Patent Grant
8022040
1. Field of the Invention
The present invention generally relates to the field of artificial bone synthesis based on hydroxyapatite binding sequences and peptides.
2. Related Art
A fundamental challenge in the field of biomineralization is to identify the short protein motifs which can specifically nucleate on or bind to the target materials. Although various protein matrices including collagens, osteopontin, and enamelogenin found in bone and dentin have been extensively studied and shown for specific nucleation of the target inorganic biominerals, understanding of the role of specific protein motifs are still limited. See L. Addadi, S. Weiner, Angew. Chem. Int. Ed. Engl. 31, 153 (1992); S. Weiner, L. Addadi, J. Mater. Chem. 7, 689 (1997); G. He, T. Dahl, A. Veis, A. George, Nat. Mater. 2. 552 (2003); C. E. Ye, K. R. Rattray, K. J. Warne, J. Gordon, J. Sodek, G. K. Hunter, H. Goldberg, J Bio. Chem. 278, 7949 (2003); and S. Mann, Biomimetic Materials Chemistry; VCH: New York, (1996). The long encrypted peptide chains hinder direct incorporation of protein matrices into functional building blocks in organic/inorganic hybrid composite materials.
One of the most promising methods to identify the specific short peptide binding motifs against the unknown inorganic or organic surfaces is phage display. See Whaley, S. R.; English, D. S.; Hu, E. L. Barbara, P. F. Belcher, A. M. Nature 405, 665 (2000) and Lee, S.-W.; Mao, C.; Flynn, C. E.; Belcher, A. M., Science, 296, 892 (2002). Phage display is a directed evolution process for identifying short peptide binding motifs against target materials. These binding peptides can potentially template the nucleation and growth of magnetic, optical, electrical materials, self-assemble these materials in various environments, or make them biocompatible. See C. Mao, D. Solis, B. Reiss, S. Kottmann, R. Sweeney, A. Hayhurst, G. Georgiou, B. Iverson, A. Belcher, Science, 303, 213 (2004); B. Reiss, C. Mao, D. Solis, K. Ryan, T. Thomson, A. Belcher, Nano Lett., 4, 1127 (2004). Phage display peptide libraries have emerged as a powerful method in identifying such peptide agonists and antagonists. See, for example, Scott et al. (1990), Science 249: 386; Devlin et al. (1990), Science 249: 404; U.S. Pat. No. 5,223,409, issued Jun. 29, 1993; U.S. Pat. No. 5,733,731, issued Mar. 31, 1998; U.S. Pat. No. 5,498,530, issued Mar. 12, 1996; U.S. Pat. No. 5,432,018, issued Jul. 11, 1995; U.S. Pat. No. 5,338,665, issued Aug. 16, 1994; U.S. Pat. No. 5,922,545, issued Jul. 13, 1999; WO 96/40987, published Dec. 19, 1996; and WO 98/15833, published Apr. 16, 1998 (each of which is incorporated by reference).
In such libraries, random peptide sequences are displayed by fusion with coat proteins of filamentous phage. Typically, the displayed peptides are affinity-eluted against an antibody-immobilized extracellular domain of a receptor. The retained phages may be enriched by successive rounds of affinity purification and repropagation. The best binding peptides may be sequenced to identify key residues within one or more structurally related families of peptides. The peptide sequences may also suggest which residues may be safely replaced by alanine scanning or by mutagenesis at the DNA level. Mutagenesis libraries may be created and screened to further optimize the sequence of the best binders. See Lowman (1997), Ann. Rev. Biophys. Biomol. Struct. 26: 401-24.
The invention provides for a composition comprising a peptide having a hydroxyapatite (HA)-binding activity comprising an amino acid sequence having a percent homology of at least 20% with an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-267.
The invention also provides for an implantable bone growth inducing composition comprising: a matrix and at least one amino acid sequence selected from the group consisting of SEQ ID NOs: 1-267, attached thereto.
The invention further provides for a method for inhibiting mineral growth in bone, ligament, or cartilage in a mammal comprising administering to said mammal a composition comprising a pharmacologically effective amount of SEQ ID NOS: 1-267 in combination with a pharmaceutically acceptable delivery vehicle.
The invention further provides for an osteogenic device for implantation in a mammal, the device comprising: an osteogenic peptide dispersed or attached within a biocompatible, in vivo biodegradable matrix, wherein said osteogenic peptide comprises at least one of the amino acid sequences of SEQ ID NOS: 1-267.
