PHE204C−7.50393.3039−13.71731180PHE204O−7.43012.5569−14.69621181PHE204CB−5.32334.4568−14.18331182PHE204CG−4.79065.6489−14.97551183PHE204CD1−5.636.3842−15.81751184PHE204CD2−3.44316.0012−14.85991185PHE204CE1−5.11167.4353−16.57871186PHE204CE2−2.92477.0537−15.6191187PHE204CZ−3.75737.7662−16.48581188THR205N−8.30162.9986−12.631189THR205CA−8.9521.6829−12.55541190THR205C−10.27051.7051−11.76271191THR205O−11.2951.18−12.19621192THR205CB−7.98410.6757−11.89911193THR205OG1−6.75870.6175−12.63421194THR205CG2−8.6165−0.7291−11.86761195GLY206N−10.1752.1806−10.46971196GLY206CA−11.33242.192−9.58851197GLY206C−11.54940.908−8.79171198GLY206O−12.52360.7578−8.05661199GLY207N−10.5234−0.0067−8.90161200GLY207CA−10.3755−1.0644−7.92251201GLY207C−9.6759−0.488−6.69081202GLY207O−9.31880.6865−6.62081203VAL208N−9.4719−1.4096−5.67791204VAL208CA−8.7137−1.0176−4.48421205VAL208C−7.2252−1.2657−4.75911206VAL208O−6.8341−2.3528−5.19161207VAL208CB−9.1628−1.8−3.23431208VAL208CG1−8.4598−1.2244−1.99011209VAL208CG2−10.6865−1.6664−3.05261210ASN220N0.5391−14.53115.74821211ASN220CA−0.345−15.05974.71141212ASN220C−0.1301−14.41883.32481213ASN220O−0.8992−14.59512.37611214ASN220CB−1.8072−14.82715.14251215ASN220CG−2.0916−13.35535.26081216ASN220OD1−2.825−12.81374.45121217ASN220ND2−1.5115−12.68916.27531218LEU221N1.0815−13.77133.16521219LEU221CA1.2715−12.81642.05711220LEU221C1.2799−13.56070.70461221LEU221O0.9346−13.036−0.35351222LEU221CB2.6218−12.10042.2591223LEU221CG2.9041−11.04581.16781224LEU221CD13.4846−11.7071−0.09661225LEU221CD21.6457−10.22370.82871226TRP222N1.7467−14.86060.77291227TRP222CA1.8026−15.7229−0.40881228TRP222C0.3893−16.1528−0.83821229TRP222O0.1312−16.4911−1.99751230TRP222CB2.6551−16.9633−0.08951231TRP222CG3.514−17.3207−1.2691232TRP222CD13.9296−18.551−1.60561233TRP222CD24.0798−16.3703−2.29061234TRP222NE14.6819−18.4953−2.67681235TRP222CE24.8057−17.2219−3.10231236TRP222CE34.0008−14.9958−2.51131237TRP222CZ25.5389−16.7516−4.19111238TRP222CZ34.7089−14.5196−3.62151239TRP222CH25.4654−15.3749−4.43571240ASP223N−0.5353−16.27920.18871241ASP223CA−1.9239−16.5685−0.14321242ASP223C−2.5885−15.3166−0.72891243ASP223O−3.4409−15.4233−1.61131244ASP223CB−2.6696−16.90751.16231245ASP223CG−1.9071−17.92061.96611246ASP223OD1−2.0616−19.13831.68311247ASP223OD2−1.1616−17.49992.89071248ILE224N−2.193−14.0971−0.20591249ILE224CA−2.7525−12.8492−0.7441250ILE224C−2.3698−12.7895−2.23841251ILE224O−3.2148−12.5541−3.10621252ILE224CB−1.9614−11.7006−0.081253ILE224CG1−2.0125−11.75541.46071254ILE224CG2−2.415−10.3245−0.60731255ILE224CD1−3.3687−11.24431.98051256LEU225N−1.0318−13.0064−2.53711257LEU225CA−0.5436−12.7541−3.90121258LEU225C−1.2766−13.7007−4.87951259LEU225O−1.6357−13.3264−5.99931260LEU225CB0.9715−13.0185−3.92131261LEU225CG1.7156−11.6713−3.85611262LEU225CD11.4854−10.9979−2.48971263LEU225CD23.2213−11.907−4.06491264ILE226N−1.4518−15.0023−4.44561265ILE226CA−2.0745−15.9965−5.31711266ILE226C−3.5714−15.6726−5.51671267ILE226O−4.1698−15.9481−6.55871268ILE226CB−1.8899−17.3793−4.6621269ILE226CG1−0.3862−17.718−4.63641270ILE226CG2−2.642−18.4549−5.47021271ILE226CD1−0.1398−18.9911−3.80531272GLU227N−4.2228−15.1961−4.3881273GLU227CA−5.6282−14.8244−4.4431274GLU227C−5.8203−13.5496−5.28251275GLU227O−6.8718−13.3538−5.89441276GLU227CB−6.0543−14.5149−2.99471277GLU227CG−6.7645−15.73−2.36591278GLU227CD−5.8178−16.8723−2.13161279GLU227OE1−5.5349−17.1663−0.93951280GLU227OE2−5.3604−17.486−3.13291281ALA228N−4.7777−12.6483−5.25211282ALA228CA−4.776−11.455−6.09041283ALA228C−4.5622−11.8767−7.55981284ALA228O−5.1727−11.3474−8.49191285ALA228CB−3.5912−10.5744−5.65251286THR229N−3.6251−12.867−7.79221287THR229CA−3.3162−13.2583−9.17091288THR229C−4.5689−13.8572−9.82181289THR229O−4.9097−13.5481−10.96461290THR229CB−2.119−14.2272−9.23761291THR229OG1−2.3184−15.3492−8.37561292THR229CG2−0.825−13.4907−8.84291293TYR230N−5.2918−14.763−9.06621294TYR230CA−6.4583−15.4248−9.65471295TYR230C−7.7072−14.5029−9.75591296TYR230O−8.7572−14.8875−10.27481297TYR230CB−6.8168−16.6984−8.85491298TYR230CG−7.4666−16.426−7.49411299TYR230CD1−6.9898−17.0901−6.36091300TYR230CD2−8.5379−15.5367−7.36281301TYR230CE1−7.6126−16.9041−5.12371302TYR230CE2−9.1241−15.2992−6.1181303TYR230CZ−8.6664−15.9953−4.99731304TYR230OH−9.2605−15.7837−3.75951305ASN231N−7.5398−13.2328−9.24111306ASN231CA−8.4707−12.1217−9.46281307ASN231C−8.1441−11.3886−10.78441308ASN231O−8.9255−10.5879−11.30151309ASN231CB−8.3969−11.1441−8.27511310ASN231CG−9.4706−11.4856−7.28131311ASN231OD1−9.169−11.7934−6.14021312ASN231ND2−10.7455−11.4325−7.70861313ARG232N−6.8621−11.5676−11.26621314ARG232CA−6.3853−10.8097−12.40641315ARG232C−6.0159−9.4036−11.95611316ARG232O−6.1526−8.4293−12.69581317ARG232CB−7.3543−10.8028−13.60661318ARG232CG−7.3407−12.1783−14.29611319ARG232CD−8.3543−12.1759−15.45511320ARG232NE−8.1377−13.349−16.28131321ARG232CZ−7.7623−13.2361−17.52251322ARG232NH1−7.5672−14.3083−18.23081323ARG232NH2−7.5763−12.0707−18.06911324THR233N−5.4344−9.3387−10.70421325THR233CA−5.0346−8.0619−10.12871326THR233C−3.7566−7.5873−10.82891327THR233O−2.8805−8.3575−11.22351328THR233CB−4.8108−8.1256−8.60481329THR233OG1−3.7279−9.0059−8.29171330THR233CG2−6.0987−8.5817−7.89341331LEU234N−3.6383−6.2111−10.91291332LEU234CA−2.4212−5.6082−11.44451333LEU234C−1.4991−5.4025−10.23431334LEU234O−1.7828−4.5966−9.34611335LEU234CB−2.7335−4.2456−12.09271336LEU234CG−3.805−4.3977−13.18991337LEU234CD1−4.1814−3.0033−13.72371338LEU234CD2−3.261−5.2597−14.34511339ILE235N−0.4064−6.2504−10.19311340ILE235CA0.6017−6.192−9.13791341ILE235C1.7908−5.3356−9.61451342ILE235O2.2008−5.3498−10.7791343ILE235CB1.1155−7.6203−8.86081344ILE235CG1−0.0599−8.5572−8.51861345ILE235CG22.1354−7.6114−7.70541346ILE235CD10.4306−10.0168−8.46761347GLY236N2.42−4.6484−8.5921348GLY236CA3.6097−3.8503−8.81631349GLY236C4.4661−3.8751−7.5561350GLY236O4.0494−3.4215−6.48641351CYS237N5.5388−4.1763−7.14461352CYS237CA6.8369−4.8386−7.19511353CYS237C7.4475−4.8061−5.80551354CYS237O7.484−3.758−5.16531355CYS237CB6.5137−6.2914−7.6051356CYS237SG7.8892−6.9754−8.57471357VAL250N18.7837−1.06−3.87571358VAL250CA18.7728−1.6614−5.19681359VAL250C18.1563−0.7936−6.27551360VAL250O17.57990.2563−6.01411361VAL250CB20.2071−2.0544−5.61351362VAL250CG121.0983−0.8042−5.74591363VAL250CG220.1899−2.8323−6.94361364GLU251N18.3669−0.2148−7.32331365GLU251CA17.76650.993−7.89511366GLU251C16.2170.9991−7.94331367GLU251O15.5217−0.0022−8.131368GLU251CB18.35631.2753−9.2921369GLU251CG17.76930.3208−10.35341370GLU251CD18.039−1.1153−10.00411371GLU251OE117.0546−1.8468−9.71591372GLU251OE219.2333−1.5165−10.01811373GLY252N15.67342.2759−7.91181374GLY252CA14.25062.4954−7.69521375GLY252C13.35422.3126−8.92321376GLY252O12.45923.1102−9.19651377HIS253N13.53721.1273−9.61141378HIS253CA12.5660.6781−10.61781379HIS253C11.4865−0.1559−9.89571380HIS253O11.7404−0.8619−8.91631381HIS253CB13.2764−0.2088−11.65941382HIS253CG12.3129−0.6933−12.70511383HIS253ND111.73760.1248−13.55631384HIS253CD211.9466−1.9771−12.88171385HIS253CE110.9773−0.5897−14.32441386HIS253NE211.0523−1.7983−13.99311387ALA254N10.2237−0.0612−10.46411388ALA254CA9.1262−0.9262−10.04651389ALA254C8.9691−2.0231−11.10581390ALA254O8.8789−1.772−12.30481391ALA254CB7.8177−0.1351−9.87151392TYR255N8.9631−3.2945−10.57991393TYR255CA8.7409−4.4746−11.40811394TYR255C7.2757−4.8968−11.16621395TYR255O6.6574−4.578−10.14621396TYR255CB9.7104−5.6038−11.01171397TYR255CG11.1349−5.06−11.03721398TYR255CD111.6245−4.3411−9.94331399TYR255CD211.9459−5.2746−12.15451400TYR255CE112.9031−3.7807−9.99231401TYR255CE213.2324−4.731−12.19461402TYR255CZ13.7027−3.9676−11.12251403TYR255OH14.9665−3.3926−11.18061404THR256N6.7032−5.6869−12.14631405THR256CA5.4017−6.3105−11.89271406THR256C5.62−7.7682−11.46661407THR256O6.704−8.3411−11.57911408THR256CB4.5349−6.2455−13.16741409THR256OG13.2634−6.8578−12.9331410THR256CG25.2393−6.9521−14.34261411LEU257N4.4903−8.3735−10.9561412LEU257CA4.4405−9.7992−10.62411413LEU257C3.3352−10.3492−11.52981414LEU257O2.3071−9.7058−11.74311415LEU257CB4.0719−9.97−9.13841416LEU257CG4.449−11.3805−8.64711417LEU257CD14.42−11.398−7.10791418LEU257CD23.4361−12.4093−9.18291419THR258N3.5695−11.6026−12.06571420THR258CA2.6236−12.1467−13.0481421THR258C2.3296−13.6435−12.84721422THR258O1.6948−14.3054−13.67561423THR258CB3.0645−11.8512−14.49621424THR258OG14.2124−12.6355−14.82711425THR258CG23.3907−10.3551−14.66991426GLY259N2.8063−14.1799−11.67791427GLY259CA2.6734−15.5863−11.35131428GLY259C3.3389−15.854−10.01011429GLY259O4.304−15.195−9.61621430ILE260N2.7885−16.9007−9.30741431ILE260CA3.2533−17.2739−7.9771432ILE260C2.7416−18.6858−7.72681433ILE260O1.5506−18.9623−7.85421434ILE260CB2.6632−16.3002−6.9341435ILE260CG13.4254−14.9634−6.97431436ILE260CG22.7358−16.8838−5.50891437ILE260CD12.5596−13.8638−6.33651438LEU272N7.6295−20.2065−5.22671439LEU272CA8.2148−19.4305−6.30341440LEU272C7.2661−18.2935−6.69791441LEU272O6.0434−18.3602−6.56991442LEU272CB8.5888−20.3099−7.50791443LEU272CG9.6054−21.3716−7.05041444LEU272CD110.0036−22.2306−8.26041445LEU272CD210.8588−20.691−6.46811446VAL273N7.917−17.2324−7.29391447VAL273CA7.2358−16.0184−7.7221448VAL273C7.8155−15.6174−9.08911449VAL273O9.0208−15.6826−9.34781450VAL273CB7.4182−14.8938−6.68321451VAL273CG16.7413−13.5994−7.17331452VAL273CG28.9137−14.6382−6.41131453LYS274N6.862−15.1989−10.00271454LYS274CA7.2322−14.6979−11.31181455LYS274C7.1133−13.1683−11.28351456LYS274O6.0599−12.5689−11.5051457LYS274CB6.3006−15.2891−12.38511458LYS274CG7.1148−15.4963−13.67551459LYS274CD6.3157−14.9771−14.88441460LYS274CE7.0223−13.7456−15.48261461LYS274NZ6.9113−12.6067−14.56071462LEU275N8.3118−12.5555−10.95851463LEU275CA8.497−11.1202−11.14251464LEU275C8.6314−10.9281−12.66621465LEU275O9.183−11.7675−13.37711466LEU275CB9.7478−10.6015−10.40531467LEU275CG9.6452−10.8357−8.88281468LEU275CD18.3234−10.2695−8.32931469LEU275CD29.7528−12.336−8.54751470ARG276N8.1358−9.74−13.15431471ARG276CA8.3421−9.324−14.53311472ARG276C8.8047−7.8552−14.52951473ARG276O8.2417−6.9722−13.88361474ARG276CB7.0444−9.48−15.34551475ARG276CG7.3659−9.3005−16.83961476ARG276CD6.062−9.0872−17.62871477ARG276NE6.3734−8.4218−18.88051478ARG276CZ6.0922−7.1638−19.06031479ARG276NH15.5179−6.4638−18.12631480ARG276NH26.3917−6.5985−20.1921481ASN277N9.9012−7.6359−15.35081482ASN277CA10.3016−6.298−15.7831483ASN277C9.4382−6.0331−17.02681484ASN277O9.4635−6.8197−17.97931485ASN277CB11.7935−6.306−16.16911486ASN277CG12.2067−4.9569−16.68441487ASN277OD112.677−4.8526−17.80511488ASN277ND212.0325−3.9052−15.86381489PRO278N8.6591−4.8959−17.0421490PRO278CA7.7978−4.6224−18.19281491PRO278C8.507−3.9806−19.39441492PRO278O7.9611−3.9586−20.49961493PRO278CB6.8446−3.5703−17.59031494PRO278CG7.4474−3.0849−16.25231495PRO278CD8.643−3.9952−15.91061496TRP279N9.717−3.3532−19.13381497TRP279CA10.5405−2.8672−20.25191498TRP279C11.0577−4.086−21.02451499TRP279O11.2024−4.0388−22.24641500TRP279CB11.702−2.029−19.68781501TRP279CG11.2019−0.672−19.27771502TRP279CD19.9671−0.1697−19.44391503TRP279CD212.01850.3875−18.58881504TRP279NE19.90441.0428−18.95161505TRP279CE211.09551.4041−18.43211506TRP279CE313.340.4865−18.15591507TRP279CZ211.432.606−17.80891508TRP279CZ313.68771.6954−17.54071509TRP279CH212.75182.7248−17.36121510GLY280N11.4159−5.1697−20.2511511GLY280CA11.5344−6.5276−20.76061512GLY280C12.812−7.2554−20.34321513GLY280O12.8765−8.4845−20.33531514LYS281N13.8767−6.4156−20.07981515LYS281CA15.2169−6.9354−19.79431516LYS281C15.1794−7.7785−18.50041517LYS281O14.3936−7.5659−17.57491518LYS281CB16.1986−5.759−19.63331519LYS281CG16.1224−4.8304−20.86191520LYS281CD14.9288−3.865−20.72231521LYS281CE14.4474−3.4386−22.12151522LYS281NZ13.5748−2.261−22.01131523VAL282N16.105−8.809−18.48221524VAL282CA16.0955−9.8258−17.43381525VAL282C17.2642−9.5236−16.47791526VAL282O17.0861−9.1222−15.32831527VAL282CB16.1673−11.2512−18.01511528VAL282CG116.201−12.2832−16.87121529VAL282CG214.9202−11.505−18.88291530GLU283N18.5204−9.7489−17.02971531GLU283CA19.7139−9.1512−16.43351532GLU283C19.9054−9.6078−14.97431533GLU283O20.3128−8.8728−14.07621534GLU283CB19.699−7.6156−16.5541535GLU283CG20.3208−7.2119−17.90311536GLU283CD19.2366−6.8709−18.88271537GLU283OE118.5651−7.8146−19.37871538GLU283OE219.0641−5.6559−19.16711539TRP284N19.711−10.9701−14.80761540TRP284CA19.6307−11.5979−13.49021541TRP284C20.32−12.9674−13.57041542TRP284O20.2535−13.6941−14.56331543TRP284CB18.1888−11.6225−12.94141544TRP284CG17.91−12.8763−12.16491545TRP284CD118.4357−13.2441−10.98581546TRP284CD216.9741−13.97−12.59761547TRP284NE117.9623−14.4142−10.63351548TRP284CE217.0959−14.874−11.55961549TRP284CE316.1459−14.1717−13.70011550TRP284CZ216.3837−16.0723−11.54881551TRP284CZ315.4287−15.3733−13.69771552TRP284CH215.5441−16.2952−12.64711553LYS285N21.0285−13.3247−12.43661554LYS285CA21.9632−14.4504−12.4451555LYS285C21.1662−15.7417−12.22121556LYS285O21.0234−16.2627−11.11621557LYS285CB22.9755−14.2461−11.30191558LYS285CG23.8492−13.0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2−7.1854−21.73431860LEU339CG−16.5204−7.0397−22.50141861LEU339CD1−17.3118−5.8347−21.95841862LEU339CD2−16.225−6.8256−23.99721863LYS346N−13.6587−13.5204−9.08451864LYS346CA−14.0349−12.0861−9.05981865LYS346C−14.753−11.721−7.72481866LYS346O−15.5288−12.4919−7.15791867LYS346CB−14.8475−11.6676−10.29941868LYS346CG−13.8718−11.3517−11.44871869LYS346CD−14.6375−11.2352−12.77991870LYS346CE−13.64−10.9981−13.93041871LYS346NZ−12.7546−12.1634−14.07381872TRP347N−14.4396−10.4473−7.21031873TRP347CA−15.068−9.9379−5.95431874TRP347C−16.5675−9.6711−6.17151875TRP347O−17.1483−9.8828−7.24031876TRP347CB−14.3837−8.615−5.55511877TRP347CG−12.8879−8.754−5.56761878TRP347CD1−12.0729−8.5668−6.61771879TRP347CD2−12.022−9.1279−4.39491880TRP347NE1−10.8288−8.7702−6.26051881TRP347CE2−10.7582−9.1−4.95441882TRP347CE3−12.2542−9.4434−3.05681883TRP347CZ2−9.6178−9.3836−4.20331884TRP347CZ3−11.1126−9.7177−2.29361885TRP347CH2−9.8263−9.6862−2.85191886THR348N−17.2311−9.2235−5.04831887THR348CA−18.4309−8.3907−5.1391888THR348C−18.0481−7.0196−4.53071889THR348O−17.0874−6.9101−3.76781890THR348CB−19.6085−9.0273−4.37721891THR348OG1−19.828−10.3558−4.85851892THR348CG2−20.8846−8.1903−4.58591893TYR349N−18.8199−5.9544−4.96771894TYR349CA−18.4601−4.5467−4.72331895TYR349C−19.692−3.7778−4.22561896TYR349O−20.7812−3.8985−4.78551897TYR349CB−17.8732−3.949−6.01871898TYR349CG−17.9756−2.4268−6.0451899TYR349CD1−17.1307−1.644−5.25361900TYR349CD2−18.9219−1.8173−6.87271901TYR349CE1−17.1971−0.2503−5.33151902TYR349CE2−18.9874−0.4242−6.95111903TYR349CZ−18.10570.3584−6.20151904TYR349OH−18.13161.7425−6.32461905THR350N−19.4222−2.8685−3.20061906THR350CA−20.5275−2.1332−2.58861907THR350C−20.0198−0.8124−1.98081908THR350O−19.9987−0.6341−0.75511909THR350CB−21.212−3.0091−1.51681910THR350OG1−21.5712−4.2818−2.06171911THR350CG2−22.4841−2.3087−1.00231912GLY354N−20.21949.61251.81711913GLY354CA−20.580310.32573.02071914GLY354C−19.873711.64423.22191915GLY354O−18.939612.00262.49731916ARG355N−20.333712.35954.24271917ARG355CA−19.791513.66054.60681918ARG355C−19.481613.72086.10581919ARG355O−20.033812.9636.91761920ARG355CB−20.762614.78574.20221921ARG355CG−21.008114.74912.68241922ARG355CD−22.06715.80292.30931923ARG355NE−22.391215.68550.89871924ARG355CZ−23.60715.43870.50381925ARG355NH1−23.857415.3402−0.76791926ARG355NH2−24.577315.28851.35721927TRP356N−18.60314.65576.44081928TRP356CA−18.212414.94797.80441929TRP356C−18.415916.45597.85181930TRP356O−17.836917.19177.03651931TRP356CB−16.762714.51468.08451932TRP356CG−16.772613.05418.43471933TRP356CD1−17.539612.44999.35591934TRP356CD2−15.916211.98847.80611935TRP356NE1−17.280411.16619.38541936TRP356CE2−16.325310.85598.48491937TRP356CE3−14.938411.96756.81251938TRP356CZ2−15.77519.60278.21621939TRP356CZ3−14.382110.71266.53581940TRP356CH2−14.78869.55897.22271941GLU357N−19.320316.90448.71931942GLU357CA−19.60618.33528.861943GLU357C−19.484218.827710.29641944GLU357O−19.986218.195511.23421945GLU357CB−20.987518.68428.27671946GLU357CG−20.945618.53216.74431947GLU357CD−21.657717.2776.33041948GLU357OE1−22.709717.39285.64731949GLU357OE2−21.166916.17156.67981950LYS358N−18.812319.963810.44561951LYS358CA−18.578420.59611.73541952LYS358C−19.882520.900712.45891953LYS358O−20.766421.558411.89811954LYS358CB−17.764721.891811.5641955LYS358CG−16.345621.548111.07631956LYS358CD−15.538522.847210.90121957LYS358CE−14.120122.505210.40971958LYS358NZ−13.348323.744810.24171959ARG359N−19.98820.429513.70381960ARG359CA−21.187820.650414.49951961ARG359C−22.341319.68814.25991962ARG359O−23.452519.915314.72341963ARG359CB−21.640322.123814.53931964ARG359CG−20.470723.007315.00971965ARG359CD−20.776224.477614.67351966ARG359NE−19.5725.265814.84681967ARG359CZ−18.896625.697713.81991968ARG359NH1−17.822526.403914.01371969ARG359NH2−19.278125.43512.60431970SER360N−22.431619.068113.21681971SER360CA−23.204317.840313.09151972SER360C−22.374216.631112.66991973SER360O−22.080315.768813.48941974SER360CB−24.355718.046312.08931975SER360OG−23.82318.346610.79571976THR361N−21.969515.982611.8931977THR361CA−21.46214.653811.55051978THR361C−19.942214.474111.63961979THR361O−19.429413.425111.2721980THR361CB−21.967614.212810.16371981THR361OG1−21.477815.11089.16531982THR361CG2−23.507414.204110.14591983ALA362N−19.227615.500212.09971984ALA362CA−17.776315.432112.23951985ALA362C−17.436714.873613.62511986ALA362O−16.945615.591314.50841987ALA362CB−17.202816.849512.04771988GLY363N−17.721713.584613.80231989GLY363CA−17.498112.910615.07321990GLY363C−16.050712.789315.48861991GLY363O−15.695313.082116.62391992GLY364N−15.245512.250814.58191993GLY364CA−13.827412.101414.81311994GLY364C−13.291311.076615.79321995GLY364O−13.341611.27317.00341996GLN365N−12.887210.574616.25871997GLN365CA−12.21779.309516.53231998GLN365C−12.70768.480117.72231999GLN365O−13.26369.003218.68252000GLN365CB−10.69299.490516.63522001GLN365CG−10.1349.954115.2782002GLN365CD−8.686410.314715.43932003GLN365OE1−8.324811.467715.27232004GLN365NE2−7.84019.321815.76692005ARG366N−12.5617.128317.60942006ARG366CA−13.14456.472318.7812007ARG366C−12.88967.116320.15872008ARG366O−13.77387.095821.03152009ARG366CB−12.77424.975918.76682010ARG366CG−11.24724.788218.84462011ARG366CD−10.80114.825620.31752012ARG366NE−9.38985.154720.38692013ARG366CZ−8.57864.47921.14782014ARG366NH1−9.00323.484821.87132015ARG366NH2−7.32114.805321.18642016PHE373N−17.855411.311917.88722017PHE373CA−17.75169.881317.62622018PHE373C−19.03089.262517.05052019PHE373O−19.25688.075917.21722020PHE373CB−16.94519.038918.63572021PHE373CG−16.3247.847617.91252022PHE373CD1−15.62378.03616.71752023PHE373CD2−16.46286.563218.44452024PHE373CE1−15.0996.936116.03412025PHE373CE2−15.93545.463217.76312026PHE373CZ−15.26115.649116.55352027TRP374N−19.99058.973117.92072028TRP374CA−21.25958.369917.52522029TRP374C−22.02459.186116.49262030TRP374O−23.03688.725315.97132031TRP374CB−22.11898.219218.79482032TRP374CG−22.33289.565119.42492033TRP374CD1−21.628910.106320.43122034TRP374CD2−23.388410.562119.03132035TRP374NE1−22.103311.293620.71792036TRP374CE2−23.146111.594819.91672037TRP374CE3−24.402910.599918.07592038TRP374CZ2−23.921712.753619.91762039TRP374CZ3−25.188211.75918.0722040TRP374CH2−24.956912.806718.97572041LYS375N−21.527510.385616.19422042LYS375CA−22.167511.278915.23532043LYS375C−21.720811.176513.76152044LYS375O−22.319511.817312.89342045LYS375CB−21.794512.714915.64622046LYS375CG−22.766413.260816.70552047LYS375CD−22.524314.775316.8432048LYS375CE−23.331715.334518.02822049LYS375NZ−22.494615.329319.23642050ASN376N−20.674210.398613.47722051ASN376CA−20.217810.206812.09182052ASN376C−21.2719.336111.40822053ASN376O−22.02538.626812.08022054ASN376CB−18.82839.54412.03052055ASN376CG−17.849410.310612.87352056ASN376OD1−17.033611.046912.34382057ASN376ND2−17.920610.13514.20542058PRO377N−21.33619.367110.06612059PRO377CA−22.32918.52439.3882060PRO377C−22.0577.06239.80792061PRO377O−20.97486.756810.33282062PRO377CB−21.95858.7347.90662063PRO377CG−20.84639.80827.84032064PRO377CD−20.444610.19149.27992065GLN378N−23.02856.17379.60472066GLN378CA−22.8714.76589.98882067GLN378C−23.31973.81358.8882068GLN378O−24.21844.12788.11392069GLN378CB−23.57064.441911.3212070GLN378CG−22.64724.838112.48942071GLN378CD−23.05596.142813.11452072GLN378OE1−24.0356.751812.71442073GLN378NE2−22.28626.588314.12342074PHE379N−22.69242.64238.82492075PHE379CA−23.01171.6637.78842076PHE379C−23.10470.2518.33622077PHE379O−22.77740.0079.48982078PHE379CB−21.9641.7516.66272079PHE379CG−21.92463.17516.1182080PHE379CD1−20.99714.08866.62542081PHE379CD2−22.81683.56825.11722082PHE379CE1−20.97845.40266.15072083PHE379CE2−22.78494.87674.62842084PHE379CZ−21.87075.7965.14992085LEU380N−23.5633−0.67347.50162086LEU380CA−23.6919−2.05427.92692087LEU380C−23.0878−3.02276.93762088LEU380O−23.4873−3.05865.76962089LEU380CB−25.1596−2.41458.22422090LEU380CG−25.2241−3.76038.97222091LEU380CD1−24.5552−3.624110.35322092LEU380CD2−26.6953−4.17569.15522093LEU381N−22.1021−3.7827.39872094LEU381CA−21.5005−4.8086.57332095LEU381C−21.4522−6.07657.40472096LEU381O−21.1832−6.03018.60372097LEU381CB−20.0819−4.40196.13192098LEU381CG−20.1459−3.14525.24332099LEU381CD1−18.7168−2.67074.92222100LEU381CD2−20.8874−3.46413.9312101LEU399N−11.2797−5.88733.02562102LEU399CA−11.0656−5.28621.73182103LEU399C−11.7767−3.94231.80862104LEU399O−13.0068−3.88111.77492105LEU399CB−11.6931−6.16790.63622106LEU399CG−10.8241−6.0892−0.63292107LEU399CD1−9.5321−6.9031−0.42882108LEU399CD2−11.6064−6.6564−1.83092109VAL400N−11.7072−3.27322.95342110VAL400CA−12.3614−1.97443.09032111VAL400C−11.4375−0.79412.78352112VAL400O−10.3307−0.68253.3252113VAL400CB−13.1588−1.78824.39682114VAL400CG1−13.8429−0.40744.4122115VAL400CG2−14.2414−2.87954.49622116SER401N−11.90450.0621.87492117SER401CA−11.15541.23831.4892118SER401C−11.9922.47921.71042119SER401O−13.10492.58871.17562120SER401CB−10.66121.13330.03322121SER401OG−11.75980.8699−0.84412122LEU402N−11.48233.38152.54812123LEU402CA−12.14374.64862.85852124LEU402C−11.29895.71782.212125LEU402O−10.13255.85082.5512126LEU402CB−12.09954.79624.39432127LEU402CG−12.41026.23614.84922128LEU402CD1−13.86566.59974.50072129LEU402CD2−12.20116.34446.37172130LEU403N−11.89676.50441.32092131LEU403CA−11.17257.54740.60332132LEU403C−11.77088.93290.85652133LEU403O−12.96649.06961.04852134LEU403CB−11.1177.218−0.90122135LEU403CG−9.85897.8275−1.54952136LEU403CD1−9.56627.0971−2.8732137LEU403CD2−10.09379.3191−1.84932138GLN404N−10.92079.94710.94152139GLN404CA−11.385511.30511.17582140GLN404C−11.345312.1121−0.12692141GLN404O−10.373512.0411−0.89452142GLN404CB−10.511212.01112.2282143GLN404CG−9.018311.87661.8642144GLN404CD−8.193712.98992.44572145GLN404OE1−8.722713.99382.89452146GLN404NE2−6.861312.81042.44632147LYS405N−12.422212.8483−0.38782148LYS405CA−12.51813.6554−1.59742149LYS405C−11.79814.9875−1.42562150LYS405O−11.507415.4054−0.29972151LYS405CB−13.98513.8319−2.02912152LYS405CG−14.453712.5454−2.73382153LYS405CD−15.940312.677−3.1122154LYS405CE−16.41711.381−3.79392155LYS405NZ−16.186111.4678−5.2432156PRO406N−11.503315.637−2.5522157PRO406CA−10.813716.9279−2.57222158PRO406C−11.723618.0933−2.17862159PRO406O−12.946618.0443−2.38182160PRO406CB−10.406617.0777−4.05022161PRO406CG−11.161815.9903−4.84622162PRO406CD−11.842515.0486−3.8332163ARG407N−11.100419.1521−1.65062164ARG407CA−11.813220.3502−1.21462165ARG407C−10.962521.6281−1.31542166ARG407O−10.474122.1387−0.30262167ARG407CB−12.298620.11950.22852168ARG407CG−13.7520.61430.36052169ARG407CD−14.579719.54141.08862170ARG407NE−14.80618.41950.19552171ARG407CZ−14.129617.31390.31732172ARG407NH1−13.219717.17651.23662173ARG407NH2−14.369116.33−0.49712174HIS408N−11.011422.2129−2.23752175HIS408CA−9.824923.0234−2.55782176HIS408C−9.169923.7237−1.36492177HIS408O−8.39124.3342−1.99582178HIS408CB−10.16323.9089−3.77712179HIS408CG−9.601223.2388−4.99572180HIS408ND1−9.911222.0018−5.30882181HIS408CD2−8.746223.8055−5.86842182HIS408CE1−9.270621.7087−6.39522183HIS408NE2−8.587222.6943−6.76672184ARG409N−8.553623.516−0.93032185ARG409CA−7.322323.5699−0.14012186ARG409C−6.098322.8344−0.72382187ARG409O−4.984423.3773−0.72352188ARG409CB−7.631122.98411.25062189ARG409CG−6.510223.3632.23562190ARG409CD−6.783922.70013.59742191ARG409NE−5.68222.98364.49842192ARG409CZ−4.904822.03284.93032193AR0409NH1−5.086720.79644.56912194ARG409NH2−3.928522.32515.73722195CYS410N−6.30521.6096−1.2112196CYS410CA−5.229120.8006−1.78782197CYS410C−4.743721.339−3.13872198CYS410O−5.473421.2892−4.13332199CYS410CB−5.727619.3545−1.97332200CYS410SG−6.139918.6764−0.33842201ARG411N−3.504721.8272−3.17592202ARG411CA−2.921722.3682−4.4082203ARG411C−2.370621.2465−5.28912204ARG411O−2.33421.365−6.5212205ARG411CB−1.810523.366−4.03512206ARG411CG−2.284424.798−4.35472207ARG411CD−3.309925.296−3.3152208ARG411NE−4.46324.4149−3.26932209ARG411CZ−5.544524.6704−3.9462210ARG411NH1−5.642425.7334−4.6892211ARG411NH2−6.544123.8429−3.87912212LYS412N−2.003420.155−4.68182213LYS412CA−1.347718.9915−5.27312214LYS412C−2.270317.8226−5.63212215LYS412O−1.867716.889−6.32852216LYS412CB0.134718.7248−4.96052217LYS412CG0.979419.5622−5.93872218LYS412CD2.476619.3549−5.65052219LYS412CE3.303320.2142−6.62462220LYS412NZ4.620619.5956−6.82992221ILE419N−8.62329.53586.84542222ILE419CA−8.79539.30938.28322223ILE419C−8.84937.82398.57022224ILE419O−9.11317.03247.67082225ILE419CB−10.08319.99688.79352226ILE419CG1−11.36079.37618.18492227ILE419CG2−10.043311.51678.54292228ILE419CD1−11.41389.56476.65592229GLY420N−9.48977.2829.29862230GLY420CA−9.56575.89539.71812231GLY420C−11.02255.53339.94432232GLY420O−11.87656.38629.97512233PHE421N−11.29364.293210.08382234PHE421CA−12.66843.844510.33892235PHE421C−12.63732.637611.26912236PHE421O−11.91661.745511.0912237PHE421CB−13.51363.62099.06762238PHE421CG−12.87622.59078.14032239PHE421CD1−12.98241.22658.42572240PHE421CD2−12.18853.0146.99992241PHE421CE1−12.38160.28637.58462242PHE421CE2−11.60422.07356.14762243PHE421CZ−11.69550.71086.4442244TYR422N−13.34192.627312.24942245TYR422CA−13.40141.474213.15522246TYR422C−14.6730.725312.89632247TYR422O−15.70051.358812.66032248TYR422CB−13.42251.89614.63862249TYR422CG−12.59883.153314.92250TYR422CD1−13.1334.411614.61032251TYR422CD2−11.31393.047715.43822252TYR422CE1−12.39585.565714.88722253TYR422CE2−10.57734.201815.71752254TYR422CZ−11.12095.460615.4492255TYR422OH−10.39326.608115.74042256LEU423N−14.6042−0.556212.8742257LEU423CA−15.8179−1.323612.67192258LEU423C−16.1001−2.212813.89682259LEU423O−15.2057−2.895114.35032260LEU423CB−15.6594−2.22211.43022261LEU423CG−17.0006−2.361210.68312262LEU423CD1−16.8092−3.2789.46062263LEU423CD2−18.0756−2.966311.60552264TYR424N−17.3096−2.139714.42032265TYR424CA−17.6813−3.038515.52762266TYR424C−18.874−3.852915.01552267TYR424O−19.8515−3.268714.7372268TYR424CB−18.0616−2.193916.76022269TYR424CG−17.0839−1.030716.9132270TYR424CD1−17.37660.203616.32662271TYR424CD2−15.8977−1.196317.63282272TYR424CE1−16.48861.273816.46372273TYR424CE2−15.0125−0.124317.77562274TYR424CZ−15.31481.11517.20482275TYR424OH−14.44982.189817.37592276SER18N−29.21912.2461−11.11182277SER18CA−28.569611.9899−12.38552278SER18C−27.258511.2838−12.15552279SER18O−27.002610.8074−11.06082280SER18CB−28.311213.3475−13.06962281SER18OG−27.424214.143−12.27712282ARG19N−26.411211.2244−13.20152283ARG19CA−25.103710.6172−13.01822284ARG19C−24.050211.6653−12.79382285ARG19O−24.337612.8489−12.87062286ARG19CB−24.72959.8228−14.28242287ARG19CG−25.41638.4463−14.24552288ARG19CD−24.92167.6042−15.43522289ARG19NE−25.3846.2371−15.28152290ARG19CZ−26.18875.697−16.15042291ARG19NH1−26.58064.4696−15.97892292ARG19NH2−26.60776.3625−17.18672293ARG20N−22.810311.2111−12.52082294ARG20CA−21.710712.1564−12.42282295ARG20C−21.298312.5578−13.81222296ARG20O−20.931413.6994−14.0382297ARG20CB−20.542911.5144−11.64142298ARG20CG−19.636610.6438−12.53642299ARG20CD−20.40789.4148−13.05142300ARG20NE−20.19898.3033−12.14362301ARG20CZ−19.60597.215−12.54012302ARG20NH1−19.42996.2426−11.69582303ARG20NH2−19.18397.0845−13.7642304ALA21N−21.382911.5916−14.74812305ALA21CA−21.078811.8988−16.13282306ALA21C−22.071612.8888−16.67032307ALA21O−21.751813.5873−17.61792308ALA21CB−21.179810.5933−16.94242309SER22N−23.269512.9551−16.05222310SER22CA−24.261113.9176−16.50332311SER22C−23.682215.3066−16.53162312SER22O−23.638915.8754−17.60942313SER22CB−25.520513.8526−15.61852314SER22OG−26.065812.5317−15.65982315PRO23N−23.218315.8635−15.39022316PRO23CA−22.57117.1607−15.41632317PRO23C−21.263517.0693−16.15222318PRO23O−20.814718.0635−16.69912319PRO23CB−22.275217.4063−13.92342320PRO23CG−22.611916.1125−13.15082321PRO23CD−23.332215.1657−14.12832322GLN24N−20.660315.8634−16.17752323GLN24CA−19.43315.6899−16.93652324GLN24C−19.658616.0109−18.38892325GLN24O−18.729616.44−19.05342326GLN24CB−18.982214.2236−16.79992327GLN24CG−17.867514.121−15.74162328GLN24CD−18.119312.964−14.81762329GLN24OE1−18.180413.1523−13.61392330GLN24NE2−18.268511.7477−15.37152331GLN25N−20.901415.8186−18.87692332GLN25CA−21.190816.151−20.2622333GLN25C−20.954317.6163−20.51612334GLN25O−20.118117.9192−21.3522335GLN25CB−22.644315.7729−20.60352336GLN25CG−22.780414.244−20.73352337GLN25CD−23.939313.7462−19.91722338GLN25OE1−23.804212.7627−19.20842339GLN25NE2−25.099214.4217−20.00822340PRO26N−21.650918.5378−19.81062341PRO26CA−21.379319.9524−19.97562342PRO26C−19.935520.2396−19.67692343PRO26O−19.393521.1953−20.20822344PRO26CB−22.251520.5874−18.87422345PRO26CG−23.072219.4644−18.20352346PRO26CD−22.661718.1328−18.85882347GLN27N−19.312819.3876−18.8382348GLN27CA−17.886819.5279−18.60922349GLN27C−17.149718.9872−19.80492350GLN27O−16.450917.9906−19.70812351GLN27CB−17.508218.7621−17.32472352GLN27CG−18.259219.3411−16.112353GLN27CD−17.727520.7009−15.75922354GLN27OE1−17.118820.8629−14.71452355GLN27NE2−17.958621.6981−16.63222356TYR84N−1.97564.3397−31.01252357TYR84CA−1.44833.2203−30.25232358TYR84C−1.51532.0149−31.14582359TYR84O−2.28021.0942−30.9042360TYR84CB−2.24193.0353−28.93892361TYR84CG−1.60372.0109−27.99742362TYR84CD1−1.88012.0732−26.62882363TYR84CD2−0.75621.0093−28.48022364TYR84CE1−1.36091.1086−25.76082365TYR84CE2−0.22460.0498−27.61572366TYR84CZ−0.53260.0971−26.25442367TYR84OH−0.0121−0.8597−25.39252368PHE85N−0.68332.0379−32.20392369PHE85CA−0.66050.8992−33.10282370PHE85C−0.1316−0.33−32.42122371PHE85O0.8114−0.2439−31.65112372PHE85CB0.05021.1935−34.44062373PHE85CG1.44611.7991−34.28592374PHE85CD12.27481.8618−35.4092375PHE85CD21.9082.2915−33.06162376PHE85CE13.54692.4316−35.31732377PHE85CE23.17872.8638−32.96662378PHE85CZ4.00372.923−34.09212379ALA86N−0.7817−1.4764−32.70762380ALA86CA−0.3826−2.7278−32.08192381ALA86C−0.6149−2.7582−30.5962382ALA86O−0.7942−1.7247−29.97152383ALA86CB1.0752−3.1029−32.41172384LYS87N−0.6034−3.9801−30.0272385LYS87CA−0.671−4.0869−28.57992386LYS87C0.6572−3.6505−28.03582387LYS87O0.704−2.8939−27.07992388LYS87CB−0.8607−5.5636−28.18612389LYS87CG−2.293−6.028−28.50392390LYS87CD−2.4255−7.5123−28.11682391LYS87CE−3.8179−8.0329−28.51672392LYS87NZ−3.8456−9.4955−28.3742393ALA88N1.7382−4.1405−28.67782394ALA88CA3.0742−3.7712−28.24532395ALA88C3.3688−4.3514−26.89172396ALA88O3.2386−3.6715−25.88672397ALA88CB3.2728−2.2438−28.29092398LYS89N3.7874−5.6324−26.8842399LYS89CA4.1863−6.2498−25.63032400LYS89C5.3313−5.4685−25.05152401LYS89O5.3175−5.1573−23.87152402LYS89CB4.6519−7.6849−25.9422403LYS89CG5.1193−8.3944−24.65732404LYS89CD5.6894−9.7741−25.03292405LYS89CE6.2991−10.443−23.78812406LYS89NZ7.6382−10.9439−24.12732407ARG90N6.3187−5.1388−25.90652408ARG90CA7.4058−4.306−25.432409ARG90C6.9689−2.8753−25.28332410ARG90O5.8984−2.4983−25.73292411ARG90CB8.6259−4.4176−26.36272412ARG90CG9.4794−5.6297−25.9442413ARG90CD10.1419−5.3493−24.5822414ARG90NE10.8092−6.5457−24.10212415ARG90CZ12.0871−6.5553−23.8542416ARG90NH112.8194−5.4944−24.02812417ARG90NH212.6424−7.6489−23.42332418LEU91N7.8313−2.0836−24.62162419LEU91CA7.4596−0.7216−24.28322420LEU91C8.7270.0817−24.29322421LEU91O9.7323−0.4426−23.83792422LEU91CB7.0082−0.8199−22.81062423LEU91CG6.23270.4149−22.31252424LEU91CD15.8230.1552−20.8512425LEU91CD27.11281.6773−22.3532426HIS113N−6.4353−10.6403−22.92622427HIS113CA−7.4859−10.5959−21.92522428HIS113C−7.1733−9.4431−21.00382429HIS113O−6.1033−8.8622−21.10012430HIS113CB−7.5034−11.9014−21.10552431HIS113CG−8.8663−12.5314−21.13772432HIS113ND1−9.3863−13.1002−20.07462433HIS113CD2−9.6792−12.5864−22.21072434HIS113CE1−10.5551−13.5481−20.40692435HIS113NE2−10.784−13.2858−21.61272436GLN114N−8.1139−9.1025−20.09952437GLN114CA−7.8701−8.0172−19.15922438GLN114C−7.7198−6.6951−19.86152439GLN114O−6.6331−6.1411−19.91722440GLN114CB−6.6818−8.3332−18.22862441GLN114CG−7.1246−9.3496−17.162442GLN114CD−5.9534−9.736−16.30462443GLN114OE1−5.5315−10.8802−16.33372444GLN114NE2−5.4155−8.779−15.52742445ASP115N−8.8445−6.1879−20.40182446ASP115CA−8.7767−4.9376−21.13822447ASP115C−9.0522−3.7711−20.22842448ASP115O−10.0728−3.1112−20.34352449ASP115CB−9.7649−5.0067−22.31862450ASP115CG−9.3264−6.0903−23.26112451ASP115OD1−9.6038−7.2836−22.9642452ASP115OD2−8.7116−5.7495−24.30652453THR128N−5.20989.6232−37.9652454THR128CA−5.57849.5422−39.36652455THR128C−6.986910.0144−39.59512456THR128O−7.171811.0374−40.23442457THR128CB−5.35158.1277−39.93582458THR128OG1−6.13297.164−39.22532459THR128CG2−3.867.7591−39.82862460GLU129N−7.98529.2654−39.08642461GLU129CA−9.35839.6237−39.40222462GLU129C−9.939810.5726−38.39482463GLU129O−9.685510.4263−37.20972464GLU129CB−10.26658.3833−39.51282465GLU129CG−9.50437.2117−40.16222466GLU129CD−9.126.2042−39.1162467GLU129OE1−9.31154.9868−39.37682468GLU129OE2−8.63616.6199−38.02872469LYS130N−10.