Fine specificity of antigen binding to two class I major histocompatibility proteins (B*2705 and B*2703) differing in a single amino acid residue

Journal of Computer-Aided Molecular Design

Volumn 11, Issue 5, 1997, Pages 463-478

  Rognan, Didier ^a   Krebs, Stefan ^a   Kuonen, Oliver ^a   Lamas, José R ^b   López De Castro, José A ^b   Folkers, Gerd ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

Drug design; HLA B27; MHC; Molecular dynamics simulations

Indexed keywords

AMINO ACIDS; ANTIGENS; BIOINFORMATICS; COMPLEX NETWORKS; GENES; HYDROGEN BONDS; PEPTIDES;

AMINO ACID RESIDUES; ANTIGEN BINDING; CLASS I; DRUG DESIGN; DYNAMICS SIMULATION; HUMAN LEUCOCYTE ANTIGEN-B27; HUMAN LEUKOCYTE ANTIGEN; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR DYNAMIC SIMULATION; X-RAY STRUCTURE;

MOLECULAR DYNAMICS;

HLA B27 ANTIGEN; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; HYDROGEN BOND; IMMUNOLOGY; KINETICS; MOLECULAR GENETICS; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HLA-B27 ANTIGEN; HUMANS; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0031226806     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1007963901092     Document Type: Article

References (75)