The invention also provides for a method for directed mineral nucleation or mineralization comprising the steps of: attaching an amino acid sequence to a polymeric organic material to create a mineralized material precursor, wherein the amino acid sequence directs mineralization on the mineralized material precursor.
The invention also provides for a method for synthesizing an implantable article, comprising the steps of: attaching a biocompatible substrate with a polypeptide having a sequence selected from SEQ ID NOS: 1-267.
The term “peptide” herein refers to an amino acid sequence between 2 and 100 amino acids in length, the amino acids being joined by peptide linkages. The amino acids may be naturally and non-naturally occurring.
The terms “derived from” or “based on” herein refers to, regarding a peptide amino acid sequence, having a relationship to a HA-binding sequence described herein.
The term “substantially identical” herein refers to an amino acid sequence which differs from another amino acid sequence only by amino acid substitutions, deletions, or insertions that do not destroy the HA-binding or nucleation activity of the peptide. It also includes peptides or sequences containing the HA-binding motif.
The term “homology” or “homologous” herein refers to an amino acid sequence similarity measured by the program, BLAST (Altschul et al (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25:3389-3402 and expressed as −(% identity n/n). In measuring homology between a peptide and a peptide or protein of greater size, homology is measured only in the corresponding region; that is, the protein is regarded as only having the same general length as the peptide, allowing for gaps and insertions using default values. The term “homologous” herein refers to a percent homology of at least 20%, more preferably 40%, even more preferably 70%, up to 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.8%, and 99.9% homology. The term “substantially homologous” herein refers to a percent homology of at least 40%, more preferably 70%, even more preferably 85%, up to 91%, 92%, 93%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.8%, and 99.9% homology.
The term “mineral” herein refers to any inorganic compound, comprised of inorganic elements, including but not limited to, Ca2+, PO43−, OH−, CO32−, Cl− and other trace inorganic elements. The inorganic compound can include, but are not limited to, such compounds as crystalline, nanocrystalline or amorphous HA (Ca10(PO4)6(OH)2), calcium carbonate, and calcium phosphates with solubility behavior, under acidic and basic conditions, similar to that of HA, including but not limited to dicalcium phosphate, tricalcium phosphate, octacalcium phosphate or calcium phosphates having a stoichiometry that ranges from CaO-2P2O5 to 4CaO-P2O5, with a definite composition and definite crystalline, nanocrystalline or amorphous structure.
The term “mineralization” herein refers to integration of inorganic components onto a peptide or into a peptide-containing scaffold.
The term “scaffold” herein refers to a three-dimensional polymeric structure with mineral-binding peptides or masked mineral-binding sites along the polymer for mineral or other bone mineral attachment.
The term “nanocrystalline” herein refers to a mineral formation that is lengths-scale from 1000 nm to 1 nm which can be either crystalline or amorphous deposits.
The term “single crystalline” herein refers to solid phase materials characterized by an absence of crystal boundaries and by a uniform atomic structural arrangement. The term also includes materials composed of oriented-crystals or enlarged crystals (when the enlarged crystals are used as though they are a single-crystal or when the enlarged crystals are used individually as single-crystals).
The term “polycrystalline” herein refers to materials composed of variously oriented, and usually a large number of, small individual crystals or crystallites
The term “nucleation” herein refers to the first step of mineralization where the inorganic anions or cations are attracted or recruited to the peptides or peptide-containing three-dimensional scaffolds.
The terms “binding activity” or “ability to bind” are herein meant to describe the measure of the binding or affinity of molecules to each other.
In one embodiment of the present invention, novel short specific binding peptide motifs against single crystalline or polycrystalline HA surfaces were identified by phage display. Phage display was conducted and is schematically shown in
The peptide motifs described herein can be exploited as templates to grow HA, the major inorganic component of natural bone and teeth. In one embodiment, sequences were identified which contained periodic proline-hydroxylamino acid binding sequences similar to the Gly-Pro-Hyp (Hyp: hydroxyproline) repeats of human type I collagen, which is generally believed to provide spatial guidance for the growth of bone biominerals. Synthesized short binding peptides were further used as a template to grow HA crystals.
