Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A 02:01 allele

Molecular Immunology

Volumn 48, Issue 12-13, 2011, Pages 1461-1467

  Antunes, Dinler A ^a   Rigo, Maurício M ^a   Silva, Jader P ^a   Cibulski, Samuel P ^a   Sinigaglia, Marialva ^a   Chies, José A B ^a   Vieira, Gustavo F ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Cross reactivity; Hepatitis C virus; Immunogenicity; Structural bioinformatics

Indexed keywords

EPITOPE; HLA A ANTIGEN; T LYMPHOCYTE RECEPTOR; VIRUS PROTEIN;

ALLELE; ARTICLE; BIOINFORMATICS; COMPLEX FORMATION; COMPUTER MODEL; CROSS REACTION; CRYSTAL STRUCTURE; ELECTRICITY; GENOTYPE; HEPATITIS C VIRUS; IMMUNE RESPONSE; IMMUNOGENICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATIC ELECTRICITY; STRUCTURE ANALYSIS; VIRUS MUTATION; WILD TYPE;

ALLELES; AMINO ACID SEQUENCE; CD8-POSITIVE T-LYMPHOCYTES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HEPACIVIRUS; HEPATITIS C; HLA-A ANTIGENS; HUMANS; IMMUNITY, CELLULAR; MODELS, MOLECULAR; PRINCIPAL COMPONENT ANALYSIS; RECEPTORS, ANTIGEN, T-CELL; STATIC ELECTRICITY; VIRAL NONSTRUCTURAL PROTEINS;

HEPATITIS C VIRUS;

EID: 79957898384     PISSN: 01615890     EISSN: 18729142     Source Type: Journal    
DOI: 10.1016/j.molimm.2011.03.019     Document Type: Article

References (36)

