Patent Application
20210388119
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 2168935_ST25.bd. The text file is 152 KB, was created on Jun. 28, 2021, and is being submitted electronically via EFS-Web.
The present disclosure provides artificially designed circular tandem repeat proteins (cTRPs). The proteins are circular, handed, and include alpha-helical repeat proteins. The cTRPs have a number of uses as scaffolds for geometrically precise, arrayed presentation of cell-signaling and/or immune-related protein and peptide epitopes, as well as numerous other therapeutic, diagnostic, and nanotechnological uses.
Repeat proteins are formed by repetition of modular units of protein sub-structures. The overall structural architecture of repeat proteins is dictated by the internal geometry of the protein and the local packing of the repeat building blocks. These features are generated by underlying patterns of amino acid sequences, that themselves, are repetitive in nature.
Naturally existing repeat proteins play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The structure and identity of these repeat proteins are highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis.
The current disclosure provides repeat proteins designed purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of naturally existing repeat protein families. Because the design methodology did not rely on template sequence or structural information taken from natural repeat proteins, the resulting repeat proteins are unlike those seen in nature. More particularly, the designed repeat proteins have repetitive alpha (a)-helical structures joined by linkers. The inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini creating circular architectures. Further, the α-helical bundles of each circular α-helical repeat proteins can be either entirely left-handed or entirely right-handed. These proteins are self-folding, and have high thermostability and solubility. They are referred to herein as circular tandem repeat proteins, or “cTRPs” herein.
The disclosed cTRPs can have numerous uses as novel biomaterials. For example, the cTRPs have a number of uses as scaffolds for geometrically precise, arrayed presentation of cell-signaling and/or immune-related protein and peptide epitopes, as well as numerous other therapeutic, diagnostic, and nanotechnological uses. In particular embodiments, functional domains can be inserted between α-helical sequences and/or linker sequences without significantly altering the cTRPs' engineered parameters (e.g., circular, handed, α-helical repeats). The cTRPs can also be used as nanofilters.
The following nomenclature is used to reference specific cTRPs: “dTor_(number of structural repeats)x(number of amino acid residues within each structural repeat)(protein handedness)”. For example, “dTor_3x33L” describes a designed cTRP protein including a single protein chain containing 3 repeats of 33 repetitive amino acids, wherein the helical bundles of that cTRP are entirely left-handed. In the case that a cTRP is assembled from multiple protein subunits that each contain a fraction of the total repeats in that cTRP, the nomenclature also may indicate the number of repeats in each subunit of a multimeric assemblage, and thereby can distinguish between multimeric cTRPs that contain the same total number of repeats. For example, “dTor_12x31L_sub3” describes an assembly of 4 identical protein subunits that each have 3 left-handed repeats, that come together to create a multimeric cTRP with 12 total repeats. In contrast, “dTor_12x31L_sub4” describes an assembly of 3 identical protein subunits that each have 4 repeats, that again come together to create a multimeric cTRP with 12 total repeats. See
Repeat proteins are formed by repetition of modular units of protein sub-structures. The overall structural architecture of repeat proteins is dictated by the internal geometry of the protein and the local packing of the repeat building blocks. These features are generated by underlying patterns of amino acid sequences, that themselves, are repetitive in nature.
Naturally existing repeat proteins play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The structure and identity of these repeat proteins are highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis.
The current disclosure provides circular tandem repeat proteins (cTRPs) designed purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences or the structures of naturally existing repeat protein families. Because the design methodology did not rely on template sequence or structural information taken from natural repeat proteins, the resulting cTRPs are unlike those seen in nature. More particularly, the designed cTRPs have highly repetitive α-helical structures joined by linkers. The inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini creating circular architectures. Further, the repeated domains including the circular α-helical repeat proteins are uniformly handed. These proteins are capable of independently self-folding, and have high thermostability and solubility.
The disclosed cTRPs can have numerous uses as novel biomaterials. For example, the cTRPs have a number of uses as scaffolds for geometrically precise, arrayed presentation of cell-signaling and/or immune-related protein and peptide epitopes, as well as numerous other therapeutic, diagnostic, and nanotechnological uses. In particular embodiments, functional domains can be inserted between or within α-helical sequences and linker sequences without significantly altering the cTRPs' engineered parameters (e.g., circular, handed, α-helical repeats). The cTRPs can also be used as nanofilters. The cTRPs, methods of generation, characteristics, and uses are now described in more detail.
cTRPs disclosed herein include repetitive α-helical structures joined by linkers. Referring to, for example,
Exemplary amino acid sequences that generate an a-helix include VEELLKLAKAAYYS (SEQ ID NO: 1); VEEAYKLALKL (SEQ ID NO: 2); VEELLKLAEAAYYS (SEQ ID NO: 3); PTEALLKLIAEAK (SEQ ID NO: 4); ETEAKEEAEKALKE (SEQ ID NO: 5); STEAKEEAIKALKE (SEQ ID NO: 6); ELEAKVLAEKALKE (SEQ ID NO: 7); ETEAKLEAEKALKE (SEQ ID NO: 8); PTEVLLELIAEAS (SEQ ID NO: 9); KEEVKEKFLKELSK (SEQ ID NO: 10); KEEVKRKFLKELSK (SEQ ID NO: 11); KAEVKREFLWELSL (SEQ ID NO: 12); KEEVKEKFLAELEK (SEQ ID NO: 13); REEVKEKFLKELRK (SEQ ID NO: 14); KEEVKEKFLKELSF (SEQ ID NO: 15); KEEVKKKFWKELSL (SEQ ID NO: 16); KREVKRWFLFELRK (SEQ ID NO: 17); KAEVKLKFLFELSF (SEQ ID NO: 18); KEEVKEKFLKELFK (SEQ ID NO: 19); TTEALLILIAEAS (SEQ ID NO: 20); VEQQKQRFKELVKK (SEQ ID NO: 21); TAIAQILAIKASAK (SEQ ID NO: 22); TELERALRYAKKV (SEQ ID NO: 23); TELERALRYAVKV (SEQ ID NO: 24); TELEQALRYAKFV (SEQ ID NO: 25); LELTRALAYAKKV (SEQ ID NO: 26); TELERALRYAKLV (SEQ ID NO: 27); TELERALRYAKYV (SEQ ID NO: 28); PELEYALAYAKKV (SEQ ID NO: 29); TELERALIFAEAV (SEQ ID NO: 30); TELDRALVVYAKKV (SEQ ID NO: 31); TELERALLYAKKV (SEQ ID NO: 32); TELERALAYARLV (SEQ ID NO: 33); TELERALRYAEKV (SEQ ID NO: 34); TELERALVVYAKKV (SEQ ID NO: 35); SAIATAYIALAEYL (SEQ ID NO: 36); EALLKAIEIAIKL (SEQ ID NO: 37); SAIAEAYIALARYL (SEQ ID NO: 38); SALAQILAIYASAY (SEQ ID NO: 39); TLFLRALKLAKEV (SEQ ID NO: 40); ELYIRVLAIVAEAE (SEQ ID NO: 41); TKLELALKLALKK (SEQ ID NO: 42); KLYIEVLAIVAEAE (SEQ ID NO: 43); ELYIRVLAIVAKAE (SEQ ID NO: 44); KLYIEVLAIVAKAE (SEQ ID NO: 45); LEQALKILKVAAEL (SEQ ID NO: 46); VEEAVKRALKLKTKL (SEQ ID NO: 47); LEQALKILEVAAEL (SEQ ID NO: 48); LEQALKILEVAAKL (SEQ ID NO: 49); VEEAVKRAMKLKTKL (SEQ ID NO: 50); as well as SEQ ID NO: 124-129; 139, 140, 146 and 147.
Each repetitive α-helical structure includes 2 sequences that form an a helix. The two sequences forming a helices within each repetitive structure can be identical or can have at least 99%, at least 98%, at least 97%, at least 96%, at least 95%, at least 94%, at least 93%, at least 92%, at least 91%, at least 90% or at least 85% sequence identity to the other within the structure. Thus, in particular embodiments, a repetitive α-helical structure of a cTRP disclosed herein would include at least two sequences from SEQ ID NOs. 1-50; 124-129; 139, 140, 146 and 147 to generate an outer a helix and an inner a helix, respectively.
