Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential

Vaccine

Volumn 25, Issue 43, 2007, Pages 7530-7539

  Parida, R ^a   Shaila, M S ^a   Mukherjee, S ^a   Chandra, N R ^a   Nayak, R ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Avian influenza; Influenza vaccine; T cell epitopes

Indexed keywords

ALANYLALANYLGLYCYLALANYLALANYLVALYLLYSYLGLYCYLVALINE; ALANYLPROLYLISOLEUCYLGLUTAMYLHISTIDYLISOLEUCYLALANYLSERYLMETHIONINE; ARGINYLARGINYLASPARAGINYLTYROSYLPHENYLALANYLTHREONYLALANYLGLUTAMYLVALINE; ARGINYLLEUCYLISOLEUCYLASPARTYLPHENYLALANYLLEUCYLLYSYLASPARTYLVALINE; ASPARAGINYLPROLYLTHREONYLLEUCYLLEUCYLPHENYLALANYLLEUCYLLYSYLVALINE; EPITOPE; GLUTAMINYLALANYLTYROSYLGLUTAMINYLLYSYLARGINYLMETHIONYLGLYCYLVALINE; GLUTAMYLARGINYLASPARAGINYLGLUTAMYLGLUTAMINYLGLYCYLGLUTAMINYLTHREONYL LEUCINE; INFLUENZA VACCINE; ISOLEUCYLARGINYLHISTIDYLGLUTAMYLASPARAGINYLARGINYLMETHIONYLVALYLLEUCINE; ISOLEUCYLGLUTAMINYLMETHIONYLCYSTEINYLTHREONYLGLUTAMYLLEUCYLLYSYLLEUCINE; ISOLEUCYLMETHIONYLPHENYLALANYLSERYLASPARAGINYLLYSYLMETHIONYLALANYL ARGININE; LEUCYLARGINYLHISTIDYLPHENYLALANYLGLUTAMINYLLYSYLASPARTYLALANYLLYSINE; LEUCYLLYSYLMETHIONYLPROLYLALANYLSERYLARGINYLTYROSYLLEUCINE; METHIONYLARGINYLMETHIONYLGLYCYLASPARTYLPHENYLALANYLHISTIDYLSERYLLEUCINE; METHIONYLGLUTAMINYLISOLEUCYLARGINYLGLYCYLPHENYLALANYLVALYLTYROSYL PHENYLALANINE; METHIONYLPHENYLALANYLSERYLASPARAGINYLLYSYLMETHIONYLALANYLARGINYLLEUCINE; PEPTIDE DERIVATIVE; PHENYLALANYLMETHIONYLLEUCYLMETHIONYLPROLYLLYSYLGLUTAMINYLLYSYLVALINE; PROTEOME; SERYLARGINYLTYROSYLLEUCYLTHREONYLASPARTYLMETHIONYLTHREONYLLEUCINE; TYROSYLLEUCYLLEUCYLALANYLTRYPTOPHYLLYSYLGLUTAMINYLVALYLLEUCINE; UNCLASSIFIED DRUG; VALYLALANYLTYROSYLMETHIONYLLEUCYLGLUTAMYLARGINYLGLUTAMYLLEUCINE; VALYLARGINYLASPARTYLGLUTAMINYLARGINYLGLYCYLASPARAGINYLVALYLLEUCINE; VALYLGLYCYLTHREONYLMETHIONYLVALYLMETHIONYLGLUTAMYLLEUCYLISOLEUCINE;

ARTICLE; DRUG BINDING; DRUG DESIGN; DRUG IDENTIFICATION; HLA SYSTEM; INFLUENZA VIRUS A H5N1; PRIORITY JOURNAL;

ANIMALS; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA VACCINES; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEOME;

EID: 34848901073     PISSN: 0264410X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vaccine.2007.08.044     Document Type: Article

References (33)

