Abstract
Crystallographic structures can be thought of as snapshots of molecules in action. A book of such structural snapshots would yield a “field guide” that contributed important information about the mechanisms of enzyme action, DNA control or immunological recognition. This contribution is perhaps best highlighted by the structure of the human class I molecule, HLA-A2, which resulted in the rethinking of the process of MHC restriction and T cell recognition.1 Prior to the structure, one popular model of MHC restriction suggested that viral proteins existed on the surface of cells adjacent to the class I molecule and were thus recognized jointly by T cells. However, the crystallographic solution (or snapshot) of the structure of HLA-A2.1 showed a large cleft in the surface of the protein that appeared to bind short peptides. This, taken with the evidence that soluble viral peptides could stimulate T cells2,3 was interpreted to mean that histocompatibility molecules present small peptides to T cells.1,4 Additional snapshots now seek to understand how these molecules bind diverse sets of peptides with nanomolar dissociation constants and half-lives measured in days.
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Bjorkman PJ, Saper MA, Samraoui B et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 1987; 329: 506–512.
Townsend ARM, Gotch FM, Davey J. Cytotoxic T cells recognize fragments of the influenza nucleoprotein. Cell 1985; 42: 457–467.
Shimonkevitz R, Colon S, Kappler JW et al. Antigen recognition by H-2 restricted T cells. A tryptic fragment of ovalbumin substitutes for processed antigen. J Immunol 1984; 133: 2067–2074.
Bjorkman PJ, Saper MA, Samraoui B et al. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 1987; 329: 512–5188.
Salter RD, Norment AM, Chen BP et al. Polymorphism in the n3 domain of HLA-A molecules affects binding to CD8. Nature 1989; 338: 345–347.
Rosenstein Y, Ratnofsky S, Burakoff SJ et al. Direct evidence for binding of CD8 to HLA class I antigens. J Exp Med 1989; 169: 149–160.
Cerundolo V, Tse, AGD, Salter RD et al. CD8 independence and specificity of cytotoxic T lymphocytes restricted by HLA-Aw68.1. Proceedings of the Royal Society London Series B Biological Sciences 1991; 244: 169–177.
Blue ML, Craig KA, Anderson P et al. Evidence for specific association between class I major histocompatibility antigens and the CD8 molecules of human suppressor/cytotoxic cells. Cell 1988; 54: 413–421.
Fremont DH, Matsumura M, Stura EA et al. Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb [see comments]. Science 1992; 257: 919–927.
Collins EJ, Garboczi DN, Karpusas MN et al. The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain. Proc Natl Acad Sci USA 1995; 92: 1218–1221.
Elliott T, Elvin J, Cerundolo V et al. Structural requirements for the peptide-induced change of free major histocompatibility complex class I heavy chains. Eur J Immunol 1992; 22: 2085–2091.
Jackson MR, Song ES, Yang Y et al. Empty and peptide-containing conformers of class I major histocompatibility complex molecules expressed in Drosophila melanogaster cells. Proc Natl Acad Sci USA 1992; 89: 12117–12121.
Olsen AC, Pedersen LO, Hansen AS et al. A quantitative assay to measure the interaction between immunogenic peptides and purified class I major histocompatibility complex molecules. Eur J of Immunol 1994; 24: 385–392.
Townsend A, Elliot T, Cerundolo V et al. Assembly of MHC class I molecules analyzed in vitro. Cell 1990; 62: 285–295.
Lehman-Grube F, Dralle H, Utermohlen O et al. MHC Class I molecule-restricted presentation of viral antigen in ßZ-microglobulin-deficient mice. J Immunol 1994; 94: 595–603.
Parker KC, DiBrino M, Hull L et al. The 32-microglobulin dissociation rate is an accurate measure of the stability of MHC class I heterotrimers, and depends on which peptide is bound. J Immunol 1992; 149: 1896–1904.
Fahnestock ML, Johnson JL, Feldman RMR et al. Effects of peptide length and composition on binding to an empty class I MHC heterodimer. Biochemistry 1994; 33: 8149–8158.
