Towards the MHC-peptide combinatorics

Human Immunology

Volumn 62, Issue 5, 2001, Pages 539-556

  Kangueane, Pandjassarame ^a   Sakharkar, Meena K ^a   Kolatkar, Prasanna R ^a,b   Ren, Ee Chee ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

Binding pattern; Binding value; MHC peptide interface; Residue preference

Indexed keywords

HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; MAJOR HISTOCOMPATIBILITY ANTIGEN;

ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; GENE SEQUENCE; GENETIC POLYMORPHISM; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING;

ANIMALS; DATABASES, FACTUAL; HUMANS; HYDROGEN BONDING; MAJOR HISTOCOMPATIBILITY COMPLEX; MICE; PEPTIDES; PROTEIN BINDING;

EID: 0035020158     PISSN: 01988859     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0198-8859(01)00219-1     Document Type: Article

References (74)

1. Sette A., Nepom G.T. Antigen recognition. Curr Opin Immunol. 12:2000;77.
2. Abbas A.K., Janeway C.A. Immunology improving on nature in the twenty first century . Cell. 100:2000;129.
3. Abrams S.I., Schlom J. Rational antigen modification as a strategy to upregulate or downregulate antigen recognition. Curr Opin Immunol. 12:2000;85.
4. Pamer E., Cresswell P. Mechanisms of MHC class I restricted antigen processing Annu . Rev. Immunol. 16:1998;323.
5. Jensen P.E. Peptide binding and antigen presentation by class II histocompatibility glycoproteins. Biopolymers. 43:1997;303.
6. Joshi R.V., Zarutslie J.A., Stern L.J. A three step kinetic mechanism for peptide binding to MHC class II proteins. Biochemistry. 39:2000;3751.
7. Kasson P.M., Rabinowitz J.D., Schmitt L., Davis M.M., McConnell H.M. Kinetics of peptide binding to the class II MHC protein I-Ek. Biochemistry. 39:2000;1048.
8. Natarajan S.K., Assadi M., Nasseri S.S. Stable peptide binding to MHC class II molecule is rapid and is determined by a receptive conformation shaped by prior association with low affinity peptides. J Immunol. 162:1999;4030.
9. Springer S., Doring K., Skipper J.C., Townsend A.R., Cerundolo V. Fast association rates suggest a conformational change in the MHC class I molecule H-2Db upon peptide binding. Biochemistry. 37:1998;3001.
10. Batalia M.A., Collins E.J. Peptide binding by class I and class II MHC molecules. Biopolymers. 43:1997;281.
11. Bodmer J.G., Marsh S.G.E., Albert E.D., Bodmer W.F., Bontrop R.E., Dupont B., Erlich H.A., Hansen J.A., Mach B., Mayr W.R., Parham P., Petersdorf E.W., Sasazuki T., Schreuder G.M., Strominger J.L., Svejgaard A., Terasaki P.I. Nomenclature for factors of the HLA system, 1998. Tissue Antigens. 53:1999;407.
12. http://www.anthonynolan.org.uk.
13. http://www.ebi.ac.uk/imgt/hla.
14. Zhang C., Anderson A., DeLisi C. Structural principles that govern the peptide binding motifs of class I MHC molecules. J Mol Biol. 281:1998;929.
15. Buus S. Description and prediction of peptide-MHC binding the "human MHC project." Curr Opin Immunol. 11:1999;209.
16. Pinilla C., Martin R., Gran B., Appel J.R., Boggiano C., Wilson D.B., Houghten R.A. Exploring immunological specificity using synthetic peptide combinatorial libraries. Curr Opin Immunol. 11:1999;193.
17. Krebs S., Rognan D. From peptides to peptidomimetics design of nonpeptide ligands for major histocompatibility proteins . Pharm Acta Helv. 73:1998;173.
18. The MHC Sequencing Consortium: Complete sequence and gene map of a human major histocompatibility complex. Nature 401:921, 1999.
19. Altuvia Y., Sette A., Sidney J., Southwood S., Margalit H. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum Immunol. 58:1997;1.
20. Schueler-Furman O., Elber R., Margalit H. Knowledge-based structure prediction of MHC class I bound peptides a study of 23 complexes . Fold Des. 3:1998;549.
21. Kangueane P., Sakharkar M.K., Lim K.S., Hao H., Lin K., Chee R.E., Kolatkar P.R. Knowledge-based grouping of modeled HLA peptide complexes. Hum Immunol. 6:2000;460.
22. Milik M., Sauer D., Brunmark A.P., Yuan L., Vitiello A., Jackson M.R., Peterson P.A., Skolnick J., Glass C.A. Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nat Biotechnol. 16:1998;753.
23. Honeyman M.C., Brusic V., Stone N.L., Harrison L.C. Neural network-based prediction of candidate T-cell epitopes. Nat Biotechnol. 16:1998;966.