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ARG268NH118.4688−32.2949−2.63122780ARG268NH217.8589−30.3395−3.55052781PRO269N10.5143−27.9991−1.50132782PRO269CA9.5866−27.0874−2.13752783PRO269C10.0311−25.6531−2.09582784PRO269O10.8327−25.2856−1.25172785PRO269CB8.2973−27.2861−1.31842786PRO269CG8.542−28.4617−0.34642787PRO269CD10.0307−28.8527−0.4372788GLU270N9.5086−24.8419−3.03672789GLU270CA9.9543−23.4606−3.09692790GLU270C8.8187−22.5727−3.51482791GLU270O8.3378−22.6901−4.63022792GLU270CB11.1188−23.3223−4.09782793GLU270CG12.3248−24.1506−3.61562794GLU270CD12.7022−25.1816−4.63952795GLU270OE113.9116−25.2456−4.98332796GLU270OE211.7987−25.9258−5.10712797TYR271N8.3949−21.6792−2.59812798TYR271CA7.3008−20.7762−2.91812799TYR271C7.7473−19.7883−3.95782800TYR271O8.189−18.6948−3.65122801TYR271CB6.8694−20.0676−1.62132802TYR271CG5.9845−21.0113−0.81582803TYR271CD16.4001−21.45330.44242804TYR271CD24.7584−21.4337−1.33612805TYR271CE15.5858−22.31441.18232806TYR271CE23.9429−22.2927−0.59582807TYR271CZ4.3602−22.73750.66132808TYR271OH3.5561−23.60221.39352809SER289N17.1658−18.93−8.25382810SER289CA18.3422−19.0254−7.4082811SER289C18.4464−20.4103−6.83272812SER289O17.4627−21.1337−6.81672813SER289CB18.2595−17.9919−6.26892814SER289OG18.1295−16.678−6.81912815ASP290N19.658−20.783−6.37112816ASP290CA19.8478−22.1303−5.85612817ASP290C19.5131−23.1241−6.9362818ASP290O18.616−23.9338−6.77052819ASP290CB19.0064−22.3277−4.5772820ASP290CG19.3558−23.6273−3.91132821ASP290OD118.5143−24.5634−3.96582822ASP290OD220.4676−23.7127−3.32492823SER291N20.2476−23.0372−8.06322824SER291CA19.905−23.8381−9.2292825SER291C18.8119−23.1601−10.00252826SER291O17.6878−23.0693−9.53492827SER291CB19.5625−25.3123−8.93142828SER291OG20.6095−25.9035−8.15782829SER292N19.1722−22.6698−11.20392830SER292CA18.195−21.9554−12.00512831SER292C17.2106−22.9225−12.58742832SER292O16.0318−22.843−12.28282833SER292CB18.9224−21.2063−13.13562834SER292OG19.8986−20.3309−12.56582835SER293N17.7122−23.8448−13.43012836SER293CA16.8111−24.8207−14.00922837SER293C16.5572−25.9456−13.04392838SER293O16.5136−27.0961−13.45082839SER293CB17.3567−25.3185−15.36252840SER293OG18.6298−25.9437−15.17572841LYS294N16.3779−25.616−11.74792842LYS294CA16.0064−26.6686−10.81912843LYS294C14.5559−27.0301−10.98872844LYS294O13.9326−27.5604−10.08342845LYS294CB16.4338−26.4047−9.36132846LYS294CG15.808−25.1066−8.82362847LYS294CD16.0614−25.0134−7.30862848LYS294CE15.7922−23.576−6.83012849LYS294NZ16.1052−23.4562−5.39932850TRP295N14.0282−26.7341−12.19312851TRP295CA12.6821−27.1618−12.52192852TRP295C12.7817−28.5945−12.972853TRP295O12.2805−28.9619−14.02052854TRP295CB12.1207−26.2722−13.65242855TRP295CG12.5239−24.8384−13.45862856TRP295CD113.5624−24.2088−14.03012857TRP295CD211.8326−23.8389−12.57222858TRP295NE113.6136−22.9662−13.61742859TRP295CE212.6152−22.7131−12.74652860TRP295CE310.7148−23.8688−11.74052861TRP295CZ212.3445−21.5215−12.07382862TRP295CZ310.4389−22.6751−11.06372863TRP295CH211.2391−21.5329−11.21452864GLU296N13.4637−29.41−12.14252865GLU296CA13.6738−30.7962−12.51232866GLU296C13.6457−31.6147−11.25562867GLU296O12.8159−32.5018−11.13722868GLU296CB15.0491−30.9523−13.19042869GLU296CG15.1797−29.9717−14.37152870GLU296CD16.5672−30.0476−14.93832871GLU296OE116.7082−30.5508−16.08452872GLU296OE217.5189−29.5994−14.24452873LEU297N14.5557−31.3013−10.31022874LEU297CA14.5168−31.9927−9.03312875LEU297C13.2502−31.6135−8.32462876LEU297O13.0172−30.4371−8.09882877LEU297CB15.7497−31.6707−8.16442878LEU297CG15.873−30.1595−7.88682879LEU297CD116.8503−29.9272−6.72012880LEU297CD216.3974−29.4396−9.14262881LEU298N12.4169−32.625−8.00922882LEU298CA11.1004−32.3273−7.46832883LEU298C10.3621−31.3525−8.34612884LEU298O9.5067−30.6151−7.88442885LEU298CB11.1792−31.8834−5.99442886LEU298CG10.8252−33.0547−5.0572887LEU298CD19.3623−33.4862−5.26952888LEU298CD211.7632−34.252−5.30432889SER299N10.7258−31.3566−9.64232890SER299CA10.0974−30.4369−10.56922891SER299C9.9685−31.1633−11.88082892SER299O10.6607−30.836−12.83132893SER299CB10.9557−29.1635−10.70412894SER299OG11.1545−28.5444−9.43192895LEU307N6.3956−23.5665−16.48282896LEU307CA7.1931−22.4652−15.97352897LEU307C8.1083−21.8538−16.99292898LEU307O8.3851−22.46−18.01572899LEU307CB7.9177−22.8665−14.67522900LEU307CG8.3099−21.5991−13.89392901LEU307CD17.8988−21.7401−12.4172902LEU307CD29.832−21.3982−13.99432903ARG308N8.5562−20.6166−16.69432904ARG308CA9.3351−19.8688−17.66842905ARG308C8.5562−19.7259−18.94762906ARG308O9.1174−19.6909−20.03092907ARG308CB10.7482−20.4495−17.87962908ARG308CG11.4783−20.6338−16.53252909ARG308CD11.4961−19.3378−15.69372910ARG308NE11.6184−18.1599−16.5342911ARG308CZ12.7781−17.7454−16.95422912ARG308NH113.8705−18.3784−16.64212913ARG308NH212.8453−16.6798−17.69532914LYS309N7.2213−19.6664−18.78362915LYS309CA6.3417−19.6382−19.93662916LYS309C6.2972−18.2635−20.53742917LYS309O6.5442−18.1125−21.7232918LYS309CB4.9278−20.0332−19.46242919LYS309CG4.57−19.2689−18.17172920LYS309CD3.2022−19.7298−17.63962921LYS309CE3.0136−19.1806−16.21372922LYS309NZ1.7878−19.7429−15.62952923ASP310N5.9687−17.2608−19.70082924ASP310CA5.7973−15.9166−20.22462925ASP310C7.1124−15.3194−20.64242926ASP310O8.1451−15.9616−20.53462927ASP310CB5.1166−15.0146−19.17352928ASP310CG4.1993−15.8056−18.28382929ASP310OD14.64−16.1806−17.16452930ASP310OD23.0342−16.0465−18.69782931ASN311N7.063−14.0653−21.12962932ASN311CA8.2916−13.436−21.5792933ASN311C8.2891−11.9763−21.22192934ASN311O7.4456−11.544−20.45182935ASN311CB8.4266−13.6396−23.09992936ASN311CG8.7356−15.0815−23.38112937ASN311OD17.923−15.7738−23.97132938ASN311ND29.9227−15.549−22.95472939ASP312N9.2508−11.2127−21.78252940ASP312CA9.3773−9.8163−21.39492941ASP312C9.6773−9.7719−19.92272942ASP312O9.0169−9.0665−19.17882943ASP312CB8.0958−9.0254−21.73482944ASP312CG8.4216−7.784−22.51242945ASP312OD18.8258−6.7738−21.87682946ASP312OD28.2557−7.8116−23.76122947GLY313N10.6782−10.5659−19.49782948GLY313CA10.9377−10.6612−18.0742949GLY313C10.2069−11.8465−17.50872950GLY313O9.4537−11.6938−16.56042951SER340N−16.3887−9.2646−18.84952952SER340CA−16.9789−10.5545−18.52982953SER340C−16.0382−11.6865−18.82952954SER340O−16.4224−12.6865−19.41492955SER340CB−18.4188−10.7336−19.05752956SER340OG−18.4344−10.989−20.46452957GLN341N−14.7733−11.4999−18.4092958GLN341CA−13.7872−12.5328−18.65932959GLN341C−13.9973−13.6595−17.69172960GLN341O−13.8658−13.4705−16.49272961GLN341CB−12.3744−11.9426−18.50552962GLN341CG−12.2671−10.6679−19.36352963GLN341CD−10.834−10.3784−19.69452964GLN341OE1−10.5296−10.0819−20.83792965GLN341NE2−9.9401−10.467−18.6932966GLU342N−14.334−14.842−18.24162967GLU342CA−14.5771−15.9907−17.38592968GLU342C−13.3583−16.3002−16.56572969GLU342O−13.4924−16.6687−15.40982970GLU342CB−14.8923−17.2033−18.28052971GLU342CG−16.2407−16.984−18.9912972GLU342CD−16.5529−18.1797−19.84232973GLU342OE1−17.2257−19.1124−19.32782974GLU342OE2−16.1387−18.1828−21.03232975ALA343N−12.1655−16.1326−17.1712976ALA343CA−10.9489−16.4186−16.43252977ALA343C−10.8286−15.5741−15.19582978ALA343O−11.2757−14.4382−15.17812979ALA343CB−9.7128−16.2208−17.32842980ALA344N−10.219−16.1722−14.15342981ALA344CA−10.0489−15.4662−12.89462982ALA344C−11.3061−15.3614−12.07852983ALA344O−12.3777−15.1106−12.60662984ALA344CB−9.3563−14.097−13.03672985GLN345N−11.1378−15.5569−10.7562986GLN345CA−12.2396−15.3412−9.83542987GLN345C−12.542−13.8713−9.75072988GLN345O−11.7928−13.0625−10.27612989GLN345CB−11.831−15.8247−8.42972990GLN345CG−11.2853−17.2639−8.49492991GLN345CD−11.6086−17.9922−7.22262992GLN345OE1−12.3591−18.9535−7.24882993GLN345NE2−11.0403−17.5418−6.08992994MET351N−19.58670.1074−2.86472995MET351CA−18.99171.333−2.36142996MET351C−19.96822.156−1.57092997MET351O−21.17052.0284−1.73952998MET351CB−18.4072.171−3.51262999MET351CG−17.47893.2657−2.95393000MET351SD−17.02984.3543−4.3363001MET351CE−16.0915.592−3.39333002ARG352N−19.41693.0104−0.693003ARG352CA−20.28173.88050.0833004ARG352C−19.77835.2922−0.00363005ARG352O−18.67845.5259−0.47953006ARG352CB−20.31273.43211.55643007ARG352CG−21.07962.10311.68783008ARG352CD−21.1451.70583.1743009ARG352NE−22.41891.06783.45233010ARG352CZ−22.49390.00814.20473011ARG352NH1−23.6545−0.53094.43163012ARG352NH2−21.4306−0.51874.73693013GLU353N−20.60696.2430.46563014GLU353CA−20.17717.62890.42973015GLU353C−20.63518.34011.67123016GLU353O−21.33747.76252.48613017GLU353CB−20.72138.3284−0.83123018GLU353CG−20.0687.729−2.09193019GLU353CD−18.73078.3669−2.33653020GLU353OE1−17.71957.8583−1.78313021GLU353OE2−18.68519.3703−3.0973022SER58N4.516125.4695−12.04483023SER58CA5.885625.2609−11.60813024SER58C6.242626.247−10.53133025SER58O5.504627.1917−10.30033026SER58CB6.866225.352−12.79323027SER58OG6.832826.6638−13.36173028GLY59N7.384426.0176−9.85593029GLY59CA7.729226.9004−8.7583030GLY59C9.217227.0021−8.60043031GLY59O9.870726.0045−8.34063032SER60N9.735428.2375−8.75233033SER60CA11.155628.4693−8.54883034SER60C12.001227.647−9.4793035SER60O12.135628.0169−10.63313036SER60CB11.557328.3065−7.06943037SER60OG12.894428.7744−6.87613038LEU61N12.573426.5358−8.9743039LEU61CA13.370325.6829−9.83883040LEU61C12.474425.0345−10.85293041LEU61O12.854724.9202−12.00663042LEU61CB14.028724.5946−8.97193043LEU61CG15.154325.2173−8.12453044LEU61CD115.681824.1691−7.12783045LEU61CD216.305625.6736−9.04073046LEU62N11.266224.634−10.40833047LEU62CA10.279724.1384−11.35213048LEU62C9.989925.2189−12.35353049LEU62O9.815824.9231−13.52363050LEU62CB8.985923.8371−10.57383051LEU62CG9.18222.6054−9.67163052LEU62CD18.082122.5794−8.59473053LEU62CD29.098521.3253−10.52393054GLN63N9.960926.4803−11.88053055GLN63CA9.774427.5884−12.80053056GLN63C11.001427.8053−13.64483057GLN63O10.904728.4324−14.68723058GLN63CB9.480728.8481−11.96743059GLN63CG8.042128.7587−11.42553060GLN63CD7.732729.9547−10.57383061GLN63OE17.418229.8047−9.40483062GLN63NE27.81731.1633−11.15833063LYS64N12.158827.2732−13.2053064LYS64CA13.348527.3597−14.03523065LYS64C13.380226.1327−14.90533066LYS64O14.318425.3531−14.85283067LYS64CB14.592327.3962−13.1243068LYS64CG14.493128.5556−12.11683069LYS64CD15.239428.156−10.83133070LYS64CE14.860429.1181−9.69123071LYS64NZ15.279428.5352−8.40893072SER167N7.92086.4674−28.3373073SER167CA7.74366.2762−29.76693074SER167C7.20454.9046−30.06483075SER167O6.66534.6971−31.14013076SER167CB9.11726.4355−30.44683077SER167OG10.04585.4869−29.91253078THR168N7.35413.9725−29.10123079THR168CA6.93272.6017−29.33993080THR168C5.49612.4848−29.76883081THR168O4.71033.393−29.55183082THR168CB7.17881.756−28.07153083THR168OG16.91970.3739−28.33443084THR168CG26.27872.2329−26.91433085TYR169N5.16491.3297−30.37953086TYR169CA3.77471.0608−30.70453087TYR169C2.97151.1166−29.43963088TYR169O1.85011.5972−29.44593089TYR169CB3.6924−0.3845−31.22853090TYR169CG3.9609−0.4244−32.72793091TYR169CD15.17910.031−33.23863092TYR169CD22.9836−0.9252−33.59143093TYR169CE15.4261−0.0331−34.61223094TYR169CE23.2344−0.9998−34.96343095TYR169CZ4.4537−0.5472−35.47393096TYR169OH4.6986−0.6064−36.84033097LYS170N3.59390.6215−28.35243098LYS170CA2.91780.5885−27.07153099LYS170C2.48881.9565−26.63293100LYS170O1.42932.063−26.03953101LYS170CB3.92320.0584−26.03433102LYS170CG3.2029−0.8809−25.05163103LYS170CD4.1528−1.1913−23.88213104LYS170CE3.8263−2.5692−23.27943105LYS170NZ4.6894−2.8051−22.11333106ASN171N3.29583.0014−26.90523107ASN171CA2.95314.2881−26.32523108ASN171C3.05165.4378−27.28823109ASN171O3.2756.5589−26.85923110ASN171CB3.77894.5344−25.04683111ASN171CG3.73143.3219−24.16313112ASN171OD14.75082.6909−23.93813113ASN171ND22.53272.9848−23.65663114LEU172N2.88745.1636−28.59763115LEU172CA3.0546.2303−29.57033116LEU172C1.94487.2373−29.45263117LEU172O0.84276.9818−29.87693118LEU172CB3.10055.6355−30.99193119LEU172CG3.97396.524−31.89953120LEU172CD14.15025.8546−33.27383121LEU172CD23.31127.8991−32.09983122GLN367N−11.65847.628420.35373123GLN367CA−11.29928.099321.6783124GLN367C−11.16469.594121.71653125GLN367O−10.699610.127722.71133126GLN367CB−9.97967.435422.11053127GLN367CG−10.02257.142123.62093128GLN367CD−9.02366.07123.94793129GLN367OE1−9.40524.996724.38193130GLN367NE2−7.72556.357223.74193131LEU368N−11.575410.273720.62823132LEU368CA−11.526211.723120.64683133LEU368C−12.593612.215521.58263134LEU368O−13.745312.342121.1993135LEU368CB−11.739612.248619.21573136LEU368CG−10.438712.140918.39763137LEU368CD1−10.686612.67716.97563138LEU368CD2−9.331212.980919.0613139LEU369N−12.177912.48222.83633140LEU369CA−13.13812.872423.85523141LEU369C−13.809214.162323.4843142LEU369O−15.024114.248323.56153143LEU369CB−12.402413.036925.19933144LEU369CG−11.547811.789425.50073145LEU369CD1−10.785311.996726.82213146LEU369CD2−12.444610.541925.61423147GLN370N−13.005415.157823.05913148GLN370CA−13.588916.394222.56613149GLN370C−14.527616.068421.43813150GLN370O−15.609916.626821.36183151GLN370CB−12.420517.262622.05433152GLN370CG−12.917718.389421.12693153GLN370CD−12.766817.955219.6973154GLN370OE1−13.756417.756219.01163155GLN370NE2−11.513617.804919.23213156ASP371N−14.09115.1420.5673157ASP371CA−14.92714.75519.4463158ASP371C−16.165414.021719.88643159ASP371O−16.257213.601421.02883160ASP371CB−14.074613.84518.54743161ASP371CG−13.120414.669317.73453162ASP371OD1−13.376714.834316.51243163ASP371OD2−12.105715.141518.31283164THR372N−17.137113.879518.96323165THR372CA−18.371913.208519.33463166THR372C−18.284711.72719.09633167THR372O−18.599410.968519.99913168THR372CB−19.585313.83418.61633169THR372OG1−20.759113.056918.86793170THR372CG2−19.343313.932317.09943171SER382N−21.7125−7.23876.77743172SER382CA−21.778−8.44167.58953173SER382C−21.0627−9.61066.97683174SER382O−20.601−9.53455.84953175SER382CB−23.2573−8.79627.8323176SER382OG−23.8439−7.82128.69713177VAL383N−20.9902−10.7097.75533178VAL383CA−20.4217−11.93927.23323179VAL383C−20.6916−13.08278.1773180VAL383O−20.5488−12.92239.37763181VAL383CB−18.9717−11.75866.74223182VAL383CG1−18.0495−11.33737.89913183VAL383CG2−18.4529−13.01956.02793184TRP384N−21.1268−14.23697.63383185TRP384CA−21.5699−15.31728.49863186TRP384C−20.5212−16.38448.62193187TRP384O−19.4864−16.29137.98533188TRP384CB−22.9502−15.86668.06793189TRP384CG−22.8699−16.94517.02323190TRP384CD1−22.4297−18.20217.19243191TRP384CD2−23.2752−16.81315.57993192TRP384NE1−22.4732−18.85136.05553193TRP384CE2−22.9321−18.05085.07173194TRP384CE3−23.8559−15.81374.80083195TRP384CZ2−23.0663−18.34523.71523196TRP384CZ3−23.9929−16.13.43793197TRP384CH2−23.5757−17.32632.90193198ARG385N−20.7905−17.40569.45513199ARG385CA−19.783−18.42379.67883200ARG385C−20.499−19.71039.96723201ARG385O−20.8957−19.929711.09983202ARG385CB−19.0048−17.988210.9293203ARG385CG−17.802−18.899911.21653204ARG385CD−17.0898−18.360912.46973205ARG385NE−16.5758−17.029512.2043206ARG385CZ−16.7127−16.06913.07143207ARG385NH1−16.2541−14.885412.79333208ARG385NH2−17.3001−16.271114.21373209PRO386N−20.6675−20.57828.953210PRO386CA−21.3959−21.81319.15583211PRO386C−20.581−22.78379.96123212PRO386O−19.5745−22.416210.5463213PRO386CB−21.4659−22.35027.71453214PRO386CG−20.3189−21.65586.95293215PRO386CD−20.1001−20.3027.64793216GLU387N−21.0369−24.05039.97333217GLU387CA−20.2927−25.061610.69743218GLU387C−19.1297−25.54579.87483219GLU387O−19.0221−26.72819.59033220GLU387CB−21.2503−26.204811.08333221GLU387CG−22.2475−25.697412.14153222GLU387CD−22.8692−26.862412.85543223GLU387OE1−24.1183−27.002912.77513224GLU387OE2−22.1147−27.638113.50143225GLU388N−18.2392−24.60759.4953226GLU388CA−17.0442−25.00768.77123227GLU388C−16.0882−25.70889.70193228GLU388O−16.4578−26.036510.81833229GLU388CB−16.4101−23.75328.13663230GLU388CG−15.4454−24.15377.00373231GLU388CD−14.086−23.56547.25163232GLU388OE1−13.8775−22.3796.88563233GLU388OE2−13.2139−24.28947.80163234GLY389N−14.8465−25.94919.23673235GLY389CA−13.9185−26.739510.02943236GLY389C−13.4262−26.058311.27693237GLY389O−14.1027−25.213611.84113238ARG390N−12.2154−26.465411.70683239ARG390CA−11.6679−25.939612.94583240ARG390C−11.1701−24.534912.74233241ARG390O−9.9756−24.31312.61983242ARG390CB−10.5192−26.876413.37363243ARG390CG−9.9781−26.467514.75673244ARG390CD−10.9625−26.921315.84933245ARG390NE−10.6131−26.286317.10653246ARG390CZ−11.4716−25.541317.743247ARG390NH1−11.1289−24.988818.86573248ARG390NH2−12.6657−25.343317.26353249ARG391N−12.1066−23.568612.71443250ARG391CA−11.675−22.200412.50663251ARG391C−11.4618−21.490313.81493252ARG391O−11.8324−20.335913.95723253ARG391CB−12.6535−21.451111.58523254ARG391CG−12.843−22.218210.26613255ARG391CD−14.3048−22.06989.81653256ARG391NE−15.1209−22.959810.61793257ARG391CZ−16.3317−22.637210.96533258ARG391NH1−17.0163−23.46311.69693259ARG391NH2−16.8663−21.51110.5973260SER392N−10.8434−22.190514.78593261SER392CA−10.515−21.519716.03133262SER392C−9.222−20.773715.84053263SER392O−8.3233−20.857516.66233264SER392CB−10.4051−22.574617.14873265SER392OG−10.2618−21.927818.41493266LEU393N−9.1362−20.047814.70833267LEU393CA−7.9112−19.340814.38033268LEU393C−8.1089−18.717213.02753269LEU393O−7.5096−19.176112.06913270LEU393CB−6.6802−20.277114.42053271LEU393CG−6.7754−21.422713.38973272LEU393CD1−5.3984−22.094513.24323273LEU393CD2−7.8166−22.474213.81663274ARG394N−8.9651−17.6812.90823275ARG394CA−9.2458−17.222111.55673276ARG394C−9.8339−15.845211.38653277ARG394O−10.9908−15.747311.01163278ARG394CB−10.0227−18.256210.71293279ARG394CG−10.3857−19.531311.49733280ARG394CD−9.5337−20.712610.99533281ARG394NE−9.8601−20.99519.61083282ARG394CZ−10.0667−22.21129.19693283ARG394NH1−9.9769−23.225110.00663284ARG394NH2−10.3721−22.41427.94993285PRO395N−9.0548−14.761111.59183286PRO395CA−9.4903−13.446411.15593287PRO395C−9.5917−13.38859.65193288PRO395O−9.9065−14.37919.01153289PRO395CB−8.2908−12.575911.57973290PRO395CG−7.1218−13.520711.92513291PRO395CD−7.7492−14.898812.19343292CYS396N−9.3171−12.20559.06843293CYS396CA−9.4524−12.08767.62773294CYS396C−8.5442−11.04167.04073295CYS396O−7.3374−11.18437.15013296CYS396CB−10.9109−11.9547.14313297CYS396SG−12.0989−11.69048.48913298SER397N−9.1188−10.0026.39943299SER397CA−8.292−9.00795.73163300SER397C−9.2078−8.01295.07123301SER397O−9.3854−8.0573.86383302SER397CB−7.3971−9.70284.6833303SER397OG−6.675−8.73633.91513304VAL398N−9.8078−7.11745.88373305VAL398CA−10.8301−6.2215.36283306VAL398C−10.4519−5.5964.04793307VAL398O−9.4642−4.88413.95783308VAL398CB−11.2403−5.18296.43173309VAL398CG1−12.403−5.69857.29583310VAL398CG2−11.6695−3.83775.81963311ARG413N−3.536117.9222−5.17793312ARG413CA−4.554617.0011−5.66053313ARG413C−4.17515.563−5.43253314ARG413O−4.441514.7133−6.26763315ARG413CB−4.868417.2711−7.14883316ARG413CG−4.84618.782−7.45413317ARG413CD−6.067319.4646−6.81153318ARG413NE−6.568720.4804−7.71883319ARG413CZ−7.58720.2434−8.49453320ARG413NH1−8.006821.1749−9.2983321ARG413NH2−8.189719.0908−8.48293322LYS414N−3.526815.2994−4.28273323LYS414CA−3.09713.9421−4.0063324LYS414C−4.256613.1746−3.43163325LYS414O−4.646113.4592−2.31063326LYS414CB−1.947314.0374−2.9853327LYS414CG−1.253812.6735−2.8213328LYS414CD−0.027612.8477−1.90633329LYS414CE0.636111.4828−1.64843330LYS414NZ1.261910.9927−2.88443331PRO415N−4.824512.1984−4.17293332PRO415CA−5.927811.4283−3.63763333PRO415C−5.430510.5023−2.56513334PRO415O−4.247310.2053−2.53113335PRO415CB−6.369710.5929−4.85483336PRO415CG−5.30510.7827−5.95893337PRO415CD−4.33611.8912−5.49993338LEU416N−6.34210.0587−1.6763339LEU416CA−5.93319.1489−0.61533340LEU416C−7.00399.03220.43233341LEU416O−8.04939.65370.32883342LEU416CB−4.6199.5870.07263343LEU416CG−4.819510.8270.96793344LEU416CD1−3.521911.11251.74523345LEU416CD2−5.188712.05860.12143346LEU417N−6.70438.23121.47233347LEU417CA−7.57948.21242.62863348LEU417C−7.36499.47433.41983349LEU417O−6.30410.07363.34673350LEU417CB−7.20756.98393.48393351LEU417CG−7.74397.11084.92273352LEU417CD1−9.27496.95094.93013353LEU417CD2−7.08856.03975.81213354ALA418N−8.39339.8794.18663355ALA418CA−8.226811.06045.01233356ALA418C−7.999610.65676.43813357ALA418O−7.30511.35187.16183358ALA418CB−9.556711.83555.00523359ARG425N−18.6675−5.180114.90363360ARG425CA−19.6778−6.032814.3053361ARG425C−20.1478−7.063915.29123362ARG425O−19.5831−7.184216.36653363ARG425CB−19.0115−6.806113.15233364ARG425CG−18.7297−5.877711.95773365ARG425CD−17.818−6.627710.97183366ARG425NE−18.051−6.20439.60333367ARG425CZ−18.372−7.06298.67813368ARG425NH1−18.5431−6.64987.45793369ARG425NH2−18.5244−8.32688.9443370MET426N−21.1986−7.812714.89833371MET426CA−21.719−8.85615.7673372MET426C−22.8919−9.49915.08093373MET426O−23.8577−8.810714.79163374MET426CB−22.1868−8.257117.10933375MET426CG−21.173−8.6118.21323376MET426SD−21.2964−7.360219.52483377MET426CE−20.4539−8.288620.8413378ASN427N−22.806−10.821214.81883379ASN427CA−23.905−11.50614.14923380ASN427C−24.0585−11.011212.73653381ASN427O−24.7822−10.055212.50583382ASN427CB−25.2258−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51.67043682PHE467N−19.5915−20.0647−0.81453683PHE467CA−18.6057−19.0773−1.22173684PHE467C−18.4992−17.9348−0.25193685PHE467O−18.7028−16.7913−0.62793686PHE467CB−18.8775−18.6158−2.66653687PHE467CG−18.8007−19.8306−3.58333688PHE467CD1−19.9284−20.6341−3.77113689PHE467CD2−17.6019−20.1412−4.23023690PHE467CE1−19.8486−21.7681−4.58313691PHE467CE2−17.5246−21.272−5.04713692PHE467CZ−18.6458−22.0883−5.21853693ARG468N−18.1687−18.26131.0133694ARG468CA−18.1013−17.20922.00993695ARG468C−17.3189−17.64143.2193696ARG468O−17.2096−18.83093.46383697ARG468CB−19.5391−16.82.36193698ARG468CG−19.9077−15.54071.56293699ARG468CD−21.3668−15.63221.08693700ARG468NE−21.6434−14.4680.26753701ARG468CZ−22.7141−13.75180.44963702ARG468NH1−22.9115−12.7039−0.29363703ARG468NH2−23.5889−14.06411.35993704ASP469N−16.745−16.68343.97613705ASP469CA−15.8373−17.09255.0373706ASP469C−16.05−16.36966.33963707ASP469O−16.7493−15.37126.38623708ASP469CB−14.3729−16.97774.5713709ASP469CG−13.9302−18.20863.83023710ASP469OD1−12.8642−18.76714.1993711ASP469OD2−14.6368−18.63222.87823712LEU470N−15.4321−16.9187.40613713LEU470CA−15.6036−16.37988.74783714LEU470C−14.9378−15.05268.99183715LEU470O−14.3951−14.4358.08943716LEU470CB−17.0618−16.45269.26363717LEU470CG−17.5558−15.10049.82793718LEU470CD1−17.8156−14.10918.68453719LEU470CD2−18.8011−15.219210.72183720TRP471N−15.0438−14.635610.26973721TRP471CA−14.7445−13.270310.65523722TRP471C−13.4505−13.148211.39553723TRP471O−12.402−13.445210.84763724TRP471CB−15.0216−12.17789.60473725TRP471CG−15.8341−11.071610.21053726TRP471CD1−15.4677−9.786810.32723727TRP471CD2−17.2153−11.19110.79693728TRP471NE1−16.4268−9.095310.88913729TRP471CE2−17.4766−9.889611.183730TRP471CE3−18.1224−12.230810.99363731TRP471CZ2−18.6801−9.530211.78623732TRP471CZ3−19.3127−11.888511.6473733TRP471CH2−19.5898−10.567112.02563734LYS472N−13.5592−12.713412.66623735LYS472CA−12.3709−12.528113.48153736LYS472C−11.6523−11.265213.0913737LYS472O−11.6137−10.944211.91433738LYS472CB−11.4541−13.767713.48823739LYS472CG−10.8259−13.954714.88053740LYS472CD−9.2936−13.841414.78553741LYS472CE−8.8943−12.408714.38923742LYS472NZ−7.4446−12.208814.51543743GLN473N−11.084−10.505414.04933744GLN473CA−11.1305−10.922115.44063745GLN473C−12.4414−10.547116.06843746GLN473O−12.6715−9.379316.33953747GLN473CB−9.9771−10.220416.18193748GLN473CG−9.5473−11.069917.39163749GLN473CD−8.0631−11.293917.35493750GLN473OE1−7.6174−12.427517.2893751GLN473NE2−7.2768−10.203517.3983752LEU474N−13.3061−11.551716.30783753LEU474CA−14.5666−11.233316.95323754LEU474C−14.5097−11.449718.4343755LEU474O−13.7945−12.31918.90573756LEU474CB−15.7761−11.999716.38933757LEU474CG−15.5066−13.514416.3583758LEU474CD1−16.8462−14.261616.23723759LEU474CD2−14.6256−13.849615.14153760LYS475N−15.2938−10.636219.16393761LYS475CA−15.3764−10.846720.5943762LYS475C−16.4623−11.853420.84513763LYS475O−17.5127−11.500821.35763764LYS475CB−15.6919−9.507221.28763765LYS475CG−14.3884−8.731321.55143766LYS475CD−14.1716−7.671620.4553767LYS475CE−13.5279−8.313919.21243768LYS475NZ−13.2432−7.266218.22133769LEU476N−16.2048−13.127420.48493770LEU476CA−17.2074−14.136820.77233771LEU476C−17.3598−14.277222.25383772LEU476O−16.3956−14.558922.94613773LEU476CB−16.9055−15.504420.12843774LEU476CG−17.8622−16.613920.62513775LEU476CD1−17.4057−17.214421.96793776LEU476CD2−19.3105−16.105520.74993777SER477N−18.6041−14.071422.71573778SER477CA−18.8438−14.152124.13953779SER477C−18.8661−15.57624.60743780SER477O−19.5043−16.416523.99513781SER477CB−20.1921−13.48424.45273782SER477OG−20.1822−12.168823.89633783GLN478N−18.1605−15.837525.72253784GLN478CA−18.2964−17.138926.34773785GLN478C−19.6603−17.18426.97693786GLN478O−20.2313−18.252727.12213787GLN478CB−17.1909−17.31427.40783788GLN478CG−15.7783−17.144726.80393789GLN478CD−15.6896−17.540125.35583790GLN478OE1−15.394−16.706624.51563791GLN478NE2−15.947−18.824325.05033792LYS479N−20.1891−15.98927.31263793LYS479CA−21.5695−15.900127.75793794LYS479C−22.518−16.300626.66013795LYS479O−22.093−16.681925.58093796LYS479CB−21.9024−14.468428.23083797LYS479CG−21.1271−13.406427.42573798LYS479CD−19.8093−13.088428.1583799LYS479CE−18.6074−13.367927.2393800LYS479NZ−18.3823−12.221926.34743801VAL480N−23.8296−16.216126.95253802VAL480CA−24.8025−16.679625.97893803VAL480C−25.9383−15.693625.89773804VAL480O−25.7435−14.523526.18713805VAL480CB−25.2777−18.086526.40483806VAL480CG1−26.1324−18.734425.29953807VAL480CG2−24.0673−18.998826.68153808PHE481N−27.1361−16.170325.50113809PHE481CA−28.2686−15.268825.38713810PHE481C−28.5777−14.610826.69953811PHE481O−28.5512−15.266327.72893812PHE481CB−29.5093−16.046424.90953813PHE481CG−30.6455−15.113524.49873814PHE481CD1−30.405−13.764824.22313815PHE481CD2−31.9427−15.62224.39693816PHE481CE1−31.4575−12.92923.84573817PHE481CE2−32.9913−14.792823.99083818PHE481CZ−32.7463−13.448423.70083819HIS482N−28.8647−13.294926.64253820HIS482CA−29.1666−12.571227.86573821HIS482C−28.0142−12.668328.8273822HIS482O−28.2101−12.910230.00763823HIS482CB−30.4761−13.091328.49323824HIS482CG−31.6535−12.803927.60783825HIS482ND1−32.6249−13.67427.45673826HIS482CD2−31.8465−11.671726.90443827HIS482CE1−33.4945−13.144626.65623828HIS482NE2−33.1102−12.002526.30463829LYS483N−26.7884−12.490428.2993830LYS483CA−25.6324−12.632929.16363831LYS483C−24.6189−11.588328.80833832LYS483O−24.1628−11.543527.67663833LYS483CB−25.0266−14.044229.03633834LYS483CG−26.1005−15.094229.37543835LYS483CD−25.5128−16.510329.24943836LYS483CE−26.6608−17.535929.26143837LYS483NZ−26.1029−18.895329.22653838GLN484N−24.2798−10.742329.80143839GLN484CA−23.3352−9.671529.53383840GLN484C−22.0236−10.225229.06073841GLN484O−21.606−11.279629.51163842GLN484CB−23.0998−8.803730.78393843GLN484CG−24.4469−8.337431.3673844GLN484CD−24.5187−8.722632.81623845GLN484OE1−25.3451−9.539333.18823846GLN484NE2−23.647−8.131133.65293847ASP485N−21.3878−9.50128.12253848ASP485CA−20.1652−10.022127.54223849ASP485C−18.9649−9.699728.38513850ASP485O−19.0926−9.097929.43953851ASP485CB−20.0082−9.469326.11313852ASP485CG−21.1396−9.917225.23013853ASP485OD1−21.3088−9.301524.14423854ASP485OD2−21.8672−10.875525.61063855ARG486N−17.7821−10.122227.89963856ARG486CA−16.5738−9.91528.67683857ARG486C−15.3703−10.269627.85243858ARG486O−15.4489−11.14827.00823859ARG486CB−16.5904−10.777329.95543860ARG486CG−16.9669−12.225929.59183861ARG486CD−16.9507−13.116330.84593862ARG486NE−16.4438−14.42330.47033863ARG486CZ−15.4104−14.94131.06813864ARG486NH1−14.9709−16.103530.68753865ARG486NH2−14.8105−14.315932.03833866GLY487N−14.2495−9.565828.10933867GLY487CA−13.0384−9.84827.35743868GLY487C−12.5891−11.255427.62133869GLY487O−12.254−11.966626.68773870SER488N−12.6035−11.651228.913871SER488CA−12.2732−13.026529.24283872SER488C−13.2361−13.945628.54773873SER488O−12.8507−15.026728.13243874SER488CB−12.4306−13.205530.76383875SER488OG−11.5098−12.353731.453876GLY489N−14.4953−13.489128.40563877GLY489CA−15.4568−14.292727.67783878GLY489C−15.3005−14.094926.19743879GLY489O−16.3031−13.956525.5193880TYR490N−14.0514−14.090225.69143881TYR490CA−13.8643−13.999324.25153882TYR490C−12.8647−15.031123.80463883TYR490O−12.3326−15.749124.63673884TYR490CB−13.3901−12.591923.83513885TYR490CG−14.4754−11.541624.06033886TYR490CD1−14.1148−10.260724.48563887TYR490CD2−15.8226−11.844323.84633888TYR490CE1−15.0993−9.299624.72923889TYR490CE2−16.8117−10.896424.11783890TYR490CZ−16.4483−9.622924.5623891TYR490OH−17.4285−8.677924.83753892LEU491N−12.6034−15.117222.48313893LEU491CA−11.6638−16.12922.02453894LEU491C−11.252−15.945620.59023895LEU491O−12.0934−15.919119.70643896LEU491CB−12.1723−17.560222.30263897LEU491CG−13.3597−17.945621.39643898LEU491CD1−13.8683−19.339121.80693899LEU491CD2−14.5076−16.930521.54163900ASN492N−9.9258−15.823420.38283901ASN492CA−9.4009−15.675819.03363902ASN492C−7.9853−16.195819.00183903ASN492O−7.4131−16.404120.05933904ASN492CB−9.4086−14.198718.59513905ASN492CG−10.7986−13.632918.56863906ASN492OD1−11.1194−12.787119.38683907ASN492ND2−11.639−14.092117.62463908TRP493N−7.3666−16.440517.82693909TRP493CA−8.033−16.168116.56623910TRP493C−6.9975−15.778915.54213911TRP493O−6.647−14.611415.49163912TRP493CB−8.8914−17.350816.07323913TRP493CG−9.8756−17.863217.08553914TRP493CD1−11.2065−17.707217.04573915TRP493CD2−9.5666−18.648418.33213916TRP493NE1−11.7642−18.270918.08783917TRP493CE2−10.8239−18.826518.87773918TRP493CE3−8.4064−19.139818.92893919TRP493CZ2−11.0102−19.495520.08633920TRP493CZ3−8.5843−19.810720.14473921TRP493CH2−9.8554−19.977920.71393922GLU494N−6.4974−16.726914.71943923GLU494CA−5.4994−16.343813.73043924GLU494C−5.5057−17.243512.52553925GLU494O−5.0583−18.376812.59853926GLU494CB−4.0923−16.247614.34993927GLU494CG−3.7763−14.782514.71353928GLU494CD−4.102−13.846713.58243929GLU494OE1−4.7641−12.809613.85113930GLU494OE2−3.7091−14.146912.42293931GLN495N−6.0364−16.703511.40973932GLN495CA−6.304−17.516610.23573933GLN495C−7.2692−16.81829.31663934GLN495O−7.338−15.59969.32543935GLN495CB−5.0369−17.97769.4933936GLN495CG−4.8209−19.48769.72113937GLN495CD−6.0634−20.27759.41573938GLN495OE1−6.5357−21.017510.26273939GLN495NE2−6.6081−20.12678.1953940LEU496N−8.0384−17.60078.53273941LEU496CA−9.0582−16.98577.69643942LEU496C−10.3289−17.78587.75093943LEU496O−10.2675−18.99727.88423944LEU496CB−8.595−16.83496.23523945LEU496CG−7.3993−15.86846.143946LEU496CD1−6.9522−15.76364.67043947LEU496CD2−7.801−14.47326.65333948HIS497N−11.4883−17.09967.67013949HIS497CA−12.7528−17.78127.91093950HIS497C−12.8025−18.19459.35413951HIS497O−12.5097−19.33589.67083952HIS497CB−12.9863−18.99536.98653953HIS497CG−14.3988−19.49857.11363954HIS497ND1−14.9898−19.65368.27693955HlS497CD2−15.1943−19.83476.08073956HIS497CE1−16.1873−20.09318.05163957HIS497NE2−16.3672−20.22026.81623958ALA498N−13.1814−17.242910.22723959ALA498CA−13.1595−17.51511.65423960ALA498C−14.0791−18.629112.07383961ALA498O−14.7686−19.206111.2483962ALA498CB−13.566−16.21512.37133963ALA499N−14.0686−18.91313.39313964ALA499CA−14.9678−19.910613.95543965ALA499C−14.5838−20.211615.37753966ALA499O−13.7636−19.516815.9573967ALA499CB−14.9691−21.233613.16883968MET500N−15.1933−21.27615.93933969MET500CA−14.9391−21.604617.33193970MET500C−15.426−20.475418.19443971MET500O−14.7312−20.020719.08883972MET500CB−13.4583−21.953217.57913973MET500CG−13.3701−22.975918.72613974MET500SD−12.7965−22.123220.22183975MET500CE−12.6583−23.578421.29963976ARG501N−16.6523−20.017717.87953977ARG501CA−17.1808−18.849418.55713978ARG501C−18.6731−18.825618.36813979ARG501O−19.2805−19.865718.16643980ARG501CB−16.5623−17.612817.87273981ARG501CG−15.1516−17.341718.42883982ARG501CD−14.67−15.965117.93763983ARG501NE−13.573−16.115316.99933984ARG501CZ−13.7607−16.582415.79853985ARG501NH1−12.7489−16.682914.98933986ARG501NH2−14.9398−16.949515.39193987GLU502N−19.2645−17.614918.41573988GLU502CA−20.6847−17.490418.14193989GLU502C−20.9358−18.016616.76043990GLU502O−21.946−18.654816.52133991GLU502CB−21.034−15.99218.18233992GLU502CG−22.4733−15.762417.68823993GLU502CD−22.4706−15.328116.25123994GLU502OE1−23.0568−16.06215.41183995GLU502OE2−21.886−14.250615.9583996ALA503N−19.9852−17.754215.84833997ALA503CA−20.1081−18.348514.53553998ALA503C−19.1648−19.514214.43313999ALA503O−18.1384−19.523115.0954000ALA503CB−19.7811−17.262413.50064001GLY504N−19.5234−20.516913.60784002GLY504CA−18.6468−21.669713.49784003GLY504C−19.42−22.957313.43084004GLY504O−20.6152−22.952913.18384005ARG505N−18.7084−24.080113.64884006ARG505CA−19.3631−25.368613.52314007ARG505C−20.074−25.717314.79924008ARG505O−19.5131−26.377115.65974009ARG505CB−18.3277−26.441813.13534010ARG505CG−19.0675−27.727112.724011ARG505CD−18.0544−28.843112.40854012ARG505NE−17.7481−28.840310.98984013ARG505CZ−16.5174−28.854110.56674014ARG505NH1−16.2831−28.8439.28824015ARG505NH2−15.5188−28.875111.40024016HIS506N−21.3392−25.270714.90514017HIS506CA−22.0972−25.583816.1034018HIS506C−23.5704−25.411215.86494019HIS506O−23.9709−24.866614.84814020HIS506CB−21.6667−24.644717.24754021HIS506CG−21.8326−23.221416.80024022HIS506ND1−20.8661−22.567316.1994023HIS506CD2−22.9533−22.490716.95194024HIS506CE1−21.3155−21.382915.93184025HIS506NE2−22.4991−21.274216.33574026ARG507N−24.3781−25.876716.83814027ARG507CA−25.8061−25.630716.75294028ARG507C−26.0315−24.181817.07954029ARG507O−26.2062−23.825518.23434030ARG507CB−26.5313−26.530217.77194031ARG507CG−26.5793−27.976817.24794032ARG507CD−27.4735−28.817618.1774033ARG507NE−27.5376−30.181817.68594034ARG507CZ−27.1634−31.182318.42984035ARG507NH1−27.2354−32.390817.95634036ARG507NH2−26.7191−30.995319.63814037LYS508N−26.0164−23.338916.034038LYS508CA−26.1133−21.91116.27114039LYS508C−27.4339−21.515816.86294040LYS508O−28.4323−22.188216.66014041LYS508CB−25.8432−21.107214.98944042LYS508CG−24.5525−21.619214.32974043LYS508CD−24.0293−20.570213.33574044LYS508CE−22.737−21.113312.70564045LYS508NZ−23.0643−22.166411.73374046SER509N−27.4122−20.406317.62264047SER509CA−28.6287−19.982618.2894048SER509C−29.2901−18.863117.53684049SER509O−28.8376−18.478716.47084050SER509CB−28.2766−19.531919.71924051SER509OG−27.1009−18.7219.69174052TRP510N−30.3851−18.335118.11354053TRP510CA−31.0793−17.252517.44364054TRP510C−31.6712−16.340118.47314055TRP510O−31.5666−15.133618.3284056TRP510CB−32.1576−17.821316.5064057TRP510CG−31.5471−17.964315.14314058TRP510CD1−31.6121−19.033314.33464059TRP510CD2−30.7387−16.914314.43024060TRP510NE1−30.9688−18.787913.21984061TRP510CE2−30.4479−17.543613.2354062TRP510CE3−30.3098−15.623714.73714063TRP510CZ2−29.7138−16.908512.23374064TRP510CZ3−29.5691−14.9813.73834065TRP510CH2−29.298−15.600212.50964066SER511N−32.2648−16.921619.53454067SER511CA−32.6247−16.093520.67144068SER511C−31.3371−15.56921.2394069SER511O−31.1914−14.369421.40394070SER511CB−33.3761−16.939521.71814071SER511OG−32.5848−18.060422.12394072CYS512N−30.3893−16.493121.49714073CYS512CA−29.054−16.068821.87874074CYS512C−28.4923−15.233820.76544075CYS512O−27.8063−14.261321.03364076CYS512CB−28.1483−17.305422.02884077CYS512SG−28.9325−18.539323.10754078GLY513N−28.8125−15.614519.50984079GLY513CA−28.404−14.796518.37964080GLY513C−28.8091−13.367318.60364081GLY513O−28.0983−12.460418.2024082HIS514N−29.9612−13.185619.27584083HIS514CA−30.3937−11.843319.60824084HIS514C−29.7979−11.444720.93084085HIS514O−30.5143−11.087821.85244086HIS514CB−31.9352−11.814319.65574087HIS514CG−32.5477−12.250418.35494088HIS514ND1−33.8314−12.510118.26444089HIS514CD2−31.8956−12.421117.1884090HIS514CE1−34.0697−12.861117.04064091HIS514NE2−33.0067−12.831316.37394092THR515N−28.4557−11.500521.02244093THR515CA−27.8194−11.006722.22934094THR515C−26.3531−10.759422.02574095THR515O−25.697−11.465821.27714096THR515CB−28.1139−11.841623.49384097THR515OG1−27.8485−11.063524.6644098THR515CG2−27.2537−13.11923.52844099ARG516N−25.8659−9.720122.72634100ARG516CA−24.4561−9.384722.67534101ARG516C−24.1989−8.683123.97784102ARG516O−24.063−7.470424.01494103ARG516CB−24.1919−8.461421.46794104ARG516CG−24.1308−9.288320.16984105ARG516CD−22.8747−10.178320.18634106ARG516NE−23.2084−11.508919.71884107ARG516CZ−22.8227−11.931918.55064108ARG516NH1−23.1216−13.141318.18964109ARG516NH2−22.1438−11.182317.73444110ALA517N−24.1631−9.489525.05884111ALA517CA−24.1682−8.933926.40274112ALA517C−25.5826−8.554626.73084113ALA517O−26.1868−9.163227.59944114ALA517CB−23.1864−7.764326.61394115GLY518N−26.1113−7.552226.00264116GLY518CA−27.5232−7.244426.13714117GLY518C−28.2821−7.960825.05544118GLY518O−27.716−8.26324.01734119CYS519N−29.5766−8.234525.30954120CYS519CA−30.3711−8.951924.32594121CYS519C−30.5352−8.127523.07774122CYS519O−31.4697−7.349922.97564123CYS519CB−31.7408−9.236324.97474124CYS519SG−32.8006−10.116523.78934125THR520N−29.6209−8.311922.10694126THR520CA−29.7507−7.562220.86944127THR520C−30.8517−8.125620.01014128THR520O−31.5034−9.080520.39944129THR520CB−28.394−7.568320.13344130THR520OG1−28.4296−6.67819.01494131THR520CG2−28.0242−8.985819.65614132LEU521N−31.0527−7.524518.82054133LEU521CA−31.9831−8.099917.86034134LEU521C−33.3511−8.328818.44544135LEU521O−33.9048−9.408818.31064136LEU521CB−31.4089−9.388817.23274137LEU521CG−29.882−9.297917.03954138LEU521CD1−29.3723−10.601816.39994139LEU521CD2−29.53−8.111716.12234140ILE522N−33.8974−7.292619.11034141ILE522CA−35.2004−7.461219.73074142ILE522C−35.9061−6.137819.79264143ILE522O−37.0732−6.058219.44524144ILE522CB−35.056−8.007121.16694145ILE522CG1−34.1288−7.10522.00534146ILE522CG2−34.5223−9.451821.14944147ILE522CD1−34.4094−7.31423.50484148ARG523N−35.1764−5.099620.2464149ARG523CA−35.7994−3.801220.43754150ARG523C−36.2561−3.192219.14124151ARG523O−35.9804−3.723718.07724152ARG523CB−34.7842−2.867821.12384153ARG523CG−34.2737−3.523422.42144154ARG523CD−32.8623−2.996922.73864155ARG523NE−32.2864−3.769623.82444156ARG523CZ−31.2373−4.517523.63714157ARG523NH1−30.746−5.188724.63644158ARG523NH2−30.6715−4.60722.46914159GLN524N−36.9758−2.058119.24234160GLN524CA−37.4924−1.447518.02984161GLN524C−37.30610.042918.06584162GLN524O−36.82460.591619.04364163GLN524CB−38.9918−1.764717.86484164GLN524CG−39.2516−3.270618.06374165GLN524CD−39.684−3.516519.48054166GLN524OE1−38.9756−4.166720.2314167GLN524NE2−40.8636−2.993519.8606