Referring to
In one embodiment, it is contemplated that sequences can be made which are substantially identical to the peptides (SEQ ID NOS: 1-267) listed herein, but still retain the essential HA-binding activity exhibited by the peptides described herein. Thus, in one embodiment, the invention provides for a peptide that binds HA, having a length of 5-15 amino acid residues, wherein the peptide comprises (1) at least one amino acid residue having a hydroxyl side chain, wherein if there is more than one residue having a hydroxyl side chain, that another residue having a hydroxyl side chain occurs every 2-7 residues; and (2) at least one positively-charged residue. In another embodiment, the peptide further comprises (3) at least one residue having an amide side chain. Furthermore, in one preferred embodiment, the distances between the alpha carbons of at least two hydroxylated or amide (side-chain)-containing amino acid residues should closely match the lattice parameters of HA of 9.42 Å, to within at least 0.5 to 2.5 Å. In another preferred embodiment, the distances between the oxygens of at least two hydroxylated amino acid residues closely matches unit cell distance of single crystal HA on (100) face (9.42 Å) and/or the average distance between neighboring hydroxyproline (Hyp, O) residues (10.10±0.84 Å) in a collagen-like peptide (1CAG, SEQ ID NO: 268, having the sequence, POGPOGPOGPOGPOAPOGPOGPOGPOGPOG (P=Pro, O=Hydroxyproline, G=Gly)), to within at least 0.5 to 2.5 Å. The crystal and molecular structure of this collagen-like peptide was characterized to 1.9 Å resolution by J. Bella, M. Eaton, B. Brodsky, H. M. Berman, Science 266, 75 (1994).
In another embodiment, it is further contemplated that substantially identical peptides can be made to each of the disclosed peptides from each round of selection by systematically making conserved substitutions. For example, using the color-coding in
In another embodiment, homologous peptides to any of the peptides of the invention having a percent homology of at least 20%, more preferably at least 40%, even more preferably at least 70%, more preferably up to 85%, most preferably at least 93% homologous, while retaining HA-binding activity. In a preferred embodiment, substantially homologous peptides share a percent homology of at least 40%, more preferably 70%, even more preferably 85%, up to 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.8%, and 99.9% homology, to any of the disclosed peptide sequences and having the ability to bind HA.
In another embodiment, it is further contemplated that the peptides of the invention may be flanked by other amino acids such as cysteines, histidines or glycines, or amino acid sequence which does not destroy or interfere with the HA-binding or nucleation activity of the peptides. For example, the peptides can be constrained and flanked by cysteines on both ends, such as the constrained Single 14 peptide, SEQ ID NO: 267. In another embodiment, the peptides can be attached to biomolecules or materials for binding, labeling or identification including biotin, streptavidin, oligonucleotides, other known sequence, antibodies, nanoparticles, nanocrystals, nanospheres, polyethylene glycols, lipids, biomolecules, and the like. It is further contemplated that the peptides can be attached to the biomolecules through means of linking molecules or flanking amino acid sequence. In one embodiment, the peptides are linked to biotin through means of a linking amino acid sequence, GGGK, thereby producing a peptide having a sequence such as Control Peptide 1, NPYHPTIPQSVH-GGGK-biotin (SEQ ID NO: 269).
The functional binding activity of HA-binding peptides of the invention can be illustrated in several assays, for example the method used in Example 2. Any peptide shown by flow cytometry to have a relative intensity of fluorescence above the background is said to have mineral or HA-binding activity.
One main characteristic of the HA-binding peptides of the invention is the periodic display of the hydroxyl or amide (side chain) residues. Most of the 7-mer binding peptides identified (22 out of 27) have pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains at approximately every two to three residues. In addition, when the dominant 7-mer binding sequences are compared with those of the 12-mers, key amino acid patterns were found to be highly conserved. Specifically, Asn, Tyr, Pro, Thr, Leu and Ser appeared at positions 1, 2, 3, 4, 5, and 7 in the 7-mer constrained binding peptides; these residues also appeared at positions 1, 3, 5, 6, 7, and 10, respectively, in the 12-mer linear binding peptides.
Another characteristic of the 12-mer dominant binding sequences is periodic occurrence of proline and hydroxyl/amide (side chain) residues. These pseudo-repetitive sequences resembled the (Gly-Pro-Hyp)n repeat of human type I collagen, a major component of the extracellular matrices of natural bone.
For example, the most dominant 12-mer binding peptide (NPYHPTIPQSVH, SEQ ID NO: 208) emerged after the fourth round of screening showing the periodic display of prolines (position 2, 5, and 8) and hydroxylated residues (position 3, 6 and 10). Compared with dominant 7-mer constrained binding peptide (CNYPTLKSC, SEQ ID NO: 267; two cysteines form a disulfide bond) isolated under the same experimental conditions, both dominant binding peptides exhibited remarkable conserved amino acid sequences (Asn, Tyr, Pro, Thr, Ile/Leu, and Ser). Considering the lack of hydroxyproline residue in the phage libraries, the sequence similarity between the isolated peptide and the most frequent GPO (Gly-Pro-Hyp) repeat of type I collagen is rather striking. Type I collagen is believed to guide controlled growth of HA in natural bone. Therefore the fact that the single 15 peptide was identified via directed evolutionary screening processes from billions of candidates suggests that the presence of a collagen-like binding peptide motif in the present peptides imparts specific recognition of single crystal HA surfaces.
