Identification of discontinuous antigenic determinants on proteins based on shape complementarities

Journal of Molecular Recognition

Volumn 20, Issue 2, 2007, Pages 113-121

  Rapberger, Ronald ^a   Lukas, Arno ^b   Mayer, Bernd ^a,b  

^a UNIVERSITY OF VIENNA   (Austria)

^b Emergentec Biodevelopment GmbH   (Austria)

Author keywords

Antigen; B cell; Epitope; Molecular recognition; Prediction

Indexed keywords

EID: 34248594570     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.819     Document Type: Article

References (45)

1. Agadjanyan MG, Ghochikyan A, Petrushina I, Vasilevko V, Movsesyan N, Mkrtichyan M, Saing T, Cribbs DH. 2005. Prototype Alzheimer's disease vaccine using the immunodominant B cell epitope from beta-amyloid and promiscuous T cell epitope pan HLA DR-binding peptide. J. Immunol. 174: 1580-1586.
2. Agresti A. 1992. A survey of exact inference for contegency tables. Stat. Sci. 7: 131-153.
3. Alix AJ. 1999. Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine 18: 311-314.
4. Barlow DJ, Edwards MS, Thornton JM. 1986. Continuous and discontinuous protein antigenic determinants. Nature 322: 747-748.
5. Batori V, Friis EP, Nielsen H, Roggen EL. 2006. An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context. J. Mol. Recognit. 19: 21-29.
6. Beckmann C, Brittnacher M, Ernst R, Mayer-Hamblett N, Miller SI, Burns JL. 2005. Use of phage display to identify potential Pseudomonas aeruginosa gene products relevant to early cystic fibrosis airway infections. Infect. Immun. 73: 444-452.
7. Benjamin DC. 1995. B-cell epitopes: fact and fiction. Adv. Exp. Med. Biol. 386: 95-108.
8. Blythe MJ, Flower DR. 2005. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci. 14: 246-248.
9. Camacho CJ, Zhang C. 2005. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 21: 2534-2536.
10. Coley AM, Parisi K, Masciantonio R, Hoeck J, Casey JL, Murphy VJ, Harris KS, Batchelor AH, Anders RF, Foley M. 2006. The most polymorphic residue on Plasmodium falciparum apical membrane antigen 1 determines binding of an invasion-inhibitory antibody. Infect. Immun. 74: 2628-2636.
11. Dakappagari NK, Pyles J, Parihar R, Carson WE, Young DC, Kaumaya PT. 2003. A chimeric multi-human epidermal growth factor receptor-2 B cell epitope peptide vaccine mediates superior antitumor responses. J. Immunol. 170: 4242-4253.
12. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q, Knezevich C, Xie L, Chen L, Feng Z, Green RK, Flippen-Anderson JL, Westbrook J, Berman HM, Bourne PE. 2005. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33: D233-D237.
13. Gonzalez S, Vina L, Nazabal C, Chinea G, Caballero E, Musacchio A. 2000. B-cell epitope mapping of the Neisseria meningitidis P64k protein using overlapping peptides. Biotechnol. Appl. Biochem. 32(Part 1): 1-8.
14. Greenspan NS, Di Cera E. 1999. Defining epitopes: it's not as easy as it seems. Nat. Biotechnol. 17: 936-937.
15. Guthridge JM, Young K, Gipson MG, Sarrias MR, Szakonyi G, Chen XS, Malaspina A, Donoghue E, James JA, Lambris JD, Moir SA, Perkins SJ, Holers VM. 2001. Epitope mapping using the X-ray crystallographic structure of complement receptor type 2 (CR2)/C D21: identification of a highly inhibitory monoclonal antibody that directly recognizes the CR2-C3d interface. J. Immunol. 167: 5758-5766.
16. Harada K, Ikegami T. 2000. Evolution of specificity in an immune network. J. Theor. Biol. 203: 439-449.
17. Hopp TP, Woods KR. 1983. A computer program for predicting protein antigenic determinants. Mol. Immunol. 20: 483-489.
18. Horsfall AC, Hay FC, Soltys AJ, Jones MG. 1991. Epitope mapping. Immunol. Today 12: 211-213.