Disclosed engineered cTRPs that contain a circular architecture represent a target for rational, geometry-guided design of structural repeats for several reasons. Closure results from simple constraints on the inter-repeat geometry: if the transformation between successive repeats is considered as being composed of a rotation (curvature) about an axis together with a translation (rise) parallel to that axis, then the rise must equal zero and the curvature multiplied by the number of repeats must equal 360°. Circular structures are stabilized by interactions between the first and last repeats, obviating the need for capping repeats to maintain solubility and making them more tolerant than open repeat architectures to imperfections in the designed geometry. Thus, in particular embodiments, a circular protein (e.g., a protein having a circular architecture) is one wherein the N-terminal and C-terminal ends of the protein are naturally found within 10 Å following expression and folding. In particular embodiments, a circular protein is one wherein the N-terminal and C-terminal ends of the protein are naturally found within 10 Å; within 9 Å; within 8 Å; within 7 Å; within 6 Å; within 5 Å; within 4 Å; within 3 Å; within 2 Å; within 1 Å; or within 0.5 Å; following expression and folding. Naturally found means that the cTRP is self-folding. In particular embodiments, a circular protein is one designated as such by the teachings of Kajava, A. V. Tandem repeats in proteins: from sequence to structure. J. Struct. Biol. 179, 279-288, doi:10.1016/j.jsb.2011.08.009 (2012).
cTRPs offer the advantages of rotational symmetry (for example, in generating higher-order assemblies) with the added control provided by a covalent linkage between subunits. Conversely, and as described in more detail elsewhere herein, it is possible to convert a monomeric cTRP array into a symmetrical protein assembly by truncation (for example, converting a toroidal protein containing ‘n’ repeats into an equivalent homodimeric assembly containing ‘n/2’ repeats per subunit) if economy of protein length is required.
To generate the cTRPs disclosed herein, an approach to geometry-guided repeat protein design (
Designs with left-handed bundles (e.g., left-handed proteins;
Six monomeric repeat architectures have been initially selected for experimental characterization: a left-handed 3-repeat family (dTor_3x33L: designed Toroid with three 33-residue repeats, left-handed (
Crystal structures for the five monomeric repeat architectures were determined (
Comparison of the design models to the experimental crystal structures shows that four of the initially characterized designs formed left-handed α-helical toroids with the intended geometries (
The feasibility of splitting monomeric designs into fragments that can assemble symmetrically to reform complete toroids including multiple copies of identical subunits was explored (see, for example,
An alternative in either case would be for the monomers to associate as head-to-tail dimers to form a single larger ring, (akin to the tetrameric ring formed by the 3-repeat dTor_9x31L_sub3 construct), with concomitant breakage of the intra-monomer interactions between terminal repeats that are observed in the crystalline state. Given the stable, well-packed nature of the 3× and 6× designs, it was hypothesized that such an association mode would be disfavored due to loss of favorable packing interactions and energetic strain caused by the altered curvature of a larger ring. To evaluate this hypothesis in the case of the 3-repeat construct 3x33L_2-2, multiple independent symmetric folding simulations were performed in order to model the structure of a 6-repeat ring composed of two copies of the 3-repeat construct; for comparison, the same simulation protocol to model the 3-repeat construct forming a 3-repeat ring as designed was used. Analysis of packing quality and per-residue energies in these simulations suggests that the 6-repeat dimerization mode is indeed significantly less favorable than the 3.
The structurally characterized 9x31L design was selected to split into a small 3-repeat subfragment. The 3-repeat subfragments were expected to form a trimeric assembly. This 3-repeat fragment was expressed, purified, and formed diffraction-quality crystals. Upon determination of the experimental structure, it was discovered that the design fragment formed an unexpected crystal packing arrangement composed of linked tetrameric rings (i.e., including a total of 12 repeats per ring,
The current database of solved protein structures was analyzed to assess the uniqueness of the disclosed designed cTRPs in terms of global similarity and bundle handedness.
DALI searches: Representative models from each of the design families were submitted to the DALI server. Holm & Rosenstrom, Nucleic Acids Research 38, W545-W549, (2010). For the left-handed bundles, top Z-scores ranged from 3 to 5 with relatively short alignments that did not cover substantial portions of the design or matched PDB structure. For the right-handed design dTor_6x33R, on the other hand, the top Z-scores exceeded 11.0 and top alignments were longer, although sequence identities were low (5-20%) and RMSD's were high (above 6 Å). Top-scoring matches were found primarily to right-handed helical bundles assembled from hairpins (as is dTor_6x33R), however toroidal (closed circular) structures were not found (by visual inspection of the top few matches).
To minimize the likelihood of missing a similar structure, multiple databases were consulted. Representatives from the SCOPe (Fox, et al., Nucleic Acids Res 42, D304-309, (2014)) a/a toroid fold (a.102), the CATH a/a barrel architecture, the ECOD (Cheng, et al., PLoS Comput Biol 10, e1003926, (2014)) a/a toroid topology, and the RepeatsDB (Di Domenico, et al., Nucleic Acids Res 42, D352357, (2014)) α-barrel classification were visually inspected.
The SCOPe database contains two folds already classified by handedness: a.118, the α-α superhelix fold, described as having a right-handed superhelix, and a.298, the left-handed α-α superhelix fold. The a.118 fold class is composed 24 superfamilies, which include canonical α-helical repeats such as the Armadillo and TPR families. By contrast, the a.298 fold includes only the TAL effector-like family, composed of DNA-binding domains from plant-pathogenic bacteria (and designed variants thereof). These are not circular structures.
In the ECOD database, a superhelices are collected together into a single top-level grouping. Representative structures and domain boundaries (410 total) for this grouping were downloaded and analyzed using Rosetta to determine the handedness of the bundle. Visual inspection of all domains identified as potentially left-handed revealed that the only proteins containing multiple complete turns of the solenoid belonged to the mitochondrial mTERF and TAL effector families. Again, these are not circular structures. In ECOD these two homology-level families are grouped together at the “possible homology” (“X”) level, and indeed there are similarities in their overall structures and modes of DNA binding. Finally, representatives of the α-solenoid (111.3) grouping were analyzed in RepeatsDB (48 domains) and no left-handed bundles were found.
It is worth mentioning that a few α-helical barrel structures (for example, PDB ID 1okc) were encountered for which it was difficult to assign a handedness because the α-helices composing the barrel follow an up-down path rather than twisting around a bundle axis (in other words, the helices do not form a true solenoid/super-helical structure, a fact which is supported by the SCOPe and ECOD classifications of 1okc).
Successful design of several left-handed cTRPs demonstrates that the apparent absence of this fold from the current database of solved structures is not due to constraints imposed by the helical solenoid architecture or the toroidal geometry.
In particular embodiments, the left-handedness of particular cTRPs is due in part to the use of inter-helical turns whose geometry naturally imparts a handedness to the resulting helical bundle. The 3-residue ‘GBB’ (aL-1313) turn type used in particular embodiments prefers a left-handed dihedral twist between the connected helices, while the ‘GB’ turn found in dTor_6x33R correlates with right-handed geometry (
Based on the foregoing, and as stated, in particular embodiments linkers between a helix residues can utilize a GBB format. In particular embodiments, the G residue is glycine. In particular embodiments, the G residue is not isoleucine or valine. In particular embodiments, the B residues are selected from serine, threonine, asparagine, or glutamine.
In particular embodiments, repetitive a-helical structures joined by linkers can be formed from sequences selected from:
Additional examples include SEQ ID NO: 130-134; 141-144; and 148.
SEQ ID NOs: 51-70; 117-123; 135-138; and 145 provide exemplary repetitively patterned amino acid sequences that create cTRPs. In particular embodiments, adjacent structural repeats can include sequences that are identical or that have at least 99%, at least 98%, at least 97%, at least 96%, at least 95%, at least 94%, at least 93%, at least 92%, at least 91%, at least 90% or at least 85% sequence identity to the adjacent structural repeat. Methods to determine sequence identity are described below.
As will be understood by one of ordinary skill in the art, variants of the cTRP sequences, that do not alter the circular, handed and repetitive structural nature of the proteins can also be used. Indeed, variants of all protein sequences disclosed herein can be used, so long as the variation does not render the protein unfit for its intended purpose.
“Variants” include protein sequences having one or more amino acid additions, deletions, stop positions, or substitutions, as compared to a protein sequence disclosed elsewhere herein.
