The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

Protein Engineering, Design and Selection

Volumn 26, Issue 10, 2013, Pages 599-609

  Kunik, Vered ^a   Ofran, Yanay ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

antibody antigen interactions; antigen binding regions; complementarity determining regions; epitopes

Indexed keywords

AMINO ACID COMPOSITIONS; ANTIBODY-ANTIGEN INTERACTIONS; ANTIGEN BINDING; COMPLEMENTARITY-DETERMINING REGIONS; EPITOPE PREDICTIONS; INDISTINGUISHABILITY; PROTEIN-PROTEIN INTERFACE; STABILIZING INTERACTIONS;

AMINO ACIDS; ANTIBODIES; CELL ENGINEERING;

EPITOPES;

AMINO ACID; EPITOPE;

AMINO ACID COMPOSITION; ANTIGEN ANTIBODY COMPLEX; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SURFACE PROPERTY;

ANTIBODY-ANTIGEN INTERACTIONS; ANTIGEN BINDING REGIONS; COMPLEMENTARITY DETERMINING REGIONS; EPITOPES;

ANTIBODIES; ANTIBODY SPECIFICITY; COMPUTATIONAL BIOLOGY; EPITOPES;

EID: 84885006229     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzt027     Document Type: Article

References (71)

1. Al-Lazikani, B., Lesk, A.M. and Chothia, C. (1997) J. Mol. Biol., 273, 927-948.
2. Almagro, J.C. (2004) J. Mol. Recognit., 17, 132-143.
3. Azad, R.K. and Lawrence, J.G. (2007) Nucleic Acids Res., 35, 4629-4639.
4. Barderas, R., Desmet, J., Timmerman, P., Meloen, R., Casal, J.I., et al. (2008) Proc. Natl Acad. Sci., 105, 9029-9034.
5. Barrios, Y., Jirholt, P. and Ohlin, M. (2004) J. Mol. Recognit., 17, 332-338.
6. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res., 28, 235-242.
7. Berzofsky, J.A. (1985) Science, 229, 932-940.
8. Birtalan, S., Zhang, Y., Fellouse, F.A., Shao, L., Schaefer, G. and Sidhu, S.S. (2008) J. Mol. Biol., 377, 1518-1528.
9. Blythe, M.J. and Flower, D.R. (2005) Protein Sci., 14, 246-248.
10. Burkovitz, A., Leiderman, O., Sela-Culang, I., Byk, G. and Ofran, Y. (2012) J. Immunol., 190, 2327-2334.
11. Capra, J.A. and Singh, M. (2007) Bioinformatics, 23, 1875-1882.
12. Chakrabarti, P. and Janin, J. (2002) Proteins, 47, 334-343.
13. Chothia, C. (1976) J. Mol. Biol., 105, 1-12.
14. Chothia, C. and Lesk, A.M. (1987) J. Mol. Biol., 196, 901-917.
15. Chothia, C., Lesk, A.M., Tramontano, A., et al. (1989) Nature, 342, 877-883.
16. Cohen, G.H., Silverton, E.W., Padlan, E.A., Dyda, F., Wibbenmeyer, J.A., Willson, R.C. and Davies, D.R. (2005) Acta Crystallogr. D, Biol. Crystallogr., 61, 628-633.
17. Collis, A.V., Brouwer, A.P. and Martin, A.C. (2003) J. Mol. Biol., 325, 337-354.
18. Crowley, P.B. and Golovin, A. (2005) Proteins, 59, 231-239.
19. Fellouse, F.A., Wiesmann, C. and Sidhu, S.S. (2004) Proc. Natl Acad. Sci. USA, 101, 12467-12472.
20. Fellouse, F.A., Barthelemy, P.A., Kelley, R.F. and Sidhu, S.S. (2006) J. Mol. Biol., 357, 100-114.
21. Greenbaum, J.A., Andersen, P.H., Blythe, M., et al. (2007) J. Mol. Recognit., 20, 75-82.
22. Grosse, I., Bernaola-Galván, P., Carpena, P., Román- Roldán, R., Oliver, J. and Stanley, H.E. (2002) Phys. Rev. E, Stat. Nonlin. Soft Matter Phys., 65, 041905.
23. Guerois, R., Nielsen, J.E. and Serrano, L. (2002) J. Mol. Biol., 320, 369-387.
24. Hubbard, S. and Thornton, J. (1992-6). http://www.bioinf.manchester.ac. uk/naccess/
25. Janin, J. and Chothia, C. (1990) J. Biol. Chem., 265, 16027-16030.
26. Jones, S. and Thornton, J.M. (1995) Prog. Biophys. Mol. Biol., 63, 31-65.
27. Jones, S. and Thornton, J.M. (1996) Proc. Natl Acad. Sci. USA, 93, 13-20.
28. Jones, S. and Thornton, J.M. (1997a) J. Mol. Biol., 272, 121-132.
29. Jones, S. and Thornton, J.M. (1997b) J. Mol. Biol., 272, 133-143.
30. Kabat, E.A., Wu, T.T., Bilofsky, H., Reid-Miller, M. and Perry, H. (1983) Natl Inst. Health, Bathesda.
31. Kawashima, S. and Kanehisa, M. (2000) Nucleic Acids Res., 28, 374.
32. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2008) Chem. Rev., 108, 1225-1244.
33. Kringelum, J.V., Nielsen, M., Padkjaer, S.B. and Lund, O. (2012) Mol. Immunol., 53, 24-34.
34. Kunik, V., Peters, B. and Ofran, Y. (2012a) PLoS Comput. Biol., 8, e1002388.
35. Kunik, V., Ashkenazi, S. and Ofran, Y. (2012b) Nucleic Acids Res., 40, W521-W524.
36. Kuroda, D., Shirai, H., Kobori, M. and Nakamura, H. (2008) Proteins, 73, 608-620.
37. Kuroda, D., Shirai, H., Jacobson, M.P. and Nakamura, H. (2012) Protein Eng. Des. Sel., 25, 507-521.
38. Laver, W.G., Air, G.M., Webster, R.G. and Smith-Gill, S.J. (1990) Cell, 61, 553-556.
39. Lefranc, M.P., Pommie, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc, G. (2003) Dev. Comp. Immunol., 27, 55-77.
40. Lin, J. (1991) IEEE Trans. Inf. Theory, 145, 145-151.
41. Lo Conte, L., Chothia, C. and Janin, J. (1999) J. Mol. Biol., 285, 2177-2198.
42. Lollier, V., Denery-Papini, S., Larre, C. and Tessier, D. (2011) Mol. Immunol., 48, 577-585.
43. MacCallum, R.M., Martin, A.C. and Thornton, J.M. (1996) J. Mol. Biol., 262, 732-745.
44. McCoy, A.J., Chandana Epa, V. and Colman, P.M. (1997) J. Mol. Biol., 268, 570-584.
45. Neuvirth, H., Raz, R. and Schreiber, G. (2004) J. Mol. Biol., 338, 181-199.
46. North, B., Lehmann, A. and Dunbrack, R.L., Jr (2011) J. Mol. Biol., 406, 228-256.
47. Novotny, J., Handschumacher, M., Haber, E., Bruccoleri, R.E., Carlson, W.B., Fanning, D.W., Smith, J.A. and Rose, G.D. (1986) Proc. Natl Acad. Sci. USA, 83, 226-230.
48. Ofran, Y. (2009) Prediction of Protein Interaction Sites. Computational Protein-Protein Interactions. Boca Raton: CRC Press.
49. Ofran, Y. and Rost, B. (2003) J. Mol. Biol., 325, 377-387.
50. Ofran, Y., Schlessinger, A. and Rost, B. (2008) J. Immunol., 181, 6230-6235.
51. Padlan, E.A., Abergel, C. and Tipper, J.P. (1995) FASEB J., 9, 133-139.
52. Ponomarenko, J.V. and Bourne, P.E. (2007) BMC Struct. Biol., 7, 64.
53. Raghunathan, G., Smart, J., Williams, J. and Almagro, J.C. (2012) J. Mol. Recognit., 25, 103-113.
54. Ravishankar, R.V., Chakravarti, D., Samina, L., Animesh, R. and Alpan, R. (2009) PLoS ONE, 4, e5344.
55. Rubinstein, N.D., Mayrose, I., Halperin, D., Yekutieli, D., Gershoni, J.M. and Pupko, T. (2008) Mol. Immunol., 45, 3477-3489.
56. Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F. and Serrano, L. (2005) Nucleic Acids Res., 33, W382-W388.
57. Sela-Culang, I., Alon, S. and Ofran, Y. (2012) J. Immunol., 189, 4890-4899.
58. Shannon, C.E. (1948) Bell Syst. Tech. J., 27, 379-423; see also pp. 623-656.
59. Sheinerman, F.B., Norel, R. and Honig, B. (2000) Curr. Opin. Struct. Biol., 10, 153-159.
60. Soga, S., Kuroda, D., Shirai, H., Kobori, M. and Hirayama, N. (2010) Protein Eng. Des. Sel., 23, 441-448.
61. Sun, J., Xu, T., Wang, S., Li, G., Wu, D. and Cao, Z. (2011) Immunome Res., 7, 1-11.
62. Van Regenmortel, M.H.V. (2009) Methods Mol. Biol., 524, 3-20.
63. Vargas-Madrazo, E., Lara-Ochoa, F. and Almagro, J.C. (1995) J. Mol. Biol., 254, 497-504.
64. West, A.P., Diskin, R., Nussenzweig, M.C. and Bjorkman, P.J. (2012) Proc. Natl Acad. Sci. USA, 109, E2083-E2090.
65. Wu, T.T. and Kabat, E.A. (1970) J. Exp. Med., 132, 211-250.
66. Wu, T.T., Johnson, G. and Kabat, E.A. (1993) Proteins, 16, 1-7.
67. Xu, D., Tsai, C.J. and Nussinov, R. (1997a) Protein Eng., 10, 999-1012.
68. Xu, D., Lin, S.L. and Nussinov, R. (1997b) J. Mol. Biol., 265, 68-84.
69. Zemlin, M., Klinger, M., Link, J., Zemlin, C., Bauer, K., Engler, J.A., Schroeder, H.W. and Kirkham, P.M. (2003) J. Mol. Biol., 334, 733-749.
70. Zhao, L. and Li, J. (2010) BMC Struct. Biol., 10(Suppl 1), S6.
71. Zhao, L., Wong, L. and Li, J. (2011) IEEE/ACM Trans. Comput. Biol. Bioinf., 8, 1483-1494.