24. Mamitsuka H. Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models. Proteins. 33:1998;460.
25. Parker K.C., Shields M., DiBrino M., Brooks A., Coligan J.E. Peptide binding to MHC class I molecules implications for antigenic peptide prediction . Immunol Res. 14:1995;34.
26. Schafer J.R., Jesdale B.M., George J.A., Kouttab N.M., De Groot A.S. Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix. Vaccine. 16:1998;1880.
27. Lo Conte L., Ailey B., Hubbard T.J., Brenner S.E., Murzin A.G., Chothia C. SCOP a structural classification of proteins database . Nucleic Acids Res. 28:2000;257.
28. Brenner S.E., Barken D., Levitt M. The PRESAGE database for structural genomics. Nucleic Acids Res. 27:1999;251.
29. Jones S., Thornton J.M. Principles of protein-protein interactions. Proc Natl Acad Sci USA. 93:1996;13.
30. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235.
31. http://www.rcsb.org/pdb.
32. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.E., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The protein data bank a computer-based archival file for macromolecular structures . J Mol Biol. 112:1977;535.
33. Madden D.R., Garboczi D.N., Wiley D.C. The antigenic identity of peptide-MHC complexes a comparison of the conformations of five viral peptides presented by HLA-A2 . Cell. 75:1993;693.
34. Gao G.F., Tormo J., Gerth U.C., Wyer J.R., McMichael A.J., Stuart D.I., Bell J.I., Jones E.Y., Jakobsen B.K. Crystal structure of the complex between human CD8 alpha (alpha) and HLA-A2. Nature. 387:1997;630.
35. Garboczi D.N., Ghosh P., Utz U., Fan Q.R., Biddison W.E., Wiley D.C. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature. 384:1996;134.
36. Ding Y.H., Smith K.J., Garboczi D.N., Utz U., Biddison W.E., Wiley D.C. Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. Immunity. 8:1998;403.
37. Zhao R., Loftus D.J., Appella E., Collins E.J. Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry. J Exp Med. 189:1999;359.
38. Bouvier M., Guo H.C., Smith K.J., Wiley D.C. Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino or carboxyl-terminal group substituted by a methyl group. Proteins. 33:1998;97.
39. Collins E.J., Garboczi D.N., Wiley D.C. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature. 371:1994;626.
40. Collins E.J., Garboczi D.N., Karpusas M.N., Wiley D.C. 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. 92:1995;1218.
41. Reid S.W., McAdam S., Smith K.J., Klenerman P., O'Callaghan C.A., Harlos K., Jakobsen B.K., McMichael A.J., Bell J.I., Stuart D.I., Jones E.Y. Antagonist HIV-1 Gag peptides induce structural changes in HLA B8. J Exp Med. 184:1996;2279.
42. Madden D.R., Gorga J.C., Strominger J.L., Wiley D.C. The three-dimensional structure of HLA-B27 at 2 1 A resolution suggests a general mechanism for tight peptide binding to MHC . Cell. 70:1992;1035.
43. Smith K.J., Reid S.W., Stuart D.I., McMichael A.J., Jones E.Y., Bell J.I. An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501. Immunity. 4:1996;203.
44. Menssen R., Orth P., Ziegler A., Saenger W. Decamer like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus. J Mol Biol. 285:1999;645.
45. Smith K.J., Reid S.W., Harlos K., McMichael A.J., Stuart D.I., Bell J.I., Jones E.Y. Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Immunity. 4:1996;215.
46. Ghendler Y., Teng M.K., Liu J.H., Witte T., Liu J., Kim K.S., Kern P., Chang H.C., Wang J.H., Reinherz E.L. Differential thymic selection outcomes stimulated by focal structural alteration in peptide/major histocompatibility complex ligands. Proc Natl Acad Sci USA. 95:1998;10061.
47. Fremont D.H., Matsumura M., Stura E.A., Peterson P.A., Wilson I.A. Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. Science. 257:1992;919.
48. Speir J.A., Abdel-Motal U.M., Jondal M., Wilson I.A. Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL. Immunity. 10:1999;51.
49. Fremont D.H., Stura E.A., Matsumura M., Peterson P.A., Wilson I.A. Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Proc Natl Acad Sci USA. 92:1995;2479.
50. Zhao R., Loftus D.J., Appella E., Collins E.J. Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry. J Exp Med. 189:1999;359.