An amino acid substitution can be a conservative or a non-conservative substitution. Variants of protein sequence disclosed herein can include those having one or more conservative amino acid substitutions. A “conservative substitution” or “conservative amino acid substitution” involves a substitution found in one of the following conservative substitutions groups: Group 1: Alanine (Ala; A), Glycine (Gly; G), Serine (Ser; S), Threonine (Thr; T); Group 2: Aspartic acid (Asp; D), Glutamic acid (Glu; E); Group 3: Asparagine (Asn; N), Glutamine (Gln; Q); Group 4: Arginine (Arg; R), Lysine (Lys; K), Histidine (His; H); Group 5: Isoleucine (Ile; I), Leucine (Leu; L), Methionine (Met; M), Valine (Val; V); and Group 6: Phenylalanine (Phe; F), Tyrosine (Tyr; Y), Tryptophan (Trp; W).
Additionally, amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing). For example, an aliphatic grouping may include, for purposes of substitution, G, A, V, L, and I. Other groups including amino acids that are considered conservative substitutions for one another include: sulfur-containing: M and C; acidic: D, E, N, and Q; small aliphatic, nonpolar or slightly polar residues: A, S, T, P, and G; polar, negatively charged residues and their amides: D, N, E, and Q; polar, positively charged residues: H, R, and K; large aliphatic, nonpolar residues: M, L, I, V, and C; and large aromatic residues: F, Y, and W.
Non-conservative substitutions include those that significantly affect: the structure of the peptide backbone in the area of the alteration (e.g., the α-helical or beta-sheet structure); the charge or hydrophobicity of the molecule at the target site; or the bulk of the side chain. Non-conservative substitutions which in general are expected to produce the greatest changes in the protein's properties are those in which (i) a hydrophilic residue (e.g. S or T) can be substituted for (or by) a hydrophobic residue (e.g. L, I, F, V, or A); (ii) a C or P can be substituted for (or by) any other residue; (iii) a residue having an electropositive side chain (e.g. K, R, or H) can be substituted for (or by) an electronegative residue (e.g. Q or D); or (iv) a residue having a bulky side chain (e.g. F), can be substituted for (or by) one not having a bulky side chain, (e.g. G). Additional information is found in Creighton (1984) Proteins, W.H. Freeman and Company.
Variants of protein sequences disclosed herein also include proteins with at least 70% sequence identity, at least 80% sequence identity, at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 96% sequence identity, at least 97% sequence identity, at least 98% sequence identity, or at least 99% sequence identity to a protein sequence disclosed herein.
“Percent(%) amino acid sequence identity” with respect to the sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared. For example, % amino acid sequence identity values generated using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology, 266:460-480 (1996)) uses several search parameters, most of which are set to the default values. Those that are not set to default values (i.e., the adjustable parameters) are set with the following values: overlap span=1, overlap fraction=0.125, word threshold (T)=11 and scoring matrix BLOSUM62.
In addition to being circular, handed, and structurally repetitive, the cTRPs disclosed herein exhibit self-folding, high thermostability, and high solubility. Self-folding means that the cTRPs fold without any need for inclusion of additional folding domains or subunits (e.g., additional protein domains physically appended to the cTRP construct, or independently added protein folding chaperones such as GroEL/GroES or redox-dependent folding cofactors such as thioredoxin). High thermostability means that the proteins retain their overall secondary structure (including alpha-helices) and tertiary structures (defined by their size and shape) at temperatures as high as 95° C. High solubility means that the proteins can be concentrated to levels of 1 mg/mL or higher at physiological pH and salt concentrations without formation of soluble protein aggregates or protein precipitate.
Examination of the crystalline arrangements formed by the cTRPs shows the creation of specific 1- and 2-dimensional assemblies: both the monomeric 9x31L and 12x31L crystals have channels extending continuously through the crystal formed from the pores in vertical stacks of proteins (
The disclosed cTRPs have applications as scaffolds for binding and catalysis and as building blocks for higher-order assemblies. Amino acids lining the central pores can be mutated to introduce binding or catalytic functionalities and/or sites of chemical modification. The modular symmetry of monomeric toroids can be exploited to array interaction surfaces with prescribed geometries: a designed interface on the external face of the 12x31L design, for example, could be replicated with 2, 3, 4, or 6-fold symmetry by repeating the interfacial mutations throughout the full sequence. Thus monomeric toroids could replace multimeric assemblies as symmetry centers in the assembly of protein cages; by breaking the symmetry of the interaction surfaces it is possible to create more complex heterotypic assemblies with non-uniform placement of functional sites. For example, SEQ ID NOs: 71; 72; and 149-151 provide inserted functional domains and
In particular embodiments cTRPs include one or more functional domain. Examples of functional domains that can be incorporated into cTRPs include peptide binding domains (such as SH2 and SH3 domains), phosphotyrosine binding domains, LIM domains, SAM domains, PDZ domains, FERM domains, Pleckstrin homology domains, VWV domains, oligosaccharide binding (OB) domains, Immunoglobulin domains (IgG), single chain MHC proteins, tumor specific antigens (such as CD19 or ROR1), receptor ectodomains, isolated antigenic or adjuvant peptides, small molecule ligand binding domains (e.g., maltose binding protein) and enzyme domains (for example, trypsin). In particular embodiments the functional domains include SH2, Protein L, cytokines (e.g., IL-2; IL-17c, IL-3); Notch ligands (e.g., Delta or Jagged); immunogenic peptides (e.g., SEQ ID NO: 116); and/or peptide adjuvants (e.g., SEQ ID NO: 115).
In embodiments incorporating functional domains, linkers can be utilized between the scaffold cTRP sequence and the functional domain sequence. Linkers can be used that fuse domains together and result in stably expressed, functional proteins. Examples of linkers can be found in Chen et al., Adv Drug Deliv Rev. 2013 Oct. 15; 65(10): 1357-1369._Linkers can be flexible, rigid, or semi-rigid, depending on the desired functional domain presentation to a target. Commonly used flexible linkers include Gly-Ser linkers such as SEQ ID NO: 152, SEQ ID NO: 153 and SEQ ID NO: 160. Additional examples include: GGGGSGGGGS (SEQ ID NO: 161); GGGSGGGS (SEQ ID NO: 162); and GGSGGS (SEQ ID NO: 163).
In some situations, flexible linkers may be incapable of maintaining a distance or positioning of functional domains needed for a particular use. In these instances, rigid or semi-rigid linkers may be useful. Examples of rigid or semi-rigid linkers include proline-rich linkers. In particular embodiments, a proline-rich linker is a peptide sequence having more proline residues than would be expected based on chance alone. In particular embodiments, a proline-rich linker is one having at least 30%, at least 35%, at least 36%, at least 39%, at least 40%, at least 48%, at least 50%, or at least 51% proline residues. Particular examples of proline-rich linkers include fragments of proline-rich salivary proteins (PRPs).
The rigidity of protein linkers refers to the degree of flexibility of the protein backbone over the entire length of a short, single chain protein as measured by the average root-mean-square (RMS) (RMSfluct) of all internal torsion angles (Φ, ψ) over the length of a given single chain protein linker.
RMSfluct of a torsion angle is the standard deviation of the torsion angle value about the time-averaged value in a CHARMm molecular dynamics simulation, wherein RMSfluct is calculated as follows:
where f refers to the frame number, N is the total number of frames in the trajectory file, and of and θave are the current value and the average value for the torsion angle, respectively.
“CHARMm” (Chemistry at HARvard Macromolecular Mechanics) refers to a computer simulation engine (see Brooks et al., (1983) J Comp Chem 4: 187-217; MacKerell, et al., (1998) J. Phys. Chem. B 102(18): 3586-3616; and “CHARMM: The Energy Function and Its Parameterization with an Overview of the Program”, by MacKerell et al., in The Encyclopedia of Computational Chemistry, Volume 1, 271-277, by Paul von Raque Schleyer et al., editors (John Wiley & Sons: Chichester, United Kingdom (1998)); and Brooks, et al., (2009) J. Comp. Chem., 30:1545-1615 (2009).
In particular embodiments, the average RMSfluct can be calculated using the formula: (average RMSfluct phi (Φ)+average RMSfluct psi (ψ))/2. The average RMS fluctuation of all internal backbone torsion angles over the length of the protein can be used to quantify the rigidity of the protein linker. The more rigid the protein is the smaller the average RMS fluctuation should be due to a more limited conformational space accessible to the protein.