In addition, these binding peptide sequences tended to possess positively charged residues rather than negatively charged residues. Up till now, the negatively charged groups found in many acidic non-collagenous ECM proteins have been postulated to be important in regulating the biomineralization process in natural bone. Favorable electrostatic interactions between the positively charged residues and the negatively charged HA surfaces under physiological pH (pH 7.5) may be a driving force.
It is known that many ECM proteins in calcified tissues (e.g. sialoprotein, phosphosphoryn, amelogenin) are rich in phosphoserine, aspartate, and glutamate residues. These negatively charged residues may be involved in enriching local calcium ions and templating the nucleation of amorphous minerals and their subsequent ripening into more stable crystalline structures.
In addition, it is found that when the sequences are similar, 7-mer constrained viruses generally exhibit better binding affinity than the linear peptides, presumably due to the lack of the structural flexibility. Titering experiments in Example 2 and the results shown in
In our phage display against single crystal HA, the a and b faces of the whisker type HA (
The peptides of the invention are listed herein according to the round of phage display selection that the peptide was identified. The 7-mer peptides, recited herein and selected from constrained 7-mer libraries, were flanked on both ends by cysteine residues. The cysteines are shown in the Figures. The asterisks in place of residues at various positions in the peptides below indicate that any residue may be placed at the position.
The peptides may be made and purified by methods known in the art, preferably by in vitro automated synthesis, but also by recombinant DNA methods. Furthermore, these peptides can be synthesized using D- or L-amino acids and selected non-natural or other modified amino acids, as is known in the art, in order to synthesize peptides which can act upon targets in the body and be degraded if necessary, yet do not interfere with normal protein function. The peptides can be stored in lyophilized form and dissolved in aqueous buffers or water prior to use. For the purposes of experimental use, the peptides can be dissolved in sterilized water or buffer. In addition, suitable buffers or diluents should be capable of solubilizing the active peptide, preferably at a suitable pH to prevent the peptide from precipitating out of solution too easily.
In one embodiment, the invention further contemplates the use of the peptides tagged with detectable agents including, but not limited to, antibodies, radioanalogs, products or compounds having distinctive absorption, fluorescence, or chemi-luminescence properties, such as rhodamine, fluorescein, green fluorescent protein (GFP) or semiconductor nanocrystal beads. Peptides tagged with such detectable agents would be useful for studying and monitoring the peptides and their effectiveness in templated nucleation of HA.
One embodiment of the present invention involves preparing a library of HA-binding peptides for use with complex solutions and mixtures of minerals to create HA on a surface material. Because of the HA-binding activity of the present peptides, they may be immobilized on soluble or insoluble solid, bulk or polymeric scaffolds or matrices. It is contemplated that the HA-binding peptides can be attached covalently or non-covalently, including physical adsorption, to biomolecules or biomaterials, either organic, inorganic or organic-inorganic composites.
Examples of such polymeric scaffolds include using the monomers and co-monomers disclosed in U.S. Pat. Application Pub. No. 2004/0161444, filed on Dec. 18, 2003, which is hereby incorporated by reference in its entirety. It is contemplated that the peptides of the invention can be attached to co-monomers in the formation of such polymeric scaffolds to be displayed on the scaffolds to promote mineralization. Furthermore, it is contemplated that the peptides of the invention can be used in conjunction with other known peptides or agents in the art for the promotion of mineralization. For example, Bab, et al., in U.S. Pat. No. 6,479,460, and Rodan, et al., in U.S. Pat. No. 5,461,034, which are hereby incorporated by reference in their entirety, disclose synthetic peptides, pseudopeptides, and pharmaceutical compositions having osteogenic activity which can be attached to the co-monomers as functional groups to make the biomimetic composites. Different co-monomers may also be used to control porosity, the concentration of nucleation sites, and other properties.
In another aspect, the scaffold can be coated with at least one material such as gold, avidin, streptavidin, carboxymethyl groups, dextran or collagen to promote the stable attachment of the peptide to the scaffold. In one embodiment, the scaffold is coated with streptavidin and the peptide is biotinylated, whereby the peptide attaches to the scaffold through the binding of biotin and the streptavidin-coating.