Falk K, Rotzchke O, Rammensee H-G. Cellular peptide composition governed by major histocompatibility complex class I molecules. Nature 1990; 351: 290–296.
Jardetzky TS, Lane WS, Robinson RA et al. Identification of self peptides bound to purified HLA-B27. Nature 1991; 353: 326–329.
Lowe J, Stock D, Jap B et al. Crystal structure of the 20S proteosome from the archaeon T. acidophilum at 3.4A resolution. Science 1995; 268: 533–539.
Momburg F, Neefles JJ, Hammerling GJ. Peptide selection by the MHCencoded TAP transporters. Cur Opin Immunol 1994; 6: 32–37.
Young AC, Zhang W, Sacchettini JC et al. The three-dimensional structure of H-2Db at 2.4A resolution: implications for antigen-determinant selection. Cell 1994; 76: 39–50.
Garrett TP, Saper MA, Bjorkman PJ et al. Specificity pockets for the side chains of peptide antigens in HLA- Aw68 [see comments]. Nature 1989; 342: 692–696.
Madden DR, Gorga JC, Strominger JL et al. The three-dimensional structure of HLA-B27 at 2.1A resolution suggests a general mechanism for tight peptide binding to MHC. Cell 1992; 70: 1035–1048.
Gorga JC, Madden DR, Prendergast JK et al. Crystallization and preliminary X-ray diffraction studies of the human major histocompatibility antigen HLA-B27. Proteins 1992; 12: 87–90.
Hunt DF, Henderson RA, Shabanowitz J et al. Characterization of peptides bound to the Class I MHC molecule HLA-A2.1 by mass spectrometry. Science 1992; 255: 1261–1263.
Stura EA, Matsumura M, Fremont DH et al. Crystallization of murine major histocompatibility complex class I H- 2Kb with single peptides. J Mol Biol 1992; 228: 975–982.
Parker KC, Carreno BM, Sestak L et al. Peptide binding to HLA-A2 and HLA-B27 isolated from E. coli: reconstitution of HLA-A2 and HLA-B27 heavy chain/ß2-microglobulin complexes requires specific peptides. J Biol Chem 1992; 267: 5451–5459.
Zhang W, Young AC, Imarai M et al. Crystal structure of the major histocompatibility complex class I H- 2Kb molecule containing a single viral peptide: implications for peptide binding and T cell receptor recognition. Proc Natl Acad Sci USA 1992; 89: 8403–8407.
Garboczi DN, Hung DT, Wiley DC. HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proc Natl Acad Sci USA 1992; 89: 3429–3433.
Madden DR, Garboczi DN, Wiley DC. The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2 [published erratum appears in Cell 1994 Jan 28;76(2):following 410]. Cell 1993; 75: 693–708.
Guo HC, Jardetzky TS, Garrett TP et al. Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle [see comments]. Nature 1992; 360: 364–366.
Chen Y et al. Naturally processed peptides longer than 9 amino acid residues bind to the class I MHC molecule HLA-A2.1 with high affinity and in different conformations. J Immunol 1994; 152: 2874–2881.
Collins EJ, Garboczi DN, Wiley DC. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 1994; 371: 626–629.
Bouvier M, Wiley DC. Importance of antigenic peptide N- and C-termini to the stability of class I MHC molecules. Science 1994; 265: 398–402.
Guo HC, Madden DR, Silver ML et al. Comparison of the P2 specificity pocket in three human histocompatibility antigens: HLA-A*6801, HLA-A*0201, and HLA-B*2705. Proc Natl Acad Sci USA 1993; 90: 8053–8057.
Latron F, Pazmany L, Morrison J et al. A critical role for conserved residues in the cleft of HLA-A2 in presentation of a nonapeptide to T cells. Science 1992; 257: 964–967.
Rojo S, Garcia F, Villadangos JA et al. Changes in the repertoire of peptides bound to HLA-B27 subtypes and to site-specific mutants inside and outside pocket B. J Exp Med 1993; 177: 613–620.
Colbert RA, Rowland JS, McMichael AJ et al. Allele-specific B pocket transplant in class I major histocompatibility complex protein changes requirement for anchor residue at P2 of peptide. Proc Natl Acad Sci USA 1993; 90: 6879–6883.