[1496]

21

TABLE V

Atom No
Residue
Atom name
x coord
y coord
z coord

1
LYS12
CA
−26.781
19.61
−5.574

2
LYS12
C
−27.853
18.529
−5.301

3
LYS12
N
−27.307
20.9
−5.159

4
LYS12
O
−27.815
17.778
−4.324

5
LYS12
CB
−25.462
19.387
−4.819

6
LYS12
CG
−24.469
18.447
−5.526

7
LYS12
CD
−24.861
16.966
−5.511

8
LYS12
CE
−23.82
16.057
−6.165

9
LYS12
NZ
−22.573
16.005
−5.369

10
LEU13
N
−28.901
18.567
−6.21

11
LEU13
CA
−30.014
17.612
−6.169

12
LEU13
C
−29.844
16.617
−7.329

13
LEU13
O
−29.62
15.424
−7.12

14
LEU13
CB
−31.372
18.325
−6.222

15
LEU13
CG
−31.708
19.142
−4.957

16
LEU13
CD1
−33.003
19.928
−5.179

17
LEU13
CD2
−31.852
18.264
−3.713

18
ALA14
N
−29.896
17.156
−8.611

19
ALA14
CA
−30.062
16.233
−9.738

20
ALA14
C
−28.974
15.148
−9.82

21
ALA14
O
−29.304
13.976
−10.052

22
ALA14
CB
−30.199
16.966
−11.065

23
PRO15
N
−27.648
15.468
−9.615

24
PRO15
CA
−26.614
14.433
−9.739

25
PRO15
C
−26.577
13.384
−8.613

26
PRO15
O
−25.683
12.539
−8.564

27
PRO15
CB
−25.291
15.205
−9.757

28
PRO15
CG
−25.689
16.611
−10.179

29
PRO15
CD
−27.049
16.79
−9.529

30
ARG16
N
−27.611
13.432
−7.698

31
ARG16
CA
−27.889
12.313
−6.808

32
ARG16
C
−28.719
11.222
−7.523

33
ARG16
O
−28.811
10.092
−7.04

34
ARG16
CB
−28.669
12.759
−5.565

35
ARG16
CG
−27.998
13.889
−4.779

36
ARG16
CD
−28.841
14.271
−3.563

37
ARG16
NE
−28.553
15.641
−3.125

38
ARG16
CZ
−28.879
16.152
−1.919

39
ARG16
NH1
−28.577
17.443
−1.675

40
ARG16
NH2
−29.498
15.43
−0.966

41
TYR17
N
−29.447
11.628
−8.629

42
TYR17
CA
−30.387
10.734
−9.307

43
TYR17
C
−30.365
10.753
−10.847

44
TYR17
O
−30.892
9.844
−11.493

45
TYR17
CB
−31.82
10.861
−8.763

46
TYR17
CG
−32.42
12.247
−8.83

47
TYR17
CD1
−33.026
12.713
−10.005

48
TYR17
CD2
−32.399
13.079
−7.7

49
TYR17
CE1
−33.605
13.985
−10.05

50
TYR17
CE2
−32.976
14.348
−7.743

51
TYR17
CZ
−33.575
14.791
−8.915

52
TYR17
OH
−34.113
16.045
−8.919

53
SER18
N
−29.786
11.842
−11.463

54
SER18
CA
−29.362
11.756
−12.86

55
SER18
C
−28.037
10.969
−12.906

56
SER18
O
−27.418
10.622
−11.898

57
SER18
CB
−29.251
13.135
−13.513

58
SER18
OG
−28.18
13.894
−12.961

59
ARG19
N
−27.608
10.612
−14.178

60
ARG19
CA
−26.407
9.799
−14.302

61
ARG19
C
−25.186
10.715
−14.173

62
ARG19
O
−25.093
11.798
−14.749

63
ARG19
CB
−26.36
9.052
−15.639

64
ARG19
CG
−27.385
7.915
−15.684

65
ARG19
CD
−27.352
7.176
−17.017

66
ARG19
NE
−28.229
5.993
−17.009

67
ARG19
CZ
−29.584
6.014
−17.06

68
ARG19
NH1
−30.264
4.849
−17.011

69
ARG19
NH2
−30.28
7.164
−17.165

70
ARG20
N
−24.137
10.172
−13.44

71
ARG20
CA
−23.074
11.059
−12.946

72
ARG20
C
−22.105
11.601
−14.025

73
ARG20
O
−21.196
12.384
−13.749

74
ARG20
CB
−22.298
10.391
−11.796

75
ARG20
CG
−21.451
9.183
−12.222

76
ARG20
CD
−21.741
7.92
−11.41

77
ARG20
NE
−21.225
7.976
−10.034

78
ARG20
CZ
−21.316
6.918
−9.177

79
ARG20
NH1
−20.707
6.953
−7.974

80
ARG20
NH2
−22.006
5.801
−9.504

81
ALA21
N
−22.342
11.167
−15.311

82
ALA21
CA
−21.702
11.786
−16.466

83
ALA21
C
−22.401
13.094
−16.884

84
ALA21
O
−21.802
13.973
−17.513

85
ALA21
CB
−21.7
10.815
−17.638

86
SER22
N
−23.748
13.189
−16.596

87
SER22
CA
−24.595
14.209
−17.204

88
SER22
C
−24.187
15.655
−16.886

89
SER22
O
−24.338
16.517
−17.76

90
SER22
CB
−26.076
14.009
−16.861

91
SER22
OG
−26.564
12.755
−17.346

92
PRO23
N
−23.727
15.993
−15.627

93
PRO23
CA
−23.271
17.363
−15.354

94
PRO23
C
−21.806
17.591
−15.778

95
PRO23
O
−21.311
18.716
−15.797

96
PRO23
CB
−23.413
17.512
−13.839

97
PRO23
CG
−23.201
16.095
−13.327

98
PRO23
CD
−23.881
15.239
−14.385

99
GLN24
N
−21.082
16.438
−16.016

100
GLN24
CA
−19.678
16.471
−16.414

101
GLN24
C
−19.544
16.633
−17.939

102
GLN24
O
−18.62
17.275
−18.441

103
GLN24
CB
−18.95
15.209
−15.942

104
GLN24
CG
−18.96
15.085
−14.417

105
GLN24
CD
−18.096
13.933
−13.964

106
GLN24
OE1
−16.973
14.097
−13.504

107
GLN24
NE2
−18.651
12.698
−14.155

108
GLN25
N
−20.485
15.967
−18.706

109
GLN25
CA
−20.388
15.96
−20.167

110
GLN25
C
−20.253
17.391
−20.748

111
GLN25
O
−19.364
17.623
−21.581

112
GLN25
CB
−21.577
15.23
−20.803

113
GLN25
CG
−21.36
13.719
−20.86

114
GLN25
CD
−22.653
13.001
−21.172

115
GLN25
OE1
−23.272
12.342
−20.342

116
GLN25
NE2
−23.097
13.155
−22.455

117
PRO26
N
−21.115
18.387
−20.32

118
PRO26
CA
−20.991
19.766
−20.799

119
PRO26
C
−19.946
20.596
−20.02

120
PRO26
O
−20.004
21.825
−19.936

121
PRO26
CB
−22.395
20.35
−20.632

122
PRO26
CG
−22.91
19.622
−19.398

123
PRO26
CD
−22.368
18.214
−19.591

124
GLN27
N
−18.849
19.895
−19.569

125
GLN27
CA
−17.613
20.528
−19.115

126
GLN27
C
−16.463
19.898
−19.929

127
GLN27
O
−15.331
19.73
−19.484

128
GLN27
CB
−17.416
20.396
−17.603

129
GLN27
CG
−18.523
21.051
−16.774

130
GLN27
CD
−18.442
22.561
−16.807

131
GLN27
OE1
−17.735
23.205
−16.038

132
GLN27
NE2
−19.197
23.17
−17.767

133
GLN28
N
−16.808
19.71
−21.262

134
GLN28
CA
−15.945
19.054
−22.232

135
GLN28
C
−16.691
18.924
−23.579

136
GLN28
O
−16.447
19.642
−24.544

137
GLN28
CB
−14.567
19.723
−22.419

138
GLN28
CG
−14.595
21.247
−22.555

139
GLN28
CD
−13.26
21.765
−23.043

140
GLN28
OE1
−13.065
22.155
−24.189

141
GLN28
NE2
−12.242
21.746
−22.12

142
ASP29
N
−17.633
17.907
−23.602

143
ASP29
CA
−18.243
17.418
−24.852

144
ASP29
C
−17.114
16.809
−25.738

145
ASP29
O
−15.94
16.761
−25.373

146
ASP29
CB
−19.095
18.476
−25.541

147
ASP29
CG
−20.157
17.743
−26.352

148
ASP29
OD1
−21.32
17.755
−25.873

149
ASP29
OD2
−19.723
17.189
−27.416

150
PHE30
N
−17.515
16.262
−26.934

151
PHE30
CA
−16.585
15.682
−27.911

152
PHE30
C
−17.336
15.656
−29.244

153
PHE30
O
−16.883
16.173
−30.268

154
PHE30
CB
−16.091
14.297
−27.475

155
PHE30
CG
−15.177
13.595
−28.452

156
PHE30
CD1
−13.793
13.795
−28.41

157
PHE30
CD2
−15.69
12.688
−29.387

158
PHE30
CE1
−12.94
13.077
−29.25

159
PHE30
CE2
−14.838
11.962
−30.221

160
PHE30
CZ
−13.461
12.156
−30.153

161
GLU31
N
−18.571
15.047
−29.206

162
GLU31
CA
−19.371
14.861
−30.403

163
GLU31
C
−19.84
16.233
−30.919

164
GLU31
O
−19.914
16.467
−32.129

165
GLU31
CB
−20.581
13.945
−30.146

166
GLU31
CG
−20.204
12.473
−29.906

167
GLU31
CD
−19.422
12.179
−28.631

168
GLU31
OE1
−18.905
11.018
−28.535

169
GLU31
OE2
−19.275
13.143
−27.826

170
ALA32
N
−20.23
17.156
−29.959

171
ALA32
CA
−20.695
18.481
−30.361

172
ALA32
C
−19.529
19.381
−30.805

173
ALA32
O
−19.719
20.395
−31.476

174
ALA32
CB
−21.475
19.175
−29.256

175
LEU33
N
−18.285
19.002
−30.336

176
LEU33
CA
−17.064
19.644
−30.808

177
LEU33
C
−16.734
19.113
−32.211

178
LEU33
O
−16.436
19.883
−33.13

179
LEU33
CB
−15.891
19.427
−29.85

180
LEU33
CG
−16.068
20.121
−28.484

181
LEU33
CD1
−14.97
19.656
−27.528

182
LEU33
CD2
−16.034
21.645
−28.603

183
LEU34
N
−16.806
17.743
−32.408

184
LEU34
CA
−16.484
17.2
−33.728

185
LEU34
C
−17.468
17.783
−34.767

186
LEU34
O
−17.124
18.027
−35.925

187
LEU34
CB
−16.582
15.672
−33.798

188
LEU34
CG
−15.405
14.894
−33.178

189
LEU34
CD1
−15.661
13.393
−33.352

190
LEU34
CD2
−14.056
15.246
−33.805

191
ALA35
N
−18.765
17.953
−34.31

192
ALA35
CA
−19.818
18.481
−35.163

193
ALA35
C
−19.724
20.006
−35.38

194
ALA35
O
−20.487
20.59
−36.158

195
ALA35
CB
−21.195
18.145
−34.609

196
GLU36
N
−18.78
20.682
−34.645

197
GLU36
CA
−18.303
22.015
−35.021

198
GLU36
C
−17.186
21.785
−36.053

199
GLU36
O
−17.234
22.262
−37.192

200
GLU36
CB
−17.861
22.801
−33.778

201
GLU36
CG
−17.443
24.24
−34.073

202
GLU36
CD
−16.03
24.44
−34.627

203
GLU36
OE1
−15.172
23.573
−34.311

204
GLU36
OE2
−15.902
25.463
−35.368

205
CYS37
N
−16.146
20.978
−35.621

206
CYS37
CA
−14.854
21.039
−36.301

207
CYS37
C
−14.982
20.521
−37.736

208
CYS37
O
−14.408
21.084
−38.67

209
CYS37
CB
−13.796
20.222
−35.56

210
CYS37
SG
−13.318
20.986
−33.971

211
LEU38
N
−15.724
19.365
−37.893

212
LEU38
CA
−15.839
18.71
−39.193

213
LEU38
C
−16.86
19.396
−40.122

214
LEU38
O
−16.939
19.086
−41.311

215
LEU38
CB
−16.189
17.219
−39.063

216
LEU38
CG
−14.967
16.304
−38.849

217
LEU38
CD1
−14.173
16.629
−37.586

218
LEU38
CD2
−15.421
14.844
−38.807

219
ARG39
N
−17.699
20.323
−39.529

220
ARG39
CA
−18.489
21.215
−40.371

221
ARG39
C
−17.655
22.435
−40.786

222
ARG39
O
−17.723
22.893
−41.927

223
ARG39
CB
−19.765
21.696
−39.67

224
ARG39
CG
−20.879
20.645
−39.722

225
ARG39
CD
−22.192
21.193
−39.164

226
ARG39
NE
−22.073
21.461
−37.731

227
ARG39
CZ
−22.814
22.311
−37

228
ARG39
NH1
−22.502
22.479
−35.699

229
ARG39
NH2
−23.855
22.991
−37.519

230
ASN40
N
−16.956
23.056
−39.765

231
ASN40
CA
−16.365
24.376
−39.99

232
ASN40
C
−15.001
24.28
−40.69

233
ASN40
O
−14.541
25.23
−41.324

234
ASN40
CB
−16.187
25.141
−38.682

235
ASN40
CG
−17.481
25.764
−38.204

236
ASN40
OD1
−18.559
25.676
−38.782

237
ASN40
ND2
−17.346
26.478
−37.045

238
GLY41
N
−14.267
23.143
−40.414

239
GLY41
CA
−12.89
23.005
−40.854

240
GLY41
C
−11.898
23.611
−39.86

241
GLY41
O
−10.739
23.874
−40.176

242
CYS42
N
−12.38
23.728
−38.571

243
CYS42
CA
−11.519
24.131
−37.462

244
CYS42
C
−10.8
22.878
−36.938

245
CYS42
O
−11.253
21.744
−37.079

246
CYS42
CB
−12.322
24.733
−36.301

247
CYS42
SG
−13.088
26.325
−36.732

248
LEU43
N
−9.636
23.151
−36.236

249
LEU43
CA
−9.096
22.166
−35.302

250
LEU43
C
−9.601
22.594
−33.916

251
LEU43
O
−9.9
23.761
−33.659

252
LEU43
CB
−7.562
22.161
−35.29

253
LEU43
CG
−6.909
21.736
−36.619

254
LEU43
CD1
−5.39
21.902
−36.521

255
LEU43
CD2
−7.243
20.293
−36.997

256
PHE44
N
−9.616
21.585
−32.979

257
PHE44
CA
−10.012
21.847
−31.602

258
PHE44
C
−8.796
22.437
−30.875

259
PHE44
O
−7.718
21.842
−30.797

260
PHE44
CB
−10.433
20.557
−30.896

261
PHE44
CG
−10.682
20.72
−29.416

262
PHE44
CD1
−11.728
21.521
−28.942

263
PHE44
CD2
−9.854
20.066
−28.491

264
PHE44
CE1
−11.942
21.656
−27.57

265
PHE44
CE2
−10.09
20.179
−27.123

266
PHE44
CZ
−11.134
20.973
−26.663

267
GLU45
N
−9.013
23.684
−30.325

268
GLU45
CA
−8.117
24.256
−29.33

269
GLU45
C
−8.867
24.183
−27.994

270
GLU45
O
−10.022
24.587
−27.87

271
GLU45
CB
−7.785
25.72
−29.653

272
GLU45
CG
−6.759
25.864
−30.78

273
GLU45
CD
−5.434
25.234
−30.385

274
GLU45
OE1
−4.99
25.529
−29.227

275
GLU45
OE2
−4.95
24.381
−31.195

276
ASP46
N
−8.134
23.636
−26.957

277
ASP46
CA
−8.68
23.586
−25.607

278
ASP46
C
−8.389
24.957
−24.968

279
ASP46
O
−7.252
25.424
−24.869

280
ASP46
CB
−8.053
22.452
−24.808

281
ASP46
CG
−8.813
22.241
−23.517

282
ASP46
OD1
−8.966
23.266
−22.785

283
ASP46
OD2
−9.206
21.058
−23.267

284
THR47
N
−9.545
25.589
−24.549

285
THR47
CA
−9.557
26.883
−23.87

286
THR47
C
−9.369
26.703
−22.354

287
THR47
O
−9.032
27.646
−21.638

288
THR47
CB
−10.923
27.57
−24.096

289
THR47
OG1
−11.445
27.165
−25.369

290
THR47
CG2
−10.813
29.09
−24.071

291
SER48
N
−9.771
25.476
−21.842

292
SER48
CA
−9.616
25.195
−20.406

293
SER48
C
−8.158
24.878
−20.053

294
SER48
O
−7.708
25.08
−18.927

295
SER48
CB
−10.481
23.997
−20.005

296
SER48
OG
−11.808
24.115
−20.522

297
PHE49
N
−7.444
24.246
−21.05

298
PHE49
CA
−6.033
23.891
−20.932

299
PHE49
C
−5.262
24.642
−22.045

300
PHE49
O
−4.968
24.108
−23.124

301
PHE49
CB
−5.884
22.368
−21.029

302
PHE49
CG
−4.649
21.869
−20.32

303
PHE49
CD1
−4.611
21.823
−18.919

304
PHE49
CD2
−3.528
21.454
−21.044

305
PHE49
CE1
−3.482
21.342
−18.255

306
PHE49
CE2
−2.404
20.966
−20.375

307
PHE49
CZ
−2.382
20.901
−18.983

308
PRO50
N
−4.967
25.977
−21.797

309
PRO50
CA
−4.379
26.826
−22.826

310
PRO50
C
−2.846
26.69
−22.873

311
PRO50
O
−2.174
26.135
−22.003

312
PRO50
CB
−4.778
28.243
−22.411

313
PRO50
CG
−4.787
28.153
−20.889

314
PRO50
CD
−5.383
26.774
−20.646

315
ALA51
N
−2.291
27.32
−23.972

316
ALA51
CA
−0.862
27.308
−24.27

317
ALA51
C
−0.137
28.512
−23.632

318
ALA51
O
0.623
29.243
−24.266

319
ALA51
CB
−0.667
27.281
−25.782

320
THR52
N
−0.343
28.652
−22.272

321
THR52
CA
0.396
29.632
−21.46

322
THR52
C
1.448
28.845
−20.633

323
THR52
O
1.924
27.777
−21.027

324
THR52
CB
−0.56
30.482
−20.595

325
THR52
OG1
−1.056
29.691
−19.513

326
THR52
CG2
−1.734
31.065
−21.37

327
LEU53
N
1.866
29.437
−19.452

328
LEU53
CA
2.574
28.681
−18.418

329
LEU53
C
1.6
28.189
−17.317

330
LEU53
O
1.975
27.466
−16.389

331
LEU53
CB
3.658
29.545
−17.754

332
LEU53
CG
4.727
30.104
−18.714

333
LEU53
CD1
5.702
30.996
−17.939

334
LEU53
CD2
5.501
29
−19.432

335
SER54
N
0.291
28.613
−17.427

336
SER54
CA
−0.681
28.479
−16.33

337
SER54
C
−1.097
27.015
−16.162

338
SER54
O
−1.541
26.571
−15.109

339
SER54
CB
−1.966
29.285
−16.585

340
SER54
OG
−1.692
30.559
−17.187

341
SER55
N
−1.042
26.303
−17.334

342
SER55
CA
−1.355
24.887
−17.495

343
SER55
C
−0.139
24.005
−17.146

344
SER55
O
−0.226
22.783
−17.014

345
SER55
CB
−1.784
24.668
−18.951

346
SER55
OG
−1.052
25.563
−19.803

347
ILE56
N
1.066
24.675
−17.053

348
ILE56
CA
2.278
24.001
−16.601

349
ILE56
C
2.33
24.124
−15.072

350
ILE56
O
2.39
23.12
−14.359

351
ILE56
CB
3.557
24.544
−17.287

352
ILE56
CG1
3.357
24.643
−18.815

353
ILE56
CG2
4.77
23.668
−16.944

354
ILE56
CD1
4.592
25.09
−19.577

355
GLY57
N
2.367
25.424
−14.596

356
GLY57
CA
2.7
25.698
−13.211

357
GLY57
C
4.2
25.489
−12.997

358
GLY57
O
4.879
24.744
−13.702

359
SER58
N
4.733
26.171
−11.92

360
SER58
CA
6.169
26.079
−11.675

361
SER58
C
6.538
26.776
−10.355

362
SER58
O
6.339
27.974
−10.161

363
SER58
CB
6.996
26.674
−12.826

364
SER58
OG
6.453
27.908
−13.297

365
GLY59
N
7.11
25.938
−9.41

366
GLY59
CA
7.488
26.438
−8.1

367
GLY59
C
8.997
26.684
−7.979

368
GLY59
O
9.805
25.782
−7.739

369
SER60
N
9.412
27.977
−8.223

370
SER60
CA
10.761
28.487
−7.965

371
SER60
C
11.834
27.742
−8.76

372
SER60
O
12.293
28.182
−9.813

373
SER60
CB
11.133
28.6
−6.484

374
SER60
OG
12.351
29.365
−6.324

375
LEU61
N
12.211
26.514
−8.255

376
LEU61
CA
13.268
25.74
−8.903

377
LEU61
C
12.877
25.429
−10.352

378
LEU61
O
13.704
25.396
−11.26

379
LEU61
CB
13.547
24.434
−8.149

380
LEU61
CG
14.084
24.624
−6.716

381
LEU61
CD1
14.196
23.264
−6.022

382
LEU61
CD2
15.443
25.326
−6.691

383
LEU62
N
11.543
25.141
−10.533

384
LEU62
CA
11.016
24.696
−11.813

385
LEU62
C
10.583
25.875
−12.708

386
LEU62
O
10.123
25.694
−13.835

387
LEU62
CB
9.873
23.701
−11.583

388
LEU62
CG
10.292
22.481
−10.728

389
LEU62
CD1
9.07
21.645
−10.371

390
LEU62
CD2
11.333
21.609
−11.429

391
GLN63
N
10.796
27.141
−12.19

392
GLN63
CA
10.621
28.352
−12.999

393
GLN63
C
11.905
28.667
−13.786

394
GLN63
O
11.905
29.443
−14.74

395
GLN63
CB
10.28
29.576
−12.132

396
GLN63
CG
8.901
29.468
−11.493

397
GLN63
CD
8.643
30.538
−10.459

398
GLN63
OE1
8.52
30.29
−9.262

399
GLN63
NE2
8.574
31.811
−10.947

400
LYS64
N
13.058
28.134
−13.247

401
LYS64
CA
14.394
28.557
−13.668

402
LYS64
C
14.973
27.615
−14.741

403
LYS64
O
15.964
27.927
−15.399

404
LYS64
CB
15.316
28.621
−12.437

405
LYS64
CG
14.863
29.702
−11.435

406
LYS64
CD
15.239
29.355
−9.991

407
LYS64
CE
14.471
30.217
−8.988

408
LYS64
NZ
14.487
29.568
−7.652

409
LEU65
N
14.366
26.377
−14.827

410
LEU65
CA
14.828
25.348
−15.748

411
LEU65
C
14.299
25.454
−17.198

412
LEU65
O
15.052
25.083
−18.109

413
LEU65
CB
14.562
23.925
−15.22

414
LEU65
CG
15.32
23.551
−13.931

415
LEU65
CD1
14.885
22.157
−13.472

416
LEU65
CD2
16.838
23.581
−14.107

417
PRO66
N
12.985
25.815
−17.464

418
PRO66
CA
12.437
25.65
−18.822

419
PRO66
C
12.087
26.965
−19.575

420
PRO66
O
10.97
27.132
−20.083

421
PRO66
CB
11.167
24.841
−18.536

422
PRO66
CG
10.629
25.517
−17.279

423
PRO66
CD
11.893
25.854
−16.493

424
PRO67
N
13.064
27.918
−19.775

425
PRO67
CA
12.782
29.095
−20.588

426
PRO67
C
12.822
28.72
−22.081

427
PRO67
O
13.391
27.717
−22.509

428
PRO67
CB
13.909
30.063
−20.243

429
PRO67
CG
15.085
29.13
−19.974

430
PRO67
CD
14.441
27.918
−19.309

431
ARG68
N
12.179
29.621
−22.908

432
ARG68
CA
12.145
29.51
−24.371

433
ARG68
C
11.217
28.398
−24.898

434
ARG68
O
11.203
28.074
−26.089

435
ARG68
CB
13.525
29.367
−25.038

436
ARG68
CG
14.512
30.474
−24.677

437
ARG68
CD
15.852
30.291
−25.393

438
ARG68
NE
16.958
30.148
−24.436

439
ARG68
CZ
17.252
29.02
−23.743

440
ARG68
NH1
18.155
29.105
−22.735

441
ARG68
NH2
16.701
27.826
−23.987

442
LEU69
N
10.338
27.861
−23.97

443
LEU69
CA
9.584
26.677
−24.351

444
LEU69
C
8.561
27.022
−25.444

445
LEU69
O
8.092
28.147
−25.609

446
LEU69
CB
8.961
25.93
−23.163

447
LEU69
CG
8.04
26.719
−22.211

448
LEU69
CD1
6.717
27.144
−22.848

449
LEU69
CD2
7.734
25.845
−20.99

450
GLN70
N
8.218
25.944
−26.234

451
GLN70
CA
7.169
26.042
−27.225

452
GLN70
C
6.106
25.004
−26.851

453
GLN70
O
6.376
23.939
−26.294

454
GLN70
CB
7.673
25.793
−28.652

455
GLN70
CG
8.902
26.625
−29.028

456
GLN70
CD
10.18
25.816
−28.919

457
GLN70
OE1
10.366
24.784
−29.564

458
GLN70
NE2
11.135
26.334
−28.095

459
TRP71
N
4.834
25.353
−27.245

460
TRP71
CA
3.735
24.391
−27.223

461
TRP71
C
3.541
24.022
−28.697

462
TRP71
O
3.381
24.894
−29.553

463
TRP71
CB
2.456
25.02
−26.68

464
TRP71
CG
2.454
25.224
−25.191

465
TRP71
CD1
2.869
26.355
−24.508

466
TRP71
CD2
1.907
24.336
−24.212

467
TRP71
NE1
2.537
26.21
−23.186

468
TRP71
CE2
1.903
25.006
−22.992

469
TRP71
CE3
1.334
23.052
−24.262

470
TRP71
CZ2
1.291
24.491
−21.846

471
TRP71
CZ3
0.686
22.535
−23.136

472
TRP71
CH2
0.656
23.252
−21.947

473
LYS72
N
3.624
22.679
−28.983

474
LYS72
CA
3.494
22.16
−30.348

475
LYS72
C
2.42
21.068
−30.347

476
LYS72
O
2.092
20.469
−29.321

477
LYS72
CB
4.83
21.592
−30.849

478
LYS72
CG
5.858
22.692
−31.13

479
LYS72
CD
7.126
22.114
−31.759

480
LYS72
CE
8.191
23.186
−31.926

481
LYS72
NZ
9.428
22.568
−32.457

482
ARG73
N
1.871
20.801
−31.584

483
ARG73
CA
1.094
19.583
−31.812

484
ARG73
C
2.115
18.449
−32.15

485
ARG73
O
3.335
18.648
−32.191

486
ARG73
CB
0.057
19.819
−32.924

487
ARG73
CG
−1
20.889
−32.607

488
ARG73
CD
−2.153
20.364
−31.751

489
ARG73
NE
−3.204
21.384
−31.608

490
ARG73
CZ
−4.491
21.125
−31.262

491
ARG73
NH1
−4.929
19.909
−30.901

492
ARG73
NH2
−5.372
22.129
−31.273

493
PRO74
N
1.613
17.176
−32.386

494
PRO74
CA
2.532
16.075
−32.691

495
PRO74
C
3.204
16.037
−34.08

496
PRO74
O
4.339
15.537
−34.178

497
PRO74
CB
1.692
14.815
−32.46

498
PRO74
CG
0.722
15.264
−31.377

499
PRO74
CD
0.364
16.664
−31.838

500
PRO75
N
2.518
16.432
−35.214

501
PRO75
CA
3.119
16.245
−36.536

502
PRO75
C
4.309
17.176
−36.837

503
PRO75
O
5.012
17.021
−37.836

504
PRO75
CB
1.974
16.435
−37.528

505
PRO75
CG
1.003
17.338
−36.786

506
PRO75
CD
1.147
16.902
−35.335

507
GLU76
N
4.55
18.16
−35.895

508
GLU76
CA
5.745
18.993
−35.974

509
GLU76
C
6.967
18.157
−35.531

510
GLU76
O
8.116
18.48
−35.833

511
GLU76
CB
5.704
20.206
−35.021

512
GLU76
CG
4.624
21.241
−35.323

513
GLU76
CD
3.326
20.806
−34.659

514
GLU76
OE1
2.924
21.524
−33.694

515
GLU76
OE2
2.825
19.744
−35.135

516
LEU77
N
6.674
17.174
−34.601

517
LEU77
CA
7.698
16.407
−33.913

518
LEU77
C
7.993
15.098
−34.656

519
LEU77
O
9.151
14.751
−34.894

520
LEU77
CB
7.281
16.104
−32.465

521
LEU77
CG
7.016
17.359
−31.608

522
LEU77
CD1
6.472
16.945
−30.239

523
LEU77
CD2
8.274
18.211
−31.436

524
HIS78
N
6.902
14.283
−34.897

525
HIS78
CA
7.056
12.996
−35.577

526
HIS78
C
6.321
13.054
−36.919

527
HIS78
O
5.266
13.665
−37.072

528
HIS78
CB
6.494
11.831
−34.748

529
HIS78
CG
7.297
11.485
−33.533

530
HIS78
ND1
6.849
10.582
−32.599

531
HIS78
CD2
8.531
11.874
−33.051

532
HIS78
CE1
7.78
10.503
−31.605

533
HIS78
NE2
8.817
11.265
−31.855

534
SER79
N
6.896
12.292
−37.918

535
SER79
CA
6.39
12.314
−39.296

536
SER79
C
5.22
11.341
−39.492

537
SER79
O
4.445
11.438
−40.442

538
SER79
CB
7.51
11.959
−40.277

539
SER79
OG
8.239
10.828
−39.793

540
ASN80
N
5.183
10.301
−38.59

541
ASN80
CA
4.117
9.304
−38.557

542
ASN80
C
3.642
9.227
−37.097

543
ASN80
O
4.05
8.344
−36.336

544
ASN80
CB
4.652
7.957
−39.044

545
ASN80
CG
3.555
6.92
−39.15

546
ASN80
OD1
2.364
7.137
−38.952

547
ASN80
ND2
4.004
5.678
−39.506

548
PRO81
N
2.793
10.222
−36.654

549
PRO81
CA
2.231
10.173
−35.311

550
PRO81
C
1.077
9.157
−35.31

551
PRO81
O
0.264
9.064
−36.229

552
PRO81
CB
1.737
11.592
−35.063

553
PRO81
CG
1.329
12.074
−36.452

554
PRO81
CD
2.346
11.41
−37.374

555
GLN82
N
1.042
8.343
−34.196

556
GLN82
CA
0.079
7.257
−34.071

557
GLN82
C
−0.393
7.201
−32.612

558
GLN82
O
0.262
7.684
−31.692

559
GLN82
CB
0.687
5.91
−34.478

560
GLN82
CG
1.026
5.81
−35.967

561
GLN82
CD
−0.208
5.864
−36.841

562
GLN82
OE1
−1.346
5.673
−36.422

563
GLN82
NE2
0.056
6.091
−38.163

564
PHE83
N
−1.617
6.574
−32.457

565
PHE83
CA
−2.289
6.467
−31.154

566
PHE83
C
−2.105
5.038
−30.619

567
PHE83
O
−1.725
4.817
−29.472

568
PHE83
CB
−3.772
6.838
−31.314

569
PHE83
CG
−4.503
7.095
−30.019

570
PHE83
CD1
−4.162
8.191
−29.213

571
PHE83
CD2
−5.58
6.284
−29.64

572
PHE83
CE1
−4.89
8.472
−28.055

573
PHE83
CE2
−6.306
6.572
−28.483

574
PHE83
CZ
−5.965
7.666
−27.693

575
TYR84
N
−2.472
4.037
−31.493

576
TYR84
CA
−2.292
2.612
−31.215

577
TYR84
C
−2.348
1.943
−32.592

578
TYR84
O
−3.064
2.387
−33.49

579
TYR84
CB
−3.419
2.024
−30.349

580
TYR84
CG
−3.01
1.729
−28.926

581
TYR84
CD1
−3.451
2.547
−27.877

582
TYR84
CD2
−2.2
0.621
−28.633

583
TYR84
CE1
−3.109
2.253
−26.556

584
TYR84
CE2
−1.846
0.336
−27.314

585
TYR84
CZ
−2.305
1.151
−26.286

586
TYR84
OH
−1.942
0.839
−25.008

587
PHE85
N
−1.583
0.803
−32.722

588
PHE85
CA
−1.557
0.054
−33.976

589
PHE85
C
−1.018
−1.353
−33.675

590
PHE85
O
0.157
−1.675
−33.809

591
PHE85
CB
−0.869
0.752
−35.162

592
PHE85
CG
0.567
1.2
−35.04

593
PHE85
CD1
1.526
0.717
−35.943

594
PHE85
CD2
0.952
2.184
−34.122

595
PHE85
CE1
2.828
1.22
−35.939

596
PHE85
CE2
2.257
2.675
−34.109

597
PHE85
CZ
3.192
2.205
−35.026

598
ALA86
N
−2.007
−2.183
−33.163

599
ALA86
CA
−1.777
−3.512
−32.605

600
ALA86
C
−1.378
−3.41
−31.12

601
ALA86
O
−1.093
−2.352
−30.564

602
ALA86
CB
−0.813
−4.383
−33.405

603
LYS87
N
−1.392
−4.628
−30.458

604
LYS87
CA
−1.132
−4.726
−29.017

605
LYS87
C
0.379
−4.824
−28.732

606
LYS87
O
0.853
−4.568
−27.626

607
LYS87
CB
−1.863
−5.937
−28.42

608
LYS87
CG
−3.355
−5.643
−28.213

609
LYS87
CD
−4.1
−6.829
−27.594

610
LYS87
CE
−5.384
−6.375
−26.912

611
LYS87
NZ
−6.065
−7.531
−26.331

612
ALA88
N
1.123
−5.333
−29.781

613
ALA88
CA
2.584
−5.318
−29.775

614
ALA88
C
3.128
−6.294
−28.7

615
ALA88
O
2.602
−7.389
−28.494

616
ALA88
CB
3.115
−3.89
−29.745

617
LYS89
N
4.291
−5.911
−28.057

618
LYS89
CA
4.945
−6.782
−27.079

619
LYS89
C
5.754
−5.89
−26.126

620
LYS89
O
5.385
−5.663
−24.971

621
LYS89
CB
5.825
−7.83
−27.788

622
LYS89
CG
6.606
−8.738
−26.825

623
LYS89
CD
7.485
−9.72
−27.607

624
LYS89
CE
8.029
−10.844
−26.742

625
LYS89
NZ
9.338
−10.527
−26.142

626
ARG90
N
6.881
−5.351
−26.721

627
ARG90
CA
7.917
−4.637
−25.989

628
ARG90
C
7.456
−3.225
−25.613

629
ARG90
O
6.494
−2.665
−26.128

630
ARG90
CB
9.216
−4.573
−26.818

631
ARG90
CG
10.046
−5.857
−26.712

632
ARG90
CD
10.86
−5.887
−25.426

633
ARG90
NE
11.405
−7.218
−25.152

634
ARG90
CZ
12.701
−7.569
−25.276

635
ARG90
NH1
13.526
−6.914
−26.122

636
ARG90
NH2
13.203
−8.576
−24.542

637
LEU91
N
8.235
−2.676
−24.617

638
LEU91
CA
7.904
−1.434
−23.919

639
LEU91
C
9.226
−0.664
−23.931

640
LEU91
O
10.235
−1.123
−23.392

641
LEU91
CB
7.475
−1.815
−22.498

642
LEU91
CG
6.487
−0.843
−21.846

643
LEU91
CD1
5.945
−1.465
−20.56

644
LEU91
CD2
7.114
0.509
−21.527

645
ASP92
N
9.214
0.48
−24.704

646
ASP92
CA
10.404
1.319
−24.881

647
ASP92
C
11.496
0.478
−25.612

648
ASP92
O
11.245
−0.57
−26.213

649
ASP92
CB
10.877
1.95
−23.572

650
ASP92
CG
9.809
2.796
−22.89

651
ASP92
OD1
9.046
3.441
−23.668

652
ASP92
OD2
9.837
2.781
−21.626

653
LEU93
N
12.768
1.028
−25.618

654
LEU93
CA
13.922
0.28
−26.105

655
LEU93
C
14.741
−0.175
−24.876

656
LEU93
O
14.723
−1.344
−24.474

657
LEU93
CB
14.753
1.108
−27.099

658
LEU93
CG
14.023
1.446
−28.416

659
LEU93
CD1
14.893
2.381
−29.261

660
LEU93
CD2
13.669
0.2
−29.23

661
CYS94
N
15.447
0.831
−24.233

662
CYS94
CA
16.324
0.577
−23.09

663
CYS94
C
16.131
1.7
−22.062

664
CYS94
O
15.357
1.583
−21.113

665
CYS94
CB
17.803
0.423
−23.481

666
CYS94
SG
18.154
−1.146
−24.337

667
GLN95
N
16.809
2.875
−22.309

668
GLN95
CA
16.828
3.977
−21.343

669
GLN95
C
15.595
4.88
−21.519

670
GLN95
O
15.666
6.101
−21.667

671
GLN95
CB
18.128
4.782
−21.468

672
GLN95
CG
19.35
3.971
−21.037

673
GLN95
CD
20.631
4.716
−21.332

674
GLN95
OE1
21.398
4.387
−22.23

675
GLN95
NE2
20.868
5.796
−20.532

676
GLY96
N
14.387
4.241
−21.336

677
GLY96
CA
13.113
4.941
−21.412

678
GLY96
C
12.794
5.775
−20.17

679
GLY96
O
11.648
5.904
−19.733

680
ILE97
N
13.836
6.527
−19.667

681
ILE97
CA
13.733
7.329
−18.442

682
ILE97
C
13.041
8.673
−18.791

683
ILE97
O
13.56
9.771
−18.609

684
ILE97
CB
15.122
7.531
−17.772

685
ILE97
CG1
15.926
6.211
−17.692

686
ILE97
CG2
14.949
8.124
−16.362

687
ILE97
CD1
17.34
6.378
−17.148

688
VAL98
N
11.751
8.517
−19.265

689
VAL98
CA
10.927
9.621
−19.757

690
VAL98
C
9.429
9.286
−19.558

691
VAL98
O
8.531
9.843
−20.19

692
VAL98
CB
11.221
9.994
−21.234

693
VAL98
CG1
12.475
10.859
−21.382

694
VAL98
CG2
11.335
8.767
−22.145

695
GLY99
N
9.185
8.415
−18.514

696
GLY99
CA
7.875
7.865
−18.235

697
GLY99
C
7.657
7.649
−16.74

698
GLY99
O
8.578
7.612
−15.928

699
ASP100
N
6.324
7.452
−16.42

700
ASP100
CA
5.893
7.06
−15.077

701
ASP100
C
5.918
5.515
−15.027

702
ASP100
O
5.893
4.805
−16.031

703
ASP100
CB
4.487
7.593
−14.83

704
ASP100
CG
4.12
7.565
−13.351

705
ASP100
OD1
3.671
8.643
−12.877

706
ASP100
OD2
4.264
6.429
−12.793

707
CYS101
N
5.865
4.992
−13.749

708
CYS101
CA
5.769
3.556
−13.534

709
CYS101
C
4.373
3.044
−13.937

710
CYS101
O
4.226
1.887
−14.348

711
CYS101
CB
6.133
3.221
−12.089

712
CYS101
SG
6.148
1.438
−11.724

713
TRP102
N
3.29
3.904
−13.831

714
TRP102
CA
1.957
3.399
−14.203

715
TRP102
C
1.878
3.08
−15.714

716
TRP102
O
1.076
2.263
−16.17

717
TRP102
CB
0.751
4.239
−13.763

718
TRP102
CG
0.781
5.685
−14.133

719
TRP102
CD1
1.058
6.715
−13.259

720
TRP102
CD2
0.498
6.294
−15.401

721
TRP102
NE1
1.069
7.893
−13.955

722
TRP102
CE2
0.713
7.668
−15.262

723
TRP102
CE3
0.088
5.808
−16.661

724
TRP102
CZ2
0.584
8.568
−16.325

725
TRP102
CZ3
−0.042
6.694
−17.735

726
TRP102
CH2
0.205
8.052
−17.567

727
PHE103
N
2.748
3.808
−16.5

728
PHE103
CA
2.834
3.674
−17.967

729
PHE103
C
3.477