In particular embodiments, a rigid protein linker refers to a linker having an average RMSfluct of 25 or less, 20 or less 15 or less when measured using CHARMm modeling over a production run of 200 picoseconds (ps). In particular embodiments, a semi-rigid protein linker refers to a linker having an average RMSfluct of 45-25 when measured using CHARMm modeling over a production run of 200 picoseconds (ps).
As indicated, there are many possible uses of the disclosed cTRPs for synthetic biology and bioengineering (Mak, et al., Science 335, 716-719, (2012); Deng, et al., Science 335, 720-723, (2012); Barkan, et al., PLoS Genet. 8, e1002910, doi:10.1371/journal.pgen.1002910 (2012); Reichen et al., J. Struct. Biol. 185, 147-162, (2014); Wierenga, FEBS Lett. 492, 193-198 (2001)). Exemplary applications for the cTRPs include the incorporation and display of multiple copies of protein or peptide ligands for use in cell-stimulating growth factors and in vaccine development. Without being bound by theory, it is hypothesized that the display complex arrangements of multiple peptide and/or protein moieties onto stable protein nanoparticles, with well-defined symmetry and distances separating those individual components, will facilitate the creation of growth factor reagents and vaccines with exceptional biological activity as a result of (i) formation of high avidity interactions at the cell surface, and (ii) the potential to induce clustering of receptor complexes when the nanoparticle encounters its extracellular targets in vivo.
Cell manufacturing (e.g., the expansion of hematopoietic stem cells (and especially from limiting starting pools of such cells such as infant cord blood)) involves the addition of mixtures of cytokines and growth factors in various combinations to cell cultures. The overall biological activities of commercial cytokine and growth factor preparations in cell culture are suboptimal, being limited by the hostile environment of the cell incubator and media (which results in rapid protein degradation) and low activity in the wide-open spaces and volumes of the incubator (which negates the close intercellular distances that govern cytokine action in a living body). Therefore, the consumption, cost and effectiveness of these reagents is a clear target for improvement by a next generation of improved cell culture reagents, such as the cTRPs described herein. When used for cell manufacturing, the extreme physical and thermal stability of the underlying cTRP protein scaffolds (which have been shown to remain intact at temperatures up to 95° C.) greatly increases the stability and lifetime of the molecules used during manufacturing.
In particular embodiments, a variable number of copies of a well-characterized peptide binding domain (SH2 and/or SH3 domains) can be displayed on the surface of cTRPs (e.g., dTor_12x31L). SH2 domains are protein domains that can bind particular peptides or proteins motifs that contain a phosphorylated tyrosine. SH3 domains are protein domains that can bind particular peptides or protein motifs that contain two or more prolines. In particular embodiments the SH2 domain displayed on the surface of cTRPs is derived from the human Nck2 adapter protein, and binds a peptide with the sequence EHIpYDEVAAD (SEQ ID NO: 159). See, for example,
In particular embodiments, a variable number of copies of a well-characterized small ligand binding protein (Protein L) can be displayed on the surface of cTRPs (e.g., dTor_12x31L). Protein L exhibits very well-studied binding affinity and specificity towards IgG, and also has been used extensively as a model system for protein folding and stability (Kobe & Kajava, Trends Biochem. Sci. 25, 509-515 (2000); Main, et al., Structure 11, 497-508 (2003)).
In particular embodiments a variable number of copies of IL-2 can be displayed on the surface of cTRPs disclosed herein. IL-2 is a cytokine that stimulates various cell types, including T cells. In particular embodiments cTRPs that display IL-2 functional domains can be useful for stimulating T cells. In particular embodiments display of multiple copies of IL-2 on the surface of cTRPs can enhance IL-2 activity.
In particular embodiments, a variable number of copies of the IL-17c cytokine can be displayed on cTRPs disclosed herein. IL-17c has recently been shown to act as a potent neural growth factor. Because signaling is believed to be driven by ligand binding-induced multimerization of cell-surface IL-17RA and IL-17RE receptors, it is hypothesized that the presence of multiple copies IL-17c on the surface of the cTRPs can enhance signaling activity of the ligand.
In particular embodiments, a variable number of copies of IL-3 can be displayed on the surface of cTRPs disclosed herein. IL-3 is a cytokine that stimulates cells of the myeloid lineage, such as monocytes and dendritic cells. An example of an IL-3 sequence is SEQ ID NO: 173. In particular embodiments, cTRPs that display IL-3 functional domains can be useful for stimulating cells of the myeloid lineage.
In particular embodiments, a variable number of copies of Notch ligands (e.g. Delta or Jagged), or fragments and combinations thereof, can be displayed on the surface of cTRPs. Notch is a transmembrane protein with an extracellular EGF domain and intracellular domains that are involved in signaling. Notch proteins can be involved in embryogenesis and cell fate decisions, such as hematopoietic progenitor cell differentiation. Notch ligands such as Delta and Jagged can interact with Notch to influence cell differentiation. An example of a human Delta (also known as Delta-like protein) is SEQ ID NO: 174. An example of a human Jagged protein is SEQ ID NO: 175. The extracellular domains of Delta and Jagged proteins can interact with the extracellular domain of Notch protein. In particular embodiments, the extracellular domains of Notch and/or Jagged can be displayed on the surface of cTRPs.
In particular embodiments a functional domain linked to a cTRP can be a single chain MHC (scMHC) harboring an immunogenic peptide. MHC molecules are heterodimers (alpha chain and beta chain) that are expressed on the surface of cells and present peptides/antigens to T cells. There are several classes of MHC molecules and the best studied are class I and class II. Class I MHC molecules are expressed by all nucleated cells, and present non-self peptides. Class II MHC molecules are expressed on antigen presenting cells, and can present both self and non-self peptides. Single chain, scMHC molecules can be recombinant MHC proteins wherein functional fragments of an MHC alpha chain and an MHC beta chain are expressed from the same polypeptide. In particular embodiments the MHC alpha and beta chains can be derived from class I MHC molecules. In particular embodiments, the MHC alpha chain domain can be SEQ ID NO: 165. In particular embodiments, the MHC beta chain domain can be SEQ ID NO: 166. In particular embodiments, the immunogenic peptide can be derived from human cytomegalovirus. In particular embodiments, the immunogenic cytomegalovirus peptide can be NLVPMVATV (SEQ ID NO: 167)
In particular embodiments, a variable number of immunogenic peptide vaccine candidates (e.g., derived from a mutated growth factor receptor that acts as a commonly observed cancer-associated neoantigen) on one surface, along with multiple copies of a peptide adjuvant (e.g., derived from the HMGB1 high mobility group box protein) on the other can be displayed on cTRPs disclosed herein. For example, LEEKKGNYWTDHC (SEQ ID NO: 116) is an immunogenic peptide derived from in-frame deletion of exons 2 to 7 in the EGFR gene that results in an oncogenic growth factor receptor while also creating a high-frequency neoantigen across a wide variety of tumor types. This peptide is already very well studied as a peptide vaccine for treatment of Glioblastoma multiforme under the trade name ‘Rindopepimut’ (Boersma & Pluckthun, Curr. Opin. Biotechnol. 22, 849-857, (2011); Ramisch, et al., Proc. Natl. Acad. Sci. USA 111, 17875-17880, (2014). The peptide adjuvant (termed ‘HP91; sequence DPNAPKRPPSAFFLFCSE (SEQ ID NO: 115)), which is derived from the B box domain of HMGB1 and induces activation of human and murine dendritic cells) can also be displayed. As described in Grove, et al., (Curr. Opin. Struct. Biol. 18, 507-515, (2008)) one of the simplest tests of immunogenicity of a vaccine candidate/adjuvant combination is an ELISPOT assay to monitor the activation of dendritic cells in vitro, as a function of the addition of the vaccine candidate molecules.
In particular embodiments, cTRPs can be linked to a detectable label. Detectable labels can be detected following administration to a subject using imaging techniques. Examples of imaging techniques include magnetic resonance imaging (MRI), magnetic resonance tomography (MRT), positron emission tomography (PET), computer tomography (CT), single-photon emission computed tomography (SPECT) and optical imaging, such as x-ray.
Detectable labels can include any suitable label or detectable group detectable by, for example, optical, spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Such detectable labels include radiolabels (e.g., 355 1251 32p, 3 H, 140, 1311), radioacoustic labels, enzyme labels (e.g., horseradish peroxidase, hydrolases, alkaline phosphatase), chemiluminescence labels, fluorescence labels (e.g., rhodamine, phycoerythrin, fluorescein, fluorescent proteins, Texas red), fluorescent proteins (e.g. a green fluorescent protein or one of its many modified forms), gold beads, magnetic beads (e.g. Dynabeads™), and biotin (with labeled avidin or streptavidin).