Engelhard V. Structure of peptides associated with class I and class II MHC molecules. Ann Rev Immunol 1994; 12: 181–207.
Rohren EM, Pease LR, Ploegh HL et al. Polymorphisms in pockets of major histocompatibility complex class I molecules influence peptide preference. J Exp Med 1993; 177: 1713–1721.
Rovero P et al. The importance of secondary anchor residue motifs of HLA class I proteins: a chemometric approach. Mol Immunol 1994; 31: 549–554.
Van Bleek GM, Nathenson SG. The structure of the antigen-binding groove of major histocompatibility complex class I molecules determines specific selection of self-peptides. Proc Natl Acad Sci USA 1991; 88: 11032–11036.
Ruppert J, Sidney J, Celis E et al. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 1993; 74: 929–937.
Saito Y, Peterson PA, Matsumura M. Quantitation of peptide anchor residue contributions to class I major histocompatibility complex molecule binding. J Biol Chem 1993; 268: 21309–21317.
Cerundolo V, Elliot T, Elvin J et al. The binding affinity and dissociation rates of peptides for class I major histocompatibility complex molecules. Eur J Immunol 1991; 21: 2069–2075.
Silver ML, Guo H-C, Strominger JL et al. Atomic structure of a human MHC molecule presenting an influenza virus peptide. Nature 1992; 360: 367–369.
Solheim JC, Carreno BM, Smith JD et al. Binding of peptides lacking consensus anchor residue alters H-2Ld serologic recognition. J Immunol 1993; 151: 5387–5397.
Brown JH, Jardetzky TS, Gorga JC et al. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1 [see comments]. Nature 1993; 364: 33–39.
Bakke O, Dobberstein B. MHC class II-associated invariant chain contains a sorting signal for endosomal compartments. Cell 1990; 63: 707–716.
Blum JS, Cresswell P. Role for intracellular proteases in the processing and transport of class II HLA antigens. Proc Natl Acad Sci USA 1988; 85: 3975–3979.
Lotteau V, Teyton L, Peleraux A et al. Intracellular transport of class II MHC molecules directed by invariant chain. Nature 1990; 348: 600–605.
Maric MA, Taylor MD, Blum JS. Endosomal aspartic proteinases are required for invariant-chain processing. Proc Natl Acad Sci USA 1994; 91: 2171–2175.
Odorizzi CG, Trowbridge IS, Xue L et al. Sorting signals in the MHC class II invariant chain cytoplasmic tail and transmembrane region determine trafficking to an endocytic processing compartment. J Cell Biol 1994; 126: 317–330.
Konig R, Huang L-Y, Germain RN. MHC Class II interaction with CD4 mediated by a region analogous to the MHC class I binding site for CD8 Nature 1992; 356: 796–798.
Cammarota G, Scheirle A, Takacs B et al. Identification of a CD4 binding site on the beta 2 domain of HLA-DR molecules. Nature 1992; 356: 799–801.
Chicz RM, Urban RG, Lane WS et al. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature 1992; 358: 764–768.
Rudensky AY, Preston-Hurlburt P, al-Ramadi BK et al. Truncation variants of peptides isolated from MHC class II molecules suggest sequence motifs. Nature 1992; 359: 429–431.
Stern LJ, Wiley DC. The human class II MHC protein HLA-DRI Assembles as empty 043 heterodimers in the absence of antigenic peptide. Cell 1992; 68: 465–477.
Stern LJ, Brown JH, Jardetzky TS et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 1994; 368: 215–221.
Alexander J et al. Functional consequences of engagement of the T cell receptor by low affinity ligands. J Immunol 1993; 150: 1–7.
O’Sullivan D et al. On the interaction of promiscuous antigenic peptides with different DR alleles. Identification of common structural motifs. J Immunol 1991; 147: 2663–2669.
Jardetzky TS, Gorga JC, Busch R et al. Peptide Binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO 1990; 9: 1797–1803.