In one embodiment, the peptide is attached to the scaffold by means of an oligonucleotide. In this embodiment, the oligonucleotide is biotinylated and attaches to the scaffold through the binding of biotin and the streptavidin-coating. In one aspect, the peptide would further comprise flanking amino acid sequences. In another aspect, the invention further comprises a peptide or protein bound to the peptide by means of a polyhistidine tag.
These HA-binding peptides are expected to be further incorporated into three dimensional organic matrices or cellular environment to orchestrate and regulate the growth or inhibition of the bone structures. Prokaryotic or eukaryotic cell line can be modified by insertion of the short DNA motifs which can express the HA binding peptides. Structural biology also needs to be considered in this in vivo and ex vivo system to display short peptide motifs outside of cellular membranes.
In one embodiment, osteoblasts can be genetically engineered to express the HA-binding peptides. The engineered osteoblasts can then be applied in cell-based treatments of bone defects such as where there is deficient bone growth. The display of the peptides outside the cellular membranes will direct nucleation and mineral growth to the applied areas.
In another embodiment, the HA-binding peptides can be attached onto a scaffold, such as an artificial bone scaffold implant. If such implant is then inserted into a subject, the peptides would direct nucleation of HA in vivo, thus encouraging the integration of the implant with natural bone. Thus, in practice it is contemplated that an implantable structure be formed in vitro and adapted to fit a particular area of bony structure to be repaired or reconstructed. The peptides can be attached to the scaffold, or attached to a surface on a scaffold. After mineralization, the mineralized structure is implanted into the subject in the recipient site. Alternatively, the peptide coated substrates can be implanted to induce mineralization in vivo. Then, the implant can be attached to the bony structure under physiological conditions, such as the modification or mediation of osteoclasts and osteoblasts which express the HA-binding peptides, as described above.
In addition to the utilization of the HA-binding peptides for biomimetic bone synthesis, it is also possible to exploit the inhibitory potential of these peptides in HA crystal growth where these peptides may be coupled with the nucleation frontline. When these peptides are incorporated with soluble polymer matrices, the HA binding peptides can block the nucleation frontline so that the crystal growth can not be propagated further to form elongated crystals. These peptides can also be coated onto organic and inorganic nanoparticles or nanospheres and injected into areas where the HA-deposition needs to be reduced.
In another embodiment, HA-binding peptides are coated, combined, bound or adsorbed with a pharmaceutically acceptable delivery vehicle and injected into interstitial spaces where HA deposition needs to be reduced. Examples of such pharmaceutically acceptable delivery vehicles includes but are not limited to biopolymers, polymethacrylates, a biodegradable polyester, an aqueous polymeric hydrogel or microgel, nanoparticles or nanospheres.
In order to identify the short peptide specific binding motifs, phage display was performed against the single crystal HA surface. Procedures known in the art were used for phage display. The basic procedure used for phage display selection is schematically shown in
The combinatorial library comprises M13 phage having genetically altered proteins featured at the pIII units. Equal amount of three different types of phage library suspensions, 7-mer, 7-mer constrained, 12-mer (Ph.D.-7, Ph.D. c7c, and Ph.D. 12 libraries obtained from New England Biolabs), were mixed to generate more than 6.7×109 diversity of randomized amino acid library and suspended in 10 μl each in 1 mL TBST (0.1%).
Single crystalline hydroxyapatite crystals were incubated with 10 μl of each three library suspensions and then washed with buffer and TWEEN20 in the bioselection step.
Synthesis of single crystalline hydroxyapatite. Single crystalline HA crystal were synthesized by molten salt synthesis, as described in A. Tas, J. Ame. Ceramic Soc., 84, 295 (2001), which is hereby incorporated by reference. The preparation of single crystal hydroxyapatite whiskers was achieved by molten salt synthesis with a potassium sulfate flux at 1190° C. In a typical procedure, commercial polycrystalline HA powders were dry-mixed with potassium sulfate at a K2SO4-to-HA weight ratio of 1.6. The mixture was placed in a clean alumina crucible and heated in a furnace from room temperature to 1190° C. at a rate of 5° C./min. After holding the temperature at 1190° C. for 3.5 h, the sample was cooled naturally to room temperature within the shut-off furnace. The single crystal HA whiskers were separated from the solidified mass by washing the mass with MilliQ water at 90° C. for three times. The whiskers were then air-dried and characterized by SEM, EDS and XRD. As shown in
To remove potential CaCO3 impurities on HA, HA surfaces were etched using 0.2 M Gly-HCl (pH 2.2) immediately prior to biopanning. This etching condition was also used to elute the bound phage from HA.