2.303
−18.263

730
PHE103
O
3.184
1.626
−19.246

731
PHE103
CB
3.697
4.823
−18.521

732
PHE103
CG
3.647
5.182
−19.989

733
PHE103
CD1
2.98
4.439
−20.966

734
PHE103
CD2
4.345
6.338
−20.391

735
PHE103
CE1
3.011
4.843
−22.306

736
PHE103
CE2
4.371
6.743
−21.725

737
PHE103
CZ
3.701
5.994
−22.684

738
LEU104
N
4.471
1.954
−17.371

739
LEU104
CA
5.153
0.669
−17.416

740
LEU104
C
4.232
−0.452
−16.89

741
LEU104
O
4.292
−1.604
−17.331

742
LEU104
CB
6.453
0.729
−16.608

743
LEU104
CG
7.691
1.153
−17.425

744
LEU104
CD1
7.519
2.468
−18.183

745
LEU104
CD2
8.893
1.266
−16.486

746
ALA105
N
3.406
−0.101
−15.834

747
ALA105
CA
2.56
−1.101
−15.193

748
ALA105
C
1.429
−1.517
−16.151

749
ALA105
O
1.062
−2.692
−16.237

750
ALA105
CB
1.951
−0.585
−13.898

751
ALA106
N
0.819
−0.484
−16.85

752
ALA106
CA
−0.432
−0.724
−17.57

753
ALA106
C
−0.204
−1.675
−18.754

754
ALA106
O
−1.054
−2.479
−19.141

755
ALA106
CB
−1.013
0.582
−18.097

756
LEU107
N
1.009
−1.53
−19.398

757
LEU107
CA
1.321
−2.176
−20.673

758
LEU107
C
1.718
−3.678
−20.575

759
LEU107
O
2.258
−4.293
−21.501

760
LEU107
CB
2.384
−1.374
−21.433

761
LEU107
CG
1.878
−0.061
−22.059

762
LEU107
CD1
3.035
0.663
−22.753

763
LEU107
CD2
0.74
−0.303
−23.051

764
GLN108
N
1.244
−4.303
−19.443

765
GLN108
CA
1.063
−5.742
−19.321

766
GLN108
C
−0.337
−6.131
−19.827

767
GLN108
O
−0.557
−7.222
−20.355

768
GLN108
CB
1.183
−6.173
−17.853

769
GLN108
CG
2.621
−6.422
−17.41

770
GLN108
CD
3.582
−5.274
−17.628

771
GLN108
OE1
4.64
−5.424
−18.24

772
GLN108
NE2
3.248
−4.089
−17.05

773
ALA109
N
−1.359
−5.255
−19.525

774
ALA109
CA
−2.772
−5.614
−19.668

775
ALA109
C
−3.291
−5.495
−21.117

776
ALA109
O
−4.39
−5.022
−21.399

777
ALA109
CB
−3.596
−4.765
−18.713

778
LEU110
N
−2.462
−6.089
−22.051

779
LEU110
CA
−2.756
−6.142
−23.476

780
LEU110
C
−2.279
−7.502
−24.017

781
LEU110
O
−1.669
−7.63
−25.075

782
LEU110
CB
−2.121
−5.001
−24.287

783
LEU110
CG
−2.629
−3.591
−23.935

784
LEU110
CD1
−1.731
−2.934
−22.892

785
LEU110
CD2
−2.658
−2.71
−25.186

786
ALA111
N
−2.72
−8.579
−23.265

787
ALA111
CA
−2.753
−9.915
−23.857

788
ALA111
C
−4.101
−10.024
−24.608

789
ALA111
O
−4.773
−9.031
−24.91

790
ALA111
CB
−2.558
−10.955
−22.762

791
LEU112
N
−4.465
−11.29
−25.015

792
LEU112
CA
−5.86
−11.58
−25.354

793
LEU112
C
−6.414
−12.161
−24.046

794
LEU112
O
−5.918
−13.188
−23.572

795
LEU112
CB
−5.952
−12.64
−26.461

796
LEU112
CG
−5.261
−12.256
−27.785

797
LEU112
CD1
−5.34
−13.427
−28.769

798
LEU112
CD2
−5.866
−11.005
−28.417

799
HIS113
N
−7.43
−11.444
−23.451

800
HIS113
CA
−7.821
−11.611
−22.048

801
HIS113
C
−6.923
−10.665
−21.229

802
HIS113
O
−5.785
−10.341
−21.566

803
HIS113
CB
−7.778
−13.012
−21.426

804
HIS113
CG
−8.611
−14.02
−22.134

805
HIS113
ND1
−8.095
−14.823
−23.122

806
HIS113
CD2
−9.929
−14.406
−22.032

807
HIS113
CE1
−9.092
−15.645
−23.555

808
HIS113
NE2
−10.212
−15.424
−22.906

809
GLN114
N
−7.504
−10.22
−20.054

810
GLN114
CA
−6.884
−9.215
−19.194

811
GLN114
C
−6.983
−7.797
−19.8

812
GLN114
O
−6.316
−6.849
−19.385

813
GLN114
CB
−5.444
−9.521
−18.747

814
GLN114
CG
−5.258
−10.965
−18.283

815
GLN114
CD
−4.009
−11.203
−17.462

816
GLN114
OE1
−4.009
−11.949
−16.481

817
GLN114
NE2
−2.866
−10.614
−17.913

818
ASP115
N
−7.986
−7.644
−20.739

819
ASP115
CA
−8.063
−6.457
−21.592

820
ASP115
C
−8.661
−5.284
−20.776

821
ASP115
O
−9.86
−5.006
−20.77

822
ASP115
CB
−8.938
−6.751
−22.812

823
ASP115
CG
−8.176
−7.678
−23.745

824
ASP115
OD1
−8.126
−8.901
−23.421

825
ASP115
OD2
−7.654
−7.126
−24.764

826
ILE116
N
−7.728
−4.588
−20.009

827
ILE116
CA
−8.165
−3.488
−19.133

828
ILE116
C
−8.463
−2.254
−20.018

829
ILE116
O
−9.325
−1.423
−19.726

830
ILE116
CB
−7.086
−3.125
−18.066

831
ILE116
CG1
−6.977
−4.238
−16.998

832
ILE116
CG2
−7.362
−1.775
−17.38

833
ILE116
CD1
−5.89
−3.988
−15.958

834
LEU117
N
−7.566
−2.046
−21.058

835
LEU117
CA
−7.268
−0.678
−21.504

836
LEU117
C
−8.491
0.028
−22.113

837
LEU117
O
−8.609
1.255
−22.1

838
LEU117
CB
−6.122
−0.667
−22.53

839
LEU117
CG
−4.72
−0.396
−21.943

840
LEU117
CD1
−4.559
1.055
−21.489

841
LEU117
CD2
−4.346
−1.348
−20.81

842
SER118
N
−9.408
−0.805
−22.71

843
SER118
CA
−10.624
−0.306
−23.348

844
SER118
C
−11.65
0.289
−22.366

845
SER118
O
−12.654
0.877
−22.767

846
SER118
CB
−11.286
−1.413
−24.169

847
SER118
OG
−11.43
−2.584
−23.363

848
ARG119
N
−11.355
0.143
−21.025

849
ARG119
CA
−12.143
0.802
−19.988

850
ARG119
C
−11.707
2.275
−19.855

851
ARG119
O
−12.455
3.127
−19.381

852
ARG119
CB
−11.894
0.161
−18.62

853
ARG119
CG
−12.335
−1.297
−18.522

854
ARG119
CD
−11.739
−1.974
−17.293

855
ARG119
NE
−12.298
−1.457
−16.042

856
ARG119
CZ
−11.803
−0.482
−15.244

857
ARG119
NH1
−10.711
0.247
−15.555

858
ARG119
NH2
−12.452
−0.258
−14.089

859
VAL120
N
−10.362
2.488
−20.094

860
VAL120
CA
−9.706
3.779
−19.884

861
VAL120
C
−9.694
4.555
−21.214

862
VAL120
O
−9.932
5.766
−21.253

863
VAL120
CB
−8.269
3.569
−19.347

864
VAL120
CG1
−7.529
4.896
−19.144

865
VAL120
CG2
−8.281
2.797
−18.023

866
VAL121
N
−9.242
3.824
−22.299

867
VAL121
CA
−8.985
4.393
−23.615

868
VAL121
C
−10.137
3.956
−24.546

869
VAL121
O
−10.169
2.831
−25.059

870
VAL121
CB
−7.629
3.889
−24.177

871
VAL121
CG1
−7.284
4.624
−25.476

872
VAL121
CG2
−6.481
4.066
−23.177

873
PRO122
N
−11.151
4.858
−24.793

874
PRO122
CA
−12.257
4.516
−25.681

875
PRO122
C
−11.727
4.64
−27.122

876
PRO122
O
−11.655
5.707
−27.736

877
PRO122
CB
−13.34
5.54
−25.351

878
PRO122
CG
−12.56
6.749
−24.854

879
PRO122
CD
−11.376
6.132
−24.132

880
LEU123
N
−11.265
3.444
−27.648

881
LEU123
CA
−10.478
3.372
−28.894

882
LEU123
C
−11.285
3.658
−30.198

883
LEU123
O
−11.001
3.142
−31.278

884
LEU123
CB
−9.802
1.984
−29.007

885
LEU123
CG
−8.58
1.794
−28.085

886
LEU123
CD1
−8.246
0.307
−27.948

887
LEU123
CD2
−7.356
2.544
−28.613

888
ASN124
N
−12.211
4.68
−30.117

889
ASN124
CA
−12.829
5.29
−31.3

890
ASN124
C
−12.104
6.607
−31.619

891
ASN124
O
−12.689
7.68
−31.747

892
ASN124
CB
−14.341
5.477
−31.162

893
ASN124
CG
−14.79
6.026
−29.825

894
ASN124
OD1
−14.992
7.218
−29.597

895
ASN124
ND2
−14.98
5.078
−28.858

896
GLN125
N
−10.738
6.468
−31.766

897
GLN125
CA
−9.826
7.606
−31.832

898
GLN125
C
−8.631
7.22
−32.717

899
GLN125
O
−8.277
6.051
−32.867

900
GLN125
CB
−9.337
7.976
−30.426

901
GLN125
CG
−10.449
8.556
−29.557

902
GLN125
CD
−9.954
8.892
−28.177

903
GLN125
OE1
−9.565
10.014
−27.87

904
GLN125
NE2
−9.96
7.87
−27.275

905
SER126
N
−7.977
8.292
−33.292

906
SER126
CA
−6.903
8.121
−34.272

907
SER126
C
−6.247
9.491
−34.529

908
SER126
O
−6.72
10.537
−34.089

909
SER126
CB
−7.434
7.571
−35.601

910
SER126
OG
−6.393
7.517
−36.579

911
PHE127
N
−5.107
9.413
−35.315

912
PHE127
CA
−4.435
10.605
−35.843

913
PHE127
C
−4.861
10.96
−37.282

914
PHE127
O
−4.327
11.876
−37.907

915
PHE127
CB
−2.908
10.456
−35.78

916
PHE127
CG
−2.362
10.971
−34.47

917
PHE127
CD1
−2.161
10.109
−33.388

918
PHE127
CD2
−2.091
12.334
−34.312

919
PHE127
CE1
−1.653
10.589
−32.181

920
PHE127
CE2
−1.612
12.819
−33.096

921
PHE127
CZ
−1.378
11.946
−32.035

922
THR128
N
−5.945
10.264
−37.77

923
THR128
CA
−6.502
10.531
−39.093

924
THR128
C
−8.034
10.544
−38.983

925
THR128
O
−8.707
11.526
−39.309

926
THR128
CB
−5.992
9.555
−40.178

927
THR128
OG1
−5.571
8.303
−39.635

928
THR128
CG2
−4.785
10.13
−40.915

929
GLU129
N
−8.608
9.393
−38.494

930
GLU129
CA
−10.035
9.112
−38.601

931
GLU129
C
−10.811
10.009
−37.614

932
GLU129
O
−11.205
9.625
−36.517

933
GLU129
CB
−10.335
7.629
−38.31

934
GLU129
CG
−9.759
6.652
−39.339

935
GLU129
CD
−8.271
6.311
−39.226

936
GLU129
OE1
−7.929
5.198
−39.697

937
GLU129
OE2
−7.53
7.208
−38.687

938
LYS130
N
−11.005
11.296
−38.093

939
LYS130
CA
−11.731
12.34
−37.373

940
LYS130
C
−10.877
12.95
−36.242

941
LYS130
O
−11.355
13.334
−35.177

942
LYS130
CB
−13.126
11.929
−36.873

943
LYS130
CG
−13.995
11.284
−37.956

944
LYS130
CD
−15.417
11.04
−37.448

945
LYS130
CE
−16.274
10.388
−38.522

946
LYS130
NZ
−17.636
10.16
−37.984

947
TYR131
N
−9.562
13.204
−36.609

948
TYR131
CA
−8.563
13.568
−35.589

949
TYR131
C
−8.9
14.925
−34.947

950
TYR131
O
−8.836
15.109
−33.729

951
TYR131
CB
−7.175
13.608
−36.26

952
TYR131
CG
−6.046
14.306
−35.541

953
TYR131
CD1
−5.831
14.159
−34.166

954
TYR131
CD2
−5.155
15.104
−36.281

955
TYR131
CE1
−4.787
14.844
−33.54

956
TYR131
CE2
−4.101
15.77
−35.655

957
TYR131
CZ
−3.927
15.641
−34.285

958
TYR131
OH
−2.881
16.305
−33.712

959
ALA132
N
−9.049
15.977
−35.833

960
ALA132
CA
−9.562
17.291
−35.428

961
ALA132
C
−8.797
18.069
−34.324

962
ALA132
O
−9.201
19.152
−33.891

963
ALA132
CB
−11.05
17.221
−35.103

964
GLY133
N
−7.619
17.503
−33.892

965
GLY133
CA
−6.856
18.065
−32.802

966
GLY133
C
−7.431
17.783
−31.41

967
GLY133
O
−7.144
18.534
−30.47

968
ILE134
N
−8.174
16.624
−31.274

969
ILE134
CA
−8.908
16.289
−30.044

970
ILE134
C
−8.793
14.785
−29.724

971
ILE134
O
−8.765
13.926
−30.603

972
ILE134
CB
−10.397
16.728
−30.16

973
ILE134
CG1
−11.124
16.686
−28.801

974
ILE134
CG2
−11.169
15.94
−31.224

975
ILE134
CD1
−12.511
17.313
−28.847

976
PHE135
N
−8.83
14.489
−28.371

977
PHE135
CA
−8.833
13.117
−27.856

978
PHE135
C
−9.685
13.073
−26.568

979
PHE135
O
−10.012
14.085
−25.944

980
PHE135
CB
−7.413
12.624
−27.534

981
PHE135
CG
−6.553
12.377
−28.746

982
PHE135
CD1
−5.529
13.267
−29.088

983
PHE135
CD2
−6.777
11.255
−29.554

984
PHE135
CE1
−4.741
13.032
−30.215

985
PHE135
CE2
−6.003
11.033
−30.691

986
PHE135
CZ
−4.989
11.924
−31.023

987
ARG136
N
−10.009
11.798
−26.139

988
ARG136
CA
−10.796
11.546
−24.941

989
ARG136
C
−10.416
10.231
−24.233

990
ARG136
O
−9.984
9.248
−24.834

991
ARG136
CB
−12.308
11.593
−25.207

992
ARG136
CG
−12.821
10.558
−26.217

993
ARG136
CD
−14.35
10.528
−26.238

994
ARG136
NE
−14.865
9.659
−27.303

995
ARG136
CZ
−16.136
9.742
−27.779

996
ARG136
NH1
−16.503
8.988
−28.829

997
ARG136
NH2
−17.054
10.552
−27.241

998
PHE137
N
−10.687
10.254
−22.871

999
PHE137
CA
−10.321
9.168
−21.959

1000
PHE137
C
−11.354
9.108
−20.824

1001
PHE137
O
−11.947
10.111
−20.421

1002
PHE137
CB
−8.944
9.385
−21.316

1003
PHE137
CG
−7.793
9.34
−22.287

1004
PHE137
CD1
−7.236
10.527
−22.776

1005
PHE137
CD2
−7.258
8.117
−22.706

1006
PHE137
CE1
−6.147
10.489
−23.643

1007
PHE137
CE2
−6.162
8.083
−23.57

1008
PHE137
CZ
−5.604
9.269
−24.035

1009
TRP138
N
−11.51
7.859
−20.254

1010
TRP138
CA
−12.345
7.665
−19.064

1011
TRP138
C
−11.447
7.497
−17.827

1012
TRP138
O
−10.396
6.86
−17.86

1013
TRP138
CB
−13.233
6.421
−19.182

1014
TRP138
CG
−14.47
6.651
−19.997

1015
TRP138
CD1
−14.621
6.385
−21.343

1016
TRP138
CD2
−15.731
7.146
−19.529

1017
TRP138
NE1
−15.902
6.7
−21.705

1018
TRP138
CE2
−16.607
7.155
−20.616

1019
TRP138
CE3
−16.213
7.579
−18.276

1020
TRP138
CZ2
−17.942
7.566
−20.511

1021
TRP138
CZ3
−17.545
7.994
−18.155

1022
TRP138
CH2
−18.395
7.984
−19.257

1023
PHE139
N
−11.973
8.052
−16.675

1024
PHE139
CA
−11.306
7.973
−15.369

1025
PHE139
C
−12.384
7.696
−14.306

1026
PHE139
O
−13.538
8.118
−14.423

1027
PHE139
CB
−10.641
9.303
−14.98

1028
PHE139
CG
−9.331
9.613
−15.658

1029
PHE139
CD1
−9.286
10.091
−16.972

1030
PHE139
CD2
−8.136
9.507
−14.936

1031
PHE139
CE1
−8.072
10.481
−17.539

1032
PHE139
CE2
−6.928
9.916
−15.495

1033
PHE139
CZ
−6.896
10.405
−16.798

1034
TRP140
N
−11.939
7.013
−13.188

1035
TRP140
CA
−12.701
7.014
−11.929

1036
TRP140
C
−12.057
8.105
−11.072

1037
TRP140
O
−10.834
8.217
−11.006

1038
TRP140
CB
−12.571
5.667
−11.208

1039
TRP140
CG
−13.383
5.54
−9.948

1040
TRP140
CD1
−14.64
4.977
−9.842

1041
TRP140
CD2
−12.984
5.899
−8.615

1042
TRP140
NE1
−14.998
4.949
−8.521

1043
TRP140
CE2
−14.019
5.533
−7.753

1044
TRP140
CE3
−11.825
6.474
−8.053

1045
TRP140
CZ2
−13.959
5.73
−6.367

1046
TRP140
CZ3
−11.752
6.684
−6.671

1047
TRP140
CH2
−12.806
6.317
−5.841

1048
HIS141
N
−12.917
8.884
−10.331

1049
HIS141
CA
−12.408
9.837
−9.352

1050
HIS141
C
−13.458
10.025
−8.248

1051
HIS141
O
−14.635
10.302
−8.48

1052
HIS141
CB
−12.141
11.23
−9.934

1053
HIS141
CG
−11.032
11.334
−10.919

1054
HIS141
ND1
−9.75
10.877
−10.725

1055
HIS141
CD2
−11.005
11.901
−12.174

1056
HIS141
CE1
−9.024
11.237
−11.83

1057
HIS141
NE2
−9.754
11.864
−12.721

1058
TYR142
N
−12.985
9.871
−6.958

1059
TYR142
CA
−13.632
10.526
−5.814

1060
TYR142
C
−15.113
10.164
−5.57

1061
TYR142
O
−15.861
10.868
−4.883

1062
TYR142
CB
−13.428
12.057
−5.844

1063
TYR142
CG
−11.989
12.464
−5.617

1064
TYR142
CD1
−11.292
13.263
−6.54

1065
TYR142
CD2
−11.335
12.063
−4.448

1066
TYR142
CE1
−9.96
13.636
−6.306

1067
TYR142
CE2
−10.014
12.428
−4.224

1068
TYR142
CZ
−9.338
13.215
−5.142

1069
TYR142
OH
−8.073
13.56
−4.798

1070
GLY143
N
−15.476
8.919
−6.043

1071
GLY143
CA
−16.832
8.412
−5.971

1072
GLY143
C
−17.655
8.645
−7.241

1073
GLY143
O
−18.883
8.482
−7.266

1074
ASN144
N
−16.955
8.951
−8.384

1075
ASN144
CA
−17.596
9.151
−9.681

1076
ASN144
C
−16.688
8.618
−10.801

1077
ASN144
O
−15.464
8.573
−10.704

1078
ASN144
CB
−17.922
10.63
−9.913

1079
ASN144
CG
−19.33
11.081
−9.576

1080
ASN144
OD1
−19.774
12.166
−9.944

1081
ASN144
ND2
−20.118
10.253
−8.821

1082
TRP145
N
−17.387
8.237
−11.939

1083
TRP145
CA
−16.681
8.01
−13.204

1084
TRP145
C
−16.708
9.355
−13.94

1085
TRP145
O
−17.634
10.157
−13.793

1086
TRP145
CB
−17.356
6.938
−14.068

1087
TRP145
CG
−16.948
5.548
−13.681

1088
TRP145
CD1
−17.601
4.704
−12.805

1089
TRP145
CD2
−15.793
4.843
−14.152

1090
TRP145
NE1
−16.89
3.535
−12.723

1091
TRP145
CE2
−15.768
3.603
−13.515

1092
TRP145
CE3
−14.756
5.154
−15.056

1093
TRP145
CZ2
−14.741
2.671
−13.713

1094
TRP145
CZ3
−13.723
4.237
−15.269

1095
TRP145
CH2
−13.715
3.018
−14.599

1096
VAL146
N
−15.638
9.562
−14.788

1097
VAL146
CA
−15.39
10.871
−15.385

1098
VAL146
C
−14.852
10.644
−16.812

1099
VAL146
O
−13.837
9.963
−17.003

1100
VAL146
CB
−14.358
11.689
−14.569

1101
VAL146
CG1
−14.207
13.097
−15.155

1102
VAL146
CG2
−14.719
11.766
−13.081

1103
PRO147
N
−15.549
11.254
−17.843

1104
PRO147
CA
−15.043
11.286
−19.215

1105
PRO147
C
−14.214
12.571
−19.39

1106
PRO147
O
−14.723
13.693
−19.373

1107
PRO147
CB
−16.31
11.349
−20.067

1108
PRO147
CG
−17.313
12.106
−19.2

1109
PRO147
CD
−16.917
11.758
−17.771

1110
VAL148
N
−12.848
12.386
−19.479

1111
VAL148
CA
−11.973
13.532
−19.714

1112
VAL148
C
−11.758
13.62
−21.235

1113
VAL148
O
−11.456
12.641
−21.92

1114
VAL148
CB
−10.63
13.404
−18.97

1115
VAL148
CG1
−9.735
14.62
−19.234

1116
VAL148
CG2
−10.856
13.273
−17.459

1117
VAL149
N
−11.918
14.896
−21.747

1118
VAL149
CA
−11.758
15.208
−23.164

1119
VAL149
C
−10.691
16.306
−23.249

1120
VAL149
O
−10.646
17.256
−22.459

1121
VAL149
CB
−13.078
15.659
−23.809

1122
VAL149
CG1
−12.86
15.9
−25.303

1123
VAL149
CG2
−14.181
14.618
−23.583

1124
ILE150
N
−9.774
16.139
−24.272

1125
ILE150
CA
−8.459
16.763
−24.18

1126
ILE150
C
−7.864
16.991
−25.584

1127
ILE150
O
−8.123
16.277
−26.552

1128
ILE150
CB
−7.579
15.931
−23.204

1129
ILE150
CG1
−7.164
14.539
−23.729

1130
ILE150
CG2
−6.394
16.721
−22.679

1131
ILE150
CD1
−5.892
14.481
−24.561

1132
ASP151
N
−7.006
18.07
−25.645

1133
ASP151
CA
−6.201
18.426
−26.811

1134
ASP151
C
−4.805
17.775
−26.706

1135
ASP151
O
−4.388
17.224
−25.683

1136
ASP151
CB
−6.032
19.945
−26.887

1137
ASP151
CG
−5.19
20.42
−25.713

1138
ASP151
OD1
−4.284
21.264
−25.964

1139
ASP151
OD2
−5.384
19.863
−24.585

1140
ASP152
N
−4.025
17.991
−27.816

1141
ASP152
CA
−2.677
17.478
−27.987

1142
ASP152
C
−1.662
18.603
−28.256

1143
ASP152
O
−0.641
18.39
−28.91

1144
ASP152
CB
−2.65
16.414
−29.084

1145
ASP152
CG
−3.094
16.94
−30.439

1146
ASP152
OD1
−2.806
16.218
−31.441

1147
ASP152
OD2
−3.733
18.037
−30.439

1148
ARG153
N
−1.855
19.793
−27.564

1149
ARG153
CA
−0.747
20.739
−27.456

1150
ARG153
C
0.246
20.139
−26.438

1151
ARG153
O
−0.025
20.021
−25.241

1152
ARG153
CB
−1.151
22.137
−26.954

1153
ARG153
CG
−1.674
23.084
−28.031

1154
ARG153
CD
−3.156
22.953
−28.326

1155
ARG153
NE
−3.946
24.076
−27.803

1156
ARG153
CZ
−4.465
24.31
−26.588

1157
ARG153
NH1
−4.293
23.508
−25.537

1158
ARG153
NH2
−5.257
25.397
−26.457

1159
LEU154
N
1.429
19.688
−26.982

1160
LEU154
CA
2.505
19.144
−26.165

1161
LEU154
C
3.541
20.264
−25.943

1162
LEU154
O
3.869
21.026
−26.862

1163
LEU154
CB
3.194
17.955
−26.85

1164
LEU154
CG
2.267
16.758
−27.143

1165
LEU154
CD1
3.043
15.674
−27.891

1166
LEU154
CD2
1.648
16.167
−25.875

1167
PRO155
N
4.111
20.347
−24.685

1168
PRO155
CA
5.113
21.362
−24.364

1169
PRO155
C
6.512
20.815
−24.687

1170
PRO155
O
6.887
19.688
−24.347

1171
PRO155
CB
4.968
21.566
−22.858

1172
PRO155
CG
4.548
20.186
−22.366

1173
PRO155
CD
3.654
19.668
−23.481

1174
VAL156
N
7.327
21.709
−25.354

1175
VAL156
CA
8.68
21.349
−25.743

1176
VAL156
C
9.633
22.52
−25.452

1177
VAL156
O
9.287
23.695
−25.577

1178
VAL156
CB
8.788
20.883
−27.216

1179
VAL156
CG1
7.781
19.785
−27.562

1180
VAL156
CG2
8.635
22.013
−28.231

1181
ASN157
N
10.914
22.138
−25.11

1182
ASN157
CA
12.032
23.084
−25.07

1183
ASN157
C
12.942
22.663
−26.224

1184
ASN157
O
13.399
21.524
−26.322

1185
ASN157
CB
12.82
23.005
−23.768

1186
ASN157
CG
12.778
24.303
−22.999

1187
ASN157
OD1
12.36
24.37
−21.846

1188
ASN157
ND2
13.288
25.39
−23.643

1189
GLU158
N
13.114
23.635
−27.193

1190
GLU158
CA
14.111
23.471
−28.257

1191
GLU158
C
13.939
22.143
−29.043

1192
GLU158
O
14.864
21.58
−29.619

1193
GLU158
CB
15.539
23.711
−27.735

1194
GLU158
CG
15.875
25.194
−27.503

1195
GLU158
CD
15.163
25.954
−26.384

1196
GLU158
OE1
14.01
25.532
−26.053

1197
GLU158
OE2
15.803
26.929
−25.881

1198
ALA159
N
12.617
21.738
−29.135

1199
ALA159
CA
12.147
20.492
−29.732

1200
ALA159
C
12.26
19.213
−28.87

1201
ALA159
O
11.813
18.139
−29.278

1202
ALA159
CB
12.681
20.249
−31.14

1203
GLY160
N
12.833
19.347
−27.627

1204
GLY160
CA
12.798
18.281
−26.635

1205
GLY160
C
11.549
18.465
−25.774

1206
GLY160
O
11.176
19.573
−25.389

1207
GLN161
N
10.863
17.298
−25.497

1208
GLN161
CA
9.536
17.315
−24.877

1209
GLN161
C
9.627
17.448
−23.346

1210
GLN161
O
10.562
16.979
−22.701

1211
GLN161
CB
8.748
16.054
−25.271

1212
GLN161
CG
8.339
16.079
−26.748

1213
GLN161
CD
7.893
14.73
−27.264

1214
GLN161
OE1
6.724
14.462
−27.521

1215
GLN161
NE2
8.897
13.818
−27.434

1216
LEU162
N
8.539
18.094
−22.773

1217
LEU162
CA
8.479
18.432
−21.343

1218
LEU162
C
7.22
17.826
−20.681

1219
LEU162
O
6.667
18.336
−19.709

1220
LEU162
CB
8.471
19.955
−21.132

1221
LEU162
CG
9.695
20.714
−21.671

1222
LEU162
CD1
9.416
22.218
−21.608

1223
LEU162
CD2
10.961
20.379
−20.884

1224
VAL163
N
6.852
16.608
−21.195

1225
VAL163
CA
5.733
15.782
−20.703

1226
VAL163
C
6.309
14.359
−20.709

1227
VAL163
O
7.323
14.092
−21.364

1228
VAL163
CB
4.505
16.045
−21.609

1229
VAL163
CG1
3.751
14.822
−22.116

1230
VAL163
CG2
3.528
16.978
−20.898

1231
PHE164
N
5.641
13.412
−19.96

1232
PHE164
CA
6.097
12.023
−19.996

1233
PHE164
C
5.696
11.42
−21.353

1234
PHE164
O
4.599
11.614
−21.871

1235
PHE164
CB
5.51
11.16
−18.874

1236
PHE164
CG
6.08
11.364
−17.485

1237
PHE164
CD1
5.246
11.166
−16.374

1238
PHE164
CD2
7.433
11.648
−17.25

1239
PHE164
CE1
5.739
11.272
−15.071

1240
PHE164
CE2
7.928
11.755
−15.947

1241
PHE164
CZ
7.081
11.568
−14.858

1242
VAL165
N
6.676
10.652
−21.956

1243
VAL165
CA
6.617
10.292
−23.37

1244
VAL165
C
7.345
8.961
−23.613

1245
VAL165
O
8.126
8.471
−22.805

1246
VAL165
CB
7.223
11.381
−24.302

1247
VAL165
CG1
6.328
12.612
−24.414

1248
VAL165
CG2
8.64
11.794
−23.892

1249
SER166
N
7.079
8.398
−24.848

1250
SER166
CA
7.919
7.347
−25.421

1251
SER166
C
7.498
7.205
−26.902

1252
SER166
O
6.799
8.053
−27.462

1253
SER166
CB
7.877
6.045
−24.628

1254
SER166
OG
8.632
5.033
−25.298

1255
SER167
N
8.079
6.144
−27.575

1256
SER167
CA
8.464
6.287
−28.98

1257
SER167
C
8.573
4.942
−29.715

1258
SER167
O
9.355
4.741
−30.642

1259
SER167
CB
9.76
7.099
−29.116

1260
SER167
OG
10.789
6.523
−28.311

1261
THR168
N
7.578
4.041
−29.385

1262
THR168
CA
7.352
2.822
−30.159

1263
THR168
C
5.861
2.433
−30.103

1264
THR168
O
4.999
3.146
−29.584

1265
THR168
CB
8.308
1.676
−29.773

1266
THR168
OG1
8.098
0.575
−30.674

1267
THR168
CG2
8.139
1.18
−28.343

1268
TYR169
N
5.555
1.224
−30.708

1269
TYR169
CA
4.235
0.981
−31.326

1270
TYR169
C
3.133
0.935
−30.247

1271
TYR169
O
1.952
1.171
−30.479

1272
TYR169
CB
4.186
−0.38
−32.048

1273
TYR169
CG
4.901
−0.542
−33.373

1274
TYR169
CD1
5.939
0.286
−33.819

1275
TYR169
CD2
4.514
−1.623
−34.188

1276
TYR169
CE1
6.569
0.048
−35.046

1277
TYR169
CE2
5.137
−1.86
−35.414

1278
TYR169
CZ
6.16
−1.023
−35.835

1279
TYR169
OH
6.741
−1.283
−37.041

1280
LYS170
N
3.604
0.444
−29.05

1281
LYS170
CA
2.798
0.211
−27.851

1282
LYS170
C
2.744
1.483
−26.973

1283
LYS170
O
1.97
1.612
−26.026

1284
LYS170
CB
3.513
−0.903
−27.078

1285
LYS170
CG
2.592
−1.758
−26.213

1286
LYS170
CD
3.445
−2.788
−25.473

1287
LYS170
CE
2.645
−3.746
−24.614

1288
LYS170
NZ
3.578
−4.381
−23.651

1289
ASN171
N
3.768
2.368
−27.234

1290
ASN171
CA
4.157
3.465
−26.36

1291
ASN171
C
3.766
4.86
−26.88

1292
ASN171
O
3.772
5.831
−26.123

1293
ASN171
CB
5.673
3.426
−26.177

1294
ASN171
CG
6.106
2.591
−24.996

1295
ASN171
OD1
6.751
1.552
−25.119

1296
ASN171
ND2
5.736
3.079
−23.775

1297
LEU172
N
3.56
4.976
−28.242

1298
LEU172
CA
3.524
6.295
−28.877

1299
LEU172
C
2.334
7.141
−28.378

1300
LEU172
O
1.156
6.825
−28.533

1301
LEU172
CB
3.413
6.16
−30.41

1302
LEU172
CG
4.79
6.179
−31.103

1303
LEU172
CD1
4.705
5.551
−32.493

1304
LEU172
CD2
5.329
7.605
−31.219

1305
PHE173
N
2.709
8.282
−27.695

1306
PHE173
CA
1.821
9.402
−27.38

1307
PHE173
C
0.666
9.132
−26.405

1308
PHE173
O
0.273
10.019
−25.637

1309
PHE173
CB
1.276
10.121
−28.626

1310
PHE173
CG
2.341
10.844
−29.423

1311
PHE173
CD1
2.506
10.572
−30.787

1312
PHE173
CD2
3.148
11.827
−28.829

1313
PHE173
CE1
3.466
11.258
−31.533

1314
PHE173
CE2
4.118
12.501
−29.574

1315
PHE173
CZ
4.274
12.219
−30.927

1316
TRP174
N
0.023
7.916
−26.48

1317
TRP174
CA
−1.29
7.75
−25.846

1318
TRP174
C
−1.183
8.012
−24.328

1319
TRP174
O
−2.097
8.524
−23.68

1320
TRP174
CB
−1.927
6.381
−26.136

1321
TRP174
CG
−1.211
5.23
−25.501

1322
TRP174
CD1
−0.168
4.507
−26.045

1323
TRP174
CD2
−1.461
4.683
−24.201

1324
TRP174
NE1
0.247
3.582
−25.124

1325
TRP174
CE2
−0.482
3.72
−23.964

1326
TRP174
CE3
−2.406
4.949
−23.187

1327
TRP174
CZ2
−0.367
3.063
−22.735

1328
TRP174
CZ3
−2.329
4.256
−21.975

1329
TRP174
CH2
−1.31
3.34
−21.745

1330
GLY175
N
0.002
7.587
−23.752

1331
GLY175
CA
0.236
7.682
−22.325

1332
GLY175
C
0.629
9.101
−21.926

1333
GLY175
O
0.44
9.536
−20.791

1334
ALA176
N
1.254
9.821
−22.928

1335
ALA176
CA
1.572
11.239
−22.756

1336
ALA176
C
0.261
12.029
−22.715

1337
ALA176
O
0.075
12.979
−21.955

1338
ALA176
CB
2.429
11.734
−23.913

1339
LEU177
N
−0.676
11.617
−23.645

1340
LEU177
CA
−1.98
12.249
−23.72

1341
LEU177
C
−2.785
11.896
−22.451

1342
LEU177
O
−3.58
12.7
−21.959

1343
LEU177
CB
−2.706
11.834
−25

1344
LEU177
CG
−2.049
12.401
−26.277

1345
LEU177
CD1
−2.554
11.649
−27.507

1346
LEU177
CD2
−2.312
13.898
−26.435

1347
LEU178
N
−2.592
10.625
−21.934

1348
LEU178
CA
−3.28
10.202
−20.707

1349
LEU178
C
−2.707
10.975
−19.493

1350
LEU178
O
−3.431
11.346
−18.565

1351
LEU178
CB
−3.153
8.688
−20.509

1352
LEU178
CG
−3.953
8.098
−19.331

1353
LEU178
CD1
−5.449
8.386
−19.425

1354
LEU178
CD2
−3.751
6.582
−19.292

1355
GLU179
N
−1.337
11.179
−19.493

1356
GLU179
CA
−0.666
11.977
−18.452

1357
GLU179
C
−1.269
13.394
−18.502

1358
GLU179
O
−1.645
13.991
−17.49

1359
GLU179
CB
0.855
11.976
−18.681

1360
GLU179
CG
1.656
12.821
−17.692

1361
GLU179
CD
2.28
14.011
−18.424

1362
GLU179
OE1
3.48
13.853
−18.808

1363
GLU179
OE2
1.514
15.003
−18.568

1364
LYS180
N
−1.378
13.922
−19.776

1365
LYS180
CA
−1.856
15.282
−19.97

1366
LYS180
C
−3.353
15.369
−19.581

1367
LYS180
O
−3.847
16.402
−19.118

1368
LYS180
CB
−1.6
15.696
−21.418

1369
LYS180
CG
−2.039
17.119
−21.728

1370
LYS180
CD
−1.673
17.5
−23.169

1371
LYS180
CE
−2.371
18.765
−23.644

1372
LYS180
NZ
−3.814
18.529
−23.623

1373
ALA181
N
−4.117
14.246
−19.843

1374
ALA181
CA
−5.532
14.194
−19.486

1375
ALA181
C
−5.69
14.205
−17.958

1376
ALA181
O
−6.638
14.765
−17.406

1377
ALA181
CB
−6.199
12.946
−20.04

1378
TYR182
N
−4.741
13.478
−17.262

1379
TYR182
CA
−4.747
13.443
−15.796

1380
TYR182
C
−4.457
14.878
−15.312

1381
TYR182
O
−5.095
15.396
−14.394

1382
TYR182
CB
−3.706
12.448
−15.261

1383
TYR182
CG
−3.807
11.985
−13.822

1384
TYR182
CD1
−2.727
11.247
−13.3

1385
TYR182
CD2
−4.931
12.18
−13.008

1386
TYR182
CE1
−2.776
10.707
−12.013

1387
TYR182
CE2
−4.982
11.63
−11.721

1388
TYR182
CZ
−3.915
10.88
−11.242

1389
TYR182
OH
−3.965
10.288
−10.012

1390
ALA183
N
−3.434
15.531
−15.988

1391
ALA183
CA
−3.038
16.884
−15.608

1392
ALA183
C
−4.202
17.867
−15.839

1393
ALA183
O
−4.4
18.834
−15.1

1394
ALA183
CB
−1.832
17.348
−16.408

1395
LYS184
N
−4.981
17.64
−16.97

1396
LYS184
CA
−5.99
18.628
−17.348

1397
LYS184
C
−7.037
18.763
−16.233

1398
LYS184
O
−7.581
19.841
−15.989

1399
LYS184
CB
−6.679
18.274
−18.681

1400
LYS184
CG
−7.882
19.184
−18.979

1401
LYS184
CD
−8.472
18.994
−20.377

1402
LYS184
CE
−9.794
19.745
−20.487

1403
LYS184
NZ
−10.324
19.656
−21.85

1404
LEU185
N
−7.438
17.574
−15.652

1405
LEU185
CA
−8.502
17.579
−14.661

1406
LEU185
C
−7.993
18.015
−13.276

1407
LEU185
O
−8.758
18.521
−12.443

1408
LEU185
CB
−9.19
16.216
−14.574

1409
LEU185
CG
−10.637
16.334
−14.048

1410
LEU185
CD1
−11.596
16.865
−15.116

1411
LEU185
CD2
−11.116
14.98
−13.546

1412
SER186
N
−6.679
17.712
−12.974

1413
SER186
CA
−6.082
18.2
−11.73

1414
SER186
C
−5.982
19.731
−11.809

1415
SER186
O
−6.408
20.446
−10.901

1416
SER186
CB
−4.744
17.544
−11.396

1417
SER186
OG
−3.726
17.894
−12.319

1418
GLY187
N
−5.389
20.215
−12.954

1419
GLY187
CA
−5.295
21.628
−13.244

1420
GLY187
C
−4.073
21.958
−14.088

1421
GLY187
O
−4.101
22.845
−14.942

1422
SER188
N
−2.929
21.274
−13.737

1423
SER188
CA
−1.635
21.633
−14.299

1424
SER188
C
−0.634
20.464
−14.245

1425
SER188
O
−0.86
19.395
−13.679

1426
SER188
CB
−1.08