1. Heemels, M.T. and Ploegh, H.L., Annu. Rev. Biochem., 64 (1995) 643.
2. Bjorkman, P.J., Saper, M.A., Samraoui, B., Bennet, W.S., Strominger, J.L. and Wiley, D.C., Nature, 329 (1987) 506.
3. Falk, K., Rötzschke, O., Stevanovic, S., Jung, G. and Rammensee, H.-G., Nature, 351 (1991) 290.
4. Spies, T., Bresnahan, M., Bahram, S., Arnold, D., Blank, G., Mellins, E., Pious, D. and DeMars, R., Nature, 348 (1990) 744.
5. Stern, L.J. and Wiley, D.C., Structure, 2 (1994) 245.
6. Madden, D.R., Annu. Rev. Immunol., 13 (1995) 587.
7. Corr, M., Boyd, L.F., Frankel, S.R., Kozlowski, S., Padlan, E.A. and Margulies, D.H., J. Exp. Med., 176 (1992) 1681.
8. Huczo, E.L., Bodnar, W.M., Benjamin, D., Sakaguchi, K., Zhu, NZ., Shabanowitz, J., Henderson, R.A., Appella, E., Hunt, D.F. and Engelhard, D., J. Immunol., 151 (1993) 2572.
9. Rognan, D., Scapozza, L., Folkers, G. and Daser, A., Biochemistry, 33 (1994) 11476.
10. Chelvanayagam, G., Jakobsen, I.B., Gao, X. and Easteal, S., Protein Eng., 9 (1996) 1151.
11. Brewerton, D.A., Hart, F.D., Nicholls, A. and Sturrock, R.D., Lancet 2, (1973) 994.
12. Todd, J.A., Bell, J.I. and McDevitt, H.O., Nature, 329 (1987) 599.
13. Wordsworth, B.P., Lanchbury, J.S., Sakkas, L.I., Welsh, K.I., Panayi, G.S. and Bell, J.I., Proc. Natl. Acad. Sci. USA, 86 (1989) 10049.
14. Hill, A.V.S., Elvin, J., Willis, A.C., Aidoo, M., Allsopp, C.E.M., Gotch, F.M., Gao, X.M., Takiguchi, M., Greenwood, B.M., Townsend, A.R.M., McMichael, A.J. and Whittle, H.C., Nature, 360 (1992) 434.
15. Benjamin, R. and Parham, P., Immunol. Today, 11 (1990) 137.
16. Kingsley, G. and Sieper, J., Immunol. Today, 14 (1993) 387.
17. López-Larrea, C., Sujirachato, K., Mehra, N.K., Chiewsilp, P., Isarangkura, D., Kanga, O., Dominguez, O., Coto, E., Peña, M., Setién, F. and Gonzales-Roces, S., Tissue Antigens, 45 (1995) 169.
18. Nasution, A.R., Mardjuadi, A., Kunmartini, S., Suryadhana, N.G., Setyohadi, B., Sudarsono, D., Lardy, N.M. and Feltkamp, T.E.W, J. Rheumatol., 24 (1997) 1111.
19. D'Amato, M., Fiorillo, M.T., Carcassi, C., Mathieu, A., Zuccarelli, A., Bitti, P.P., Tosi, R. and Sorrentino, R., Eur. J. Immunol., 25 (1995) 3199.
20. Jardetzky, T.S., Lane, W.S., Robinson, R.A., Madden, D.R. and Wiley, D.C., Nature, 353 (1991) 326.
21. Rojo, S., Garcia, F., Villadangos, J.A. and López de Castro, J.A., J. Exp. Med., 177 (1993) 613.
22. Rötzchke, O., Falk, K., Stevanovic, S., Gnau, V., Jung, G. and Rammensee, H.G., Immunogenetics, 39 (1994) 74.
23. Boisgérault, F., Tieng, V., Stolzenberg, M.C., Dulphy, N., Khalil, I., Tamouza, R., Charron, D. and Toubert, A., J. Clin. Invest., 98 (1996) 2764.
24. Garcia, F., Marina, A. and López de Castro, J.A., Tissue Antigens, 49 (1997) 215.
25. Garcia, F., Galocha, B., Villadangos, J.A., Lamas, J.R., Albar, J.P., Marina, A. and López de Castro, J.A., Tissue Antigens, 49 (1997) 580.
26. Fiorillo, M.T., Meadows, L., D'Amato, M., Shabanowitz, J., Hunt, D.F., Apella, E. and Sorrentino, R., Eur. J. Immunol., 27 (1997) 368.
27. Parker, K.C., Biddison, W.E. and Coligan, J.E., Biochemistry, 33 (1994) 7736.
28. Villadangos, J.A., Galocha, B., Garcia, F., Albar, J.P. and López de Castro, J.A., Eur. J. Immunol., 25 (1995) 2370.
29. Galocha, B., Lamas, J.R., Villadangos, J.A., Albar, J.P. and López de Castro, J.A., Tissue Antigens, 48 (1996) 509.
30. Raghavan, M., Lebron, J., Johnson, J. and Bjorkman, P., Protein Sci., 5 (1996) 2080.
31. Madden, D.R., Gorga, J.C., Strominger, J.L. and Wiley, D.C., Nature, 353 (1991) 321.
32. Madden, D.R., Gorga, J.C., Strominger, J.L. and Wiley, D.C., Cell, 70 (1992) 1035.
33. López, D., García-Hoyo, R. and López de Castro, J.A., J. Immunol., 152 (1994) 5557.
34. Villadangos, J.A., Galocha, B., García-Hoyo, R., López, D., Garcia, F. and López de Castro, J.A., Eur. J. Immunol., 24 (1994) 2548.
35. Colbert, R.A., Rowland-Jones, S.L., McMichael, A.J. and Frelinger, J.A., Immunity, 1 (1994) 121.
36. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr., E.F., Brice, M.D., Rodgers, J.M., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
37. Rognan, D., Zimmermann, N., Jung, G. and Folkers, G., Eur. J. Biochem., 208 (1992) 101.
38. Rognan, D., Scapozza, L., Folkers, G. and Daser, A., Proc. Natl. Acad. Sci. USA, 92 (1995) 753.
39. Collins, E.J., Garboczi, D.N., Karpusas, M.N. and Wiley, D.C., Proc. Natl. Acad. Sci. USA, 92 (1995) 1218.
40. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L., J. Chem. Phys., 70 (1983) 926.
41. Pearlman, D.A., Case, D.A., Caldwell, J.C., Seibel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A., AMBER 4.0, University of California, San Francisco, CA, U.S.A., 1992.
42. Besler, B.H., Merz, K.M. and Kollman, P.A., J. Comput. Chem., 11 (1990) 431.
43. SYBYL, release 6.2, TRIPOS Associates Inc., St. Louis, MO, U.S.A.
44. Stewart, J.J.P., J. Comput.-Aided Mol. Design, 4 (1990) 1.
45. Dewar, M.J.S. and Thiel, W., J. Am. Chem. Soc., 99 (1977) 4899.
46. Ryckaert, J.P., Cicotti, G. and Berendsen, H.J.C., J. Comput. Phys., 23 (1977) 327.
47. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R., J. Chem. Phys., 81 (1984) 3684.
48. Klapper, I., Hagstrom, R., Fine, R., Sharp, K. and Honig, B., Proteins Struct. Fund. Genet., (1986) 47.
49. Warwicker, J. and Watson, H.C., J. Mol. Biol., 157 (1982) 671.
50. Gilson, M.K. and Honig, B., Proteins Struct. Funct. Genet., 4 (1988) 7.
51. Gilson, M.K., Sharp, K. and Honig, B., J. Comput. Chem., 9 (1988) 327.
52. Ljunggren, H.G., Stam, N.J., Ohlen, C., Neefjes, J.J., Hoglund, P., Heemels, M.T., Bastin, J., Schumacher, T.N., Townsend, A., Karre, K. and Ploegh, H.L., Nature, 46 (1990) 476.
53. Ellis, S.A., Taylor, C. and McMichael, A., Hum. Immunol., 5 (1982) 49.
54. van Gunsteren, W.F. and Berendsen, H.J.C., Angew. Chem., Int. Ed. Engl., 29 (1990) 992.
55. Madden, D.R., Garboczi, D.N. and Wiley, D.C., Cell, 75 (1993) 693.
56. 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. and Jones, E.Y., J. Exp. Med., 184 (1996) 2279.
57. Rovero, P., Vigano, S., Pegorado, S., Revoltella, R., Riganelli, D., Fruci, D., Greco, G., Butler, R. and Tanigaki, N., J. Pept. Sci., 1 (1995) 266.
58. Brunne, R.M., Berndt, K.D., Güntert, P., Wüthrich, K. and van Gunsteren, W.F., Proteins Struct. Funct. Genet., 23 (1995) 49.
59. Fox, T. and Kollman, P.A., Proteins Struct. Funct. Genet., 25 (1996) 315.
60. Gallego, J., Ortiz, A.R., de Pascual-Teresa, B. and Gago, F., J. Comput.-Aided Mol. Design, 11 (1997) 114.
61. Taylor, N.R. and von Itzstein, M., J. Comput.-Aided Mol. Design, 10 (1996) 233.
62. Bash, P.A., Singh, U.C., Langridge, R. and Kollman, P.A., Science, 236 (1987) 564.
63. Garcia, F., Marina, A., Albar, J.P. and López de Castro, J.A., Tissue Antigens, 49 (1997) 23.
64. Guichard, G., Calbo, S., Muller, S., Kourilsky, P., Briand, J.-P. and Abastado, J.-P., J. Biol. Chem., 270 (1995) 26057.
65. Guichard, G., Connan, F., Graff, R., Ostankovitch, M., Muller, S., Guillet, J.-G, Choppin, F. and Briand, J.-P., J. Med. Chem., 39 (1996) 2030.
66. Garboczi, D.N., Ghosh, P., Utz, U., Fan, Q.R., Biddison, W.E. and Wiley, D.C., Nature, 384 (1996) 134.
67. Weiss, G.A., Collins, E.J., Garboczi, D.N., Wiley, D.C. and Schreiber, S.L., Chem. Biol., 2 (1995) 401.
68. Bouvier, M. and Wiley, D.C., Proc. Natl. Acad. Sci. USA, 93 (1996) 4583.
69. Adorini, L., Muller, S., Cardinaux, F., Lehmann, P.V., Falcioni, F. and Nagy, Z.A., Nature, 334 (1988) 623.
70. De Magistris, M.T., Alexander, J., Coggeshall, M., Altman, A., Gaeta, F.C.A., Grey, H.M. and Sette, A., Cell, 68 (1992) 625.
71. Rognan, D., Habilitationsschrift, ETH Zürich, Zürich, Switzerland, 1997.
72. Saper, M.A., Bjorkman, P.J. and Wiley, D.C., J. Mol. Biol., 219 (1991) 277.
73. Kraulis, P.J., J. Appl. Crystallogr., 24 (1991) 846.
74. Merritt, E.A. and Murphy, M.E.P., Acta Crystallogr., D50 (1994) 869.
75. Connolly, M.J., J. Appl. Crystallogr., 16 (1983) 548.