19. Huang J, Honda W. 2006. CED: a conformational epitope database. BMC Immunol. 7: 7-14.
20. Hubbard SJ, Thornton JM. 1993. 'NACCESS'. Computer Program, Department of Biochemistry and Molecular Biology, University College London.
21. Jameson BA, Wolf H. 1988. The antigenic index: a novel algorithm for predicting antigenic determinants. Comput. Appl. Biosci. 4: 181-186.
22. Jerne NK. 1960. Immunological speculations. Annu. Rev. Microbiol. 14: 341-358.
23. Krchnak V, Mach O, Maly A. 1989. Computer prediction of B-cell determinants from protein amino acid sequences based on incidence of beta turns. Methods Enzymol. 178: 586-611.
24. Kulkarni-Kale U, Bhosle S, Kolaskar AS. 2005. CEP: a conformational epitope prediction server. Nucleic Acids Res. 33: W168-W171.
25. Lee B, Richards FM. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55: 379-400.
26. Lundkvist A, Meisel H, Koletzki D, Lankinen H, Cifire F, Geldmacher A, Sibold C, Gott P, Vaheri A, Kruger DH, Ulrich R. 2002. Mapping of B-cell epitopes in the nucleocapsid protein of Puumala hantavirus. Viral Immunol. 15: 177-192.
27. Maiti R, Van Domselaar GH, Zhang H, Wishart DS. 2004. SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 32: W590-W594.
28. Mitchell JC, Kerr R, Ten Eyck LF. 2001. Rapid atomic density methods for molecular shape characterization. J. Mol. Graph. Model. 19: 325-330, 388-390.
29. Moreau V, Granier C, Villard S, Laune D, Molina F. 2006. Discontinuous epitope prediction based on mimotope analysis. Bioinformatics 22: 1088-1095.
30. Morris K. 2005. B-cell epitope booster for HIV vaccine hope. Lancet Infect. Dis. 5: 11.
31. Novotny J, Handschumacher M, Haber E, Bruccoleri RE, Carlson WB, Fanning DW, Smith JA, Rose GD. 1986. Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains). Proc. Natl. Acad. Sci. USA 83: 226-230.
32. Odorico M, Pellequer JL. 2003. BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit. 16: 20-22.
33. Padlan EA. 1996. X-ray crystallography of antibodies. Adv. Protein Chem. 49: 57-133.
34. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A. 2005. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 3: 379-381.
35. Pickersgill RW. 1988. A rapid method of calculating charge-charge interaction energies in proteins. Protein Eng. 2: 247-248.
36. Saha S, Bhasin M, Raghava GP. 2005. Bcipep: a database of B-cell epitopes. BMC Genomics 6: 79-85.
37. Sali A, Blundell TL. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
38. Schlessinger A, Ofran Y, Yachdav G, Rost B. 2006. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. 34: D777-D780.
39. Schreiber A, Humbert M, Benz A, Dietrich U. 2005. 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J. Comput. Chem. 26: 879-887.
40. Sollner J, Mayer B. 2006. Machine learning approaches for prediction of linear B-cell epitopes on proteins. J. Mol. Recognit. 19: 200-208.
41. Van Regenmortel MHV. 1986. Which structural features determine protein antigenicity? Trends Biochem. Sci. 11: 36-39.
42. Van Regenmortel MHV. 1996. Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods 9: 465-472.
43. Weichhart T, Horky M, Sollner J, Gangl S, Henics T, Nagy E, Meinke A, von Gabain A, Fraser CM, Gill SR, Hafner M, von Ahsen U. 2003. Functional selection of vaccine candidate peptides from Staphylococcus aureus whole-genome expression libraries in vitro. Infect. Immun. 71: 4633-4641.
44. Welling GW, Weijer WJ, van der Zee R, Welling-Wester S. 1985. Prediction of sequential antigenic regions in proteins. FEBS. Lett. 188: 215-218.
45. Westbrook J, Feng Z, Chen L, Yang H, Berman HM. 2003. The Protein Data Bank and structural genomics. Nucleic Acids Res. 31: 489-491.