22.931
−13.683

1427
SER188
OG
−1.317
23.08
−12.285

1428
TYR189
N
0.559
20.686
−14.923

1429
TYR189
CA
1.584
19.634
−14.924

1430
TYR189
C
2.307
19.583
−13.564

1431
TYR189
O
2.837
18.545
−13.161

1432
TYR189
CB
2.64
19.809
−16.024

1433
TYR189
CG
2.104
19.641
−17.427

1434
TYR189
CD1
2.367
20.614
−18.397

1435
TYR189
CD2
1.388
18.501
−17.808

1436
TYR189
CE1
1.864
20.5
−19.69

1437
TYR189
CE2
0.894
18.376
−19.107

1438
TYR189
CZ
1.125
19.379
−20.036

1439
TYR189
OH
0.641
19.22
−21.301

1440
GLU190
N
2.384
20.786
−12.876

1441
GLU190
CA
3.168
20.899
−11.632

1442
GLU190
C
2.609
19.903
−10.583

1443
GLU190
O
3.317
19.387
−9.715

1444
GLU190
CB
3.086
22.345
−11.112

1445
GLU190
CG
3.854
22.683
−9.83

1446
GLU190
CD
5.371
22.781
−9.988

1447
GLU190
OE1
5.914
21.822
−10.607

1448
GLU190
OE2
5.92
23.794
−9.457

1449
ASP191
N
1.247
19.682
−10.688

1450
ASP191
CA
0.426
19.049
−9.662

1451
ASP191
C
0.887
17.614
−9.366

1452
ASP191
O
0.648
17.058
−8.296

1453
ASP191
CB
−1.033
18.939
−10.123

1454
ASP191
CG
−1.597
20.089
−10.935

1455
ASP191
OD1
−2.749
19.891
−11.438

1456
ASP191
OD2
−0.842
21.096
−11.106

1457
LEU192
N
1.439
16.958
−10.45

1458
LEU192
CA
1.598
15.508
−10.482

1459
LEU192
C
2.801
15.062
−9.63

1460
LEU192
O
2.951
13.901
−9.246

1461
LEU192
CB
1.795
15.005
−11.92

1462
LEU192
CG
0.622
15.292
−12.882

1463
LEU192
CD1
0.972
14.781
−14.281

1464
LEU192
CD2
−0.69
14.659
−12.415

1465
GLN193
N
3.748
16.036
−9.4

1466
GLN193
CA
4.968
15.752
−8.659

1467
GLN193
C
4.574
15.629
−7.176

1468
GLN193
O
4.262
16.607
−6.498

1469
GLN193
CB
5.987
16.876
−8.833

1470
GLN193
CG
6.408
17.051
−10.293

1471
GLN193
CD
6.947
18.435
−10.567

1472
GLN193
OE1
8.067
18.62
−11.029

1473
GLN193
NE2
6.061
19.431
−10.274

1474
SER194
N
4.539
14.329
−6.718

1475
SER194
CA
3.995
13.858
−5.439

1476
SER194
C
2.514
13.433
−5.505

1477
SER194
O
1.863
13.182
−4.484

1478
SER194
CB
4.308
14.701
−4.189

1479
SER194
OG
3.332
15.722
−3.907

1480
GLY195
N
2.041
13.202
−6.782

1481
GLY195
CA
1.101
12.127
−7.04

1482
GLY195
C
1.928
10.845
−7.219

1483
GLY195
O
3.15
10.857
−7.377

1484
GLN196
N
1.186
9.688
−7.163

1485
GLN196
CA
1.797
8.377
−7.026

1486
GLN196
C
0.965
7.331
−7.793

1487
GLN196
O
−0.253
7.41
−7.969

1488
GLN196
CB
1.808
7.923
−5.553

1489
GLN196
CG
2.661
8.755
−4.601

1490
GLN196
CD
2.095
8.793
−3.196

1491
GLN196
OE1
1.964
9.849
−2.572

1492
GLN196
NE2
1.777
7.59
−2.63

1493
VAL197
N
1.681
6.168
−8.084

1494
VAL197
CA
1.01
5.06
−8.774

1495
VAL197
C
−0.116
4.492
−7.891

1496
VAL197
O
−1.095
3.91
−8.354

1497
VAL197
CB
1.965
3.914
−9.166

1498
VAL197
CG1
2.893
4.344
−10.297

1499
VAL197
CG2
2.792
3.356
−8.003

1500
SER198
N
0.102
4.647
−6.537

1501
SER198
CA
−0.789
4.109
−5.523

1502
SER198
C
−2.164
4.782
−5.597

1503
SER198
O
−3.17
4.207
−5.178

1504
SER198
CB
−0.199
4.308
−4.12

1505
SER198
OG
0.213
5.664
−3.897

1506
GLU199
N
−2.127
6.1
−6.024

1507
GLU199
CA
−3.344
6.848
−6.325

1508
GLU199
C
−3.753
6.559
−7.786

1509
GLU199
O
−4.916
6.304
−8.108

1510
GLU199
CB
−3.127
8.357
−6.167

1511
GLU199
CG
−2.568
8.791
−4.805

1512
GLU199
CD
−1.449
9.818
−4.893

1513
GLU199
OE1
−0.876
9.96
−6.007

1514
GLU199
OE2
−1.141
10.415
−3.814

1515
ALA200
N
−2.74
6.657
−8.734

1516
ALA200
CA
−3.103
6.771
−10.149

1517
ALA200
C
−3.797
5.49
−10.633

1518
ALA200
O
−4.67
5.494
−11.502

1519
ALA200
CB
−1.874
7.023
−11.007

1520
LEU201
N
−3.322
4.319
−10.067

1521
LEU201
CA
−3.888
3.038
−10.447

1522
LEU201
C
−5.325
2.882
−9.906

1523
LEU201
O
−6.103
2.079
−10.432

1524
LEU201
CB
−3.011
1.864
−9.998

1525
LEU201
CG
−1.642
1.78
−10.709

1526
LEU201
CD1
−0.767
0.732
−10.018

1527
LEU201
CD2
−1.779
1.433
−12.193

1528
VAL202
N
−5.667
3.646
−8.801

1529
VAL202
CA
−7.065
3.737
−8.368

1530
VAL202
C
−7.818
4.513
−9.456

1531
VAL202
O
−8.867
4.067
−9.927

1532
VAL202
CB
−7.246
4.416
−6.992

1533
VAL202
CG1
−8.72
4.645
−6.65

1534
VAL202
CG2
−6.578
3.6
−5.892

1535
ASP203
N
−7.254
5.713
−9.85

1536
ASP203
CA
−8.006
6.652
−10.692

1537
ASP203
C
−8.397
5.992
−12.047

1538
ASP203
O
−9.411
6.314
−12.673

1539
ASP203
CB
−7.187
7.906
−10.97

1540
ASP203
CG
−7.174
8.932
−9.842

1541
ASP203
OD1
−8.293
9.238
−9.338

1542
ASP203
OD2
−6.035
9.446
−9.607

1543
PHE204
N
−7.478
5.086
−12.557

1544
PHE204
CA
−7.72
4.42
−13.845

1545
PHE204
C
−8.653
3.196
−13.671

1546
PHE204
O
−9.343
2.734
−14.585

1547
PHE204
CB
−6.418
3.901
−14.479

1548
PHE204
CG
−5.392
4.96
−14.801

1549
PHE204
CD1
−5.721
6.123
−15.505

1550
PHE204
CD2
−4.062
4.771
−14.4

1551
PHE204
CE1
−4.747
7.093
−15.756

1552
PHE204
CE2
−3.099
5.749
−14.641

1553
PHE204
CZ
−3.439
6.913
−15.318

1554
THR205
N
−8.498
2.525
−12.471

1555
THR205
CA
−9.181
1.26
−12.237

1556
THR205
C
−10.57
1.499
−11.629

1557
THR205
O
−11.559
0.925
−12.094

1558
THR205
CB
−8.375
0.292
−11.355

1559
THR205
OG1
−7.023
0.205
−11.813

1560
THR205
OG2
−8.953
−1.117
−11.399

1561
GLY206
N
−10.57
2.248
−10.471

1562
GLY206
CA
−11.736
2.417
−9.612

1563
GLY206
C
−11.773
1.408
−8.46

1564
GLY206
O
−12.704
1.354
−7.66

1565
GLY207
N
−10.674
0.575
−8.411

1566
GLY207
CA
−10.481
−0.4
−7.359

1567
GLY207
C
−9.701
0.191
−6.19

1568
GLY207
O
−9.342
1.364
−6.144

1569
VAL208
N
−9.446
−0.722
−5.185

1570
VAL208
CA
−8.721
−0.33
−3.977

1571
VAL208
C
−7.241
−0.71
−4.177

1572
VAL208
O
−6.892
−1.808
−4.614

1573
VAL208
CB
−9.326
−1.027
−2.736

1574
VAL208
CG1
−8.569
−0.683
−1.451

1575
VAL208
CG2
−10.802
−0.645
−2.557

1576
THR209
N
−6.341
0.271
−3.793

1577
THR209
CA
−4.903
−0.012
−3.717

1578
THR209
C
−4.681
−0.655
−2.348

1579
THR209
O
−5.049
−0.111
−1.308

1580
THR209
CB
−4.045
1.266
−3.824

1581
THR209
OG1
−4.047
1.727
−5.178

1582
THR209
CG2
−2.587
1.029
−3.45

1583
MET210
N
−4.037
−1.872
−2.386

1584
MET210
CA
−3.614
−2.558
−1.167

1585
MET210
C
−2.079
−2.547
−1.22

1586
MET210
O
−1.446
−3.248
−2.012

1587
MET210
CB
−4.185
−3.983
−1.139

1588
MET210
CG
−4.994
−4.283
0.122

1589
MET210
SD
−3.932
−4.483
1.581

1590
MET210
CE
−5.23
−4.677
2.828

1591
THR211
N
−1.497
−1.595
−0.405

1592
THR211
CA
−0.058
−1.513
−0.171

1593
THR211
C
0.329
−2.517
0.925

1594
THR211
O
−0.404
−2.788
1.874

1595
THR211
CB
0.362
−0.109
0.315

1596
THR211
OG1
−0.653
0.417
1.181

1597
THR211
CG2
0.568
0.868
−0.834

1598
ILE212
N
1.606
−3.032
0.784

1599
ILE212
CA
2.161
−3.992
1.731

1600
ILE212
C
3.653
−3.623
1.842

1601
ILE212
O
4.439
−3.679
0.89

1602
ILE212
CB
1.996
−5.467
1.269

1603
ILE212
CG1
0.544
−5.787
0.842

1604
ILE212
CG2
2.459
−6.409
2.391

1605
ILE212
CD1
0.323
−7.224
0.389

1606
ASN213
N
4.051
−3.196
3.097

1607
ASN213
CA
5.445
−2.852
3.377

1608
ASN213
C
6.198
−4.176
3.565

1609
ASN213
O
6.374
−4.712
4.655

1610
ASN213
CB
5.591
−1.95
4.597

1611
ASN213
CG
5.543
−0.495
4.194

1612
ASN213
OD1
4.56
0.217
4.374

1613
ASN213
ND2
6.679
−0.011
3.606

1614
LEU214
N
6.631
−4.743
2.372

1615
LEU214
CA
6.849
−6.196
2.257

1616
LEU214
C
7.948
−6.786
3.164

1617
LEU214
O
8.071
−8
3.325

1618
LEU214
CB
7.21
−6.524
0.797

1619
LEU214
CG
6.781
−7.924
0.322

1620
LEU214
CD1
5.264
−8.091
0.35

1621
LEU214
CD2
7.299
−8.169
−1.097

1622
ALA215
N
8.799
−5.866
3.743

1623
ALA215
CA
9.746
−6.28
4.771

1624
ALA215
C
9.004
−6.749
6.035

1625
ALA215
O
9.443
−7.658
6.743

1626
ALA215
CB
10.69
−5.138
5.114

1627
GLU216
N
7.856
−6.051
6.362

1628
GLU216
CA
6.965
−6.512
7.432

1629
GLU216
C
6.126
−7.656
6.824

1630
GLU216
O
4.964
−7.535
6.437

1631
GLU216
CB
6.095
−5.354
7.928

1632
GLU216
CG
5.351
−5.703
9.216

1633
GLU216
CD
4.479
−4.568
9.76

1634
GLU216
OE1
4.149
−4.705
10.973

1635
GLU216
OE2
4.185
−3.649
8.948

1636
ALA217
N
6.837
−8.845
6.702

1637
ALA217
CA
6.304
−9.929
5.891

1638
ALA217
C
5.088
−10.522
6.619

1639
ALA217
O
5.13
−10.958
7.768

1640
ALA217
CB
7.341
−11.017
5.666

1641
HIS218
N
3.921
−10.47
5.876

1642
HIS218
CA
2.657
−10.92
6.446

1643
HIS218
C
2.558
−12.444
6.27

1644
HIS218
O
3.016
−13.043
5.297

1645
HIS218
CB
1.464
−10.242
5.762

1646
HIS218
CG
1.262
−8.812
6.152

1647
HIS218
ND1
2.268
−7.905
6.403

1648
HIS218
CD2
0.101
−8.086
6.327

1649
HIS218
CE1
1.678
−6.716
6.736

1650
HIS218
NE2
0.368
−6.792
6.683

1651
GLY219
N
1.808
−13.081
7.253

1652
GLY219
CA
1.951
−14.522
7.447

1653
GLY219
C
1.238
−15.416
6.431

1654
GLY219
O
1.25
−16.64
6.533

1655
ASN220
N
0.606
−14.742
5.413

1656
ASN220
CA
−0.097
−15.41
4.321

1657
ASN220
C
0.08
−14.582
3.033

1658
ASN220
O
−0.798
−14.425
2.188

1659
ASN220
CB
−1.55
−15.706
4.677

1660
ASN220
CG
−2.411
−14.472
4.791

1661
ASN220
OD1
−3.291
−14.195
3.978

1662
ASN220
ND2
−2.161
−13.678
5.875

1663
LEU221
N
1.381
−14.127
2.838

1664
LEU221
CA
1.657
−13.17
1.758

1665
LEU221
C
1.537
−13.871
0.395

1666
LEU221
O
1.097
−13.298
−0.603

1667
LEU221
CB
3.045
−12.546
1.961

1668
LEU221
CG
3.463
−11.398
1.019

1669
LEU221
CD1
4.053
−11.903
−0.296

1670
LEU221
CD2
2.349
−10.38
0.782

1671
TRP222
N
2.049
−15.157
0.345

1672
TRP222
CA
1.983
−15.898
−0.921

1673
TRP222
C
0.519
−16.115
−1.317

1674
TRP222
O
0.144
−16.108
−2.489

1675
TRP222
CB
2.717
−17.243
−0.832

1676
TRP222
CG
3.702
−17.433
−1.948

1677
TRP222
CD1
3.681
−18.413
−2.923

1678
TRP222
CD2
4.845
−16.612
−2.211

1679
TRP222
NE1
4.778
−18.245
−3.728

1680
TRP222
CE2
5.502
−17.153
−3.312

1681
TRP222
CE3
5.376
−15.448
−1.617

1682
TRP222
CZ2
6.677
−16.608
−3.831

1683
TRP222
CZ3
6.521
−14.861
−2.163

1684
TRP222
CH2
7.167
−15.439
−3.249

1685
ASP223
N
−0.329
−16.336
−0.26

1686
ASP223
CA
−1.732
−16.674
−0.436

1687
ASP223
C
−2.439
−15.457
−1.071

1688
ASP223
O
−3.327
−15.585
−1.915

1689
ASP223
CB
−2.365
−17.05
0.899

1690
ASP223
CG
−1.492
−17.936
1.793

1691
ASP223
OD1
−2.122
−18.723
2.549

1692
ASP223
OD2
−0.241
−17.716
1.707

1693
ILE224
N
−2.011
−14.218
−0.61

1694
ILE224
CA
−2.557
−12.964
−1.141

1695
ILE224
C
−2.205
−12.885
−2.64

1696
ILE224
O
−3.014
−12.473
−3.475

1697
ILE224
CB
−2.02
−11.714
−0.388

1698
ILE224
CG1
−2.573
−11.676
1.05

1699
ILE224
CG2
−2.385
−10.409
−1.116

1700
ILE224
CD1
−1.906
−10.642
1.947

1701
LEU225
N
−0.9
−13.202
−2.961

1702
LEU225
CA
−0.423
−13.139
−4.339

1703
LEU225
C
−1.047
−14.261
−5.206

1704
LEU225
O
−1.184
−14.141
−6.428

1705
LEU225
CB
1.105
−13.173
−4.41

1706
LEU225
CG
1.79
−11.79
−4.36

1707
LEU225
CD1
1.338
−10.9
−3.204

1708
LEU225
CD2
3.308
−11.981
−4.304

1709
ILE226
N
−1.398
−15.419
−4.543

1710
ILE226
CA
−2.158
−16.482
−5.211

1711
ILE226
C
−3.569
−15.908
−5.494

1712
ILE226
O
−4.099
−16.024
−6.603

1713
ILE226
CB
−2.153
−17.799
−4.401

1714
ILE226
CG1
−0.769
−18.483
−4.52

1715
ILE226
CG2
−3.251
−18.76
−4.869

1716
ILE226
CD1
−0.545
−19.602
−3.512

1717
GLU227
N
−4.195
−15.25
−4.447

1718
GLU227
CA
−5.531
−14.679
−4.634

1719
GLU227
C
−5.479
−13.627
−5.764

1720
GLU227
O
−6.373
−13.499
−6.603

1721
GLU227
CB
−6.066
−13.998
−3.364

1722
GLU227
CG
−7.271
−14.723
−2.779

1723
GLU227
CD
−6.902
−15.919
−1.909

1724
GLU227
OE1
−6.286
−15.606
−0.837

1725
GLU227
OE2
−7.305
−17.042
−2.336

1726
ALA228
N
−4.374
−12.795
−5.728

1727
ALA228
CA
−4.271
−11.646
−6.618

1728
ALA228
C
−4.181
−12.118
−8.08

1729
ALA228
O
−4.639
−11.458
−9.016

1730
ALA228
CB
−3.029
−10.841
−6.274

1731
THR229
N
−3.461
−13.284
−8.258

1732
THR229
CA
−3.262
−13.877
−9.57

1733
THR229
C
−4.478
−14.672
−10.083

1734
THR229
O
−4.599
−14.866
−11.298

1735
THR229
CB
−1.972
−14.717
−9.672

1736
THR229
OG1
−1.776
−15.533
−8.52

1737
THR229
CG2
−0.729
−13.851
−9.858

1738
TYR230
N
−5.375
−15.178
−9.154

1739
TYR230
CA
−6.665
−15.726
−9.594

1740
TYR230
C
−7.839
−14.716
−9.578

1741
TYR230
O
−8.954
−15.009
−10.022

1742
TYR230
CB
−7.009
−17.12
−9.043

1743
TYR230
CG
−7.495
−17.25
−7.62

1744
TYR230
CD1
−6.708
−17.904
−6.661

1745
TYR230
CD2
−8.779
−16.824
−7.252

1746
TYR230
CE1
−7.187
−18.111
−5.364

1747
TYR230
CE2
−9.252
−17.022
−5.955

1748
TYR230
CZ
−8.453
−17.658
−5.02

1749
TYR230
OH
−8.933
−17.814
−3.747

1750
ASN231
N
−7.53
−13.45
−9.12

1751
ASN231
CA
−8.366
−12.287
−9.435

1752
ASN231
C
−7.876
−11.655
−10.756

1753
ASN231
O
−8.659
−11.094
−11.523

1754
ASN231
CB
−8.348
−11.242
−8.326

1755
ASN231
CG
−9.222
−10.039
−8.619

1756
ASN231
OD1
−8.789
−8.888
−8.614

1757
ASN231
ND2
−10.546
−10.28
−8.837

1758
ARG232
N
−6.507
−11.647
−10.936

1759
ARG232
CA
−5.833
−11
−12.059

1760
ARG232
C
−5.824
−9.478
−11.843

1761
ARG232
O
−6.255
−8.671
−12.672

1762
ARG232
CB
−6.345
−11.407
−13.448

1763
ARG232
CG
−6.11
−12.893
−13.724

1764
ARG232
CD
−6.664
−13.312
−15.077

1765
ARG232
NE
−6.351
−14.717
−15.369

1766
ARG232
CZ
−5.132
−15.175
−15.748

1767
ARG232
NH1
−4.95
−16.509
−15.884

1768
ARG232
NH2
−4.091
−14.362
−16.01

1769
THR233
N
−5.206
−9.094
−10.668

1770
THR233
CA
−4.818
−7.708
−10.41

1771
THR233
C
−3.502
−7.41
−11.169

1772
THR233
O
−2.874
−8.268
−11.79

1773
THR233
CB
−4.613
−7.455
−8.905

1774
THR233
OG1
−3.54
−8.265
−8.436

1775
THR233
CG2
−5.843
−7.771
−8.071

1776
LEU234
N
−3.086
−6.084
−11.103

1777
LEU234
CA
−1.673
−5.76
−11.307

1778
LEU234
C
−1.027
−5.808
−9.904

1779
LEU234
O
−1.659
−5.515
−8.885

1780
LEU234
CB
−1.478
−4.37
−11.924

1781
LEU234
CG
−2.119
−4.193
−13.316

1782
LEU234
CD1
−1.98
−2.738
−13.772

1783
LEU234
CD2
−1.502
−5.121
−14.364

1784
ILE235
N
0.303
−6.192
−9.912

1785
ILE235
CA
1.03
−6.564
−8.693

1786
ILE235
C
2.451
−6.001
−8.879

1787
ILE235
O
3.222
−6.474
−9.721

1788
ILE235
CB
1.117
−8.11
−8.538

1789
ILE235
CG1
−0.254
−8.808
−8.634

1790
ILE235
CG2
1.846
−8.473
−7.234

1791
ILE235
CD1
−0.173
−10.328
−8.602

1792
GLY236
N
2.759
−4.917
−8.08

1793
GLY236
CA
4.011
−4.19
−8.235

1794
GLY236
C
4.421
−3.56
−6.91

1795
GLY236
O
3.603
−3.04
−6.148

1796
CYS237
N
5.725
−3.547
−6.529

1797
CYS237
CA
6.857
−4.283
−7.087

1798
CYS237
C
8.063
−3.78
−6.284

1799
CYS237
O
7.91
−3.319
−5.153

1800
CYS237
CB
6.703
−5.791
−6.864

1801
CYS237
SG
7.471
−6.738
−8.199

1802
GLN238
N
9.292
−3.94
−6.884

1803
GLN238
CA
10.552
−3.904
−6.105

1804
GLN238
C
11.444
−4.893
−6.899

1805
GLN238
O
10.903
−5.735
−7.626

1806
GLN238
CB
11.161
−2.511
−5.884

1807
GLN238
CG
10.422
−1.538
−4.952

1808
GLN238
CD
10.355
−1.958
−3.489

1809
GLN238
OE1
11.034
−1.48
−2.583

1810
GLN238
NE2
9.443
−2.924
−3.213

1811
THR239
N
12.807
−4.866
−6.7

1812
THR239
CA
13.655
−5.762
−7.512

1813
THR239
C
13.612
−7.169
−6.901

1814
THR239
O
13.197
−8.155
−7.508

1815
THR239
CB
15.092
−5.205
−7.588

1816
THR239
OG1
14.982
−3.829
−7.972

1817
THR239
CG2
15.953
−5.988
−8.57

1818
HIS240
N
14.09
−7.248
−5.61

1819
HIS240
CA
14.281
−8.527
−4.914

1820
HIS240
C
12.978
−8.912
−4.203

1821
HIS240
O
12.88
−9.04
−2.985

1822
HIS240
CB
15.458
−8.418
−3.936

1823
HIS240
CG
16.743
−8.341
−4.684

1824
HIS240
ND1
17.417
−9.453
−5.129

1825
HIS240
CD2
17.479
−7.272
−5.144

1826
HIS240
CE1
18.495
−9.005
−5.838

1827
HIS240
NE2
18.56
−7.693
−5.865

1828
SER241
N
11.916
−9.112
−5.071

1829
SER241
CA
10.542
−9.313
−4.607

1830
SER241
C
10.161
−10.799
−4.555

1831
SER241
O
9.027
−11.208
−4.801

1832
SER241
CB
9.546
−8.498
−5.441

1833
SER241
OG
8.59
−7.843
−4.604

1834
GLY242
N
11.138
−11.604
−4.005

1835
GLY242
CA
10.886
−12.991
−3.685

1836
GLY242
C
11.518
−13.984
−4.646

1837
GLY242
O
11.058
−15.12
−4.768

1838
GLU243
N
12.701
−13.574
−5.222

1839
GLU243
CA
13.646
−14.531
−5.795

1840
GLU243
C
14.662
−14.811
−4.652

1841
GLU243
O
14.268
−14.833
−3.474

1842
GLU243
CB
14.083
−14.032
−7.179

1843
GLU243
CG
12.878
−14.115
−8.149

1844
GLU243
CD
13.078
−14.26
−9.661

1845
GLU243
OE1
13.914
−13.477
−10.185

1846
GLU243
OE2
12.38
−15.174
−10.223

1847
LYS244
N
15.967
−15.146
−4.963

1848
LYS244
CA
16.915
−15.495
−3.891

1849
LYS244
C
18.043
−14.481
−3.601

1850
LYS244
O
18.714
−14.546
−2.563

1851
LYS244
CB
17.58
−16.87
−4.126

1852
LYS244
CG
16.585
−18.033
−4.084

1853
LYS244
CD
17.202
−19.34
−3.557

1854
LYS244
CE
16.229
−20.489
−3.773

1855
LYS244
NZ
16.694
−21.744
−3.179

1856
ILE245
N
18.33
−13.6
−4.621

1857
ILE245
CA
19.704
−13.1
−4.817

1858
ILE245
C
20.105
−12.091
−3.705

1859
ILE245
O
19.301
−11.591
−2.912

1860
ILE245
CB
19.866
−12.645
−6.297

1861
ILE245
CG1
19.798
−13.898
−7.213

1862
ILE245
CG2
21.135
−11.843
−6.591

1863
ILE245
CD1
19.972
−13.612
−8.696

1864
LEU246
N
21.47
−11.909
−3.553

1865
LEU246
CA
22.04
−11.035
−2.526

1866
LEU246
C
21.875
−9.555
−2.918

1867
LEU246
O
21.604
−9.188
−4.057

1868
LEU246
CB
23.526
−11.357
−2.297

1869
LEU246
CG
23.787
−12.752
−1.695

1870
LEU246
CD1
25.282
−13.077
−1.762

1871
LEU246
CD2
23.311
−12.848
−0.244

1872
GLU247
N
22.06
−8.689
−1.856

1873
GLU247
CA
21.764
−7.257
−1.941

1874
GLU247
C
22.653
−6.574
−0.877

1875
GLU247
O
23.403
−7.203
−0.125

1876
GLU247
CB
20.257
−7.031
−1.687

1877
GLU247
CG
19.585
−6.072
−2.672

1878
GLU247
CD
19.777
−4.615
−2.3

1879
GLU247
OE1
18.747
−3.984
−1.931

1880
GLU247
OE2
20.979
−4.202
−2.313

1881
ASN248
N
22.551
−5.209
−0.847

1882
ASN248
CA
23.218
−4.331
0.109

1883
ASN248
C
22.391
−3.063
0.424

1884
ASN248
O
22.479
−2.526
1.53

1885
ASN248
CB
24.616
−3.956
−0.38

1886
ASN248
CG
25.697
−4.59
0.469

1887
ASN248
OD1
26.558
−3.934
1.047

1888
ASN248
ND2
25.696
−5.956
0.515

1889
GLY249
N
21.675
−2.496
−0.615

1890
GLY249
CA
20.704
−1.458
−0.326

1891
GLY249
C
19.996
−0.918
−1.571

1892
GLY249
O
20.588
−0.612
−2.604

1893
LEU250
N
18.631
−0.761
−1.405

1894
LEU250
CA
17.733
−0.144
−2.382

1895
LEU250
C
17.442
−1.024
−3.615

1896
LEU250
O
16.294
−1.159
−4.043

1897
LEU250
CB
18.165
1.266
−2.829

1898
LEU250
CG
18.419
2.269
−1.685

1899
LEU250
CD1
18.916
3.597
−2.264

1900
LEU250
CD2
17.174
2.512
−0.832

1901
VAL251
N
18.555
−1.5
−4.273

1902
VAL251
CA
18.487
−2.051
−5.63

1903
VAL251
C
18.664
−0.876
−6.614

1904
VAL251
O
19.193
0.189
−6.286

1905
VAL251
CB
19.538
−3.173
−5.802

1906
VAL251
CG1
20.982
−2.666
−5.845

1907
VAL251
CG2
19.264
−4.06
−7.016

1908
GLU252
N
18.244
−1.121
−7.904

1909
GLU252
CA
18.313
−0.099
−8.931

1910
GLU252
C
17.064
0.805
−8.898

1911
GLU252
O
16.015
0.521
−8.32

1912
GLU252
CB
18.559
−0.724
−10.313

1913
GLU252
CG
17.381
−1.462
−10.947

1914
GLU252
CD
16.937
−2.788
−10.337

1915
GLU252
OE1
16.583
−3.673
−11.176

1916
GLU252
OE2
16.902
−2.853
−9.067

1917
GLY253
N
17.189
1.972
−9.635

1918
GLY253
CA
16.143
2.98
−9.629

1919
GLY253
C
15.005
2.579
−10.561

1920
GLY253
O
14.857
3.072
−11.678

1921
HIS254
N
14.186
1.593
−10.045

1922
HIS254
CA
13.164
0.948
−10.863

1923
HIS254
C
12.181
0.227
−9.928

1924
HIS254
O
12.461
−0.07
−8.768

1925
HIS254
CB
13.814
−0.05
−11.838

1926
HIS254
CG
13.022
−0.295
−13.075

1927
HIS254
ND1
12.803
0.665
−14.031

1928
HIS254
CD2
12.416
−1.427
−13.576

1929
HIS254
CE1
12.073
0.088
−15.029

1930
HIS254
NE2
11.843
−1.182
−14.795

1931
ALA255
N
10.976
−0.101
−10.519

1932
ALA255
CA
10.04
−1.017
−9.884

1933
ALA255
C
9.562
−1.974
−10.98

1934
ALA255
O
9.432
−1.627
−12.151

1935
ALA255
CB
8.88
−0.293
−9.228

1936
TYR256
N
9.353
−3.256
−10.524

1937
TYR256
CA
9.061
−4.376
−11.419

1938
TYR256
C
7.558
−4.671
−11.306

1939
TYR256
O
6.814
−4.032
−10.559

1940
TYR256
CB
9.918
−5.601
−11.046

1941
TYR256
CG
11.385
−5.477
−11.403

1942
TYR256
CD1
12.185
−4.472
−10.843

1943
TYR256
CD2
11.987
−6.408
−12.262

1944
TYR256
CE1
13.533
−4.357
−11.178

1945
TYR256
CE2
13.343
−6.305
−12.583

1946
TYR256
CZ
14.104
−5.269
−12.053

1947
TYR256
OH
15.418
−5.186
−12.413

1948
THR257
N
7.096
−5.697
−12.106

1949
THR257
CA
5.751
−6.245
−11.912

1950
THR257
C
5.882
−7.767
−11.761

1951
THR257
O
6.862
−8.39
−12.172

1952
THR257
CB
4.785
−5.826
−13.033

1953
THR257
OG1
3.438
−6.226
−12.762

1954
THR257
CG2
5.178
−6.346
−14.404

1955
LEU258
N
4.796
−8.365
−11.156

1956
LEU258
CA
4.758
−9.801
−10.82

1957
LEU258
C
3.657
−10.421
−11.703

1958
LEU258
O
2.578
−9.849
−11.876

1959
LEU258
CB
4.477
−9.917
−9.316

1960
LEU258
CG
5.035
−11.17
−8.621

1961
LEU258
CD1
5.351
−10.838
−7.159

1962
LEU258
CD2
4.036
−12.324
−8.672

1963
THR259
N
3.969
−11.634
−12.313

1964
THR259
CA
3.099
−12.191
−13.367

1965
THR259
C
2.945
−13.737
−13.36

1966
THR259
O
2.503
−14.372
−14.326

1967
THR259
CB
3.424
−11.686
−14.802

1968
THR259
OG1
4.665
−12.213
−15.307

1969
THR259
CG2
3.491
−10.171
−14.94

1970
GLY260
N
3.177
−14.344
−12.141

1971
GLY260
CA
3.017
−15.778
−11.933

1972
GLY260
C
3.617
−16.24
−10.601

1973
GLY260
O
4.34
−15.515
−9.914

1974
ILE261
N
3.277
−17.542
−10.254

1975
ILE261
CA
3.485
−18.055
−8.884

1976
ILE261
C
3.328
−19.605
−8.878

1977
ILE261
O
2.85
−20.201
−9.849

1978
ILE261
CB
2.487
−17.336
−7.933

1979
ILE261
CG1
2.935
−17.375
−6.465

1980
ILE261
CG2
1.049
−17.849
−8.094

1981
ILE261
CD1
2.357
−16.213
−5.673

1982
ARG262
N
3.751
−20.227
−7.708

1983
ARG262
CA
3.281
−21.535
−7.183

1984
ARG262
C
4.264
−22.043
−6.083

1985
ARG262
O
5.187
−21.344
−5.659

1986
ARG262
CB
3.005
−22.6
−8.255

1987
ARG262
CG
4.269
−23.015
−9.005

1988
ARG262
CD
3.951
−23.82
−10.255

1989
ARG262
NE
3.381
−22.955
−11.296

1990
ARG262
CZ
3.328
−23.325
−12.598

1991
ARG262
NH1
2.901
−22.461
−13.537

1992
ARG262
NH2
3.705
−24.548
−13.015

1993
LYS263
N
4.005
−23.303
−5.575

1994
LYS263
CA
4.937
−24.024
−4.693

1995
LYS263
C
5.465
−25.246
−5.468

1996
LYS263
O
4.778
−25.813
−6.32

1997
LYS263
CB
4.195
−24.458
−3.421

1998
LYS263
CG
5.102
−25.081
−2.357

1999
LYS263
CD
4.339
−25.363
−1.061

2000
LYS263
CE
5.27
−25.934
0

2001
LYS263
NZ
4.644
−25.802
1.335

2002
VAL264
N
6.718
−25.681
−5.083

2003
VAL264
CA
7.326
−26.916
−5.581

2004
VAL264
C
8.106
−27.592
−4.428

2005
VAL264
O
8.335
−27.036
−3.352

2006
VAL264
CB
8.248
−26.692
−6.807

2007
VAL264
CG1
7.47
−26.229
−8.04

2008
VAL264
CG2
9.396
−25.727
−6.504

2009
THR265
N
8.554
−28.869
−4.72

2010
THR265
CA
9.554
−29.535
−3.884

2011
THR265
C
10.787
−29.809
−4.756

2012
THR265
O
10.694
−30.025
−5.965

2013
THR265
CB
8.991
−30.793
−3.206

2014
THR265
OG1
9.877
−31.233
−2.175

2015
THR265
CG2
8.73
−31.956
−4.153

2016
CYS266
N
11.978
−29.812
−4.061

2017
CYS266
CA
13.284
−29.87
−4.714

2018
CYS266
C
14.097
−30.88
−3.895

2019
CYS266
O
14.691
−30.581
−2.86

2020
CYS266
CB
13.989
−28.509
−4.7

2021
CYS266
SG
13.206
−27.305
−5.819

2022
LYS267
N
13.961
−32.195
−4.31

2023
LYS267
CA
14.689
−33.299
−3.673

2024
LYS267
C
14.286
−33.478
−2.192

2025
LYS267
O
15.01
−34.029
−1.367

2026
LYS267
CB
16.213
−33.232
−3.892

2027
LYS267
CG
16.663
−34.184
−5.011

2028
LYS267
CD
18.157
−34.036
−5.317

2029
LYS267
CE
18.571
−34.928
−6.481

2030
LYS267
NZ
20.005
−34.709
−6.786

2031
HIS268
N
12.97
−33.132
−1.95

2032
HIS268
CA
12.274
−33.231
−0.667

2033
HIS268
C
12.482
−32.006
0.241

2034
HIS268
O
11.993
−31.959
1.37

2035
HIS268
CB
12.498
−34.526
0.134

2036
HIS268
CG
12.281
−35.759
−0.675

2037
HIS268
ND1
13.322
−36.468
−1.223

2038
HIS268
CD2
11.152
−36.446
−1.061

2039
HIS268
CE1
12.789
−37.516
−1.915

2040
HIS268
NE2
11.478
−37.53
−1.837

2041
ARG269
N
13.176
−30.951
−0.316

2042
ARG269
CA
13.144
−29.618
0.276

2043
ARG269
C
12.021
−28.86
−0.454

2044
ARG269
O
12.043
−28.758
−1.688

2045
ARG269
CB
14.46
−28.861
0.046

2046
ARG269
CG
15.662
−29.559
0.684

2047
ARG269
CD
16.953
−28.794
0.405

2048
ARG269
NE
18.104
−29.474
1.018

2049
ARG269
CZ
19.385
−29.046
0.903

2050
ARG269
NH1
20.373
−29.744
1.502

2051
ARG269
NH2
19.706
−27.938
0.204

2052
PRO270
N
11.014
−28.293
0.298

2053
PRO270
CA
9.987
−27.465
−0.337

2054
PRO270
C
10.563
−26.091
−0.7

2055
PRO270
O
11.354
−25.501
0.037

2056
PRO270
CB
8.9
−27.291
0.729

2057
PRO270
CG
9.144
−28.441
1.697

2058
PRO270
CD
10.654
−28.613
1.67

2059
GLU271
N
10.059
−25.54
−1.864

2060
GLU271
CA
10.405
−24.182
−2.273

2061
GLU271
C
9.161
−23.549
−2.941

2062
GLU271
O
8.302
−24.202
−3.534

2063
GLU271
CB
11.647
−24.106
−3.183

2064
GLU271
CG
12.953
−24.496
−2.481

2065
GLU271
CD
14.184
−24.134
−3.291

2066
GLU271
OE1
14.842
−23.104
−2.938

2067
GLU271
OE2
14.491
−24.885
−4.272

2068
TYR272
N
9.087
−22.177
−2.79

2069
TYR272
CA
7.922
−21.389
−3.21

2070
TYR272
C
8.368
−20.54
−4.407

2071
TYR272
O
9.278
−19.715
−4.286

2072
TYR272
CB
7.46
−20.467
−2.073

2073
TYR272
CG
6.69
−21.185
−0.988

2074
TYR272
CD1
7.353
−21.902
0.018

2075
TYR272
CD2
5.289
−21.136
−0.972

2076
TYR272
CE1
6.629
−22.565
1.011

2077
TYR272
CE2
4.562
−21.773
0.033

2078
TYR272
CZ
5.241
−22.492
1.008

2079
TYR272
OH
4.541
−23.204
1.947

2080
LEU273
N
7.728
−20.835
−5.606

2081
LEU273
CA
8.076
−20.123
−6.831

2082
LEU273
C
7.317
−18.786
−6.864

2083
LEU273
O
6.155
−18.677
−6.464

2084
LEU273
CB
7.669
−20.839
−8.137

2085
LEU273
CG
8.109
−22.294
−8.354

2086
LEU273
CD1
7.859
−22.713
−9.808

2087
LEU273
CD2
9.577
−22.515
−8.047

2088
VAL274
N
8.026
−17.773
−7.475

2089
VAL274
CA
7.432
−16.492
−7.872

2090
VAL274
C
7.657
−16.369
−9.387

2091
VAL274
O
8.406
−17.132
−9.998

2092
VAL274
CB
8.092
−15.34
−7.081

2093
VAL274
CG1
7.194
−14.107
−6.99

2094
VAL274
CG2
9.471
−14.952
−7.61

2095
LYS275
N
7.044
−15.285
−9.983

2096
LYS275
CA
7.464
−14.86
−11.304

2097
LYS275
C
7.322
−13.332
−11.429

2098
LYS275
O
6.235
−12.753
−11.4

2099
LYS275
CB
6.633
−15.505
−12.406

2100
LYS275
CG
7.255
−15.212
−13.764

2101
LYS275
CD
6.224
−15.112
−14.878

2102
LYS275
CE
6.828
−14.538
−16.146

2103
LYS275
NZ
7.123
−13.098
−16.004

2104
LEU276
N
8.531
−12.693
−11.629

2105
LEU276
CA
8.634
−11.276
−11.95

2106
LEU276
C
8.444
−11.093
−13.474

2107
LEU276
O
8.563
−12.011
−14.289

2108
LEU276
CB
10.025
−10.736
−11.562

2109
LEU276
CG
10.275
−10.475
−10.064

2110
LEU276
CD1
9.462
−9.29
−9.559

2111
LEU276
CD2
10.031
−11.687
−9.173

2112
ARG277
N
8.207
−9.79
−13.855

2113
ARG277
CA
8.528
−9.281
−15.18

2114
ARG277
C
9.232
−7.926
−14.936

2115
ARG277
O
8.825
−7.1
−14.115

2116
ARG277
CB
7.289
−9.089
−16.071

2117
ARG277
CG
7.647
−8.941
−17.558

2118
ARG277
CD
6.742
−7.976
−18.331

2119
ARG277
NE
7.367
−7.619
−19.624

2120
ARG277
CZ
7.335
−6.381
−20.171

2121
ARG277
NH1
6.551
−5.395
−19.697

2122
ARG277
NH2
8.113
−6.055
−21.217

2123
ASN278
N
10.335
−7.719
−15.749

2124
ASN278
CA
10.937
−6.394
−15.894

2125
ASN278
C
10.093
−5.697
−16.971

2126
ASN278
O
9.954
−6.213
−18.087

2127
ASN278
CB
12.38
−6.516
−16.379

2128
ASN278
CG
12.947
−5.17
−16.753

2129
ASN278
OD1
13.081
−4.819
−17.922