Based on the foregoing, it is anticipated that cTRPs disclosed herein can be formulated into compositions for administration to a subject. Subjects can include humans, veterinary animals (dogs, cats, reptiles, birds, etc.) livestock (horses, cattle, goats, pigs, chickens, etc.) and research animals (monkeys, rats, mice, fish, etc.).
Compositions include at least one repeat protein and at least one pharmaceutically acceptable carrier. In particular embodiments, the compositions include repeat proteins of at least 0.1%-99% w/v of the composition or from 0.1% w/w-99% w/w of composition.
Exemplary generally used pharmaceutically acceptable carriers include any and all absorption delaying agents, antioxidants, binders, buffering agents, bulking agents or fillers, chelating agents, coatings, disintegration agents, dispersion media, gels, isotonic agents, lubricants, preservatives, salts, solvents or co-solvents, stabilizers, surfactants, and/or delivery vehicles.
Exemplary antioxidants include ascorbic acid, methionine, and vitamin E. Exemplary buffering agents include citrate buffers, succinate buffers, tartrate buffers, fumarate buffers, and/or gluconate buffers. An exemplary chelating agent is EDTA. Exemplary isotonic agents include polyhydric sugar alcohols including trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol, or mannitol. Exemplary preservatives include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, and/or octadecyldimethylbenzyl ammonium chloride.
Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the repeat proteins or helps to prevent denaturation or adherence to the container wall. Typical stabilizers can include polyhydric sugar alcohols; amino acids, such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, and threonine.
For injection, compositions can be formulated as aqueous solutions, such as in buffers including Hanks' solution, Ringer's solution, or physiological saline. The aqueous solutions can contain formulatory agents such as suspending, stabilizing, and/or dispersing agents. Alternatively, the formulation can be in lyophilized and/or powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
For oral administration, the compositions can be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like. For oral solid formulations such as powders, capsules and tablets, suitable excipients include binders (gum tragacanth, acacia, cornstarch, gelatin), fillers such as sugars, e.g. lactose, sucrose, mannitol and sorbitol. If desired, disintegrating agents can be added, such as corn starch, potato starch, alginic acid, cross-linked polyvinylpyrrolidone, agar, or alginic acid. If desired, solid dosage forms can be sugar-coated or enteric-coated using standard techniques. Flavoring agents can also be used.
Compositions can be formulated as an aerosol. In one embodiment, the aerosol is provided as part of an anhydrous, liquid or dry powder inhaler. Aerosol sprays from pressurized packs or nebulizers can also be used with a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. Capsules and cartridges of gelatin for use in an inhaler or insufflator may also be formulated containing a powder mix of repeat proteins and a suitable powder base such as lactose or starch.
Compositions can also be formulated as depot preparations. Depot preparations can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salts.
Additionally, compositions can be formulated as sustained-release systems utilizing semipermeable matrices of solid polymers including at least one cTRP. Various sustained-release materials have been established and are well known by those of ordinary skill in the art.
Any composition disclosed herein can advantageously include any other pharmaceutically acceptable carriers which include those that do not produce significantly adverse, allergic, or other untoward reactions that outweigh the benefit of administration. Exemplary pharmaceutically acceptable carriers and formulations are disclosed in Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990. Moreover, formulations can be prepared to meet sterility, pyrogenicity, general safety, and purity standards as required by U.S. FDA Office of Biological Standards and/or other relevant foreign regulatory agencies.
Example 1. Methods. Computational design. The repeat module design process applied here includes an initial “diversification” round of large-scale sampling followed by filtering and clustering and then a second “intensification” round of sampling focused on successful topologies identified in the first round.
Fragment assembly: Starting backbone models for sequence design are built using a fragment assembly protocol which is based on the standard Rosetta ab initio protocol (Simons, et al., J Mol Biol 268, 209-225, (1997)) with the following modifications: (1) fragment replacement moves are performed symmetrically across all repeats, guaranteeing that backbone torsion angles are identical at corresponding positions across repeats; (2) a pseudo-energy term (equal to the deviation between actual and desired curvature, in degrees, plus the deviation in rise multiplied by a factor of 5) is added to the potential to favor satisfaction of the geometric constraints; (3) the amino acid sequence used for low-resolution scoring is assigned randomly at the start of each simulation from secondary-structure specific distributions (helix: Ala+Ile+Leu+Asp+Ser, turn: Gly+Ser), which has the effect of increasing the diversity in helix packing distances and geometries compared with using a constant sequence such as poly-Val or poly-Leu.
Providing supplemental method information regarding fragment assembly, first round designs sampled helix lengths from 7 to 20 residues, turn lengths from 1 to 5 residues, and total repeat lengths ranging from 20 to 40 residues. At the start of each independent first round design trajectory the lengths of the secondary structure elements and turns are chosen randomly, defining the target secondary structure of the repeat module and its length. Together with the number of repeats, this defines the total length of the protein and the complete secondary structure, which is used to select 3 and 9 residue backbone fragments for use in the low-resolution fragment assembly phase.
Sequence design: The low-resolution fragment assembly simulation is followed by an all-atom sequence design stage including two cycles alternating between fixed-backbone sequence design and fixed-sequence structure relaxation. Symmetry of backbone and side chain torsion angles and sequence identities is maintained across all repeats. Since the starting backbones for design are built by relatively coarse sampling in a low-resolution potential, sequences designed with the standard all-atom potential are dominated by small amino acids and the resulting structures tend to be under-packed. To correct for this tendency, a softened Lennard-Jones potential (Dantas, et al., J Mol Biol 366, 1209-1221, (2007)) is used for the sequence design steps, while the standard potential is used during the relaxation step. The Rosetta “score12prime” weights set was used for these design calculations.
Filtering and clustering: Final design models (typically 10-100,000) are first sorted by per-residue energy (total energy divided by the number of residues, to account for varying repeat length) and the top 20% are filtered for packing quality, satisfaction of buried polar groups, and sequence-structure compatibility via a fast, low-resolution symmetric refolding test (40 trajectories, requiring at least 1 under a length-dependent RMSD threshold). Designs that pass these filters are clustered by C-α RMSD (allowing for register shifts when aligning helices with unequal lengths) in order to identify recurring architectures. The clusters are ranked by averaging residue energy, packing quality, and refolding success over all cluster members.
Providing supplemental method information regarding filtering and clustering, the following filtering thresholds were used: sasapack_score<0.5, #buried unsatisfied donors per repeat<1.5, #buried unsatisfied acceptors per repeat<0.5, refolding RMSD threshold of 2 Angstroms for 3-repeat designs, and 4 Angstroms for larger designs.
Resampling: During the second round of designs, representative topologies from successful design clusters are specifically resampled by enforcing their helix and turn lengths as well as their turn conformations (defined using a 5-state, coarse-grained backbone torsion alphabet (Wintjens, et al., J Mol Biol 255, 235-253, (1996))) during fragment selection.
Providing supplemental method information regarding resampling, the following boundaries were used for the coarse-grained Ramachandran alphabet1 (
‘A’=(phi<=0, −125<psi<=50), ‘B’=(phi<=0, psi>50 or psi<=−125); ‘G’=(phi>0, −100<psi<=100); ‘E’=(phi>0, psi>100 or psi<=−100), and ‘O’=(|omega|<90).
Large-scale refolding: Selected low-energy designs from the second round that pass the filters described above are evaluated by a large-scale refolding test in which 2,000-10,000 ab initio models are built by standard (asymmetric) fragment assembly followed by all-atom relaxation. Success is measured by assessing the fraction of low energy ab initio models with RMSDs to the design model under a length-dependent threshold.
Symmetry-breaking in the central pore: For designed toroids with an open, polar central pore, perfect symmetry may not allow optimal electrostatic interactions between nearby side chains corresponding to the same repeat position in successive repeats. Symmetry-breaking mutations were therefore explored at a handful of inward-pointing positions via fixed-backbone sequence design simulations in which the length of the repeating sequence unit was doubled/tripled (for example, whereas perfect 6-fold repeat symmetry would require KKKKKK (SEQ ID NO: 156) or EEEEEE (SEQ ID NO: 157), doubling the repeat length permits charge complementarity with KEKEKE (SEQ ID NO: 158)). Solutions from these designs were accepted if they significantly lowered the total energy.