Biopanning procedure. 4 mg of single crystal HA particles were etched using glycine-HCl (200 mM, pH 2.2) for overnight and washed six times with Tris-buffered saline (TBS) before the biopanning. The HA crystals were incubated with 10 μl of each three library suspensions (Ph.D 12, Ph.D. 7, and Ph.D. C.7C™, New England Biolab, Mass.) in 1 ml TBST (0.1%) suspension for 30 min with slow rocking. Thereafter, the HA particles were washed 10 times with TBST (0.1%) to wash off all nonbinding phages. The bound phages were eluted from the HA particles by incubation at room temperature in 1 ml of 0-0.2 M glycine-HCl (pH 2.2) for 10 min. The eluted phages were neutralized with 150 μl of 1M TBS (pH 9.1). The eluted phages were amplified with E. coli (ER2738) for 4.5 hours in LB medium. Similar biopanning procedures were also performed against commercial polycrystalline HA powders.
The DNA of randomly selected phages was analyzed to identify the peptide expressed on phage pIII units. Selected phage DNA analysis results for each round are shown in the tables of FIG. 7-11. DNA analysis of randomly selected phages from 1st round selection (
In our phage display against single crystal HA, the a and b faces of the whisker type HA crystals were targeted for combinatorial screening. Binding amino acids sequences were found to systematically contain periodic hydroxyl and amide residues. For the 12-mer linear type library, these hydroxyl/amide side chain residues were also coupled with the rigid proline, reminiscent of the major repeating sequences in type I collagen. After the fourth round of screening, several amino acid sequences resulting from the randomly selected viruses showed more conserved sequences from the 7-mer constrained and 12-mer linear libraries (
Binding peptides against the polycrystalline HA, which has crystallographically impure surfaces, were also obtained. The selected binding peptide, SEQ ID NO: 264, having the sequence, Tyr-Met-Gly-Phe-Tyr-Ala-Pro-Arg-Phe-Pro-His-Tyr, (Poly 3) was also screened and compared with two single crystalline dominant HA binding sequences named single 14 and 15 using two binding assays. The sequences of the other peptides are Asn-Tyr-Pro-Thr-Leu-Lys-Ser (SEQ ID NO: 200, W4a-4-14, Single 14) and Asn-Pro-Tyr-His-Pro-Thr-Ile-Pro-Gln-Ser-Val-His (SEQ ID NO: 208, W4a-4-15, Single 15) and WILD type phage, which does not have an inserted peptides unit. A constrained single 14 peptide (SEQ ID NO: 267) having two cysteines, one on each end, was used.
As described in Example 1, 4 mg of single crystalline HA was freshly etched to remove carbonated contaminates and incubated with 1×1010 pfu of phage of constrained W4a-4-14 (Single 14), W4a-4-15 (single 15), HA-4-3 (poly 3), wild type (wild) phages suspension. After washing off with TBST (0.5%) ten times, the bound phage was eluted using glycine-HCl (mM, pH 2.2) and titered to count number of bound phage. The titering result is shown in
Fluorescence intensity of binding viruses on HA surfaces was measured using flow cytometry (
Correspondingly, HA crystals with bound phage were labeled and imaged by fluorescence. After 30 min incubation of 4 mg/ml of HA crystals with ˜1010 pfu/ml of phages containing single 14, single 15, poly3, or the wild type phage, which does not have peptide inserts, the phage bound to HA surfaces was labeled using R-phycoerythrin-labeled monoclonal pVIII antibody, and imaged by fluorescence microscope (
After 30 minutes incubation of 4 mg/ml of HA crystals with ˜1010 pfu/ml of each phage, CLP7, CLP12, or the wild type phages, the HA crystals were washed ten times with Tris-buffered saline solution (pH 7.5) contained 0.5% Tween 20. The phage bound to HA surfaces was labeled by R-phycoerythrin-conjugated monoclonal pVIII antibody (Amersham Pharmacia Biotech, UK), and the fluorescence images were acquired (Nikon fluorescence microscope, Japan) and the fluorescence intensity was quantified by FACS Calibur flow cytometer (BD Biosciences, Calif.).