2130
ASN278
ND2
13.226
−4.345
−15.705

2131
PRO279
N
9.541
−4.466
−16.682

2132
PRO279
CA
8.574
−3.868
−17.602

2133
PRO279
C
9.153
−3.581
−18.99

2134
PRO279
O
8.444
−3.571
−19.998

2135
PRO279
CB
8.162
−2.571
−16.921

2136
PRO279
CG
8.254
−2.911
−15.445

2137
PRO279
CD
9.464
−3.83
−15.371

2138
TRP280
N
10.496
−3.269
−18.983

2139
TRP280
CA
11.252
−2.927
−20.181

2140
TRP280
C
11.773
−4.151
−20.963

2141
TRP280
O
12.441
−4.014
−21.997

2142
TRP280
CB
12.425
−1.995
−19.834

2143
TRP280
CG
12.051
−0.559
−19.634

2144
TRP280
CD1
11.011
0.111
−20.238

2145
TRP280
CD2
12.756
0.413
−18.852

2146
TRP280
NE1
11.062
1.433
−19.885

2147
TRP280
CE2
12.088
1.633
−18.993

2148
TRP280
CE3
13.913
0.373
−18.044

2149
TRP280
CZ2
12.486
2.793
−18.323

2150
TRP280
CZ3
14.341
1.535
−17.391

2151
TRP280
CH2
13.626
2.723
−17.518

2152
GLY281
N
11.411
−5.382
−20.457

2153
GLY281
CA
11.425
−6.582
−21.268

2154
GLY281
C
12.714
−7.392
−21.278

2155
GLY281
O
12.875
−8.304
−22.095

2156
LYS282
N
13.616
−7.04
−20.301

2157
LYS282
CA
14.908
−7.695
−20.115

2158
LYS282
C
14.766
−8.868
−19.119

2159
LYS282
O
13.791
−9.007
−18.381

2160
LYS282
CB
15.966
−6.676
−19.648

2161
LYS282
CG
16.466
−5.772
−20.791

2162
LYS282
CD
15.559
−4.566
−21.044

2163
LYS282
CE
15.714
−4.002
−22.451

2164
LYS282
NZ
14.659
−2.99
−22.664

2165
VAL283
N
15.825
−9.754
−19.149

2166
VAL283
CA
15.911
−10.959
−18.324

2167
VAL283
C
17.177
−10.793
−17.449

2168
VAL283
O
17.109
−10.559
−16.244

2169
VAL283
CB
15.921
−12.225
−19.213

2170
VAL283
CG1
15.998
−13.494
−18.366

2171
VAL283
CG2
14.674
−12.299
−20.104

2172
GLU284
N
18.379
−10.886
−18.141

2173
GLU284
CA
19.583
−10.233
−17.632

2174
GLU284
C
20.03
−10.638
−16.205

2175
GLU284
O
20.417
−9.814
−15.373

2176
GLU284
CB
19.515
−8.702
−17.837

2177
GLU284
CG
19.846
−8.253
−19.27

2178
GLU284
CD
18.886
−8.593
−20.412

2179
GLU284
OE1
18.035
−9.506
−20.171

2180
GLU284
OE2
19.025
−7.906
−21.459

2181
TRP285
N
20.155
−12.004
−15.985

2182
TRP285
CA
20.932
−12.497
−14.842

2183
TRP285
C
21.761
−13.735
−15.237

2184
TRP285
O
21.657
−14.301
−16.323

2185
TRP285
CB
20.117
−12.623
−13.545

2186
TRP285
CG
19.575
−13.984
−13.239

2187
TRP285
CD1
20.1
−14.89
−12.334

2188
TRP285
CD2
18.396
−14.581
−13.783

2189
TRP285
NE1
19.303
−16.003
−12.321

2190
TRP285
CE2
18.241
−15.827
−13.175

2191
TRP285
CE3
17.431
−14.167
−14.72

2192
TRP285
CZ2
17.159
−16.669
−13.441

2193
TRP285
CZ3
16.37
−15.024
−15.03

2194
TRP285
CH2
16.238
−16.257
−14.401

2195
LYS286
N
22.694
−14.106
−14.287

2196
LYS286
CA
23.764
−15.067
−14.54

2197
LYS286
C
23.324
−16.517
−14.251

2198
LYS286
O
23.999
−17.284
−13.562

2199
LYS286
CB
24.995
−14.701
−13.688

2200
LYS286
CG
25.529
−13.29
−13.965

2201
LYS286
CD
26.7
−12.953
−13.039

2202
LYS286
CE
27.191
−11.531
−13.271

2203
LYS286
NZ
28.293
−11.237
−12.323

2204
GLY287
N
22.185
−16.93
−14.91

2205
GLY287
CA
21.742
−18.311
−14.832

2206
GLY287
C
20.289
−18.461
−15.26

2207
GLY287
O
19.729
−17.631
−15.971

2208
ASP288
N
19.681
−19.612
−14.781

2209
ASP288
CA
18.234
−19.828
−14.932

2210
ASP288
C
17.649
−20.449
−13.637

2211
ASP288
O
16.602
−21.088
−13.602

2212
ASP288
CB
17.889
−20.638
−16.168

2213
ASP288
CG
16.404
−20.537
−16.444

2214
ASP288
OD1
15.815
−21.581
−16.865

2215
ASP288
OD2
15.809
−19.437
−16.223

2216
TRP289
N
18.357
−20.074
−12.511

2217
TRP289
CA
17.877
−20.166
−11.129

2218
TRP289
C
19.03
−19.498
−10.338

2219
TRP289
O
19.797
−18.685
−10.878

2220
TRP289
CB
17.536
−21.597
−10.681

2221
TRP289
CG
16.279
−21.693
−9.854

2222
TRP289
CD1
15.892
−20.886
−8.8

2223
TRP289
CD2
15.271
−22.707
−9.975

2224
TRP289
NE1
14.706
−21.358
−8.3

2225
TRP289
CE2
14.29
−22.451
−9.016

2226
TRP289
CE3
15.125
−23.852
−10.78

2227
TRP289
CZ2
13.16
−23.26
−8.852

2228
TRP289
CZ3
14.018
−24.69
−10.599

2229
TRP289
CH2
13.041
−24.39
−9.659

2230
SER290
N
19.145
−19.799
−9.004

2231
SER290
CA
20.299
−19.398
−8.195

2232
SER290
C
20.188
−20.151
−6.87

2233
SER290
O
19.141
−20.146
−6.229

2234
SER290
CB
20.369
−17.892
−7.938

2235
SER290
OG
20.955
−17.227
−9.058

2236
ASP291
N
21.338
−20.833
−6.53

2237
ASP291
CA
21.456
−21.969
−5.601

2238
ASP291
C
22.001
−23.178
−6.401

2239
ASP291
O
22.889
−23.913
−5.967

2240
ASP291
CB
20.238
−22.329
−4.751

2241
ASP291
CG
19.008
−22.859
−5.469

2242
ASP291
OD1
17.956
−22.999
−4.741

2243
ASP291
OD2
19.125
−23.137
−6.697

2244
SER292
N
21.344
−23.438
−7.59

2245
SER292
CA
21.699
−24.591
−8.422

2246
SER292
C
20.931
−24.457
−9.74

2247
SER292
O
19.801
−24.911
−9.91

2248
SER292
CB
21.375
−25.923
−7.735

2249
SER292
OG
22.418
−26.301
−6.832

2250
SER293
N
21.606
−23.736
−10.724

2251
SER293
CA
20.846
−23.111
−11.818

2252
SER293
C
20.023
−24.1
−12.653

2253
SER293
O
19.033
−23.732
−13.285

2254
SER293
CB
21.757
−22.335
−12.787

2255
SER293
OG
21.239
−21.017
−13.017

2256
SER294
N
20.552
−25.369
−12.751

2257
SER294
CA
19.9
−26.41
−13.529

2258
SER294
C
18.95
−27.304
−12.721

2259
SER294
O
18.437
−28.308
−13.229

2260
SER294
CB
20.925
−27.265
−14.275

2261
SER294
OG
21.73
−27.996
−13.353

2262
LYS295
N
18.479
−26.832
−11.502

2263
LYS295
CA
17.627
−27.699
−10.671

2264
LYS295
C
16.164
−27.847
−11.19

2265
LYS295
O
15.295
−28.434
−10.547

2266
LYS295
CB
17.676
−27.362
−9.169

2267
LYS295
CG
16.925
−26.088
−8.807

2268
LYS295
CD
16.949
−25.757
−7.309

2269
LYS295
CE
16.153
−24.479
−7.118

2270
LYS295
NZ
16.053
−24.049
−5.734

2271
TRP296
N
15.972
−27.431
−12.491

2272
TRP296
CA
14.872
−27.88
−13.336

2273
TRP296
C
15.035
−29.371
−13.716

2274
TRP296
O
14.133
−29.981
−14.29

2275
TRP296
CB
14.8
−27.078
−14.65

2276
TRP296
CG
14.669
−25.595
−14.468

2277
TRP296
CD1
15.671
−24.659
−14.644

2278
TRP296
CD2
13.501
−24.875
−14.057

2279
TRP296
NE1
15.173
−23.419
−14.334

2280
TRP296
CE2
13.856
−23.529
−13.95

2281
TRP296
CE3
12.188
−25.254
−13.707

2282
TRP296
CZ2
12.979
−22.546
−13.477

2283
TRP296
CZ3
11.306
−24.286
−13.215

2284
TRP296
CH2
11.7
−22.956
−13.095

2285
GLU297
N
16.247
−29.961
−13.388

2286
GLU297
CA
16.539
−31.354
−13.743

2287
GLU297
C
15.677
−32.306
−12.884

2288
GLU297
O
15.277
−33.393
−13.297

2289
GLU297
CB
18.004
−31.703
−13.427

2290
GLU297
CG
19.007
−31.221
−14.472

2291
GLU297
CD
20.397
−31.304
−13.831

2292
GLU297
OE1
20.987
−30.192
−13.67

2293
GLU297
OE2
20.785
−32.465
−13.524

2294
LEU298
N
15.589
−31.926
−11.556

2295
LEU298
CA
14.981
−32.77
−10.54

2296
LEU298
C
13.519
−32.377
−10.28

2297
LEU298
O
13.091
−31.231
−10.421

2298
LEU298
CB
15.78
−32.784
−9.222

2299
LEU298
CG
16.265
−31.396
−8.743

2300
LEU298
CD1
15.964
−31.174
−7.264

2301
LEU298
CD2
17.769
−31.245
−8.989

2302
LEU299
N
12.717
−33.443
−9.879

2303
LEU299
CA
11.365
−33.264
−9.327

2304
LEU299
C
10.5
−32.443
−10.305

2305
LEU299
O
9.686
−31.581
−9.965

2306
LEU299
CB
11.374
−32.701
−7.897

2307
LEU299
CG
11.447
−33.753
−6.767

2308
LEU299
CD1
10.173
−34.597
−6.679

2309
LEU299
CD2
12.675
−34.655
−6.851

2310
SER300
N
10.666
−32.827
−11.626

2311
SER300
CA
10.223
−31.96
−12.711

2312
SER300
C
9.831
−32.797
−13.923

2313
SER300
O
10.551
−32.865
−14.918

2314
SER300
CB
11.302
−30.919
−13.047

2315
SER300
OG
11.474
−30.005
−11.938

2316
PRO301
N
8.614
−33.454
−13.838

2317
PRO301
CA
8.076
−34.181
−14.985

2318
PRO301
C
7.562
−33.163
−16.023

2319
PRO301
O
7.523
−31.942
−15.833

2320
PRO301
CB
6.982
−35.058
−14.38

2321
PRO301
CG
6.479
−34.227
−13.206

2322
PRO301
CD
7.752
−33.593
−12.669

2323
LYS302
N
7.147
−33.74
−17.215

2324
LYS302
CA
6.877
−32.868
−18.363

2325
LYS302
C
5.645
−31.983
−18.078

2326
LYS302
O
5.484
−30.869
−18.57

2327
LYS302
CB
6.672
−33.716
−19.625

2328
LYS302
CG
7.287
−33.047
−20.856

2329
LYS302
CD
7.05
−33.874
−22.119

2330
LYS302
CE
7.704
−33.225
−23.329

2331
LYS302
NZ
7.445
−34.06
−24.526

2332
GLU303
N
4.738
−32.591
−17.247

2333
GLU303
CA
3.395
−32.129
−16.953

2334
GLU303
C
3.494
−30.92
−16.005

2335
GLU303
O
2.6
−30.081
−15.915

2336
GLU303
CB
2.6
−33.255
−16.265

2337
GLU303
CG
2.426
−34.527
−17.11

2338
GLU303
CD
3.625
−35.48
−17.279

2339
GLU303
OE1
4.772
−34.963
−17.076

2340
GLU303
OE2
3.337
−36.652
−17.636

2341
LYS304
N
4.62
−30.928
−15.189

2342
LYS304
CA
4.963
−29.757
−14.397

2343
LYS304
C
5.639
−28.73
−15.32

2344
LYS304
O
5.311
−27.541
−15.299

2345
LYS304
CB
5.895
−30.123
−13.229

2346
LYS304
CG
5.971
−29.01
−12.169

2347
LYS304
CD
7.075
−29.248
−11.128

2348
LYS304
CE
8.442
−28.814
−11.643

2349
LYS304
NZ
9.501
−29.237
−10.709

2350
ILE305
N
6.707
−29.199
−16.076

2351
ILE305
CA
7.642
−28.242
−16.673

2352
ILE305
C
7.027
−27.482
−17.864

2353
ILE305
O
7.481
−26.394
−18.219

2354
ILE305
CB
9.006
−28.894
−17.018

2355
ILE305
CG1
10.144
−27.856
−16.892

2356
ILE305
CG2
9.013
−29.558
−18.397

2357
ILE305
CD1
11.534
−28.452
−17.059

2358
LEU306
N
5.999
−28.115
−18.541

2359
LEU306
CA
5.39
−27.484
−19.715

2360
LEU306
C
4.473
−26.329
−19.282

2361
LEU306
O
4.199
−25.396
−20.035

2362
LEU306
CB
4.555
−28.471
−20.543

2363
LEU306
CG
5.396
−29.398
−21.441

2364
LEU306
CD1
4.513
−30.523
−21.988

2365
LEU306
CD2
6.043
−28.646
−22.606

2366
LEU307
N
3.896
−26.466
−18.035

2367
LEU307
CA
3.011
−25.447
−17.465

2368
LEU307
C
3.873
−24.476
−16.624

2369
LEU307
O
3.586
−24.139
−15.471

2370
LEU307
CB
1.901
−26.13
−16.649

2371
LEU307
CG
0.531
−25.423
−16.742

2372
LEU307
CD1
−0.532
−26.257
−16.022

2373
LEU307
CD2
0.541
−24.005
−16.174

2374
LEU308
N
4.949
−23.941
−17.302

2375
LEU308
CA
6.035
−23.215
−16.647

2376
LEU308
C
6.876
−22.584
−17.768

2377
LEU308
O
7.035
−23.144
−18.85

2378
LEU308
CB
6.897
−24.178
−15.807

2379
LEU308
CG
6.948
−23.815
−14.312

2380
LEU308
CD1
7.362
−25.033
−13.486

2381
LEU308
CD2
7.91
−22.662
−14.059

2382
ARG309
N
7.444
−21.368
−17.44

2383
ARG309
CA
8.209
−20.556
−18.396

2384
ARG309
C
7.215
−20.097
−19.499

2385
ARG309
O
7.211
−20.57
−20.633

2386
ARG309
CB
9.475
−21.225
−18.956

2387
ARG309
CG
10.305
−22.098
−18.003

2388
ARG309
CD
10.578
−21.562
−16.604

2389
ARG309
NE
11.464
−20.401
−16.533

2390
ARG309
CZ
12.822
−20.438
−16.568

2391
ARG309
NH1
13.482
−21.55
−16.944

2392
ARG309
NH2
13.489
−19.33
−16.193

2393
LYS310
N
6.259
−19.194
−19.052

2394
LYS310
CA
4.947
−19.081
−19.688

2395
LYS310
C
4.447
−17.723
−20.214

2396
LYS310
O
3.452
−17.693
−20.947

2397
LYS310
CB
3.872
−19.736
−18.785

2398
LYS310
CG
3.685
−19.061
−17.42

2399
LYS310
CD
2.648
−17.934
−17.42

2400
LYS310
CE
2.777
−17.078
−16.165

2401
LYS310
NZ
2.02
−15.832
−16.318

2402
ASP311
N
5.044
−16.569
−19.735

2403
ASP311
CA
4.74
−15.299
−20.408

2404
ASP311
C
5.793
−15.231
−21.565

2405
ASP311
O
6.162
−16.217
−22.208

2406
ASP311
CB
4.787
−14.092
−19.465

2407
ASP311
CG
3.902
−13.966
−18.244

2408
ASP311
OD1
4.261
−13.082
−17.402

2409
ASP311
OD2
2.909
−14.74
−18.122

2410
ASN312
N
6.275
−13.977
−21.862

2411
ASN312
CA
7.564
−13.796
−22.526

2412
ASN312
C
8.052
−12.481
−21.892

2413
ASN312
O
7.388
−11.907
−21.023

2414
ASN312
CB
7.365
−13.694
−24.032

2415
ASN312
CG
8.686
−13.81
−24.752

2416
ASN312
OD1
9.415
−12.829
−24.929

2417
ASN312
ND2
9.044
−15.07
−25.117

2418
ASP313
N
9.252
−11.973
−22.353

2419
ASP313
CA
9.486
−10.538
−22.209

2420
ASP313
C
9.702
−10.172
−20.729

2421
ASP313
O
9.242
−9.152
−20.219

2422
ASP313
CB
8.356
−9.744
−22.863

2423
ASP313
CG
9.03
−8.547
−23.469

2424
ASP313
OD1
8.905
−7.459
−22.843

2425
ASP313
OD2
9.677
−8.778
−24.555

2426
GLY314
N
10.58
−11.035
−20.099

2427
GLY314
CA
10.855
−10.98
−18.679

2428
GLY314
C
10.158
−12.165
−18.019

2429
GLY314
O
9.038
−12.091
−17.509

2430
GLU315
N
10.88
−13.349
−18.127

2431
GLU315
CA
10.289
−14.613
−17.709

2432
GLU315
C
10.687
−14.949
−16.262

2433
GLU315
O
9.83
−15.216
−15.422

2434
GLU315
CB
10.576
−15.729
−18.718

2435
GLU315
CG
9.7
−16.972
−18.527

2436
GLU315
CD
8.191
−16.747
−18.473

2437
GLU315
OE1
7.717
−15.846
−19.212

2438
GLU315
OE2
7.517
−17.508
−17.705

2439
PHE316
N
12.03
−15.012
−15.961

2440
PHE316
CA
12.47
−15.188
−14.559

2441
PHE316
C
12.08
−16.622
−14.073

2442
PHE316
O
12.298
−17.599
−14.803

2443
PHE316
CB
12.074
−14.002
−13.659

2444
PHE316
CG
12.736
−12.706
−14.072

2445
PHE316
CD1
12.085
−11.8
−14.916

2446
PHE316
CD2
14.029
−12.408
−13.619

2447
PHE316
CE1
12.726
−10.628
−15.319

2448
PHE316
CE2
14.666
−11.235
−14.021

2449
PHE316
CZ
14.015
−10.347
−14.874

2450
TRP317
N
11.496
−16.719
−12.823

2451
TRP317
CA
11.006
−17.943
−12.169

2452
TRP317
C
12.038
−18.518
−11.196

2453
TRP317
O
12.339
−19.713
−11.19

2454
TRP317
CB
10.477
−19.098
−13.034

2455
TRP317
CG
9.177
−18.858
−13.717

2456
TRP317
CD1
9.014
−18.346
−14.977

2457
TRP317
CD2
7.867
−19.138
−13.223

2458
TRP317
NE1
7.687
−18.372
−15.307

2459
TRP317
CE2
6.957
−18.85
−14.244

2460
TRP317
CE3
7.371
−19.616
−11.994

2461
TRP317
CZ2
5.578
−19.027
−14.082

2462
TRP317
CZ3
5.996
−19.79
−11.817

2463
TRP317
CH2
5.113
−19.497
−12.85

2464
MET318
N
12.499
−17.644
−10.234

2465
MET318
CA
13.197
−18.156
−9.071

2466
MET318
C
12.185
−18.312
−7.905

2467
MET318
O
10.996
−18.594
−8.078

2468
MET318
CB
14.469
−17.368
−8.77

2469
MET318
CG
15.331
−17.18
−10.014

2470
MET318
SD
16.964
−16.506
−9.576

2471
MET318
CE
16.727
−14.789
−10.107

2472
THR319
N
12.757
−18.296
−6.644

2473
THR319
CA
12.098
−18.913
−5.49

2474
THR319
C
12.337
−18.067
−4.244

2475
THR319
O
13.343
−17.371
−4.135

2476
THR319
CB
12.703
−20.312
−5.228

2477
THR319
OG1
14.001
−20.424
−5.84

2478
THR319
CG2
11.866
−21.415
−5.826

2479
LEU320
N
11.403
−18.247
−3.239

2480
LEU320
CA
11.304
−17.264
−2.158

2481
LEU320
C
12.534
−17.265
−1.231

2482
LEU320
O
12.769
−18.16
−0.422

2483
LEU320
CB
10.046
−17.551
−1.315

2484
LEU320
CG
9.838
−16.663
−0.069

2485
LEU320
CD1
9.894
−15.167
−0.371

2486
LEU320
CD2
8.505
−17.02
0.596

2487
GLN321
N
13.316
−16.124
−1.361

2488
GLN321
CA
14.259
−15.744
−0.311

2489
GLN321
C
14.594
−14.23
−0.308

2490
GLN321
O
15.433
−13.779
0.472

2491
GLN321
CB
15.548
−16.59
−0.36

2492
GLN321
CG
15.855
−17.306
0.958

2493
GLN321
CD
16.904
−16.635
1.819

2494
GLN321
OE1
17.909
−17.223
2.211

2495
GLN321
NE2
16.654
−15.35
2.201

2496
ASP322
N
13.848
−13.446
−1.164

2497
ASP322
CA
14.248
−12.103
−1.611

2498
ASP322
C
14.249
−10.983
−0.562

2499
ASP322
O
14.875
−9.931
−0.719

2500
ASP322
CB
15.535
−12.116
−2.438

2501
ASP322
CG
15.34
−11.89
−3.933

2502
ASP322
OD1
14.15
−11.758
−4.35

2503
ASP322
OD2
16.426
−11.883
−4.604

2504
PHE323
N
13.365
−11.161
0.484

2505
PHE323
CA
12.822
−10.018
1.237

2506
PHE323
C
13.889
−9.399
2.172

2507
PHE323
O
13.821
−9.433
3.397

2508
PHE323
CB
11.584
−10.422
2.054

2509
PHE323
CG
10.362
−10.884
1.285

2510
PHE323
CD1
9.301
−11.438
2.022

2511
PHE323
CD2
10.212
−10.75
−0.103

2512
PHE323
CE1
8.125
−11.847
1.393

2513
PHE323
CE2
9.041
−11.175
−0.733

2514
PHE323
CZ
7.997
−11.712
0.016

2515
LYS324
N
14.906
−8.775
1.479

2516
LYS324
CA
16.059
−8.143
2.097

2517
LYS324
C
15.945
−6.647
1.722

2518
LYS324
O
15.583
−5.78
2.514

2519
LYS324
CB
17.384
−8.77
1.596

2520
LYS324
CG
17.441
−10.305
1.664

2521
LYS324
CD
18.492
−10.874
0.693

2522
LYS324
CE
18.146
−12.301
0.28

2523
LYS324
NZ
19.058
−12.75
−0.782

2524
THR325
N
16.254
−6.375
0.404

2525
THR325
CA
16.294
−5.05
−0.205

2526
THR325
C
14.889
−4.694
−0.708

2527
THR325
O
14.517
−5.055
−1.83

2528
THR325
CB
17.024
−3.925
0.565

2529
THR325
OG1
17.428
−2.899
−0.365

2530
THR325
CG2
18.294
−4.377
1.287

2531
HIS326
N
14.032
−4.082
0.182

2532
HIS326
CA
12.651
−3.745
−0.185

2533
HIS326
C
12.125
−2.627
0.715

2534
HIS326
O
12.506
−2.495
1.878

2535
HIS326
CB
11.71
−4.964
−0.039

2536
HIS326
CG
11.237
−5.489
−1.35

2537
HIS326
ND1
12.091
−5.768
−2.384

2538
HIS326
CD2
9.99
−5.805
−1.841

2539
HIS326
CE1
11.334
−6.159
−3.442

2540
HIS326
NE2
10.057
−6.237
−3.142

2541
PHE327
N
11.119
−1.865
0.135

2542
PHE327
CA
10.379
−0.87
0.91

2543
PHE327
C
8.879
−1.214
0.924

2544
PHE327
O
8.273
−1.356
1.992

2545
PHE327
CB
10.648
0.554
0.401

2546
PHE327
CG
9.97
1.626
1.224

2547
PHE327
CD1
10.239
1.762
2.594

2548
PHE327
CD2
9.058
2.506
0.626

2549
PHE327
CE1
9.585
2.734
3.353

2550
PHE327
CE2
8.404
3.477
1.386

2551
PHE327
CZ
8.663
3.588
2.75

2552
VAL328
N
8.241
−1.278
−0.304

2553
VAL328
CA
6.78
−1.405
−0.381

2554
VAL328
C
6.367
−2.087
−1.695

2555
VAL328
O
6.835
−1.75
−2.78

2556
VAL328
CB
6.081
−0.035
−0.188

2557
VAL328
CG1
6.279
0.921
−1.369

2558
VAL328
CG2
4.586
−0.186
0.103

2559
LEU329
N
5.431
−3.088
−1.541

2560
LEU329
CA
4.722
−3.699
−2.671

2561
LEU329
C
3.282
−3.186
−2.586

2562
LEU329
O
2.749
−2.915
−1.507

2563
LEU329
CB
4.817
−5.23
−2.55

2564
LEU329
CG
4.055
−6.055
−3.609

2565
LEU329
CD1
4.816
−7.344
−3.94

2566
LEU329
CD2
2.655
−6.451
−3.126

2567
LEU330
N
2.607
−3.134
−3.785

2568
LEU330
CA
1.18
−2.918
−3.839

2569
LEU330
C
0.517
−3.852
−4.863

2570
LEU330
O
1.06
−4.232
−5.901

2571
LEU330
CB
0.768
−1.455
−4.071

2572
LEU330
CG
1.329
−0.785
−5.344

2573
LEU330
CD1
0.345
0.266
−5.863

2574
LEU330
CD2
2.677
−0.104
−5.08

2575
VAL331
N
−0.782
−4.176
−4.512

2576
VAL331
CA
−1.727
−4.683
−5.49

2577
VAL331
C
−2.826
−3.621
−5.632

2578
VAL331
O
−3.195
−2.922
−4.684

2579
VAL331
CB
−2.31
−6.064
−5.13

2580
VAL331
CG1
−1.224
−7.136
−5.153

2581
VAL331
CG2
−3.01
−6.103
−3.774

2582
ILE332
N
−3.381
−3.556
−6.897

2583
ILE332
CA
−4.589
−2.77
−7.148

2584
ILE332
C
−5.721
−3.807
−7.228

2585
ILE332
O
−5.873
−4.569
−8.182

2586
ILE332
CB
−4.423
−1.846
−8.371

2587
ILE332
CG1
−5.382
−0.638
−8.329

2588
ILE332
CG2
−4.482
−2.546
−9.731

2589
ILE332
CD1
−6.855
−0.957
−8.158

2590
CYS333
N
−6.476
−3.899
−6.073

2591
CYS333
CA
−7.589
−4.832
−5.976

2592
CYS333
C
−8.783
−4.185
−6.689

2593
CYS333
O
−9.295
−3.132
−6.309

2594
CYS333
CB
−7.977
−5.116
−4.53

2595
CYS333
SG
−6.842
−6.3
−3.743

2596
LYS334
N
−9.182
−4.88
−7.816

2597
LYS334
CA
−10.111
−4.323
−8.792

2598
LYS334
C
−11.546
−4.279
−8.235

2599
LYS334
O
−11.95
−5.048
−7.365

2600
LYS334
CB
−10.11
−5.186
−10.065

2601
LYS334
CG
−8.863
−4.966
−10.925

2602
LYS334
CD
−8.707
−6.065
−11.976

2603
LYS334
CE
−7.611
−5.715
−12.971

2604
LYS334
NZ
−7.367
−6.877
−13.845

2605
LEU335
N
−12.355
−3.345
−8.864

2606
LEU335
CA
−13.81
−3.365
−8.711

2607
LEU335
C
−14.436
−4.308
−9.769

2608
LEU335
O
−13.753
−4.987
−10.536

2609
LEU335
CB
−14.404
−1.947
−8.725

2610
LEU335
CG
−14.005
−0.994
−9.87

2611
LEU335
CD1
−14.051
−1.609
−11.257

2612
LEU335
CD2
−14.918
0.238
−9.852

2613
THR336
N
−15.823
−4.328
−9.782

2614
THR336
CA
−16.561
−5.327
−10.569

2615
THR336
C
−16.279
−5.158
−12.078

2616
THR336
O
−15.707
−6.075
−12.687

2617
THR336
CB
−18.053
−5.318
−10.19

2618
THR336
OG1
−18.175
−5.305
−8.755

2619
THR336
CG2
−18.802
−6.527
−10.736

2620
PRO337
N
−16.567
−3.978
−12.736

2621
PRO337
CA
−16.139
−3.762
−14.13

2622
PRO337
C
−14.623
−3.439
−14.198

2623
PRO337
O
−14.151
−2.408
−14.688

2624
PRO337
CB
−17.009
−2.603
−14.62

2625
PRO337
CG
−17.292
−1.815
−13.346

2626
PRO337
CD
−17.465
−2.912
−12.306

2627
GLY338
N
−13.819
−4.463
−13.734

2628
GLY338
CA
−12.369
−4.376
−13.653

2629
GLY338
C
−11.676
−4.999
−14.864

2630
GLY338
O
−10.467
−4.881
−15.049

2631
LEU339
N
−12.517
−5.75
−15.649

2632
LEU339
CA
−12.165
−6.392
−16.909

2633
LEU339
C
−13.452
−6.384
−17.749

2634
LEU339
O
−14.556
−6.131
−17.257

2635
LEU339
CB
−11.709
−7.847
−16.695

2636
LEU339
CG
−10.31
−8
−16.073

2637
LEU339
CD1
−10.003
−9.479
−15.823

2638
LEU339
CD2
−9.234
−7.392
−16.971

2639
LEU340
N
−13.287
−6.756
−19.068

2640
LEU340
CA
−14.439
−6.983
−19.944

2641
LEU340
C
−14.996
−8.379
−19.597

2642
LEU340
O
−14.778
−9.384
−20.267

2643
LEU340
CB
−14.015
−6.863
−21.414

2644
LEU340
CG
−15.167
−6.977
−22.434

2645
LEU340
CD1
−16.231
−5.895
−22.245

2646
LEU340
CD2
−14.603
−6.904
−23.856

2647
SER341
N
−15.653
−8.423
−18.375

2648
SER341
CA
−16.715
−9.391
−18.078

2649
SER341
C
−16.338
−10.882
−18.154

2650
SER341
O
−17.186
−11.77
−18.227

2651
SER341
CB
−18.025
−9.094
−18.827

2652
SER341
OG
−17.834
−9.05
−20.236

2653
GLN342
N
−14.988
−11.143
−17.948

2654
GLN342
CA
−14.489
−12.484
−18.241

2655
GLN342
C
−15.049
−13.524
−17.241

2656
GLN342
O
−15.217
−13.291
−16.038

2657
GLN342
CB
−12.955
−12.548
−18.112

2658
GLN342
CG
−12.195
−11.889
−19.267

2659
GLN342
CD
−10.69
−11.852
−19.048

2660
GLN342
OE1
−9.978
−10.911
−19.398

2661
GLN342
NE2
−10.135
−12.963
−18.478

2662
GLU343
N
−15.17
−14.791
−17.779

2663
GLU343
CA
−15.785
−15.89
−17.033

2664
GLU343
C
−14.716
−16.454
−16.084

2665
GLU343
O
−14.982
−16.976
−15.005

2666
GLU343
CB
−16.253
−17.031
−17.956

2667
GLU343
CG
−17.318
−16.631
−18.981

2668
GLU343
CD
−16.779
−15.923
−20.232

2669
GLU343
OE1
−17.457
−16.091
−21.28

2670
GLU343
OE2
−15.72
−15.245
−20.048

2671
ALA344
N
−13.443
−16.438
−16.632

2672
ALA344
CA
−12.281
−16.858
−15.876

2673
ALA344
C
−11.844
−15.727
−14.926

2674
ALA344
O
−12.048
−14.533
−15.162

2675
ALA344
CB
−11.13
−17.223
−16.802

2676
ALA345
N
−11.171
−16.198
−13.811

2677
ALA345
CA
−10.751
−15.378
−12.674

2678
ALA345
C
−11.96
−14.979
−11.811

2679
ALA345
O
−13.024
−14.585
−12.3

2680
ALA345
CB
−9.926
−14.16
−13.056

2681
GLN346
N
−11.726
−15.069
−10.444

2682
GLN346
CA
−12.774
−14.685
−9.503

2683
GLN346
C
−12.841
−13.153
−9.405

2684
GLN346
O
−11.88
−12.418
−9.633

2685
GLN346
CB
−12.573
−15.264
−8.103

2686
GLN346
CG
−12.839
−16.767
−8.015

2687
GLN346
CD
−13.021
−17.178
−6.565

2688
GLN346
OE1
−13.722
−16.548
−5.776

2689
GLN346
NE2
−12.378
−18.327
−6.205

2690
LYS347
N
−14.088
−12.681
−9.037

2691
LYS347
CA
−14.468
−11.268
−9.084

2692
LYS347
C
−15.517
−11.068
−7.972

2693
LYS347
O
−15.975
−12.017
−7.333

2694
LYS347
CB
−15.011
−10.884
−10.479

2695
LYS347
CG
−14.023
−11.248
−11.595

2696
LYS347
CD
−14.491
−10.939
−13.015

2697
LYS347
CE
−13.508
−11.511
−14.04

2698
LYS347
NZ
−13.675
−12.969
−14.176

2699
TRP348
N
−15.889
−9.76
−7.745

2700
TRP348
CA
−16.666
−9.383
−6.56

2701
TRP348
C
−17.466
−8.095
−6.815

2702
TRP348
O
−17.235
−7.335
−7.758

2703
TRP348
CB
−15.803
−9.263
−5.289

2704
TRP348
CG
−14.525
−8.481
−5.421

2705
TRP348
CD1
−14.24
−7.437
−6.28

2706
TRP348
CD2
−13.347
−8.677
−4.623

2707
TRP348
NE1
−12.934
−7.071
−6.103

2708
TRP348
CE2
−12.359
−7.828
−5.115

2709
TRP348
CE3
−13.023
−9.513
−3.536

2710
TRP348
CZ2
−11.051
−7.818
−4.623

2711
TRP348
CZ3
−11.735
−9.471
−2.99

2712
TRP348
CH2
−10.755
−8.653
−3.544

2713
THR349
N
−18.461
−7.859
−5.885

2714
THR349
CA
−19.45
−6.792
−6.055

2715
THR349
C
−18.885
−5.466
−5.521

2716
THR349
O
−18.407
−5.345
−4.393

2717
THR349
CB
−20.729
−7.127
−5.256

2718
THR349
OG1
−20.996
−8.532
−5.384

2719
THR349
CG2
−21.937
−6.338
−5.745

2720
TYR350
N
−19.048
−4.388
−6.376

2721
TYR350
CA
−18.566
−3.041
−6.011

2722
TYR350
C
−19.482
−2.397
−4.937

2723
TYR350
O
−20.094
−1.341
−5.106

2724
TYR350
CB
−18.5
−2.155
−7.273

2725
TYR350
CG
−17.919
−0.767
−7.101

2726
TYR350
CD1
−16.742
−0.538
−6.376

2727
TYR350
CD2
−18.552
0.325
−7.718

2728
TYR350
CE1
−16.227
0.755
−6.246

2729
TYR350
CE2
−18.041
1.618
−7.586

2730
TYR350
CZ
−16.891
1.825
−6.839

2731
TYR350
OH
−16.434
3.104
−6.694

2732
THR351
N
−19.482
−3.031
−3.709

2733
THR351
CA
−20.34
−2.593
−2.598

2734
THR351
C
−19.646
−1.44
−1.834

2735
THR351
O
−19.535
−1.419
−0.609

2736
THR351
CB
−20.687
−3.766
−1.655

2737
THR351
OG1
−21.089
−4.902
−2.437

2738
THR351
CG2
−21.844
−3.438
−0.709

2739
MET352
N
−19.26
−0.379
−2.635

2740
MET352
CA
−18.829
0.901
−2.074

2741
MET352
C
−20.09
1.772
−1.929

2742
MET352
O
−21.078
1.635
−2.649

2743
MET352
CB
−17.791
1.551
−3

2744
MET352
CG
−17.031
2.699
−2.336

2745
MET352
SD
−15.698
3.301
−3.427

2746
MET352
CE
−14.9
4.439
−2.265

2747
ARG353
N
−20.012
2.736
−0.941

2748
ARG353
CA
−21.065
3.727
−0.741

2749
ARG353
C
−20.409
5.118
−0.686

2750
ARG353
O
−19.193
5.265
−0.578

2751
ARG353
CB
−21.866
3.44
0.534

2752
ARG353
CG
−22.613
2.105
0.469

2753
ARG353
CD
−23.63
1.995
1.594

2754
ARG353
NE
−24.282
0.679
1.613

2755
ARG353
CZ
−23.829
−0.389
2.309

2756
ARG353
NH1
−24.598
−1.488
2.418

2757
ARG353
NH2
−22.633
−0.385
2.934

2758
GLU354
N
−21.313
6.159
−0.787

2759
GLU354
CA
−20.907
7.561
−0.682

2760
GLU354
C
−21.009
8.025
0.787

2761
GLU354
O
−21.52
7.333
1.669

2762
GLU354
CB
−21.795
8.418
−1.607

2763
GLU354
CG
−21.021
8.966
−2.806

2764
GLU354
CD
−19.941
9.964
−2.419

2765
GLU354
OE1
−19.803
10.212
−1.187

2766
GLU354
OE2
−19.268
10.453
−3.384

2767
GLY355
N
−20.49
9.288
1.024

2768
GLY355
CA
−20.444
9.829
2.368

2769
GLY355
C
−20.044
11.301
2.472

2770
GLY355
O
−19.549
11.947
1.552

2771
ARG356
N
−20.278
11.835
3.732

2772
ARG356
CA
−19.973
13.22
4.076

2773
ARG356
C
−19.435
13.261
5.517

2774
ARG356
O
−19.822
12.473
6.377

2775
ARG356
CB
−21.22
14.11
4.019

2776
ARG356
CG
−21.71
14.391
2.6

2777
ARG356
CD
−23.015
15.181
2.591

2778
ARG356
NE
−24.15
14.34
3.001

2779
ARG356
CZ
−24.814
14.395
4.183

2780
ARG356
NH1
−25.871
13.564
4.361

2781
ARG356
NH2
−24.496
15.216
5.191

2782
TRP357
N
−18.54
14.291
5.734

2783
TRP357
CA
−17.903
14.556
7.028

2784
TRP357
C
−17.788
16.092
7.12

2785
TRP357
O
−16.762
16.695
6.804

2786
TRP357
CB
−16.508
13.905
7.125

2787
TRP357
CG
−16.539
12.489
7.622

2788
TRP357
CD1
−16.376
12.093
8.934

2789
TRP357
CD2
−16.724
11.29
6.859

2790
TRP357
NE1
−16.508
10.732
9.009

2791
TRP357
CE2
−16.721
10.216
7.753

2792
TRP357
CE3
−16.909
11.018
5.486

2793
TRP357
CZ2
−16.913
8.891
7.346

2794
TRP357
CZ3
−17.116
9.701
5.064

2795
TRP357
CH2
−17.119
8.656
5.983

2796
GLU358
N
−18.962
16.734
7.473

2797
GLU358
CA
−19.026
18.171
7.728

2798
GLU358
C
−18.992
18.415
9.253

2799
GLU358
O
−19.324
17.567
10.083

2800
GLU358
CB
−20.231
18.902
7.101

2801
GLU358
CG
−21.012
18.159
6.019

2802
GLU358
CD
−22.066
17.165
6.495

2803
GLU358
OE1
−22.758
16.626
5.577

2804
GLU358
OE2
−22.149
16.952
7.747

2805
LYS359
N
−18.551
19.678
9.621

2806
LYS359
CA
−18.467
20.053
11.028

2807
LYS359
C
−19.789
20.701
11.473

2808
LYS359
O
−20.366
21.552
10.792

2809
LYS359
CB
−17.316
21.036
11.288

2810
LYS359
CG
−15.946
20.357
11.18

2811
LYS359
CD
−14.806
21.321
11.516

2812
LYS359
CE
−13.46
20.611
11.454

2813
LYS359
NZ
−12.388
21.56
11.839