Structural bioinformatics: To assess similarity between design models and proteins in the structural database, searches were performed using the structure-structure comparison program DALI33 as well as consulting the protein structure classification databases CATH34, SCOPe35, and ECOD36. Further details are given elsewhere herein.
Cloning and Protein Expression. The plasmids encoding individual constructs were cloned into previously described bacterial pET15HE expression vectors (Mak et al., Science 335(6069):716-9, (2012)) including a cleavable N-terminal His-tag and an ampicillin resistance cassette.
Sequence verified plasmids were transformed into BL21(DE3)RIL E. coli cells (Agilent Technologies) and plated on LB medium with ampicillin (100 μg/mL). Colonies were individually picked and transferred to individual 10 mL aliquots of LB-Ampicillin media and shaken overnight at 37° C. Individual 10 mL aliquots of overnight cell cultures were added to individual 1 L volumes of LB-Ampicillin, which were then shaken at 37° C. until the cells reached an OD600 value of 0.6 to 0.8. The cells were chilled for 20 minutes at 4° C., then IPTG was then added to each flask to a final concentration of 0.5 mM to induce protein expression. The flasks were shaken overnight at 16° C., and then pelleted by centrifugation and stored at −20° C. until purification.
Construct dTor_6x35L(SeMet), incorporating a single Methionine residue at position 168 in the original design construct, was generated using a ‘QuikChange’ site-directed mutagenesis kit (Agilent) and corresponding protocol from the vendor. The resulting plasmid construct was again transformed into BL21(DE3)RIL E. coli cells (Agilent Technologies) and plated on LB plates including ampicillin (100 μg/mL) and chloramphenicol (35 g/mL). Subsequent cell culture and protein expression in minimal media, along with incorporation of selenomethionine was incorporated during protein expression according to reference Walden et al., Acta Crystallogr D Biol Crystallogr. April 1; 66(Pt 4): 352-357(2010).
Purification. Cell pellets from 3L of cell culture were resuspended in 60 mL of PBS solution (140 mM NaCl, 2.5 mM KCl, 10 mM NaHPO4, 2 mM KH2PO4) including 10 mM imidazole (pH 8.0). Cells were lysed via sonication and centrifuged to remove cell debris. The supernatant was passed through a 0.2 micron filter, and then incubated on a rocker platform at 4° C. for one hour after adding 3 mL of resuspended Nickel-NTA metal affinity resin (Invitrogen). After loading onto a gravity-fed column, the resin was washed with 45 mL of the same lysis buffer described above, and the protein was eluted from the column with three consecutive aliquots of PBS including 150 mM imidazole (pH 8.0). Purified protein was concentrated to 5 mg/mL to 25 mg/mL while buffer exchanging into 25 mM Tris (pH 7.5) and 200 mM NaCl and then further purified via size exclusion chromatography using HiLoad 16/60 Superdex 200 column (GE).
Protein samples were then split in half; one sample was used directly for crystallization while the other had the His-tag removed by an overnight digest with biotinylated thrombin (Novagen), prior to additional crystallization trials. The digested sample was incubated for 30 minutes with streptavidin-conjugated agarose (Novagen) to remove the thrombin. All samples were tested for purity and removal of the His-tag via SDS PAGE. The final protein samples, both with and without the N-terminal poly-histidine affinity tag, were concentrated to values of 5 mg/mL to 25 mg/mL for crystallization trials.
Solution Size and Stability Analysis. Proteins ata concentration of 4 to 10 mg/ml were run over a Superdex 75 10/300 GL column (GE Healthcare) in 25 mM Tris pH 8.0 plus 100 or 750 mM NaCl at a rate of 0.4 ml/min on an AKTAprime plus chromatography system (GE Healthcare). All fractions including eluted toroid protein (visualized via electrophoretic gel analyses) were pooled, concentrated and run over the column a second time in order to assess their solution oligomeric behavior using protein with a minimal background of contaminants. Gel filtration standards (Bio-Rad) were run over the same column in matching buffer, and the UV trace of the proteins was overlaid onto the standards using UNICORN 5 software (GE Healthcare).
For measurements of protein stability using circular dichroism (CD) spectroscopy, purified recombinant toroid constructs were diluted to between 10 to 20 μM concentration and dialyzed overnight into 10 mM potassium phosphate buffer at pH 8.0. Circular dichroism (CD) thermal denaturation experiments were performed on a JASCO J-815 CD spectrometer with a Peltier thermostat. Wavelength scans (190-250 or 260 nm) were carried out for each construct at 22° C. and 95° C. or 80° C. (see
Crystallization and Data Collection. Purified proteins were initially tested for crystallization via sparse matrix screens in 96-well sitting drops using a mosquito (TTP LabTech). Crystallization conditions were then optimized with constructs that proved capable of crystallizing in larger 24-well hanging drops. Out of 11 constructs that were purified to homogeneity, ten were crystallized, of which five yielded high quality x-ray diffraction that resulted in successful structure determination. dTor_6x35L was crystallized in 160 mM Sodium Chloride, 100 mM Bis-Tris pH 8.5 and 24% (w/v) Polyethylene Glycol 3350 at a concentration of 26 mg/mL. The crystal was transferred to a solution including 300 mM, then 500 mM Sodium Chloride and flash frozen in liquid nitrogen. Data was collected on a R-AXIS IV++ and processed on HKL20004.
dTor_6x35L(SeMet) was crystallized in 140 mM Sodium Chloride, 100 mM Tris pH 8.5 and 22% (w/v) Polyethylene Glycol 3350 at a concentration of 26 mg/mL. The crystal was transferred to a solution including 300 mM, then 500 mM Sodium Chloride and flash frozen in liquid nitrogen. Data was collected at ALS Beamline 5.0.2 at wavelength 0.9794 Angstroms and processed on HKL20004.
dTor_3x33L_2-2 was crystallized in two different conditions, producing two different crystal lattices. The first condition had 30% Polyethylene Glycol 3350, 100 mM Tris pH 6.5, 200 mM NaCl with a protein concentration of 1.8 mM. The protein was soaked in a 15% Ethylene Glycol cryoprotectant for one minute prior to being flash frozen in liquid nitrogen. Data was collected on a Saturn 944+(Rigaku) for 180 degrees at phi=0 and another 180 degrees at phi=180. Data was then processed on HKL20004 out to 1.85 Å in space group P212121.
The second condition had 45% Polyethylene Glycol 400 and 100 mM Tris pH 7.7 with a protein concentration of 1.8 mM. Protein crystal was flash frozen without being cryoprotected. Data was collected on a Saturn 944+(Rigaku) for 180 degrees at phi=0 and another 180 degrees at phi=180. Data was then processed on HKL20004 out to 1.85 Å in space group P43212.
dTor_9x31L_sub3 was crystallized in 100 mM Tris pH 8.5 and 15% (v/v) Ethanol at a concentration of 11.5 mg/mL. The crystal was transferred to a solution including 75 mM Tris pH 8.5, 7.5% (v/v) Ethanol and 25% (v/v) Glycerol and flash frozen in liquid nitrogen. Data was collected at ALS BL5.0.2 and processed on HKL20004 out to 2.9 Å in space group P 41 21 2/P 43 21 2.
dTor_9x31L was crystallized in 0.1 M Sodium Citrate pH 5.4 and 1.0 M Ammonium Phosphate Monobasic at a concentration of 8.8 mg/mL in 3 ul drops including 1 ul protein and 2 ul well solution. The crystal was transferred to a solution including the well plus 25% (v/v) Glycerol and flash frozen in liquid nitrogen. Data was collected on a Saturn 944+CCD and processed on HKL20004 out to 2.5 Å in space group P 21 21 21.
dTor_12x31L was crystallized in 0.9 M Sodium malonate pH 7.0, 0.1 M HEPES pH 7.0 and 0.5% Jeffamine ED-2001 pH 7.0 at a concentration of 8.8 mg/mL in 2 ul drops including 1 ul protein and 1 ul well solution. The crystal was transferred to a solution including 0.675 M Sodium malonate pH 7.0, 0.075 M HEPES pH 7.0, 0.375% Jeffamine ED-2001 pH 7.0 and 25% Glycerol, and flash frozen in liquid nitrogen. Data was collected on a Saturn 944+CCD and processed on HKL20004 out to 2.3 Å in space group R 3:H.