Plaque amplification was carried out according to the New England BioLabs, Inc. Ph.D.-12™ Phage Display Peptide Library Kit, Catalog #E8110S, version 2.7, pg. 12-13, as follows: (1) Dilute the ER2738 overnight culture 1:100 in LB. Dispense 1 ml diluted culture into culture tubes, one for each clone to be characterized. 10 clones from the third round are often sufficient to detect a consensus binding sequence. (2) Using a sterile wooden stick or pipet tip, stab a blue plaque and transfer to a tube containing diluted culture. Important: pick plaques from plates having no more than ˜100 plaques. This will ensure that each plaque contains a single DNA sequence. (3) Incubate tubes at 37° C. with shaking for 4.5-5 hours (no longer). (4) Optional. In addition to sequencing individual clones, the entire pool of selected phage can be sequenced. This can yield a consensus binding sequence in a single step, but only if the common sequence elements appear in the same positions within the 12-residue “window” in each clone. Add 10 μl of the unamplified eluate to 1 ml diluted overnight culture and incubate at 37° C. with shaking for 4.5-5 hours. (5) Transfer cultures to microcentrifuge tubes, centrifuge 30 seconds. Transfer the supernatant to a fresh tube and re-spin. Using a pipet, transfer the upper 80% of the supernatant to a fresh tube. This is the amplified phage stock and can be stored at 4° C. for several weeks with little loss of titer. For long-term storage, dilute 1:1 with sterile glycerol and store at −20° C.
Rapid purification of sequencing templates. This extremely rapid procedure produces template of sufficient purity for manual or automated dideoxy sequencing, without the use of phenol or chromatography. (1) Carry out the plaque amplification procedure described above. After the first centrifugation step, transfer 500 μl of the phage-containing supernatant to a fresh microfuge tube. (2) Add 200 μl PEG/NaCl. Invert to mix, and let stand at room temperature 10 minutes. (3) Centrifuge 10 minutes, discard supernatant. (4) Re-spin briefly. Carefully pipet away any remaining supernatant. (5) Suspend pellet thoroughly in 100 μl Iodide Buffer and add 250 μl ethanol. Incubate 10 minutes at room temperature. Short incubation at room temperature will preferentially precipitate single-stranded phage DNA, leaving most phage protein in solution. (6) Spin 10 minutes, discard supernatant. Wash pellet in 70% ethanol, dry briefly under vacuum. (7) Suspend pellet in 30 μl TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA]. (8) 5 μl of the resuspended template should be sufficient for manual dideoxy sequencing with 35S or 33P, or automated cycle sequencing with dye-labeled dideoxynucleotides. More or less template may be required depending on the sequencing method used.
Sequencing of the peptides. Sequencing of the peptides was performed as follows: (1) The −28 primer is recommended for manual dideoxy sequencing. The −96 primer should be used for automated sequencing. (2) The sequence being read corresponds to the anticodon strand of the template. Write out the complementary strand and check against the top strand sequence. Check that the 3rd position of each codon in the randomized region is G or T. Determine the amino acid sequence from this strand 4. (3) TAG stop codons are suppressed by glutamine in ER2738 (supE), the strain originally used to produce the library. TAG should thus be considered a glutamine codon when translating.
Assaying selected peptides for target binding by ELISA. (1) When carrying out the plaque amplification for DNA sequencing, save the remaining phage-containing supernatants at 4° C. (2) For each clone to be characterized, inoculate 20 ml of LB medium with ER2738 and incubate at 37° C. until slightly turbid. Alternatively, dilute an overnight culture of ER2738 1:100 in 20 ml LB. (3) Add 5 μl of phage supernatant to each culture and incubate at 37° C. with vigorous aeration for 4½ hours. (4) Transfer the culture to a centrifuge tube and spin 10 minutes at 10,000 rpm (Sorvall SS-34, Beckman JA-17 or equivalent). Transfer supernatant to a fresh tube and re-spin. (5) Pipet the upper 80% of the supernatant to a fresh tube and add 1/6 volume of PEG/NaCl. Allow phage to precipitate at 4° C. for at least 1 hour or overnight. (6) Spin PEG precipitation 15 minutes at 10,000 rpm at 4° C. Decant supernatant, re-spin briefly, and remove residual supernatant with a pipette. (7) Suspend the pellet in 1 ml TBS. Transfer the suspension to a microcentrifuge tube and spin for 5 minutes at 4° C. to pellet residual cells. (8) Transfer the supernatant to a fresh microcentrifuge tube and re-precipitate with 1/6 volume of PEG/NaCl. Incubate on ice 15-60 minutes. Microcentrifuge for 10 minutes at 4° C. Discard supernatant, re-spin briefly, and remove residual supernatant with a micropipet. (9) Suspend the pellet in 50 μl TBS. Titer as described in Example 2, store at 4° C.