Newcomb JR, Cresswell PJ. Characterization of endogenous peptides bond to purified HLA-DR molecules and their absence from invariant chain-associated alpha beta dimers J Immunol 1993; 150: 499–507.
Roche PA, Cresswell P. Invariant chain association with HLA-DR molecules inhibits immunogenic peptide binding Nature 1990; 345: 615–618.
Mellins E, Cameron P, Amaya M et al. A mutant human histocompatibility leukocyte antigen DR molecule associated with invariant chain peptides. Exp Med 1994; 179: 541–549.
Kozono H, White J, Clements J et al. Production of soluble MHC class II proteins with covalently bound single peptides. Nature 1994; 369: 151–154.
Marrack P, Blackman M, Kushnir E et al. The toxicity of staphlococcal enterotoxin B in mice is mediated by T cells. J Exp Med 1990; 171: 455–464.
Micusan VV, Thibodeau. Superantigens of microbial origin. J Semin Immunol 1993; 5: 3–11.
Marrack P, Winslow GM, Choi Y et al. The bacterial and mouse mammary tumor virus superantigens; two different families of proteins with the same functions. Immun Rev 1993; 131: 79–92.
Jardetzky TS, Brown JH, Gorga JC et al. Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Nature 1994; 368: 711–718.
Thibodeau J, Labreque N, Denis F et al. Binding sties for bacterial and endogenous retroviral superantigens can be dissociated on major histocompatibility complex class II molecules. J Exp Med 1994; 179: 1029–1034.
Choi Y, Lafferty JA, Clements JR et al. Selective expansion of T cells expressing V beta 2 in toxic shock syndrome. J Exp Med 1990; 172: 981–984.
Kim J, Urban RG, Strominger JL et al. Toxic shock syndrome toxin-1 complexed with a class II major histocompatibility molecule HLA-DR1. Science 1994; 266: 1870–1874.
Dellabona P, Peccoud J, Kappler J et al. Superantigens interact with MHC class II molecules outside of the antigen groove. Cell 1990; 62: 1115–1121.
Jorgenson JL, Reay PA, Ehrich EW et al. Molecular components of T cell recognition. Ann Rev Immun 1992; 10: 835–873.
Thibodeau J, Cloutier I, Lavoie PM et al. Subsets of HLA-DR1 molecules defined by SEB and TSST-1 binding. Science 1994; 266: 1874–1878.
Scholl PR, Diez A, Geha RS. Staphlococcal enterotoxin B and toxic shock toxin-1 bind to distinct sites on HLA-DR and HLA-DQ molecules. J Immunol 1989; 143: 2583–2588.
Chintagumpala MM, Mollick JA, Rich RR. Staphylococcal toxins bind to different sites on HLA-DR. J Immunol 1991; 147: 3876–3881.
Coppin HL, Carmichael P, Lombardi G et al. Position 71 in the alpha helix of the DR beta domain is predicted to influence peptide binding and plays a central role in allorecognition. Eur J Immunol 1993; 23: 343–349.
Brown JH, Jardetzky T, Saper M et al. A hypothetical model of the foreign antigen binding site of Class II histocompatibility molecules. Nature 1988; 332: 845–850.
Fremont DH, Stura EA, Matsumura M et al. Crystal structure of a H-2kb ovalbumin peptide complex in the major histocompatibility complex binding groove. Proc Natl Acad Sci USA 1995; 92: 2479–2483.
Carson M. Ribbon models of macromolecules. J Molec Graphics 1987; 5: 103–106.
Jones TA, Zou J-Y, Cowan SW et al. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst 1991; A47: 110–119.
Nicholls A, Sharp KA, Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991; 11: 281–296.
Huang CC, Pettersen EF, Klein TE. Conic: a fast renderer for space-filling moleculers with shadows. J Mol Graphics 1991; 9: 230–236.
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Collins, E.J. (1996). Crystallographic Analysis of Peptide Binding by Class I and Class II Major Histocompatibility Antigens. In: MHC Molecules: Expression, Assembly and Function. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-6462-7_8
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DOI: https://doi.org/10.1007/978-1-4684-6462-7_8
Publisher Name: Springer, Boston, MA
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