1. Thomas P.G., Keating R., Hulse-Post D.J., and Doherty P.C. Cell-mediated protection in influenza infection. Emerg Infect Dis 12 (2006) 48-54
2. Boni M.F., Gog J.R., Andreasen V., and Feldman M.W. Epidemic dynamics and antigenic evolution in a single season of influenza A. Proc Biol Sci 273 (2006) 1307-1316
3. Luke C.J., and Subbarao K. Vaccines for pandemic influenza. Emerg Infect Dis 12 (2006) 66-72
4. Fleury D., Barrere B., Bizebard T., Daniels R.S., Skehel J.J., Knossow M., et al. A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site. Nat Struct Biol 6 (1999) 530-534
5. Subbarao K., and Katz J.M. Influenza vaccines generated by reverse genetics. Curr Top Microbiol Immunol 283 (2004) 13-42
6. Webster R.G., Peiris M., Chen H., and Guan Y. H5N1 outbreaks and enzootic influenza. Emerg Infect Dis 12 (2006) 3-14
7. Kodihalli S., Justewicz D.M., Gubareva L.V., and Webster R.G. Selection of a single amino acid substitution in the hemagglutinin molecule by chicken eggs can render influenza A virus (H3) candidate vaccine ineffective. J Virol 69 (1995) 4888-4897
8. Katz J.M., and Webster R.G. Efficacy of inactivated influenza A virus (H3N2) vaccines grown in mammalian cells or embryonated eggs. J Infect Dis 160 (1989) 191-198
9. Alymova I.V., Kodihalli S., Govorkova E.A., Fanget B., and Gerdil C. Webster RG immunogenicity and protective efficacy in mice of influenza B virus vaccines grown in mammalian cells or embryonated chicken eggs. J Virol 72 (1998) 4472-4477
10. Palese P. Making better influenza virus vaccines?. Emerg Infect Dis 12 (2006) 61-65
11. Cox N.J., Tamblyn S.E., and Tam T. Influenza pandemic planning. Vaccine 21 (2003) 1801-1803
12. Webster R.G., Guan Y., and Peiris M. Characterization of H5N1 influenza viruses that continue to circulate in geese in southeastern China. J Virol 76 (2002) 118-126
13. Wan H., and Perez D.R. Quail carry sialic acid receptors compatible with binding of avian and human influenza viruses. Virology 346 (2006) 278-286
14. Korber B., LaBute M., and Yusim K. Immunoinformatics comes of age. PLoS Comput Biol 2 (2006) e71
15. Parker K.C., Bednarek M.A., and Coligan J.E. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152 (1994) 163-175
16. Rammensee H., Bachmann J., Emmerich N.P., Bachor O.A., and Stevanovic S. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50 (1999) 213-219
17. Reche P.A., Glutting J.P., and Reinherz E.L. Prediction of MHC class I binding peptides using profile motifs. Hum Immunol 63 (2002) 701-709
18. Singh H., and Raghava G.P. PROPRED: prediction of HLA-DR binding sites. Bioinformatics 17 (2001) 1236-1237
19. Reche P.A., Glutting J.P., Zhang H., and Reinherz E.L. Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 56 (2004) 405-419
20. Singh H., and Raghava G.P.S. PROPRED-I: prediction of promiscuous MHC class I binding sites. Bioinformatics 19 (2003) 1009-1014
21. Saha S., and Raghava G.P.S. Prediction of continuous B cell epitopes in an antigen using recurrent neural network. Proteins 65 (2006) 40-48
22. Peters B., Sidney J., and Sette A. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 3 (2005) e91
23. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D54 (1998) 905-921
24. Vani J., Shaila M.S., Chandra N.R., and Nayak R. A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of mycobacterium tuberculosis. Microbes Infect 8 (2006) 738-746
25. Holzhutter H.G., Frommel C., and Kloetzel P.M. A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J Mol Biol 286 (1999) 1251-1265
26. Lal G., Shaila M.S., and Nayak R. Recombinant idiotypic TCR beta chain immunization in mice generates antigen specific T cell response. Mol Immunol 43 (2006) 1549-1556
27. Chaitra M.G., Hariharaputran S., Chandra N.R., Shaila M.S., and Nayak R. Defining putative T cell epitopes from PE and PPE families of proteins of mycobacterium tuberculosis with vaccine potential. Vaccine 23 (2005) 1265-1272
28. Sencer D.J., and Millar J.D. Reflections on the 1976 swine flu vaccination program. Emerg Infect Dis 12 (2006) 29-33
29. Chen R., and Holmes E.C. Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol 23 (2006) 2336-2341
30. Vider-Shalit T., Raffaeli S., and Louzoun Y. Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome. Mol Immunol 44 (2007) 1253-1261
31. Lal G., Shaila M.S., and Nayak R. Activated mouse T cells downregulate, process and present their surface TCR to cognate anti-idiotypic CD4+ T cells. Immunol Cell Biol 84 (2006) 145-153
32. Nayak R., Mitra-Kaushik S., and Shaila M.S. Perpetuation of immunological memory: a relay hypothesis. Immunology 102 (2001) 387-395
33. Nayak R., Lal G., and Shaila M.S. Perpetuation of immunological memory: role of serum antibodies and accessory cells. Microbes Infect 7 (2005) 1276-1283