51. Glithero A., Tormo J., Haurum J.S., Arsequell G., Valencia G., Edwards J., Springer S., Townsend A., Pao Y.L., Wormald M., Dwek R.A., Jones E.Y., Elliott T. Crystal structures of two H-2Db/glycopeptide complexes suggest a molecular basis for CTL cross-reactivity. Immunity. 10:1999;63.
52. Achour A., Persson K., Harris R.A., Sundback J., Sentman C.L., Lindqvist Y., Schneider G., Karre K. The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-110 at 2 4 A resolution: implications for T cell and NK cell recognition . Immunity. 9:1998;199.
53. Speir J.A., Garcia K.C., Brunmark A., Degano M., Peterson P.A., Teyton L., Wilson I.A. Structural basis of 2C TCR allorecognition of H-2Ld peptide complexes. Immunity. 8:1998;553.
54. Murthy V.L., Stern L.J. The class II MHC protein HLA-DR1 in complex with an endogenous peptide implications for the structural basis of the specificity of peptide binding . Structure. 5:1997;1385.
55. Stern L.J., Brown J.H., Jardetzky T.S., Gorga J.C., Urban R.G., Strominger J.L., Wiley D.C. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature. 368:1994;215.
56. Jardetzky T.S., Brown J.H., Gorga J.C., Stern L.J., Urban R.G., Chi Y.I., Stauffacher C., Strominger J.L., Wiley D.C. Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Nature. 368:1994;711.
57. Smith K.J., Pyrdol J., Gauthier L., Wiley D.C., Wucherpfennig K.W. Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein. J Exp Med. 188:1998;1511.
58. Ghosh P., Amaya M., Mellins E., Wiley D.C. The structure of an intermediate in class II MHC maturation CLIP bound to HLA-DR3 . Nature. 378:1995;457.
59. Dessen A., Lawrence C.M., Cupo S., Zaller D.M., Wiley D.C. X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II. Immunity. 7:1997;473.
60. Scott C.A., Peterson P.A., Teyton L., Wilson I.A. Crystal structures of two I-Ad-peptide complexes reveal that high affinity can be achieved without large anchor residues. Immunity. 8:1998;319.
61. Lee B., Richard F.M. The interpretation of protein structures estimation of static accessibility . J Mol Biol. 55:1971;379.
62. Laskowski RA: SURFNET computer-program. London: Department of Biochemistry and Molecular Biology, University College, 1991.
63. Laskowski R.A. SURFNET a program for visualizing molecular surfaces, cavities and intermolecular interactions . J Mol Graph. 13:1995;323.
64. McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 238:1994;777.
65. Rammensee H.G., Friede T., Stevanoviic S. MHC ligands and peptide motifs first listing . Immunogenetics. 41:1995;178.
66. Jones D.T., Thornton J.M. Potential energy functions for threading. Curr Opin Struct Biol. 6:1996;210.
67. Rognan D., Lauemoller S.L., Holm A., Buus S., Tschinke V. Predicting binding affinities of protein ligands from three-dimensional models application to peptide binding to class I major histocompatibility proteins . J Med Chem. 42:1999;4650.
68. Service R.F. Structural genomics offers high-speed look at proteins. Science. 287:2000;1954.
69. Sette A., Sidney J., del Guercio M.F., Southwood S., Ruppert J., Dahlberg C., Grey H.M., Kubo R.T. Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays. Mol Immunol. 31:1994;813.
70. Lauvau G., Kakimi K., Niedermann G., Ostankovitch M., Yotnda P., Firat H., Chisari F.V., van Endert P.M. Human transporters associated with antigen processing (TAPs) select epitope precursor peptides for processing in the endoplasmic reticulum and presentation to T cells. J Exp Med. 190:1999;1227.
71. Gianfrani C., Oseroff C., Sidney J., Chesnut R.W., Sette A. Human memory CTL response specific for influenza A virus is broad and multispecific. Hum Immunol. 61:2000;438.
72. Livingston B.D., Crimi C., Fikes J., Chesnut R.W., Sidney J., Sette A. Immunization with the HBV core 18-27 epitope elicits CTL responses in humans expressing different HLA-A2 supertype molecules. Hum Immunol. 60:1999;1013.
73. Chen W., Khilko S., Fecondo J., Margulies D.H., McCluskey J. Determinant selection of major histocompatibility complex class I-restricted antigenic peptides is explained by class I-peptide affinity and is strongly influenced by nondominant anchor residues. J Exp Med. 180:1994;1471.
74. Rechenmann F. From data to knowledge. Bioinformatics. 16:2000;411.