In order to investigate the nucleation ability of these binding peptides, the major 12-mer linear binding peptide was synthesized by solid phase synthetic method and subjected to HA-mineralization on holey carbon film-coated TEM grids according to J. D. Hartgerink, E. Beniash, S. I. Stupp, Science, 294, 1684 (2001), which is hereby incorporated by reference. A schematic showing the protocol used is shown in
Referring to
In order to study kinetics of HA nucleation by this peptide suspension, time dependence nucleation was investigated by preparing parallel TEM samples where HA was nucleated for 30 min (
Selected area electron diffraction patterns clearly showed that the crystals are well crystallized yet without a preferred crystal growth orientation (inset in
In high-resolution TEM, the lattice fringe images support that well-crystallized HA was formed. The lattice spacing of the crystals was measured as 0.26 nm, matching the spacing of the (202) face of the HA crystal lattices (
Five control peptides (Table 2) were synthesized and tested to show that single-15-biotin peptide that contains the 12-mer HA binding sequence was not composition specific but sequence-specific to bind and to nucleate HA.
Using the same procedure described in Example 4 to template HA growth on holey TEM grids, synthetic peptides not attached to phage were used for a control experiment.
Control experiments of HA nucleation with the scrambled sequence (control peptide 1, SEQ ID NO: 269) by switching proline (from position 2 to 7) and isoleucine (from position 7 to 2) showed amorphous calcium phosphate deposition without any clear SAED patterns. Control peptide 2 (SEQ ID NO: 270) which substituted hydroxyl residue to aspartic acid residue also showed amorphous deposition of calcium phosphate without any clear diffraction patterns within the two hours mineralization time frame.
Control peptides 3-5 which substituted hydroxyl (peptide 3, SEQ ID NO: 271), positively charged (peptide 4, SEQ ID NO: 272), and amide side chain (peptide 5, SEQ ID NO: 273) residues to alanine generally showed low solubility in pure waters. Due to the low solubility of these peptides (control peptides 3, 4 and 5), 1.5 mg/ml peptide suspension in a cosolvent system of acetonitrile and water (1:1/v:v) was prepared and 5 μl of the suspensions were deposited and completely dried in dessicators in a day. When HA crystals were nucleated by soaking the peptide deposited TEM grids into 20 μl of mixture of mineral precursor solutions (10 μl of 5 mM Na2HPO4 and 10 μl of 10 mM CaCl2), nucleation phenomena similar to those templated by HA binding peptides were observed. When parallel control experiments were conducted using the peptide 3, 4 and 5 solutions in 100% water, control peptides 4 and 5 showed relatively bigger amorphous calcium phosphate aggregation comparing to those templated by peptides 1 and 2, but no well-crystallized crystals were observed. Peptide 3 showed reduced HA-nucleation ability with different morphology of HA crystals (
Although negatively charged amino acid residues are thought to be dominant in non-collagenous proteins (e.g. sialoproteins) in bone, (See G. K. Hunter and H. A. Goldberg, Biochem. J. 302, 175 (1994); B. L. George, et al., J. Biol. Chem. 271, 32869 (1996); and A. Veis, A. Perry, Biochemistry 6, 2409 (1967)), the HA-binding peptides identified here possess primarily positively charged residues. This is likely due to the negatively charged surfaces of target HA under physiological screening condition (pH 7.5) (
Specific spatial position of each amino acid residue could play an important role in HA-binding as shown by molecular mechanics modeling in
The present examples, methods, procedures, treatments, specific peptides, sequences, compounds and molecules are meant to exemplify and illustrate the invention and should in no way be seen as limiting the scope of the invention. Any patents or publications mentioned in this specification are indicative of levels of those skilled in the art to which the patent pertains and are hereby incorporated by reference to the same extent as if each was specifically and individually incorporated by reference for all purposes.
This application claims priority to International Application No. PCT/US2005/043214, filed Nov. 29, 2005, which claims priority to U.S. Provisional Patent Application No. 60/631,660, filed on Nov. 29, 2004, which are hereby incorporated by reference in its entirety.
This invention was made during work supported by U.S. Department of Energy under Contract Nos. DE-AC03-76SF00098 and DE-AC02-05CH11231. The government has certain rights in this invention.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/US2005/043214 | 11/29/2005 | WO | 00 | 4/22/2008 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2006/062776 | 6/15/2006 | WO | A |
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