Phasing and Refinement. The dTor_6x35L and both dTor_3x33L_2-2 structures were solved by Molecular Replacement with Phaser5 via CCP4i6 using the Rosetta-designed structure as a search model. The structures were then built and refined using Coot7 and Refmac58, respectively.
The structure of dTor_6x35L(SeMet) was solved by Molecular Replacement with Phaser5 via PHENIX9 using the best refined model of dTor_6x35L as a phasing model. The structure was then built and refined using Coot7 and PHENIX10, respectively.
The structures of dTor_9x31L_sub3 and dTor_9x31L were solved by Molecular Replacement with Phaser5 via PHENIX9 using the Rosetta-designed structure as a search model. The structure was then built and refined using Coot7 and PHENIX10, respectively.
The structure of dTor_12x31L was solved by Molecular Replacement with Phaser5 via PHENIX9 using a 4 repeat subunit the Rosetta-designed structure as a search model. The structure was then built and refined using Coot7 and PHENIX10, respectively.
Additional Supporting Methods. Design model for dTor_12x31L: The 12x31L design was constructed by duplicating the final 3 repeats of the 9x31L design. To generate a “design model” for comparison with the experimentally determined structure, the round 2 design protocol now forcing the 12x31L repeat sequence in addition to the number of repeats (Main, et al., Structure 11, 497-508 (2003)) and the helix and turn lengths (H14-L3-H11-L3) and turn conformations (GBB) was followed. Thus the sequence design steps were reduced to rotamer optimization (since the amino acid identities were fixed). This symmetric structure prediction process was repeated 10,000 times and the lowest-energy final model was taken as the computational model.
Surface mutations to enhance crystallization: For a single representative of the 3x31L and 6x31R families lattice docking and design simulations were performed to select mutations that might promote crystallization. Core positions were frozen at the design sequence. Candidate space groups were selected from those most commonly observed in the protein structural database. Theoretical models of crystal packing arrangements were built by randomly orienting the design model within the unit cell and reducing the lattice dimensions until clashes were encountered. Symmetric interface design was performed on these docked arrangements, and final designs were filtered by energy, packing, satisfaction of polar groups, and number of mutations from the original design model.
Handedness of repeat helical bundles: To compute the handedness of helical bundles formed by cTRPs, an approximate helical bundle axis curve was generated by joining the location of repeat-unit centers of mass in a sliding fashion along the protein chain. The handedness was then estimated by computing the directionality of the winding of the polypeptide chain about this axis curve.
Summary of Example 1. Example 1 described creation and characterization of cTRPs including: 3 repeats, 6 repeats, 9 repeats, and 12 repeats. Characterization included (i) protein expression and purification; (ii) size determination using gel filtration chromatography (also termed ‘size exclusion chromatography or ‘SEC’) and dynamic light scattering (‘DLS’) (iii) demonstration of thermostability using circular dichroism spectroscopy (‘CD’) and (iv) determination of high resolution molecular structures using X-ray Crystallography. Example 1 also provided demonstration that cTRPs can also be assembled from smaller protein subunits including a fraction of the total number of repeats found in the fully circularized protein constructs (e.g., generation of a circular protein including 12 repeats from the assembly of four identical subunits each including 3 repeats).
Example 2. Methods. Protein Expression and Purification. Designed constructs were cloned into a previously described bacterial expression vector, named ‘pET15HE’, which incorporates a cleavable N-terminal poly-histidine affinity tag and a thrombin cleavage site (Mak et al., Science 335(6069): 716-9, (2012)).
Sequence verified plasmids were transformed into BL21(DE3) RI L E. coli cells and plated on LB-Amp plates to grow at 37° C. Colonies were grown in 10 mL overnight cultures of LB+Amp (100 μg/mL) and diluted 1:100 the next day to a final volume of 1 L. Cell cultures were shaken at 37° C. until the cells reached an OD600 between 0.6-0.8. Cells were then incubated on ice for 30 minutes, induced with 200 mM IPTG, and incubated overnight at 16° C. Induced cells were pelleted and stored at −20° C. Successful protein induction was verified by SDS-PAGE.
Cell pellets were resuspended in a buffer including 25 mM Tris/HCl pH 7.5, 200 mM NaCl, and 5% glycerol. PMSF and benzonase (Sigma-Aldrich) were added to 1 mM concentrations prior to sonication. Cell debris was pelleted and the supernatant was filtered through a 0.20 μm filter.
His-tagged proteins were incubated with pre-equilibrated Nickel-NTA resin (3 mL bed volume), gravity-loaded onto a column, and washed with buffer including increasing concentrations of imidazole at pH 8.0. Fractions including eluted protein were concentrated and exchanged to a thrombin cleavage buffer (0.3 M NaCl, 25 mM Tris pH 7.5, and 5% v/v glycerol). The His-tag was removed with an overnight incubation at 4° C. with biotinylated thrombin. The following morning, streptavidin-conjugated agarose resin was added to the sample and incubated for 30 minutes at room temperature. Thrombin was then removed by gravity filtration over an empty column, and pure, tagless protein was collected.
Determination of apparent molecular mass using size exclusion chromatography (‘SEC’). The constructs were then concentrated to 5-20 mg/mL and passed over a size exclusion chromatography (SEC) column (15 mL Superdex 200 10/300 GL, GE Life Sciences) in the presence of 25 mM Tris/HCl pH 7.5, 200 mM NaCl, and 5% glycerol. The apparent molecular weight of the purified construct was determined based on interpolation of each construct's elution volume relative to a set of protein-based molecular weight standards.
Determination of hydrodynamic radius using Dynamic Light Scattering (‘DLS’). The average hydrodynamic radii and diameter of protein constructs were characterized by measuring the diffusion rate of those particles moving under Brownian motion. Designs were measured in 1×PBS (Phosphate buffered Saline; 10 mM P043-, 137 mM NaCl, and 2.7 mM KCl) ata protein concentration of 1 mg/mL and temperature of 25° C. on a Zetasizer Nano Series instrument (Malvern Instruments).
Determination of thermal stability using CD spectroscopy. Purified recombinant meganuclease constructs were diluted to between 10-20 μM concentration and dialyzed overnight into 10 mM potassium phosphate buffer at pH 8.0. Circular dichroism (CD) spectra were then collected on a JASCO J-815 CD spectrometer with a Peltier thermostat. Wavelength scans extending from 190-250 nm were carried out for each construct at 22° C. and 95° C.
Crystallization and Structure Determination. Protein samples, both before and after proteolytic removal of the poly-histidine purification tag, were screened for initial crystals in broad sparse matrix screens using nanoliter volume sitting drops in a Mosquito crystallization robotic platform (LabTech TTP). Promising hits were then optimized, when necessary in a larger microliter hanging drop format. Data were collected using X-rays generated either on a rotating anode MicroMax-007HF generator (Rigaku) or at the Advanced Light Source (ALS) beamline 5.0.2 (Lawrence Berkeley National Laboratory). Structures were solved via Molecular Replacement, using initial designed models, using program Phaser (Mccoy et al., J Appl Crystallogr 40: 658-674, (2007)) and went through multiple rounds of refinement and rebuilding using Refmac5 (Skubak et al., Acta Crystallogr D 60: 2196-2201, (2004)) or Phenix.refine (Afonine et al., Acta Crystallogr D 68: 352-367, (2012)) and Coot (Emsley et al., Acta Crystallogr D 66: 486-501, (2010)). Validation of final structures was performed using MolProbity (Chen et al., Acta Crystallogr D 66: 12-21, (2010)) and RCSB's validation server, and were then deposited into the RCSB (Berman et al., Nucleic Acids Res 28: 235-242 (2000)).
SAXS analyses. Purified proteins were transferred by dialysis into 150 mM NaCl, 25 mM Tris pH 8.0, 2% glycerol at protein concentrations ranging from 10 mg/mL to 2 mg/mL. SAXS data were collected on the SIBYLS small angle x-ray scattering beamline at the Advanced Light Source (Lawrence Berkeley National Laboratory) using a Pilatus3 2 M detector with exposure times of 0.5, 1, 2, and 4 seconds. Data was processed using program SCATTER.