1. Andrusier N., Mashiach E., Nussinov R., Wolfson H.J. Principles of flexible protein-protein docking. Proteins 2008, 73:271-289.
2. Antunes D.A., Vieira G.F., Rigo M.M., Cibulski S.P., Sinigaglia M., Chies J.A. Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment. PLoS One 2010, 5:e10353.
3. Bremel R.D., Homan E.J. An integrated approach to epitope analysis I: dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches. Immunome Res. 2010, 6:7.
4. Bremel R.D., Homan E.J. An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics. Immunome Res. 2010, 6:8.
5. Cucchiarini M., Kammer A.R., Grabscheid B., Diepolder H.M., Gerlach T.J., Gruner N., Santantonio T., Reichen J., Pape G.R., Cerny A. Vigorous peripheral blood cytotoxic T cell response during the acute phase of hepatitis C virus infection. Cell Immunol. 2000, 203:111-123.
6. Engler O.B., Schwendener R.A., Dai W.J., Wölk B., Pichler W., Moradpour D., Brunner T., Cerny A. A liposomal peptide vaccine inducing CD8+ T cells in HLA-A2.1 transgenic mice, which recognise human cells encoding hepatitis C virus (HCV) proteins. Vaccine 2004, 23:58-68.
7. Fytili P., Dalekos G.N., Schlaphoff V., Suneetha P.V., Sarrazin C., Zauner W., Zachou K., Berg T., Manns M.P., Klade C.S., Cornberg M., Wedemeyer H. Cross-genotype-reactivity of the immunodominant HCV CD8 T-cell epitope NS3-1073. Vaccine 2008, 26:3818-3826.
8. Gras S., Saulquin X., Reiser J.-B., Debeaupuis E., Echasserieau K., Kissenpfennig A., Legoux F., Chouquet A., Le Gorrec M., Machillot P., Neveu B., Thielens N., Malissen B., Bonneville M., Housset D. Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope. J. Immunol. 2009, 183:430-437. (Baltimore Md.: 1950).
9. Hiroishi K., Eguchi J., Ishii S., Hiraide A., Sakaki M., Doi H., Omori R., Imawari M. Immune response of cytotoxic T lymphocytes and possibility of vaccine development for hepatitis C virus infection. J. Biomed. Biotechnol. 2010, 263810. 2010.
10. Jorgensen J.L., Esser U., Fazekas de St Groth B., Reay P.A., Davis M.M. Mapping T-cell receptor-peptide contacts by variant peptide immunization of single-chain transgenics. Nature 1992, 355:224-230.
11. Kessels H.W., de Visser K.E., Tirion F.H., Coccoris M., Kruisbeek A.M., Schumacher T.N. The impact of self-tolerance on the polyclonal CD8+ T cell repertoire. J. Immunol. 2004, 172:2324-2331.
12. Korber B., LaBute M., Yusim K. Immunoinformatics comes of age. PLoS Comput. Biol. 2006, 2:e71.
13. Lechner F., Gruener N.H., Urbani S., Uggeri J., Santantonio T., Kammer A.R., Cerny A., Phillips R., Ferrari C., Pape G.R., Klenerman P. CD8+ T lymphocyte responses are induced during acute hepatitis C virus infection but are not sustained. Eur. J. Immunol. 2000, 30:2479-2487.
14. Petrey D., Honig B. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol. 2003, 374:492-509.
15. Prince A.M., Brotman B., Lee D.H., Pfahler W., Tricoche N., Andrus L., Shata M.T. Protection against chronic hepatitis C virus infection after rechallenge with homologous, but not heterologous, genotypes in a chimpanzee model. J. Infect. Dis. 2005, 192:1701-1709.
16. Rammensee H., Bachmann J., Emmerich N.P., Bachor O.A., Stevanovic S. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999, 50:213-219.
17. Rappuoli R. Reverse vaccinology. Curr. Opin. Microbiol. 2000, 3:445-450.
18. Rehermann B., Nascimbeni M. Immunology of hepatitis B virus and hepatitis C virus infection. Nat. Rev. Immunol. 2005, 5:215-229.
19. Rigo M., Antunes D., Vieira G., Chies J. MHC: Peptide Analysis: Implications on the Immunogenicity of Hantaviruses' N protein 2009, 5676. Springer, Berlin/Heidelberg, 160-163.
20. Rudolph M.G., Stanfield R.L., Wilson I.A. How TCRs bind MHCs, peptides, and coreceptors. Ann. Rev. Immunol. 2006, 24:419-466.
21. Schlaphoff V., Klade C.S., Jilma B., Jelovcan S.B., Cornberg M., Tauber E., Manns M.P., Wedemeyer H. Functional and phenotypic characterization of peptide-vaccine-induced HCV-specific CD8+ T cells in healthy individuals and chronic hepatitis C patients. Vaccine 2007, 25:6793-6806.
22. Soderholm J., Ahlen G., Kaul A., Frelin L., Alheim M., Barnfield C., Liljestrom P., Weiland O., Milich D.R., Bartenschlager R., Sallberg M. Relation between viral fitness and immune escape within the hepatitis C virus protease. Gut 2006, 55:266-274.
23. Thimme R., Bukh J., Spangenberg H.C., Wieland S., Pemberton J., Steiger C., Govindarajan S., Purcell R.H., Chisari F.V. Viral and immunological determinants of hepatitis C virus clearance, persistence, and disease. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:15661-15668.
24. Tian F., Lv F., Zhou P., Yang Q., Jalbout A.F. Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach. Prot. Pept. Lett. 2008, 15:1033-1043.
25. Tong J.C., Ren E.C. Immunoinformatics: current trends and future directions. Drug Discov. Today 2009, 14:684-689.
26. Trott O., Olson A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2009.
27. Turner S.J., Doherty P.C., McCluskey J., Rossjohn J. Structural determinants of T-cell receptor bias in immunity. Nat. Rev. Immunol. 2006, 6:883-894.
28. Vali B., Tohn R., Cohen M., Sakhdari A., Sheth P.M., Yue F.Y., Wong D., Kovacs C., Kaul R., Ostrowski M.A. Characterization of cross-reactive CD8+ T-cell recognition of HLA-A2-restricted HIV-Gag: SLYNTVATL and HCV-NS5b: ALYDVVSKL epitopes in individuals infected with Human Immunodeficiency and Hepatitis C Viruses. J. Virol. 2010, (JVI. 01743-10-).
29. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J. GROMACS: fast, flexible, and free. J. Comput. Chem. 2005, 26:1701-1718.
30. Vertuani S., Bazzaro M., Gualandi G., Micheletti F., Marastoni M., Fortini C., Canella A., Marino M., Tomatis R., Traniello S., Gavioli R. Effect of interferon-alpha therapy on epitope-specific cytotoxic T lymphocyte responses in hepatitis C virus-infected individuals. Eur. J. Immunol. 2002, 32:144-154.
31. Vieira G.F., Chies J.A. Immunodominant viral peptides as determinants of cross-reactivity in the immune system-can we develop wide spectrum viral vaccines?. Med. Hypotheses 2005, 65:873-879.
32. Vita R., Zarebski L., Greenbaum J., Emami a., Hoof H., Salimi I., Damle N., Sette R., Peters A.B. The immune epitope database 2.0. Nucleic acids Res. 2010, 38:D854-D862.
33. Wang S., Kennedy J.S., West K., Montefiori D.C., Coley S., Lawrence J., Shen S., Green S., Rothman A.L., Ennis F.A., Arthos J., Pal R., Markham P., Lu S. Cross-subtype antibody and cellular immune responses induced by a polyvalent DNA prime-protein boost HIV-1 vaccine in healthy human volunteers. Vaccine 2008, 26:1098-1110.
34. Wedemeyer H., He X.-S., Nascimbeni M., Davis A.R., Greenberg H.B., Hoofnagle J.H., Liang T.J., Alter H., Rehermann B. Impaired effector function of Hepatitis C Virus-Specific CD8+ T cells in chronic Hepatitis C Virus Infection. J. Immunol. 2002, 169:3447-3458.
35. Wedemeyer H., Mizukoshi E., Davis A.R., Bennink J.R., Rehermann B. Cross-reactivity between hepatitis C virus and Influenza A virus determinant-specific cytotoxic T cells. J. Virol. 2001, 75:11392-11400.
36. Yu C.I., Chiang B.-L. A new insight into hepatitis C vaccine development. J. Biomed. Biotechnol. 2010, 2010:548280.