2814
ARG360
N
−20.185
20.303
12.74

2815
ARG360
CA
−21.453
20.645
13.397

2816
ARG360
C
−22.571
19.638
13.049

2817
ARG360
O
−23.753
19.862
13.306

2818
ARG360
CB
−21.969
22.07
13.156

2819
ARG360
CG
−20.949
23.176
13.424

2820
ARG360
CD
−21.441
24.49
12.83

2821
ARG360
NE
−20.344
25.336
12.347

2822
ARG360
CZ
−19.678
25.135
11.181

2823
ARG360
NH1
−18.825
26.093
10.748

2824
ARG360
NH2
−19.827
24.028
10.422

2825
SER361
N
−22.132
18.433
12.534

2826
SER361
CA
−23.092
17.492
11.962

2827
SER361
C
−22.527
16.07
12.006

2828
SER361
O
−23.052
15.2
12.699

2829
SER361
CB
−23.45
17.878
10.521

2830
SER361
OG
−22.244
18.109
9.793

2831
THR362
N
−21.427
15.849
11.197

2832
THR362
CA
−20.967
14.494
10.88

2833
THR362
C
−19.496
14.261
11.248

2834
THR362
O
−19.07
13.144
11.557

2835
THR362
CB
−21.194
14.156
9.395

2836
THR362
OG1
−20.74
15.237
8.575

2837
THR362
CG2
−22.654
13.848
9.079

2838
ALA363
N
−18.642
15.337
11.141

2839
ALA363
CA
−17.212
15.227
11.413

2840
ALA363
C
−17
15.136
12.933

2841
ALA363
O
−16.552
16.058
13.607

2842
ALA363
CB
−16.435
16.394
10.824

2843
GLY364
N
−17.37
13.903
13.457

2844
GLY364
CA
−17.585
13.743
14.883

2845
GLY364
C
−16.35
13.324
15.673

2846
GLY364
O
−16.398
13.133
16.887

2847
GLY365
N
−15.212
13.151
14.922

2848
GLY365
CA
−13.952
12.741
15.498

2849
GLY365
C
−13.734
11.229
15.406

2850
GLY365
O
−14.527
10.457
14.872

2851
GLN366
N
−12.522
10.847
15.957

2852
GLN366
CA
−12.075
9.46
16.036

2853
GLN366
C
−12.217
9.004
17.5

2854
GLN366
O
−12.316
9.799
18.438

2855
GLN366
CB
−10.612
9.339
15.598

2856
GLN366
CG
−10.4
9.744
14.14

2857
GLN366
CD
−8.968
9.503
13.72

2858
GLN366
OE1
−8.143
10.402
13.608

2859
GLN366
NE2
−8.653
8.196
13.472

2860
ARG367
N
−12.109
7.634
17.701

2861
ARG367
CA
−12.65
7.006
18.916

2862
ARG367
C
−11.849
7.197
20.228

2863
ARG367
O
−11.982
6.425
21.184

2864
ARG367
CB
−12.905
5.498
18.688

2865
ARG367
CG
−11.635
4.631
18.755

2866
ARG367
CD
−11.779
3.48
19.753

2867
ARG367
NE
−10.476
3.073
20.296

2868
ARG367
CZ
−9.887
3.665
21.366

2869
ARG367
NH1
−10.429
4.7
22.025

2870
ARG367
NH2
−8.69
3.226
21.806

2871
GLN368
N
−11.05
8.313
20.291

2872
GLN368
CA
−10.37
8.732
21.509

2873
GLN368
C
−10.05
10.237
21.513

2874
GLN368
O
−9.328
10.743
22.375

2875
GLN368
CB
−9.092
7.906
21.735

2876
GLN368
CG
−8.796
7.688
23.221

2877
GLN368
CD
−7.888
6.49
23.4

2878
GLN368
OE1
−8.313
5.334
23.354

2879
GLN368
NE2
−6.565
6.78
23.545

2880
LEU369
N
−10.702
11.007
20.568

2881
LEU369
CA
−10.55
12.461
20.559

2882
LEU369
C
−11.611
13.036
21.509

2883
LEU369
O
−12.578
13.703
21.135

2884
LEU369
CB
−10.684
13.044
19.146

2885
LEU369
CG
−9.617
12.561
18.142

2886
LEU369
CD1
−9.783
13.301
16.811

2887
LEU369
CD2
−8.184
12.745
18.645

2888
LEU370
N
−11.352
12.814
22.853

2889
LEU370
CA
−12.372
12.994
23.897

2890
LEU370
C
−12.689
14.478
24.253

2891
LEU370
O
−13.159
14.812
25.339

2892
LEU370
CB
−12.003
12.227
25.183

2893
LEU370
CG
−11.831
10.701
25.034

2894
LEU370
CD1
−11.47
10.087
26.39

2895
LEU370
CD2
−13.076
10.017
24.47

2896
GLN371
N
−12.58
15.354
23.193

2897
GLN371
CA
−13.322
16.61
23.121

2898
GLN371
C
−14.711
16.324
22.524

2899
GLN371
O
−15.701
16.945
22.907

2900
GLN371
CB
−12.536
17.591
22.228

2901
GLN371
CG
−13.169
18.976
22.049

2902
GLN371
CD
−14.262
19.089
20.995

2903
GLN371
OE1
−15.348
19.606
21.238

2904
GLN371
NE2
−13.921
18.669
19.739

2905
ASP372
N
−14.704
15.511
21.402

2906
ASP372
CA
−15.799
15.527
20.44

2907
ASP372
C
−16.76
14.328
20.615

2908
ASP372
O
−16.66
13.492
21.511

2909
ASP372
CB
−15.203
15.594
19.035

2910
ASP372
CG
−16.111
16.58
18.31

2911
ASP372
OD1
−17.287
16.145
18.107

2912
ASP372
OD2
−15.588
17.709
18.076

2913
THR373
N
−17.792
14.315
19.688

2914
THR373
CA
−18.977
13.493
19.86

2915
THR373
C
−18.777
12.024
19.482

2916
THR373
O
−19.582
11.178
19.884

2917
THR373
CB
−20.195
14.049
19.085

2918
THR373
OG1
−21.431
13.373
19.431

2919
THR373
CG2
−20.056
13.997
17.571

2920
PHE374
N
−17.84
11.738
18.522

2921
PHE374
CA
−17.508
10.392
18.051

2922
PHE374
C
−18.642
9.76
17.217

2923
PHE374
O
−18.488
9.453
16.032

2924
PHE374
CB
−17.011
9.462
19.177

2925
PHE374
CG
−16.836
8.017
18.764

2926
PHE374
CD1
−16.167
7.669
17.583

2927
PHE374
CD2
−17.375
6.996
19.561

2928
PHE374
CE1
−16.096
6.336
17.182

2929
PHE374
CE2
−17.284
5.66
19.166

2930
PHE374
CZ
−16.653
5.331
17.97

2931
TRP375
N
−19.817
9.514
17.898

2932
TRP375
CA
−20.82
8.557
17.424

2933
TRP375
C
−21.755
9.084
16.323

2934
TRP375
O
−22.61
8.367
15.804

2935
TRP375
CB
−21.629
7.912
18.564

2936
TRP375
CG
−22.331
8.872
19.483

2937
TRP375
CD1
−21.851
9.306
20.704

2938
TRP375
CD2
−23.628
9.464
19.323

2939
TRP375
NE1
−22.769
10.151
21.262

2940
TRP375
CE2
−23.867
10.263
20.444

2941
TRP375
CE3
−24.638
9.38
18.341

2942
TRP375
CZ2
−25.054
10.984
20.627

2943
TRP375
CZ3
−25.831
10.092
18.509

2944
TRP375
CH2
−26.035
10.881
19.638

2945
LYS376
N
−21.516
10.383
15.928

2946
LYS376
CA
−22.219
11.011
14.814

2947
LYS376
C
−21.41
10.936
13.501

2948
LYS376
O
−21.746
11.557
12.494

2949
LYS376
CB
−22.584
12.47
15.123

2950
LYS376
CG
−23.353
12.625
16.44

2951
LYS376
CD
−23.905
14.043
16.608

2952
LYS376
CE
−24.52
14.269
17.983

2953
LYS376
NZ
−23.482
14.625
18.973

2954
ASN377
N
−20.364
10.027
13.505

2955
ASN377
CA
−19.79
9.578
12.237

2956
ASN377
C
−20.838
8.658
11.589

2957
ASN377
O
−21.536
7.917
12.289

2958
ASN377
CB
−18.536
8.733
12.44

2959
ASN377
CG
−17.282
9.556
12.579

2960
ASN377
OD1
−16.574
9.835
11.614

2961
ASN377
ND2
−16.991
9.935
13.859

2962
PRO378
N
−20.903
8.629
10.213

2963
PRO378
CA
−21.896
7.798
9.54

2964
PRO378
C
−21.427
6.334
9.541

2965
PRO378
O
−20.324
5.978
9.129

2966
PRO378
CB
−21.965
8.358
8.118

2967
PRO378
CG
−20.59
8.984
7.909

2968
PRO378
CD
−20.246
9.536
9.283

2969
GLN379
N
−22.355
5.455
10.063

2970
GLN379
CA
−22.13
4.02
10.099

2971
GLN379
C
−22.575
3.441
8.742

2972
GLN379
O
−23.457
3.955
8.053

2973
GLN379
CB
−22.913
3.342
11.236

2974
GLN379
CG
−22.593
3.905
12.627

2975
GLN379
CD
−23.27
5.236
12.913

2976
GLN379
OE1
−24.062
5.774
12.145

2977
GLN379
NE2
−22.924
5.779
14.122

2978
PHE380
N
−21.936
2.265
8.383

2979
PHE380
CA
−22.185
1.634
7.09

2980
PHE380
C
−22.63
0.18
7.295

2981
PHE380
O
−22.198
−0.546
8.188

2982
PHE380
CB
−20.949
1.658
6.181

2983
PHE380
CG
−20.569
3.043
5.716

2984
PHE380
CD1
−19.357
3.616
6.122

2985
PHE380
CD2
−21.416
3.779
4.873

2986
PHE380
CE1
−19.001
4.896
5.693

2987
PHE380
CE2
−21.056
5.057
4.443

2988
PHE380
CZ
−19.848
5.615
4.853

2989
LEU381
N
−23.534
−0.249
6.338

2990
LEU381
CA
−24.25
−1.514
6.46

2991
LEU381
C
−23.534
−2.548
5.567

2992
LEU381
O
−23.838
−2.741
4.388

2993
LEU381
CB
−25.714
−1.298
6.037

2994
LEU381
CG
−26.653
−2.459
6.414

2995
LEU381
CD1
−26.929
−2.494
7.92

2996
LEU381
CD2
−27.978
−2.326
5.66

2997
LEU382
N
−22.46
−3.169
6.173

2998
LEU382
CA
−21.835
−4.382
5.63

2999
LEU382
C
−22.284
−5.561
6.522

3000
LEU382
O
−22.899
−5.375
7.577

3001
LEU382
CB
−20.31
−4.248
5.591

3002
LEU382
CG
−19.805
−3.112
4.675

3003
LEU382
CD1
−18.293
−2.95
4.834

3004
LEU382
CD2
−20.143
−3.357
3.203

3005
SER383
N
−21.988
−6.824
6.048

3006
SER383
CA
−22.588
−8.052
6.617

3007
SER383
C
−21.629
−9.25
6.398

3008
SER383
O
−20.671
−9.146
5.623

3009
SER383
CB
−23.949
−8.315
5.955

3010
SER383
OG
−24.973
−7.4
6.396

3011
VAL384
N
−21.83
−10.37
7.195

3012
VAL384
CA
−21.372
−11.751
6.842

3013
VAL384
C
−22.079
−12.761
7.821

3014
VAL384
O
−22.425
−12.38
8.942

3015
VAL384
CB
−19.837
−11.888
6.772

3016
VAL384
CG1
−19.229
−12.214
8.117

3017
VAL384
CG2
−19.373
−12.917
5.744

3018
TRP385
N
−22.278
−14.06
7.353

3019
TRP385
CA
−22.723
−15.189
8.229

3020
TRP385
C
−21.53
−16.149
8.431

3021
TRP385
O
−20.479
−15.995
7.81

3022
TRP385
CB
−24.005
−15.93
7.763

3023
TRP385
CG
−23.947
−16.867
6.581

3024
TRP385
CD1
−23.168
−18.003
6.451

3025
TRP385
CD2
−24.804
−16.854
5.419

3026
TRP385
NE1
−23.438
−18.598
5.247

3027
TRP385
CE2
−24.405
−17.891
4.578

3028
TRP385
CE3
−25.913
−16.085
5.006

3029
TRP385
CZ2
−24.963
−18.119
3.313

3030
TRP385
CZ3
−26.5
−16.301
3.754

3031
TRP385
CH2
−26.014
−17.294
2.91

3032
ARG386
N
−21.73
−17.184
9.335

3033
ARG386
CA
−20.636
−18.069
9.763

3034
ARG386
C
−21.064
−19.578
9.786

3035
ARG386
O
−21.971
−19.986
10.516

3036
ARG386
CB
−20.162
−17.568
11.128

3037
ARG386
CG
−19.024
−18.381
11.725

3038
ARG386
CD
−18.422
−17.636
12.911

3039
ARG386
NE
−17.243
−16.862
12.502

3040
ARG386
CZ
−17.023
−15.559
12.755

3041
ARG386
NH1
−15.887
−14.992
12.315

3042
ARG386
NH2
−17.891
−14.792
13.442

3043
PRO387
N
−20.383
−20.443
8.926

3044
PRO387
CA
−20.892
−21.788
8.578

3045
PRO387
C
−20.298
−22.971
9.395

3046
PRO387
O
−19.435
−22.831
10.267

3047
PRO387
CB
−20.461
−21.931
7.113

3048
PRO387
CG
−19.113
−21.221
7.091

3049
PRO387
CD
−19.383
−20.011
7.958

3050
GLU388
N
−20.764
−24.221
9.005

3051
GLU388
CA
−20.389
−25.505
9.623

3052
GLU388
C
−19.082
−26.127
9.012

3053
GLU388
O
−18.926
−27.349
8.891

3054
GLU388
CB
−21.524
−26.554
9.497

3055
GLU388
CG
−22.909
−26.148
10.003

3056
GLU388
CD
−23.108
−26.087
11.515

3057
GLU388
OE1
−22.765
−27.093
12.197

3058
GLU388
OE2
−23.571
−24.979
11.934

3059
GLU389
N
−18.033
−25.254
8.789

3060
GLU389
CA
−16.664
−25.697
8.397

3061
GLU389
C
−15.987
−26.349
9.647

3062
GLU389
O
−16.605
−26.566
10.696

3063
GLU389
CB
−15.93
−24.498
7.763

3064
GLU389
CG
−14.713
−24.819
6.884

3065
GLU389
CD
−13.399
−24.46
7.563

3066
GLU389
OE1
−12.701
−23.533
7.064

3067
GLU389
OE2
−13.124
−25.121
8.61

3068
GLY390
N
−14.681
−26.751
9.516

3069
GLY390
CA
−14.027
−27.553
10.53

3070
GLY390
C
−13.423
−26.714
11.662

3071
GLY390
O
−14.015
−25.771
12.195

3072
ARG391
N
−12.162
−27.162
12.036

3073
ARG391
CA
−11.427
−26.628
13.18

3074
ARG391
C
−10.954
−25.21
12.832

3075
ARG391
O
−10.327
−24.927
11.809

3076
ARG391
CB
−10.224
−27.531
13.497

3077
ARG391
CG
−9.386
−27.126
14.715

3078
ARG391
CD
−10.134
−27.236
16.041

3079
ARG391
NE
−9.223
−26.995
17.173

3080
ARG391
CZ
−9.596
−27.072
18.477

3081
ARG391
NH1
−8.666
−26.907
19.442

3082
ARG391
NH2
−10.872
−27.303
18.843

3083
ARG392
N
−11.331
−24.267
13.785

3084
ARG392
CA
−11.305
−22.854
13.436

3085
ARG392
C
−10.846
−21.965
14.609

3086
ARG392
O
−11.058
−20.753
14.675

3087
ARG392
CB
−12.647
−22.412
12.835

3088
ARG392
CG
−12.793
−22.794
11.36

3089
ARG392
CD
−14.19
−22.585
10.807

3090
ARG392
NE
−15.126
−23.597
11.318

3091
ARG392
CZ
−16.472
−23.486
11.233

3092
ARG392
NH1
−17.268
−24.443
11.732

3093
ARG392
NH2
−17.067
−22.445
10.617

3094
SER393
N
−9.984
−22.596
15.478

3095
SER393
CA
−9.333
−21.934
16.611

3096
SER393
C
−7.956
−21.336
16.252

3097
SER393
O
−7.059
−21.28
17.093

3098
SER393
CB
−9.151
−22.928
17.767

3099
SER393
OG
−8.707
−22.282
18.955

3100
LEU394
N
−7.851
−20.775
14.996

3101
LEU394
CA
−6.568
−20.364
14.404

3102
LEU394
C
−6.794
−19.764
12.993

3103
LEU394
O
−6.362
−20.323
11.985

3104
LEU394
CB
−5.522
−21.52
14.394

3105
LEU394
CG
−5.762
−22.791
13.539

3106
LEU394
CD1
−4.561
−23.734
13.699

3107
LEU394
CD2
−7.04
−23.555
13.868

3108
ARG395
N
−7.593
−18.622
12.89

3109
ARG395
CA
−8.21
−18.3
11.586

3110
ARG395
C
−8.701
−16.782
11.178

3111
ARG395
O
−9.874
−16.525
10.892

3112
ARG395
CB
−9.39
−19.275
11.375

3113
ARG395
CG
−9.286
−20.806
11.46

3114
ARG395
CD
−8.562
−21.618
10.391

3115
ARG395
NE
−9.305
−21.658
9.128

3116
ARG395
CZ
−10.205
−22.574
8.688

3117
ARG395
NH1
−10.593
−23.658
9.402

3118
ARG395
NH2
−10.761
−22.39
7.476

3119
PRO396
N
−7.74
−15.79
11.005

3120
PRO396
CA
−7.983
−14.407
10.506

3121
PRO396
C
−8.425
−14.105
9.049

3122
PRO396
O
−8.923
−14.954
8.312

3123
PRO396
CB
−6.609
−13.747
10.679

3124
PRO396
CG
−5.993
−14.423
11.868

3125
PRO396
CD
−6.711
−15.746
11.993

3126
CYS397
N
−8.274
−12.755
8.692

3127
CYS397
CA
−8.72
−12.15
7.421

3128
CYS397
C
−8.328
−10.621
7.371

3129
CYS397
O
−7.924
−10.054
8.394

3130
CYS397
CB
−10.208
−12.41
7.221

3131
CYS397
SG
−11.279
−11.876
8.582

3132
SER398
N
−8.423
−9.94
6.157

3133
SER398
CA
−8.182
−8.484
6.024

3134
SER398
C
−9.232
−7.657
5.24

3135
SER398
O
−9.673
−7.98
4.142

3136
SER398
CB
−6.83
−8.139
5.399

3137
SER398
OG
−6.54
−6.747
5.627

3138
VAL399
N
−9.546
−6.441
5.84

3139
VAL399
CA
−10.484
−5.489
5.229

3140
VAL399
C
−9.877
−4.905
3.935

3141
VAL399
O
−8.669
−4.858
3.714

3142
VAL399
CB
−10.915
−4.399
6.256

3143
VAL399
CG1
−12.368
−4.572
6.703

3144
VAL399
CG2
−10.719
−2.942
5.827

3145
LEU400
N
−10.855
−4.406
3.088

3146
LEU400
CA
−10.577
−3.844
1.768

3147
LEU400
C
−11.708
−2.838
1.468

3148
LEU400
O
−12.448
−2.909
0.491

3149
LEU400
CB
−10.524
−4.964
0.726

3150
LEU400
CG
−10.008
−4.493
−0.644

3151
LEU400
CD1
−8.493
−4.301
−0.627

3152
LEU400
CD2
−10.408
−5.497
−1.721

3153
VAL401
N
−11.801
−1.835
2.407

3154
VAL401
CA
−12.723
−0.702
2.301

3155
VAL401
C
−11.844
0.483
2.736

3156
VAL401
O
−10.856
0.309
3.454

3157
VAL401
CB
−13.959
−0.896
3.208

3158
VAL401
CG1
−14.994
0.218
3.018

3159
VAL401
CG2
−14.649
−2.245
2.967

3160
SER402
N
−12.241
1.72
2.284

3161
SER402
CA
−11.36
2.883
2.401

3162
SER402
C
−12.157
4.151
2.745

3163
SER402
O
−13.38
4.229
2.642

3164
SER402
CB
−10.56
3.073
1.105

3165
SER402
OG
−11.443
3.091
−0.023

3166
LEU403
N
−11.356
5.198
3.161

3167
LEU403
CA
−11.854
6.504
3.597

3168
LEU403
C
−10.857
7.561
3.072

3169
LEU403
O
−10.423
8.519
3.706

3170
LEU403
CB
−12.133
6.514
5.096

3171
LEU403
CG
−12.702
7.82
5.681

3172
LEU403
CD1
−13.726
8.51
4.783

3173
LEU403
CD2
−13.325
7.552
7.053

3174
LEU404
N
−10.668
7.373
1.714

3175
LEU404
CA
−9.941
8.264
0.812

3176
LEU404
C
−10.818
9.529
0.723

3177
LEU404
O
−12.024
9.486
0.474

3178
LEU404
CB
−9.801
7.527
−0.53

3179
LEU404
CG
−8.834
8.136
−1.553

3180
LEU404
CD1
−8.581
7.127
−2.68

3181
LEU404
CD2
−9.37
9.432
−2.147

3182
GLN405
N
−10.159
10.714
1.016

3183
GLN405
CA
−10.916
11.95
1.155

3184
GLN405
C
−11.398
12.498
−0.194

3185
GLN405
O
−10.848
12.242
−1.26

3186
GLN405
CB
−10.152
13.044
1.92

3187
GLN405
CG
−8.982
13.679
1.17

3188
GLN405
CD
−8.409
14.848
1.941

3189
GLN405
OE1
−8.517
16.01
1.558

3190
GLN405
NE2
−7.772
14.524
3.104

3191
LYS406
N
−12.457
13.383
−0.088

3192
LYS406
CA
−12.778
14.302
−1.177

3193
LYS406
C
−12.141
15.635
−0.743

3194
LYS406
O
−12.518
16.183
0.306

3195
LYS406
CB
−14.292
14.496
−1.302

3196
LYS406
CG
−15.033
13.227
−1.744

3197
LYS406
CD
−16.543
13.452
−1.659

3198
LYS406
CE
−17.366
12.198
−1.9

3199
LYS406
NZ
−17.498
11.909
−3.337

3200
PRO407
N
−11.126
16.161
−1.511

3201
PRO407
CA
−10.416
17.373
−1.111

3202
PRO407
C
−11.214
18.633
−1.495

3203
PRO407
O
−12.201
18.619
−2.226

3204
PRO407
CB
−9.092
17.307
−1.875

3205
PRO407
CG
−9.469
16.556
−3.147

3206
PRO407
CD
−10.478
15.53
−2.653

3207
ARG408
N
−10.711
19.793
−0.93

3208
ARG408
CA
−11.226
21.121
−1.276

3209
ARG408
C
−10.01
21.966
−1.669

3210
ARG408
O
−8.867
21.71
−1.273

3211
ARG408
CB
−11.946
21.751
−0.075

3212
ARG408
CG
−13.319
21.114
0.167

3213
ARG408
CD
−13.694
21.058
1.65

3214
ARG408
NE
−14.581
19.919
1.947

3215
ARG408
CZ
−14.228
18.617
1.777

3216
ARG408
NH1
−12.974
18.264
1.444

3217
ARG408
NH2
−15.149
17.647
1.94

3218
HIS409
N
−10.29
23.114
−2.386

3219
HIS409
CA
−9.225
23.894
−3.039

3220
HIS409
C
−8.423
24.827
−2.092

3221
HIS409
O
−7.786
25.794
−2.516

3222
HIS409
CB
−9.749
24.675
−4.261

3223
HIS409
CG
−10.004
23.779
−5.431

3224
HIS409
ND1
−11.239
23.595
−6

3225
HIS409
CD2
−9.152
23.013
−6.2

3226
HIS409
CE1
−11.089
22.715
−7.037

3227
HIS409
NE2
−9.837
22.33
−7.181

3228
ARG410
N
−8.27
24.332
−0.808

3229
AHG410
CA
−7.107
24.629
0.028

3230
ARG410
C
−5.953
23.707
−0.422

3231
ARG410
O
−4.786
24.104
−0.504

3232
ARG410
CB
−7.462
24.385
1.5

3233
ARG410
CG
−6.329
24.746
2.464

3234
ARG410
CD
−6.767
24.581
3.916

3235
ARG410
NE
−5.679
24.889
4.856

3236
ARG410
CZ
−4.671
24.047
5.193

3237
ARG410
NH1
−4.554
22.815
4.655

3238
ARG410
NH2
−3.751
24.446
6.098

3239
CYS411
N
−6.287
22.387
−0.683

3240
CYS411
CA
−5.272
21.47
−1.206

3241
CYS411
C
−4.915
21.959
−2.62

3242
CYS411
O
−5.71
22.596
−3.317

3243
CYS411
CB
−5.753
20.019
−1.281

3244
CYS411
SG
−6.127
19.345
0.368

3245
ARG412
N
−3.614
21.698
−3.013

3246
ARG412
CA
−3.076
22.247
−4.266

3247
ARG412
C
−3.132
21.185
−5.377

3248
ARG412
O
−3.331
21.488
−6.55

3249
ARG412
CB
−1.624
22.739
−4.093

3250
ARG412
CG
−1.472
24.264
−3.936

3251
ARG412
CD
−1.97
24.831
−2.609

3252
ARG412
NE
−3.426
24.817
−2.508

3253
ARG412
CZ
−4.289
25.563
−3.227

3254
ARG412
NH1
−3.925
26.701
−3.841

3255
ARG412
NH2
−5.553
25.134
−3.334

3256
LYS413
N
−2.775
19.912
−4.979

3257
LYS413
CA
−2.423
18.864
−5.94

3258
LYS413
C
−3.566
17.87
−6.208

3259
LYS413
O
−3.417
16.89
−6.934

3260
LYS413
CB
−1.2
18.077
−5.447

3261
LYS413
CG
0.061
18.939
−5.336

3262
LYS413
CD
1.276
18.072
−5.005

3263
LYS413
CE
2.534
18.909
−4.838

3264
LYS413
NZ
3.687
18.012
−4.683

3265
ARG414
N
−4.745
18.116
−5.519

3266
ARG414
CA
−5.96
17.328
−5.776

3267
ARG414
C
−5.757
15.849
−5.368

3268
ARG414
O
−6.423
14.935
−5.854

3269
ARG414
CB
−6.46
17.417
−7.226

3270
ARG414
CG
−6.939
18.805
−7.644

3271
ARG414
CD
−8.386
19.082
−7.238

3272
ARG414
NE
−8.988
20.13
−8.069

3273
ARG414
CZ
−9.199
20.038
−9.405

3274
ARG414
NH1
−9.55
21.142
−10.09

3275
ARG414
NH2
−9.091
18.866
−10.056

3276
LYS415
N
−4.876
15.685
−4.308

3277
LYS415
CA
−4.204
14.401
−4.077

3278
LYS415
C
−5.175
13.385
−3.436

3279
LYS415
O
−5.764
13.646
−2.38

3280
LYS415
CB
−3.002
14.629
−3.139

3281
LYS415
CG
−2.124
13.386
−2.95

3282
LYS415
CD
−0.881
13.715
−2.115

3283
LYS415
CE
−0.054
12.499
−1.707

3284
LYS415
NZ
0.445
11.776
−2.873

3285
PRO416
N
−5.289
12.137
−4.035

3286
PRO416
CA
−6.208
11.119
−3.493

3287
PRO416
C
−5.699
10.44
−2.2

3288
PRO416
O
−5.502
9.229
−2.116

3289
PRO416
CB
−6.379
10.111
−4.639

3290
PRO416
CG
−6.094
10.922
−5.889

3291
PRO416
CD
−4.993
11.863
−5.44

3292
LEU417
N
−5.558
11.296
−1.119

3293
LEU417
CA
−5.151
10.828
0.207

3294
LEU417
C
−6.354
10.546
1.155

3295
LEU417
O
−7.531
10.596
0.797

3296
LEU417
CB
−4.029
11.711
0.793

3297
LEU417
CG
−4.428
12.987
1.563

3298
LEU417
CD1
−3.186
13.579
2.241

3299
LEU417
CD2
−5.07
14.051
0.682

3300
LEU418
N
−5.985
10.162
2.433

3301
LEU418
CA
−6.93
9.736
3.481

3302
LEU418
C
−7.686
10.961
4.037

3303
LEU418
O
−7.214
12.1
4.002

3304
LEU418
CB
−6.102
9.081
4.61

3305
LEU418
CG
−6.88
8.332
5.706

3306
LEU418
CD1
−7.557
7.083
5.159

3307
LEU418
CD2
−5.933
7.937
6.844

3308
ALA419
N
−8.902
10.672
4.638

3309
ALA419
CA
−9.558
11.629
5.528

3310
ALA419
C
−9.125
11.34
6.98

3311
ALA419
O
−8.25
12
7.538

3312
ALA419
CB
−11.072
11.637
5.361

3313
ILE420
N
−9.751
10.262
7.572

3314
ILE420
CA
−9.394
9.73
8.889

3315
ILE420
C
−9.594
8.204
8.777

3316
ILE420
O
−10.033
7.702
7.74

3317
ILE420
CB
−10.195
10.35
10.062

3318
ILE420
CG1
−11.716
10.074
10.052

3319
ILE420
CG2
−9.889
11.838
10.256

3320
ILE420
CD1
−12.536
10.817
9.009

3321
GLY421
N
−9.242
7.453
9.882

3322
GLY421
CA
−9.545
6.029
9.923

3323
GLY421
C
−10.876
5.785
10.639

3324
GLY421
O
−11.293
6.56
11.506

3325
PHE422
N
−11.516
4.611
10.28

3326
PHE422
CA
−12.881
4.271
10.723

3327
PHE422
C
−12.978
2.908
11.459

3328
PHE422
O
−12.03
2.131
11.58

3329
PHE422
CB
−13.905
4.426
9.586

3330
PHE422
CG
−13.725
3.469
8.435

3331
PHE422
CD1
−14.505
2.311
8.335

3332
PHE422
CD2
−12.772
3.732
7.443

3333
PHE422
CE1
−14.332
1.436
7.261

3334
PHE422
CE2
−12.596
2.855
6.375

3335
PHE422
CZ
−13.376
1.708
6.286

3336
TYR423
N
−14.215
2.649
12.042

3337
TYR423
CA
−14.36
1.647
13.112

3338
TYR423
C
−15.679
0.909
12.861

3339
TYR423
O
−16.769
1.43
13.102

3340
TYR423
CB
−14.392
2.292
14.525

3341
TYR423
CG
−13.436
3.454
14.663

3342
TYR423
CD1
−13.908
4.752
14.408

3343
TYR423
CD2
−12.065
3.241
14.853

3344
TYR423
CE1
−13.014
5.801
14.239

3345
TYR423
CE2
−11.166
4.292
14.683

3346
TYR423
CZ
−11.652
5.542
14.327

3347
TYR423
OH
−10.774
6.499
13.905

3348
LEU424
N
−15.555
−0.326
12.252

3349
LEU424
CA
−16.735
−1.139
11.976

3350
LEU424
C
−17.057
−2.062
13.172

3351
LEU424
O
−16.209
−2.733
13.761

3352
LEU424
CB
−16.547
−2.012
10.728

3353
LEU424
CG
−16.532
−1.242
9.395

3354
LEU424
CD1
−16.122
−2.192
8.266

3355
LEU424
CD2
−17.888
−0.613
9.07

3356
TYR425
N
−18.407
−2.132
13.465

3357
TYR425
CA
−18.935
−2.946
14.562

3358
TYR425
C
−20.066
−3.78
13.949

3359
TYR425
O
−21.154
−3.292
13.65

3360
TYR425
CB
−19.461
−2.075
15.711

3361
TYR425
CG
−18.348
−1.351
16.436

3362
TYR425
CD1
−18.103
0.007
16.184

3363
TYR425
CD2
−17.52
−2.037
17.337

3364
TYR425
CE1
−17.053
0.67
16.823

3365
TYR425
CE2
−16.465
−1.376
17.97

3366
TYR425
CZ
−16.239
−0.029
17.709

3367
TYR425
OH
−15.195
0.579
18.343

3368
ARG426
N
−19.7
−5.072
13.62

3369
ARG426
CA
−20.619
−5.985
12.935

3370
ARG426
C
−21.328
−6.886
13.962

3371
ARG426
O
−20.791
−7.22
15.016

3372
ARG426
CB
−19.831
−6.833
11.928

3373
ARG426
CG
−19.498
−6.044
10.651

3374
ARG426
CD
−18.185
−6.492
10.014

3375
ARG426
NE
−18.271
−6.602
8.552

3376
ARG426
CZ
−18.851
−7.644
7.904

3377
ARG426
NH1
−18.874
−7.652
6.555

3378
ARG426
NH2
−19.409
−8.672
8.574

3379
MET427
N
−22.589
−7.326
13.584

3380
MET427
CA
−23.458
−8.081
14.497

3381
MET427
C
−24.524
−8.836
13.668

3382
MET427
O
−25.435
−8.232
13.105

3383
MET427
CB
−24.21
−7.149
15.474

3384
MET427
CG
−23.321
−6.538
16.555

3385
MET427
SD
−24.334
−5.591
17.739

3386
MET427
CE
−23.003
−4.993
18.809

3387
ASN428
N
−24.345
−10.21
13.56

3388
ASN428
CA
−25.495
−11.121
13.342

3389
ASN428
C
−26.198
−10.914
11.983

3390
ASN428
O
−27.267
−10.315
11.873

3391
ASN428
CB
−26.504
−11.046
14.496

3392
ASN428
CG
−25.841
−11.268
15.835

3393
ASN428
OD1
−25.592
−10.354
16.617

3394
ASN428
ND2
−25.496
−12.557
16.116

3395
LYS429
N
−25.502
−11.41
10.89

3396
LYS429
CA
−25.762
−10.926
9.529

3397
LYS429
C
−25.484
−12.015
8.456

3398
LYS429
O
−25.267
−13.184
8.767

3399
LYS429
CB
−24.914
−9.658
9.352

3400
LYS429
CG
−25.731
−8.384
9.563

3401
LYS429
CD
−24.844
−7.196
9.938

3402
LYS429
CE
−25.496
−5.884
9.55

3403
LYS429
NZ
−25.222
−5.639
8.124

3404
GLU430
N
−25.568
−11.583
7.132

3405
GLU430
CA
−25.522
−12.497
5.971

3406
GLU430
C
−24.303
−12.271
5.033

3407
GLU430
O
−23.738
−11.184
4.938

3408
GLU430
CB
−26.789
−12.36
5.12

3409
GLU430
CG
−28.058
−12.739
5.875

3410
GLU430
CD
−29.177
−12.747
4.838

3411
GLU430
OE1
−29.853
−11.683
4.78

3412
GLU430
OE2
−29.261
−13.809
4.158

3413
MET431
N
−23.937
−13.375
4.265

3414
MET431
CA
−22.64
−13.472
3.578

3415
MET431
C
−22.448
−12.481
2.41

3416
MET431
O
−23.38
−11.916
1.837

3417
MET431
CB
−22.355
−14.908
3.081

3418
MET431
CG
−21.332
−15.608
3.982

3419
MET431
SD
−21.075
−17.319
3.462

3420
MET431
CE
−19.889
−17.834
4.72

3421
THR432
N
−21.117
−12.353
2.026

3422
THR432
CA
−20.633
−11.428
1

3423
THR432
C
−20.416
−12.185
−0.332

3424
THR432
O
−21.316
−12.297
−1.171

3425
THR432
CB
−19.345
−10.708
1.456

3426
THR432
OG1
−18.337
−11.689
1.747

3427
THR432
CG2
−19.559
−9.846
2.692

3428
TRP433
N
−19.203
−12.821
−0.466

3429
TRP433
CA
−18.684
−13.334
−1.741

3430
TRP433
C
−17.643
−14.447
−1.47

3431
TRP433
O
−17.445
−14.869
−0.33

3432
TRP433
CB
−18.203
−12.196
−2.66

3433
TRP433
CG
−17.287
−11.209
−2.005

3434
TRP433
CD1
−16.045
−11.47
−1.461

3435
TRP433
CD2
−17.527
−9.805
−1.836

3436
TRP433
NE1
−15.553
−10.308
−0.933

3437
TRP433
CE2
−16.424
−9.273
−1.171

3438
TRP433
CE3
−18.578
−8.933
−2.188

3439
TRP433
CZ2
−16.306
−7.916
−0.848

3440
TRP433
CZ3
−18.473
−7.572
−1.876

3441
TRP433
CH2
−17.352
−7.072
−1.22

3442
SER434
N
−17.074
−14.988
−2.607

3443
SER434
CA
−16.302
−16.245
−2.675

3444
SER434
C
−14.816
−16.052
−2.31

3445
SER434
O
−14.388
−15.017
−1.798

3446
SER434
CB
−16.474
−16.814
−4.092

3447
SER434
OG
−16.026
−15.858
−5.058

3448
SER435
N
−13.978
−17.125
−2.611

3449
SER435
CA
−12.701
−17.345
−1.906

3450
SER435
C
−11.638
−16.241
−1.942

3451
SER435
O
−10.671
−16.273
−1.174

3452
SER435
CB
−12.027
−18.653
−2.353

3453
SER435
OG
−11.566
−18.579
−3.706

3454
LEU436
N
−11.87
−15.187
−2.797

3455
LEU436
CA
−11.111
−13.952
−2.65

3456
LEU436
C
−11.359
−13.328
−1.26

3457
LEU436
O
−10.531
−12.606
−0.705

3458
LEU436
CB
−11.517
−12.903
−3.684

3459
LEU436
CG
−11.315
−13.279
−5.154

3460
LEU436
CD1
−11.864
−12.154
−6.032

3461
LEU436
CD2
−9.846
−13.513
−5.489

3462
GLY437
N
−12.62
−13.556
−0.747

3463
GLY437
CA
−13.039
−13.084
0.547

3464
GLY437
C
−12.719
−14.037
1.689

3465
GLY437
O
−13.079
−13.791
2.842

3466
SER438
N
−11.88
−15.091
1.39

3467
SER438
CA
−11.446
−16.058
2.416

3468
SER438
C
−10.602
−15.312
3.458

3469
SER438
O
−10.428
−15.716
4.604

3470
SER438
CB
−10.628
−17.205
1.821

3471
SER438
OG
−9.526
−16.709
1.058

3472
ARG439
N
−10.038
−14.168
2.939

3473
ARG439
CA
−9.286
−13.194
3.686

3474
ARG439
C
−10.124
−11.915
3.874

3475
ARG439
O
−9.563
−10.825
3.969

3476
ARG439
CB
−7.99
−12.932
2.92

3477
ARG439
CG
−6.867
−12.299
3.739

3478
ARG439
CD
−5.585
−12.165
2.925

3479
ARG439
NE
−5.069
−13.475
2.519

3480
ARG439
CZ
−5.407
−14.133
1.391

3481
ARG439
NH1
−5.1
−15.423
1.213

3482
ARG439
NH2
−6.106
−13.565
0.399

3483
GLN440
N
−11.463
−12.096
4.166

3484
GLN440
CA
−12.465
−11.035
4.403

3485
GLN440
C
−12.178
−10.022
5.552

3486
GLN440
O
−11.043
−9.693
5.896

3487
GLN440
CB
−12.943
−10.352
3.108

3488
GLN440
CG
−11.864
−9.689
2.259

3489
GLN440
CD
−12.414
−9.178
0.948

3490
GLN440
OE1
−13.474
−9.548
0.455

3491
GLN440
NE2
−11.597
−8.285
0.317

3492
PRO441
N
−13.239
−9.428
6.202

3493
PRO441
CA
−13.036
−8.136
6.862

3494
PRO441
C
−12.416
−8.117
8.287

3495
PRO441
O
−13.114
−7.991
9.295

3496
PRO441
CB
−14.447
−7.52
6.857

3497
PRO441
CG
−15.365
−8.731
6.917

3498
PRO441
CD
−14.652
−9.738
6.038

3499
PHE442
N
−11.029
−8.153
8.366

3500
PHE442
CA
−10.332
−7.805
9.62

3501
PHE442
C
−9.083
−6.896
9.496

3502
PHE442
O
−9.206
−5.679
9.672

3503
PHE442
CB
−10.116
−8.98
10.59

3504
PHE442
CG
−9.39
−8.563
11.855

3505
PHE442
CD1
−9.915
−7.563
12.689

3506
PHE442
CD2
−8.13
−9.099
12.155

3507
PHE442
CE1
−9.175
−7.076
13.767

3508
PHE442
CE2
−7.399
−8.621
13.245

3509
PHE442