Determination of ligand binding using Fluorescence Polarization (FP): Each protein construct was 2-fold serially diluted into twelve concentrations, from 23 μM to 0.011 μM, using FP Buffer (20 mM HEPES+150 mM KCl at pH7.4). A 90 uL aliquot of each concentration was mixed with 10 μL of 0.5 μM FITC-labeled peptide so the final concentrations were 20.7 μM to 0.01 μM with 50 nM peptide. Each reaction was incubated at room temperature, protected from light, for 20 minutes. FP was run using a SpectraMax M5 (Molecular Devices) at an excitation of 485 nm and emission of 525 nm. Background was subtracted from raw perpendicular and parallel fluorescence intensity, which were then converted to fluorescence polarization (mP) by the following equation:
F
∥
−F
⊥
mP=------------*1000
F
∥
+F
⊥
where, F∥=adjusted parallel intensity and F⊥=adjusted perpendicular intensity
Example 2 describes expansion of the cTRP scaffolds out to constructs including 24 repetitive α-helical structures in a single protein construct. These constructs were characterized using all the methods noted above in Example 1, except for X-ray crystallography (because crystals of these constructs do not diffract to appropriate resolution for a full analysis). Structural characterization for these constructs was instead performed using small angle X-ray scattering (‘SAXS’) analyses.
Example 2 also provides expansion of the cTRP scaffolds in the ‘3rd’ dimension (i.e. increasing their thickness, rather than their diameter) to increase the designable ‘surface area’ between each protein repeat and between the N- and C-termini of each protein subunit within those constructs. These constructs have been characterized by protein expression and purification, as well as SEC and DLS (
Example 2 also further explored the functionalization of cTRPs by grafting several different binding domains and cell signaling protein subunits onto their exterior. Particularly, variable numbers (1, 2, 4, and 6) of a peptide-binding domain (the SH2 domain from the Nck2 cell signaling adapter protein, which is 100 amino acids in size) have been incorporated into a cTRP scaffold harboring 12 repeats. This domain recognizes and binds a peptide sequence corresponding to “N-Glu-His-Ile-pTyr-Asp-Glu-Val-Ala-Ala-Asp-C”, (SEQ ID NO: 159) which was used for binding analyses. In these particular constructs, a minimum length protein linker required for folding and function of the SH2 domain functional domain appears to be 8 residues, currently GGSGGGSG (SEQ ID NO: 160).
Peptide binding function and behavior of these constructs, relative to ‘free’ SH2 domain, using both fluorescence polarization (‘FP’) and surface plasmon resonance (‘SPR’) was explored. Constructs including 4 or 6 copies of SH2 (i.e. that have a ratio of 1 SH2 per 3 repeats or 1 SH2 per 2 repeats) display aggregation behavior, presumably due to steric crowding and subtle misfolding behavior (i.e. there's not quite enough room for them to all fit). These constructs, however, still display binding activity. Conversely, constructs including 1 or 2 SH2 domains (i.e. that display a ratio of 1 SH2 per 12 or 6 repeats) are well-behaved. Thus, it is believed that a minimum ratio of SH2 inserts to repeats is ‘6’ (i.e. 6 repeats per SH2 insert are required for assembly, folding and function) is an optimized format for these embodiments. As this indicates, functionalization of the cTRPs with particular functional domains will require some experimentation and optimization. This experimentation is well within the ordinary skill level in the art following the extensive teachings provided herein. A toroid with 3 copies of SH2 within a 12-repeat cTRP and another toroid with 4 copies of SH2 within a 12-repeat cTRP, where the SH2 copies alternate between the ‘top’ and ‘bottom’ surfaces of the toroid will also be created and analyzed.
cTRPs with 12 or 24 repeats and including variable numbers of the IL-2 cytokine (a larger protein including 130 residues) have also been created. First, variable numbers (2, 3 and 4) of IL-2 were incorporated into a cTRP scaffold including 12 repeats. The construct including 2 copies of IL-2 expressed and purified well, but size analysis using SEC indicates that the protein formed large, presumably aggregated protein assemblages. The constructs including 3 or 4 copies of IL-2 expressed but formed fully insoluble inclusion bodies and were not usable in further experiments. Thus, 4 or 6 IL-2 molecules were incorporated onto a split cTRP scaffold including 24 repeats total. The construct including 4 copies of IL-2 (including four protein subunits that each include 1 copy of IL-2 embedded in 6 protein repeats) has been expressed, purified, and its size determined using SEC and DLS. It is well behaved folds into the expected dimensions and size relative to the ‘naked’ cTRP including 24 unmodified repeats. The protein is currently undergoing SAXS analysis to further examine its dimensions. Furthermore, a monomeric, ‘single-chain’ version of the 24-repeat toroid harboring 4 copies of IL-2 for a comparative analysis of size, behavior and function has been created.
A construct including 4 copies of a single-chain MHC protein harboring an immunogenic peptide from cytomegalovirus, in a cTRP including 24 repeats has also been created (see
As will be understood by one of ordinary skill in the art, each embodiment disclosed herein can comprise, consist essentially of or consist of its particular stated element, step, ingredient or component. Thus, the terms “include” or “including” should be interpreted to recite: “comprise, consist of, or consist essentially of.” The transition term “comprise” or “comprises” means includes, but is not limited to, and allows for the inclusion of unspecified elements, steps, ingredients, or components, even in major amounts. The transitional phrase “consisting of” excludes any element, step, ingredient or component not specified. The transition phrase “consisting essentially of” limits the scope of the embodiment to the specified elements, steps, ingredients or components and to those that do not materially affect the embodiment. A material effect would cause a statistically-significant reduction in the handed repetitive nature of the alpha-helical structure as measured by RMSD. Within this context, a structure is repetitive when, following stacking and comparison, the distance between corresponding atoms of the stacked outer a-helix and the stacked inner a-helix is within 2 Å.
Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. When further clarity is required, the term “about” has the meaning reasonably ascribed to it by a person skilled in the art when used in conjunction with a stated numerical value or range, i.e. denoting somewhat more or somewhat less than the stated value or range, to within a range of ±20% of the stated value; ±19% of the stated value; ±18% of the stated value; ±17% of the stated value; ±16% of the stated value; ±15% of the stated value; ±14% of the stated value; ±13% of the stated value; ±12% of the stated value; ±11% of the stated value; ±10% of the stated value; ±9% of the stated value; ±8% of the stated value; ±7% of the stated value; ±6% of the stated value; ±5% of the stated value; ±4% of the stated value; ±3% of the stated value; ±2% of the stated value; or ±1% of the stated value.
Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements.
The terms “a,” “an,” “the” and similar referents used in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.
Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member may be referred to and claimed individually or in any combination with other members of the group or other elements found herein. It is anticipated that one or more members of a group may be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.
Certain embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Of course, variations on these described embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventor expects skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
Furthermore, numerous references have been made to patents, printed publications, journal articles and other written text throughout this specification (referenced materials herein). Each of the referenced materials are individually incorporated herein by reference in their entirety for their referenced teaching.
In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention may be utilized in accordance with the teachings herein. Accordingly, the present invention is not limited to that precisely as shown and described.
The particulars shown herein are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of various embodiments of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for the fundamental understanding of the invention, the description taken with the drawings and/or examples making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.
Definitions and explanations used in the present disclosure are meant and intended to be controlling in any future construction unless clearly and unambiguously modified in the following examples or when application of the meaning renders any construction meaningless or essentially meaningless. In cases where the construction of the term would render it meaningless or essentially meaningless, the definition should be taken from Webster's Dictionary, 3rd Edition or a dictionary known to those of ordinary skill in the art, such as the Oxford Dictionary of Biochemistry and Molecular Biology (Ed. Anthony Smith, Oxford University Press, Oxford, 2004).
This application is a continuation of U.S. patent application Ser. No. 16/802,377, filed Feb. 26, 2020, which is a continuation of U.S. patent application Ser. No. 15/780,397, filed May 31, 2018, now U.S. Pat. No. 10,597,466, which is a national phase of International Patent Application No. PCT/US2016/064732, filed Dec. 2, 2016, which claims priority to U.S. Provisional Patent Application No. 62/262,146 filed Dec. 2, 2015, the entire contents of each of which are incorporated by reference herein.
This invention was made with government support under grant numbers GM106117, GM049857, and GM115545 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 62262146 | Dec 2015 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16802377 | Feb 2020 | US |
| Child | 17361087 | US | |
| Parent | 15780397 | May 2018 | US |
| Child | 16802377 | US |