CZ
−7.914
−7.601
14.042

3510
PHE443
N
−7.864
−7.47
9.167

3511
PHE443
CA
−6.592
−6.816
9.559

3512
PHE443
C
−6.519
−5.329
9.168

3513
PHE443
O
−6.065
−4.502
9.956

3514
PHE443
CB
−5.35
−7.501
8.958

3515
PHE443
CG
−4.915
−8.78
9.632

3516
PHE443
CD1
−4.499
−8.779
10.97

3517
PHE443
CD2
−4.845
−9.977
8.906

3518
PHE443
CE1
−4.053
−9.956
11.575

3519
PHE443
CE2
−4.392
−11.152
9.509

3520
PHE443
CZ
−4.002
−11.141
10.845

3521
SER444
N
−6.944
−5.024
7.889

3522
SER444
CA
−7.273
−3.663
7.462

3523
SER444
C
−6.103
−2.826
6.927

3524
SER444
O
−4.948
−2.922
7.329

3525
SER444
CB
−8.006
−2.808
8.523

3526
SER444
OG
−9.277
−3.34
8.873

3527
LEU445
N
−6.519
−1.872
6.004

3528
LEU445
CA
−5.909
−0.544
5.962

3529
LEU445
C
−7.064
0.398
6.361

3530
LEU445
O
−8.241
0.056
6.242

3531
LEU445
CB
−5.414
−0.178
4.561

3532
LEU445
CG
−4.232
−1.026
4.061

3533
LEU445
CD1
−3.967
−0.717
2.587

3534
LEU445
CD2
−2.959
−0.783
4.872

3535
GLU446
N
−6.68
1.619
6.875

3536
GLU446
CA
−7.618
2.736
7.041

3537
GLU446
C
−8.712
2.552
8.119

3538
GLU446
O
−9.611
3.382
8.283

3539
GLU446
CB
−8.281
3.187
5.724

3540
GLU446
CG
−7.293
3.445
4.588

3541
GLU446
CD
−7.919
4.079
3.345

3542
GLU446
OE1
−7.238
3.967
2.289

3543
GLU446
OE2
−9.047
4.637
3.496

3544
ALA447
N
−8.607
1.443
8.935

3545
ALA447
CA
−9.769
1.048
9.716

3546
ALA447
C
−9.445
0.063
10.841

3547
ALA447
O
−8.421
−0.612
10.864

3548
ALA447
CB
−10.827
0.409
8.815

3549
CYS448
N
−10.472
−0.034
11.766

3550
CYS448
CA
−10.613
−1.163
12.675

3551
CYS448
C
−11.992
−1.8
12.41

3552
CYS448
O
−12.953
−1.175
11.954

3553
CYS448
CB
−10.567
−0.751
14.15

3554
CYS448
SG
−8.969
−0.041
14.652

3555
GLN449
N
−12.101
−3.113
12.828

3556
GLN449
CA
−13.353
−3.852
12.697

3557
GLN449
C
−13.478
−4.789
13.901

3558
GLN449
O
−12.505
−5.372
14.383

3559
GLN449
CB
−13.392
−4.607
11.36

3560
GLN449
CG
−14.686
−5.391
11.114

3561
GLN449
CD
−14.77
−6.726
11.827

3562
GLN449
OE1
−15.787
−7.134
12.383

3563
GLN449
NE2
−13.64
−7.486
11.733

3564
GLY450
N
−14.782
−4.982
14.336

3565
GLY450
CA
−15.039
−5.922
15.4

3566
GLY450
C
−16.488
−6.393
15.59

3567
GLY450
O
−17.472
−5.878
15.069

3568
ILE451
N
−16.545
−7.431
16.511

3569
ILE451
CA
−17.782
−7.967
17.084

3570
ILE451
C
−17.402
−8.498
18.495

3571
ILE451
O
−16.283
−8.969
18.747

3572
ILE451
CB
−18.431
−9.052
16.18

3573
ILE451
CG1
−19.753
−9.581
16.776

3574
ILE451
CG2
−17.474
−10.212
15.914

3575
ILE451
CD1
−20.564
−10.47
15.844

3576
LEU452
N
−18.429
−8.406
19.42

3577
LEU452
CA
−18.457
−9.171
20.67

3578
LEU452
C
−19.38
−10.365
20.366

3579
LEU452
O
−20.564
−10.223
20.049

3580
LEU452
CB
−19.03
−8.361
21.838

3581
LEU452
CG
−17.969
−7.553
22.614

3582
LEU452
CD1
−17.285
−6.489
21.757

3583
LEU452
CD2
−18.613
−6.897
23.838

3584
ALA453
N
−18.72
−11.575
20.334

3585
ALA453
CA
−19.368
−12.823
19.955

3586
ALA453
C
−19.845
−13.573
21.207

3587
ALA453
O
−19.208
−13.543
22.263

3588
ALA453
CB
−18.397
−13.666
19.146

3589
LEU454
N
−20.992
−14.335
21.039

3590
LEU454
CA
−21.678
−14.884
22.218

3591
LEU454
C
−22.532
−16.117
21.838

3592
LEU454
O
−23.352
−16.077
20.924

3593
LEU454
CB
−22.578
−13.791
22.84

3594
LEU454
CG
−22.179
−13.341
24.254

3595
LEU454
CD1
−23.059
−12.174
24.702

3596
LEU454
CD2
−22.264
−14.459
25.287

3597
LEU455
N
−22.303
−17.232
22.626

3598
LEU455
CA
−23.037
−18.504
22.562

3599
LEU455
C
−22.923
−19.278
21.221

3600
LEU455
O
−21.809
−19.515
20.749

3601
LEU455
CB
−24.366
−18.564
23.336

3602
LEU455
CG
−25.471
−17.604
22.881

3603
LEU455
CD1
−26.844
−18.245
23.061

3604
LEU455
CD2
−25.453
−16.307
23.685

3605
ASP456
N
−24.08
−19.73
20.622

3606
ASP456
CA
−24.079
−20.807
19.612

3607
ASP456
C
−25.142
−20.552
18.52

3608
ASP456
O
−25.977
−21.383
18.16

3609
ASP456
CB
−24.277
−22.157
20.297

3610
ASP456
CG
−25.561
−22.276
21.117

3611
ASP456
OD1
−25.678
−23.357
21.757

3612
ASP456
OD2
−26.351
−21.282
21.082

3613
LEU457
N
−25.039
−19.315
17.918

3614
LEU457
CA
−26.163
−18.744
17.205

3615
LEU457
C
−26.23
−19.102
15.711

3616
LEU457
O
−25.275
−18.996
14.942

3617
LEU457
CB
−26.152
−17.21
17.303

3618
LEU457
CG
−26.172
−16.655
18.737

3619
LEU457
CD1
−26.215
−15.13
18.687

3620
LEU457
CD2
−27.342
−17.195
19.553

3621
ASN458
N
−27.517
−19.404
15.283

3622
ASN458
CA
−27.869
−19.553
13.868

3623
ASN458
C
−28.119
−18.161
13.271

3624
ASN458
O
−28.082
−17.963
12.057

3625
ASN458
CB
−29.094
−20.438
13.704

3626
ASN458
CG
−29.345
−20.88
12.281

3627
ASN458
OD1
−30.369
−20.599
11.654

3628
ASN458
ND2
−28.395
−21.678
11.711

3629
ALA459
N
−28.339
−17.149
14.183

3630
ALA459
CA
−28.623
−15.775
13.76

3631
ALA459
C
−27.383
−15.129
13.104

3632
ALA459
O
−27.454
−14.087
12.457

3633
ALA459
CB
−29.048
−14.929
14.952

3634
SER460
N
−26.191
−15.771
13.377

3635
SER460
CA
−24.923
−15.423
12.737

3636
SER460
C
−24.465
−16.523
11.762

3637
SER460
O
−23.307
−16.571
11.336

3638
SER460
CB
−23.826
−15.211
13.796

3639
SER460
OG
−24.097
−14.046
14.573

3640
GLY461
N
−25.421
−17.425
11.328

3641
GLY461
CA
−24.972
−18.751
10.942

3642
GLY461
C
−26.015
−19.652
10.301

3643
GLY461
O
−26.07
−20.852
10.568

3644
THR462
N
−26.747
−19.036
9.319

3645
THR462
CA
−27.6
−19.729
8.332

3646
THR462
C
−27.351
−18.909
7.069

3647
THR462
O
−27.307
−17.676
7.15

3648
THR462
CB
−29.076
−19.719
8.781

3649
THR462
OG1
−29.416
−21.025
9.273

3650
THR462
CG2
−30.111
−19.384
7.717

3651
MET463
N
−27.18
−19.512
5.856

3652
MET463
CA
−27.327
−20.912
5.478

3653
MET463
C
−26.033
−21.723
5.745

3654
MET463
O
−25.904
−22.367
6.789

3655
MET463
CB
−27.787
−21.064
4.019

3656
MET463
CG
−29.23
−20.624
3.748

3657
MET463
SD
−29.329
−19.017
2.886

3658
MET463
CE
−29.982
−17.973
4.209

3659
SER464
N
−25.026
−21.675
4.795

3660
SER464
CA
−23.925
−22.653
4.837

3661
SER464
C
−22.64
−22.062
4.223

3662
SER464
O
−22.496
−20.845
4.081

3663
SER464
CB
−24.372
−23.959
4.164

3664
SER464
OG
−24.026
−24.012
2.783

3665
ILE465
N
−21.628
−22.979
3.953

3666
ILE465
CA
−20.496
−22.62
3.087

3667
ILE465
C
−20.695
−23.153
1.652

3668
ILE465
O
−19.948
−22.821
0.73

3669
ILE465
CB
−19.145
−23.079
3.699

3670
ILE465
CG1
−17.945
−22.428
2.976

3671
ILE465
CG2
−19
−24.602
3.768

3672
ILE465
CD1
−16.65
−22.488
3.777

3673
GLN466
N
−21.729
−24.05
1.464

3674
GLN466
CA
−21.953
−24.678
0.166

3675
GLN466
C
−22.583
−23.712
−0.858

3676
GLN466
O
−22.796
−24.041
−2.023

3677
GLN466
CB
−22.784
−25.961
0.289

3678
GLN466
CG
−22.141
−26.997
1.216

3679
GLN466
CD
−22.575
−26.832
2.658

3680
GLN466
OE1
−21.911
−26.247
3.509

3681
GLN466
NE2
−23.792
−27.386
2.948

3682
GLU467
N
−22.787
−22.432
−0.379

3683
GLU467
CA
−23.107
−21.313
−1.25

3684
GLU467
C
−21.82
−20.77
−1.92

3685
GLU467
O
−21.881
−19.958
−2.844

3686
GLU467
CB
−23.776
−20.18
−0.456

3687
GLU467
CG
−25.224
−20.493
−0.071

3688
GLU467
CD
−25.479
−21.591
0.957

3689
GLU467
OE1
−26.685
−21.909
1.125

3690
GLU467
OE2
−24.462
−22.076
1.549

3691
PHE468
N
−20.625
−21.177
−1.354

3692
PHE468
CA
−19.297
−20.857
−1.887

3693
PHE468
C
−18.973
−19.378
−1.635

3694
PHE468
O
−18.508
−18.641
−2.502

3695
PHE468
CB
−19.081
−21.242
−3.361

3696
PHE468
CG
−19.031
−22.735
−3.584

3697
PHE468
CD1
−20.188
−23.444
−3.925

3698
PHE468
CD2
−17.824
−23.433
−3.437

3699
PHE468
CE1
−20.141
−24.826
−4.118

3700
PHE468
CE2
−17.777
−24.814
−3.637

3701
PHE468
CZ
−18.935
−25.51
−3.977

3702
ARG469
N
−19.176
−18.978
−0.326

3703
ARG469
CA
−18.955
−17.606
0.138

3704
ARG469
C
−18.233
−17.68
1.516

3705
ARG469
O
−18.179
−18.736
2.152

3706
ARG469
CB
−20.289
−16.841
0.146

3707
ARG469
CG
−20.949
−16.705
−1.238

3708
ARG469
CD
−22.418
−16.286
−1.154

3709
ARG469
NE
−22.576
−14.835
−1.038

3710
ARG469
CZ
−23.571
−14.191
−0.388

3711
ARG469
NH1
−23.577
−12.85
−0.416

3712
ARG469
NH2
−24.531
−14.828
0.309

3713
ASP470
N
−17.645
−16.493
1.966

3714
ASP470
CA
−16.41
−16.571
2.797

3715
ASP470
C
−16.38
−15.736
4.16

3716
ASP470
O
−17.401
−15.304
4.688

3717
ASP470
CB
−15.244
−16.262
1.861

3718
ASP470
CG
−14.765
−17.549
1.208

3719
ASP470
OD1
−13.791
−18.098
1.798

3720
ASP470
OD2
−15.341
−17.873
0.133

3721
LEU471
N
−15.118
−15.643
4.759

3722
LEU471
CA
−14.762
−15.476
6.201

3723
LEU471
C
−15.071
−14.186
7.029

3724
LEU471
O
−15.89
−13.351
6.66

3725
LEU471
CB
−15.013
−16.798
6.953

3726
LEU471
CG
−15.999
−16.857
8.125

3727
LEU471
CD1
−17.41
−16.426
7.758

3728
LEU471
CD2
−16.021
−18.296
8.651

3729
TRP472
N
−14.336
−14.066
8.234

3730
TRP472
CA
−14.807
−13.29
9.424

3731
TRP472
C
−13.809
−13.453
10.645

3732
TRP472
O
−13.539
−14.592
11.04

3733
TRP472
CB
−15.274
−11.864
9.136

3734
TRP472
CG
−16.065
−11.203
10.232

3735
TRP472
CD1
−15.809
−9.925
10.672

3736
TRP472
CD2
−17.245
−11.631
10.929

3737
TRP472
NE1
−16.69
−9.598
11.66

3738
TRP472
CE2
−17.645
−10.577
11.759

3739
TRP472
CE3
−18.065
−12.779
10.891

3740
TRP472
CZ2
−18.831
−10.599
12.5

3741
TRP472
CZ3
−19.274
−12.8
11.599

3742
TRP472
CH2
−19.649
−11.725
12.395

3743
LYS473
N
−13.317
−12.328
11.277

3744
LYS473
CA
−12.528
−12.244
12.559

3745
LYS473
C
−12.555
−10.73
12.919

3746
LYS473
O
−13.222
−9.962
12.208

3747
LYS473
CB
−11.089
−12.779
12.405

3748
LYS473
CG
−10.658
−13.618
13.62

3749
LYS473
CD
−9.176
−13.615
14.033

3750
LYS473
CE
−8.406
−12.325
13.805

3751
LYS473
NZ
−7.253
−12.238
14.705

3752
GLN474
N
−11.902
−10.125
13.948

3753
GLN474
CA
−11.485
−10.565
15.29

3754
GLN474
C
−12.758
−10.505
16.136

3755
GLN474
O
−13.294
−9.445
16.479

3756
GLN474
CB
−10.453
−9.581
15.879

3757
GLN474
CG
−10.067
−9.819
17.345

3758
GLN474
CD
−8.796
−10.613
17.546

3759
GLN474
OE1
−8.217
−11.236
16.662

3760
GLN474
NE2
−8.339
−10.619
18.834

3761
LEU475
N
−13.276
−11.753
16.425

3762
LEU475
CA
−14.466
−11.861
17.241

3763
LEU475
C
−14.037
−12.156
18.68

3764
LEU475
O
−13.301
−13.098
18.97

3765
LEU475
CB
−15.503
−12.844
16.703

3766
LEU475
CG
−15.106
−14.314
16.529

3767
LEU475
CD1
−16.382
−15.157
16.439

3768
LEU475
CD2
−14.241
−14.554
15.294

3769
LYS476
N
−14.52
−11.229
19.594

3770
LYS476
CA
−14.296
−11.408
21.023

3771
LYS476
C
−15.403
−12.373
21.456

3772
LYS476
O
−16.557
−11.986
21.643

3773
LYS476
CB
−14.448
−10.084
21.787

3774
LYS476
CG
−13.182
−9.226
21.871

3775
LYS476
CD
−13.144
−8.045
20.896

3776
LYS476
CE
−12.76
−8.445
19.483

3777
LYS476
NZ
−13.864
−8.18
18.544

3778
LEU477
N
−15.034
−13.706
21.475

3779
LEU477
CA
−15.975
−14.735
21.911

3780
LEU477
C
−16.033
−14.625
23.426

3781
LEU477
O
−15.074
−14.88
24.151

3782
LEU477
CB
−15.534
−16.129
21.469

3783
LEU477
CG
−16.481
−17.3
21.82

3784
LEU477
CD1
−16.3
−17.827
23.24

3785
LEU477
CD2
−17.957
−17.001
21.566

3786
SER478
N
−17.236
−14.142
23.884

3787
SER478
CA
−17.475
−13.916
25.289

3788
SER478
C
−17.836
−15.275
25.896

3789
SER478
O
−18.871
−15.882
25.619

3790
SER478
CB
−18.596
−12.9
25.497

3791
SER478
OG
−18.322
−12.077
26.646

3792
GLN479
N
−16.886
−15.779
26.773

3793
GLN479
CA
−17.03
−17.108
27.39

3794
GLN479
C
−18.077
−16.997
28.527

3795
GLN479
O
−17.791
−17.049
29.722

3796
GLN479
CB
−15.688
−17.598
27.959

3797
GLN479
CG
−14.69
−18.011
26.879

3798
GLN479
CD
−14.908
−19.453
26.483

3799
GLN479
OE1
−15.734
−19.8
25.647

3800
GLN479
NE2
−14.156
−20.36
27.173

3801
LYS480
N
−19.356
−16.773
28.067

3802
LYS480
CA
−20.517
−16.487
28.906

3803
LYS480
C
−21.77
−16.665
28.014

3804
LYS480
O
−21.677
−17.136
26.877

3805
LYS480
CB
−20.356
−15.172
29.687

3806
LYS480
CG
−19.899
−13.945
28.877

3807
LYS480
CD
−18.895
−13.069
29.654

3808
LYS480
CE
−17.427
−13.47
29.478

3809
LYS480
NZ
−16.768
−12.661
28.431

3810
VAL481
N
−22.997
−16.427
28.604

3811
VAL481
CA
−24.229
−17.002
28.043

3812
VAL481
C
−25.429
−16.015
28.089

3813
VAL481
O
−25.351
−14.874
28.538

3814
VAL481
CB
−24.567
−18.365
28.717

3815
VAL481
CG1
−23.517
−19.439
28.415

3816
VAL481
CG2
−24.767
−18.237
30.229

3817
PHE482
N
−26.597
−16.56
27.571

3818
PHE482
CA
−27.802
−15.775
27.256

3819
PHE482
C
−28.301
−14.989
28.477

3820
PHE482
O
−28.668
−15.532
29.517

3821
PHE482
CB
−28.909
−16.748
26.797

3822
PHE482
CG
−30.248
−16.149
26.442

3823
PHE482
CD1
−30.36
−15.064
25.568

3824
PHE482
CD2
−31.424
−16.738
26.933

3825
PHE482
CE1
−31.614
−14.568
25.206

3826
PHE482
CE2
−32.678
−16.249
26.563

3827
PHE482
CZ
−32.773
−15.165
25.696

3828
HIS483
N
−28.23
−13.613
28.311

3829
HIS483
CA
−28.735
−12.668
29.304

3830
HIS483
C
−27.97
−12.722
30.637

3831
HIS483
C
−28.45
−12.283
31.683

3832
HIS483
CB
−30.254
−12.74
29.528

3833
HIS483
CG
−31.073
−12.26
28.373

3834
HIS483
ND1
−32.394
−12.607
28.232

3835
HIS483
CD2
−30.826
−11.421
27.306

3836
HIS483
CE1
−32.878
−11.963
27.13

3837
HIS483
NE2
−31.948
−11.251
26.535

3838
LYS484
N
−26.657
−13.133
30.533

3839
LYS484
CA
−25.685
−12.862
31.58

3840
LYS484
C
−24.653
−11.904
30.972

3841
LYS484
C
−24.407
−11.865
29.767

3842
LYS484
CB
−25.05
−14.143
32.123

3843
LYS484
CG
−26.115
−15.069
32.724

3844
LYS484
CD
−25.513
−16.271
33.448

3845
LYS484
CE
−26.619
−17.214
33.907

3846
LYS484
NZ
−26.018
−18.377
34.601

3847
GLN485
N
−24.023
−11.091
31.9

3848
GLN485
CA
−23.392
−9.862
31.435

3849
GLN485
C
−22.075
−10.171
30.7

3850
GLN485
O
−21.35
−11.127
30.976

3851
GLN485
CB
−23.103
−8.888
32.593

3852
GLN485
CG
−24.353
−8.174
33.122

3853
GLN485
CD
−25.272
−9.063
33.935

3854
GLN485
OE1
−25.095
−10.268
34.093

3855
GLN485
NE2
−26.344
−8.412
34.475

3856
ASP486
N
−21.755
−9.213
29.744

3857
ASP486
CA
−20.474
−9.264
29.055

3858
ASP486
C
−19.431
−8.63
29.985

3859
ASP486
O
−19.696
−7.757
30.808

3860
ASP486
CB
−20.494
−8.536
27.718

3861
ASP486
CG
−20.864
−9.533
26.626

3862
ASP486
OD1
−21.919
−9.27
25.974

3863
ASP486
OD2
−20.035
−10.491
26.497

3864
ARG487
N
−18.167
−9.147
29.798

3865
ARG487
CA
−17.035
−8.814
30.649

3866
ARG487
C
−15.801
−9.489
30.029

3867
ARG487
O
−15.896
−10.495
29.316

3868
ARG487
CB
−17.223
−9.265
32.114

3869
ARG487
CG
−17.552
−10.755
32.235

3870
ARG487
CD
−17.844
−11.202
33.664

3871
ARG487
NE
−18.195
−12.636
33.704

3872
ARG487
CZ
−17.357
−13.643
33.349

3873
ARG487
NH1
−17.852
−14.883
33.153

3874
ARG487
NH2
−16.047
−13.438
33.161

3875
GLY488
N
−14.596
−8.926
30.413

3876
GLY488
CA
−13.358
−9.294
29.739

3877
GLY488
C
−12.713
−10.564
30.276

3878
GLY488
O
−11.803
−11.146
29.685

3879
SER489
N
−13.197
−10.993
31.488

3880
SER489
CA
−12.728
−12.203
32.159

3881
SER489
C
−13.311
−13.449
31.456

3882
SER489
O
−14.069
−14.252
32.002

3883
SER489
CB
−13.068
−12.139
33.651

3884
SER489
OG
−14.433
−11.726
33.865

3885
GLY490
N
−12.87
−13.583
30.151

3886
GLY490
CA
−13.229
−14.693
29.3

3887
GLY490
C
−13.465
−14.203
27.871

3888
GLY490
O
−14.604
−13.942
27.472

3889
TYR491
N
−12.286
−14.06
27.158

3890
TYR491
CA
−12.146
−13.768
25.722

3891
TYR491
C
−10.925
−14.598
25.239

3892
TYR491
O
−10.081
−15.004
26.04

3893
TYR491
CB
−11.825
−12.287
25.44

3894
TYR491
CG
−12.903
−11.243
25.626

3895
TYR491
CD1
−12.514
−9.911
25.86

3896
TYR491
CD2
−14.265
−11.515
25.474

3897
TYR491
CE1
−13.461
−8.888
25.963

3898
TYR491
CE2
−15.218
−10.499
25.599

3899
TYR491
CZ
−14.811
−9.194
25.84

3900
TYR491
OH
−15.774
−8.234
25.938

3901
LEU492
N
−10.827
−14.786
23.871

3902
LEU492
CA
−9.715
−15.511
23.231

3903
LEU492
C
−9.789
−15.324
21.697

3904
LEU492
O
−10.873
−15.114
21.145

3905
LEU492
CB
−9.668
−17.007
23.602

3906
LEU492
CG
−10.781
−17.923
23.041

3907
LEU492
CD1
−10.571
−19.357
23.543

3908
LEU492
CD2
−12.197
−17.488
23.413

3909
ASN493
N
−8.603
−15.444
20.997

3910
ASN493
CA
−8.429
−15.381
19.514

3911
ASN493
C
−6.895
−15.31
19.247

3912
ASN493
O
−6.15
−14.752
20.061

3913
ASN493
CB
−9.05
−14.117
18.881

3914
ASN493
CG
−10.391
−14.229
18.165

3915
ASN493
OD1
−10.682
−13.55
17.18

3916
ASN493
ND2
−11.348
−15.029
18.73

3917
TRP494
N
−6.359
−15.716
18.044

3918
TRP494
CA
−6.597
−17.008
17.376

3919
TRP494
C
−6.2
−16.972
15.869

3920
TRP494
O
−7.085
−17.043
15.008

3921
TRP494
CB
−5.864
−18.162
18.077

3922
TRP494
CG
−6.493
−18.602
19.362

3923
TRP494
CD1
−7.744
−19.168
19.512

3924
TRP494
CD2
−5.893
−18.577
20.663

3925
TRP494
NE1
−7.895
−19.543
20.819

3926
TRP494
CE2
−6.784
−19.19
21.546

3927
TRP494
CE3
−4.659
−18.117
21.169

3928
TRP494
CZ2
−6.494
−19.381
22.902

3929
TRP494
CZ3
−4.361
−18.287
22.526

3930
TRP494
CH2
−5.266
−18.913
23.378

3931
GLU495
N
−4.845
−16.903
15.565

3932
GLU495
CA
−4.323
−16.498
14.235

3933
GLU495
C
−4.049
−17.662
13.21

3934
GLU495
O
−3.999
−18.834
13.572

3935
GLU495
CB
−3.105
−15.573
14.392

3936
GLU495
CG
−3.338
−14.37
15.316

3937
GLU495
CD
−4.475
−13.47
14.863

3938
GLU495
OE1
−5.652
−13.786
15.24

3939
GLU495
OE2
−4.185
−12.479
14.142

3940
GLN496
N
−3.91
−17.286
11.867

3941
GLN496
CA
−4.128
−18.198
10.691

3942
GLN496
C
−5.056
−17.459
9.649

3943
GLN496
O
−4.914
−16.249
9.455

3944
GLN496
CB
−2.773
−18.562
10.06

3945
GLN496
CG
−2.739
−19.971
9.465

3946
GLN496
CD
−3.606
−20.099
8.236

3947
GLN496
OE1
−4.785
−20.438
8.302

3948
GLN496
NE2
−3.013
−19.72
7.067

3949
LEU497
N
−6.036
−18.212
9

3950
LEU497
CA
−7.082
−17.633
8.107

3951
LEU497
C
−8.492
−18.334
8.207

3952
LEU497
O
−8.592
−19.564
8.188

3953
LEU497
CB
−6.683
−17.756
6.624

3954
LEU497
CG
−5.572
−16.816
6.133

3955
LEU497
CD1
−5.241
−17.167
4.678

3956
LEU497
CD2
−5.983
−15.347
6.229

3957
HIS498
N
−9.613
−17.501
8.234

3958
HIS498
CA
−11.051
−17.916
8.02

3959
HIS498
C
−11.841
−18.503
9.278

3960
HIS498
O
−12.191
−19.685
9.35

3961
HIS498
CB
−11.123
−18.798
6.747

3962
HIS498
CG
−12.453
−19.296
6.297

3963
HIS498
ND1
−13.171
−20.239
6.994

3964
HIS498
CD2
−13.177
−19.116
5.137

3965
HIS498
CE1
−14.275
−20.556
6.265

3966
HIS498
NE2
−14.325
−19.868
5.15

3967
ALA499
N
−12.13
−17.598
10.312

3968
ALA499
CA
−12.588
−18.068
11.649

3969
ALA499
C
−14.09
−18.292
11.984

3970
ALA499
O
−15.033
−17.654
11.517

3971
ALA499
CB
−12.103
−17.133
12.772

3972
ALA500
N
−14.242
−19.215
13.024

3973
ALA500
CA
−15.505
−19.589
13.67

3974
ALA500
C
−15.146
−20.461
14.896

3975
ALA500
O
−14.092
−20.275
15.507

3976
ALA500
CB
−16.39
−20.34
12.698

3977
MET501
N
−16.081
−21.397
15.283

3978
MET501
CA
−15.902
−22.298
16.434

3979
MET501
C
−15.979
−21.489
17.736

3980
MET501
O
−15.297
−21.742
18.725

3981
MET501
CB
−14.634
−23.153
16.353

3982
MET501
CG
−14.778
−24.434
17.177

3983
MET501
SD
−13.151
−25.163
17.543

3984
MET501
CE
−12.736
−24.159
18.999

3985
ARG502
N
−16.942
−20.505
17.697

3986
ARG502
CA
−17.038
−19.447
18.694

3987
ARG502
C
−18.557
−19.172
18.805

3988
ARG502
O
−19.316
−20.076
19.158

3989
ARG502
CB
−16.146
−18.28
18.257

3990
ARG502
CG
−14.626
−18.523
18.409

3991
ARG502
CD
−13.871
−17.382
17.745

3992
ARG502
NE
−12.409
−17.446
17.791

3993
ARG502
CZ
−11.63
−18.186
16.968

3994
ARG502
NH1
−10.307
−17.933
16.92

3995
ARG3502
NH2
−12.109
−19.143
16.165

3996
GLU503
N
−19.034
−17.964
18.301

3997
GLU503
CA
−20.488
−17.651
18.368

3998
GLU503
C
−21.257
−18.617
17.459

3999
GLU503
O
−22.454
−18.869
17.584

4000
GLU503
CB
−20.749
−16.219
17.876

4001
GLU503
CG
−22.228
−15.886
17.704

4002
GLU503
CD
−22.439
−14.387
17.63

4003
GLU503
OE1
−22.748
−13.938
16.486

4004
GLU503
OE2
−22.316
−13.748
18.729

4005
ALA504
N
−20.506
−19.008
16.372

4006
ALA504
CA
−20.935
−20.061
15.492

4007
ALA504
C
−19.729
−20.986
15.274

4008
ALA504
O
−18.558
−20.607
15.372

4009
ALA504
CB
−21.442
−19.471
14.191

4010
GLY505
N
−20.091
−22.262
14.917

4011
GLY505
CA
−19.139
−23.332
14.703

4012
GLY505
C
−19.814
−24.4
13.856

4013
GLY505
O
−20.725
−24.12
13.072

4014
ARG506
N
−19.264
−25.662
14.004

4015
ARG506
CA
−19.955
−26.86
13.504

4016
ARG506
C
−20.693
−27.446
14.714

4017
ARG506
O
−20.065
−27.881
15.68

4018
ARG506
CB
−18.946
−27.862
12.938

4019
ARG506
CG
−19.611
−29.153
12.447

4020
ARG506
CD
−18.652
−30.027
11.642

4021
ARG506
NE
−18.39
−29.446
10.322

4022
ARG506
CZ
−17.684
−30.031
9.334

4023
ARG506
NH1
−17.591
−29.385
8.157

4024
ARG506
NH2
−17.083
−31.226
9.486

4025
HIS507
N
−22.069
−27.325
14.683

4026
HIS507
CA
−22.898
−27.667
15.848

4027
HIS507
C
−24.408
−27.458
15.594

4028
H1S507
O
−24.865
−26.798
14.664

4029
HIS507
CB
−22.481
−26.938
17.157

4030
HIS507
CG
−22.311
−25.457
17.051

4031
HIS507
ND1
−21.963
−24.674
18.126

4032
HIS507
CD2
−22.406
−24.57
16.004

4033
HIS507
CE1
−21.806
−23.393
17.674

4034
HIS507
NE2
−22.047
−23.299
16.384

4035
ARG508
N
−25.233
−28.045
16.547

4036
ARG508
CA
−26.681
−27.836
16.521

4037
ARG508
C
−26.953
−26.425
17.074

4038
ARG508
O
−27.094
−26.198
18.273

4039
ARG508
CB
−27.41
−28.873
17.387

4040
ARG508
CG
−27.241
−30.306
16.881

4041
ARG508
CD
−28.092
−31.273
17.698

4042
ARG508
NE
−27.858
−32.671
17.307

4043
ARG508
CZ
−26.814
−33.431
17.719

4044
ARG508
NH1
−26.724
−34.713
17.302

4045
ARG508
NH2
−25.855
−32.95
18.538

4046
LYS509
N
−26.933
−25.445
16.096

4047
LYS509
CA
−26.969
−24.029
16.467

4048
LYS509
C
−28.345
−23.634
17.061

4049
LYS509
O
−29.398
−24.176
16.727

4050
LYS509
CB
−26.716
−23.15
15.232

4051
LYS509
CG
−25.253
−23.169
14.785

4052
LYS509
CD
−25.024
−22.297
13.551

4053
LYS509
CE
−23.562
−21.957
13.328

4054
LYS509
NZ
−22.88
−22.921
12.47

4055
SER510
N
−28.295
−22.573
17.952

4056
SER510
CA
−29.498
−22.004
18.563

4057
SER510
C
−30.006
−20.796
17.746

4058
SER510
O
−29.321
−20.221
16.898

4059
SER510
CB
−29.268
−21.629
20.032

4060
SER510
OG
−28.392
−20.517
20.163

4061
TRP511
N
−31.309
−20.407
18.039

4062
TRP511
CA
−31.959
−19.289
17.34

4063
TRP511
C
−32.482
−18.271
18.358

4064
TRP511
O
−32.101
−17.099
18.366

4065
TRP511
CB
−33.115
−19.757
16.431

4066
TRP511
CG
−32.941
−19.317
15.011

4067
TRP511
CD1
−32.722
−20.154
13.938

4068
TRP511
CD2
−32.94
−17.976
14.5

4069
TRP511
NE1
−32.51
−19.383
12.827

4070
TRP511
CE2
−32.641
−18.051
13.138

4071
TRP511
CE3
−33.131
−16.699
15.07

4072
TRP511
CZ2
−32.5
−16.919
12.326

4073
TRP511
CZ3
−33.004
−15.557
14.271

4074
TRP511
CH2
−32.69
−15.668
12.919

4075
SER512
N
−33.435
−18.746
19.244

4076
SER512
CA
−34.294
−17.813
19.992

4077
SER512
C
−33.484
−16.939
20.958

4078
SER512
O
−33.897
−15.859
21.378

4079
SER512
CB
−35.369
−18.565
20.78

4080
SER512
OG
−34.785
−19.668
21.473

4081
CYS513
N
−32.281
−17.495
21.329

4082
CYS513
CA
−31.384
−16.86
22.278

4083
CYS513
C
−30.615
−15.692
21.628

4084
CYS513
O
−29.947
−14.898
22.298

4085
CYS513
CB
−30.354
−17.852
22.818

4086
CYS513
SG
−31.115
−19.286
23.643

4087
GLY514
N
−30.674
−15.588
20.256

4088
GLY514
CA
−29.821
−14.695
19.484

4089
GLY514
C
−30.244
−13.23
19.509

4090
GLY514
O
−30.297
−12.547
18.49

4091
HIS515
N
−30.4
−12.719
20.783

4092
HIS515
CA
−31.066
−11.438
21.038

4093
HIS515
C
−30.372
−10.761
22.233

4094
HIS515
O
−30.942
−9.978
22.991

4095
HIS515
CB
−32.567
−11.643
21.32

4096
HIS515
CG
−33.314
−12.194
20.15

4097
HIS515
ND1
−33.83
−13.466
20.107

4098
HIS515
CD2
−33.647
−11.648
18.927

4099
HIS515
CE1
−34.429
−13.627
18.887

4100
HIS515
NE2
−34.34
−12.543
18.154

4101
THR516
N
−29.009
−10.996
22.305

4102
THR516
CA
−28.221
−10.644
23.488

4103
THR516
C
−26.824
−10.167
23.058

4104
THR516
O
−26.179
−10.748
22.183

4105
THR516
CB
−28.127
−11.847
24.46

4106
THR516
OG1
−27.657
−11.48
25.761

4107
THR516
CG2
−27.272
−12.999
23.942

4108
ARG517
N
−26.341
−9.092
23.773

4109
ARG517
CA
−24.985
−8.515
23.652

4110
ARG517
C
−24.85
−7.641
24.913

4111
ARG517
O
−25.456
−6.566
24.999

4112
ARG517
CB
−24.819
−7.564
22.45

4113
ARG517
CG
−24.775
−8.14
21.035

4114
ARG517
CD
−23.657
−9.149
20.771

4115
ARG517
NE
−24.174
−10.51
20.9

4116
ARG517
CZ
−23.72
−11.583
20.231

4117
ARG517
NH1
−24.407
−12.739
20.281

4118
ARG517
NH2
−22.586
−11.579
19.529

4119
ALA518
N
−24.215
−8.205
25.999

4120
ALA518
CA
−24.204
−7.553
27.314

4121
ALA518
C
−25.608
−7.517
27.958

4122
ALA518
O
−25.869
−8.139
28.986

4123
ALA518
CB
−23.545
−6.175
27.309

4124
GLY519
N
−26.512
−6.701
27.309

4125
GLY519
CA
−27.93
−6.718
27.587

4126
GLY519
C
−28.688
−7.409
26.449

4127
GLY519
O
−28.14
−8.03
25.539

4128
GYS520
N
−30.062
−7.253
26.557

4129
GYS520
CA
−30.985
−7.773
25.539

4130
CYS520
C
−31.014
−6.765
24.375

4131
GYS520
O
−30.996
−5.539
24.549

4132
GYS520
CB
−32.391
−7.922
26.13

4133
GYS520
SG
−33.538
−8.817
25.043

4134
THR521
N
−31.107
−7.334
23.121

4135
THR521
CA
−31.076
−6.541
21.899

4136
THR521
C
−31.737
−7.262
20.707

4137
THR521
O
−32.218
−8.387
20.775

4138
THR521
CB
−29.655
−6.04
21.56

4139
THR521
OG1
−29.725
−5.151
20.433

4140
THR521
CG2
−28.67
−7.165
21.268

4141
LEU522
N
−31.81
−6.461
19.576

4142
LEU522
CA
−32.287
−6.938
18.274

4143
LEU522
C
−33.808
−7.211
18.26

4144
LEU522
O
−34.349
−7.886
17.388

4145
LEU522
CB
−31.478
−8.115
17.702

4146
LEU522
CG
−30
−7.79
17.401

4147
LEU522
CD1
−29.235
−9.081
17.093

4148
LEU522
CD2
−29.848
−6.812
16.235

4149
ILE523
N
−34.516
−6.48
19.199

4150
ILE523
CA
−35.973
−6.535
19.323

4151
ILE523
C
−36.545
−5.152
19.708

4152
ILE523
O
−37.73
−4.987
20

4153
ILE523
CB
−36.474
−7.617
20.317

4154
ILE523
CG1
−35.954
−7.381
21.752

4155
ILE523
CG2
−36.139
−9.03
19.829

4156
ILE523
CD1
−36.643
−8.264
22.785

4157
ARG524
N
−35.627
−4.116
19.641

4158
ARG524
CA
−36.041
−2.731
19.862

4159
ARG524
C
−36.617
−2.156
18.555

4160
ARG524
O
−36.56
−2.757
17.481

4161
ARG524
CB
−34.864
−1.887
20.374

4162
ARG524
CG
−34.488
−2.249
21.814

4163
ARG524
CD
−33.444
−1.292
22.384

4164
ARG524
NE
−33.203
−1.547
23.815

4165
ARG524
CZ
−32.502
−2.592
24.316

4166
ARG524
NH1
−32.437
−2.773
25.651

4167
ARG524
NH2
−31.859
−3.466
23.526

4168
GLN525
N
−37.257
−0.95
18.72

4169
GLN525
CA
−37.785
−0.124
17.626

4170
GLN525
CB
−39.314
−0.234
17.512

4171
GLN525
CG
−39.806
−1.609
17.056

4172
GLN525
CD
−39.88
−2.607
18.192

4173
GLN525
OE1
−40.549
−2.433
19.205

4174
GLN525
NE2
−39.152
−3.75
17.988

4175
GLN525
C
−37.468
1.347
17.904

4176
GLN525
O
−36.858
1.67
18.923

4177
GLN525
OXT
−37.884
2.231
16.996

[1497]

Number	Date	Country
60281253	Apr 2001	US
60288768	May 2001	US
60296180	Jun 2001	US
60300620	Jun 2001	US

Polynucleotide encoding a novel cysteine protease of the calpain superfamily, CAN-12, and variants thereof

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

Parent Case Info

Provisional Applications (4)