Knowledge-based virtual screening of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus genome

Journal of Theoretical Biology

Volumn 281, Issue 1, 2011, Pages 133-139

  Bi, Jianjun ^a   Yang, Huilan ^a   Yan, Huacheng ^a   Song, Rengang ^b   Fan, Jianyong ^a  

^a GUANGZHOU GENERAL HOSPITAL OF GUANGZHOU MILITARY COMMAND   (China)

^b SHENZHEN PEOPLE'S HOSPITAL   (China)

Author keywords

Affinity; Binding mode; Free energy analysis

Indexed keywords

ALANYLLEUCYLLEUCYLGLUTAMYLASPARTYLPROLYLVALYLGLYCYLTHREONINE; ARGINYLLEUCYLGLYCYLALANYLVALYLISOLEUCYLLEUCYLPHENYLALANYLVALINE; ASPARAGINYLLEUCYLTHREONYLISOLEUCYLALANYLTRYPTOPHANYLPHENYLALANYLARGINYLMETHIONINE; EPITOPE; GLYCOPROTEIN D; GLYCOPROTEIN K; HERPES SIMPLEX VACCINE; HLA A ANTIGEN; ISOLEUCYLLEUCYLPHENYLALANYLVALYLVALYLISOLEUCYLVALYLGLYCYLLEUCINE; ISOLEUCYLTHREONYLALANYLTYROSYLGLYCYLLEUCYLVALYLLEUCYLVALINE; LEUCYLLEUCYLPROLYLPROLYLGLUTAMYLLEUCYLSERYLGLUTAMYLTHREONINE; LEUCYLMETHIONYLHISTIDYLALANYLPROLYLALANYLPHENYLALANYLGLUTAMYLTHREONINE; PHENYLALANYLISOLEUCYLPROLYLGLUTAMYLASPARAGINYLGLUTAMINYLARGINYLTHREONYLVALINE; SERYLLEUCYLPROLYLISOLEUCYLTHREONYLVALYLTYROSYLTYROSYLALANINE; UNCLASSIFIED DRUG; VALYLLEUCYLLEUCYLASPARAGINYLALANYLPROLYLSERYLGLUTAMYLALANINE; VALYLVALYLISOLEUCYLVALYLGLYCYLLEUCYLHISTIDYLGLYCYLVALINE; VIRUS GLYCOPROTEIN;

DETECTION METHOD; GENOME; GENOMICS; KNOWLEDGE BASED SYSTEM; MUTATION; PEPTIDE; PREDICTION;

AMINO ACID SEQUENCE; ANTIGEN RECOGNITION; ARTICLE; BINDING AFFINITY; CD8+ T LYMPHOCYTE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG POTENCY; EPITOPE MAPPING; GENOME ANALYSIS; HERPES SIMPLEX VIRUS; KNOWLEDGE BASE; MOLECULAR MECHANICS; OPEN READING FRAME; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROCESS DEVELOPMENT; SCORING SYSTEM; SCREENING; STRUCTURE ANALYSIS; VACCINE PRODUCTION; VIRTUAL REALITY; VIRUS GENOME; VIRUS MUTATION;

AMINO ACID SEQUENCE; CALIBRATION; CD8-POSITIVE T-LYMPHOCYTES; CRYSTALLOGRAPHY, X-RAY; EPITOPES, T-LYMPHOCYTE; GENOME, VIRAL; HERPESVIRUS 1, HUMAN; HLA-A ANTIGENS; KNOWLEDGE; LINEAR MODELS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; OPEN READING FRAMES; PEPTIDES; THERMODYNAMICS; USER-COMPUTER INTERFACE; VIRAL PROTEINS;

HUMAN HERPESVIRUS 1; SIMPLEXVIRUS;

EID: 79958054226     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.04.018     Document Type: Article

References (38)

1. Baines J.D., Wills E., Jacob R.J., Pennington J., Roizman B. Glycoprotein M of herpes simplex virus 1 is incorporated into virions during budding at the inner nuclear membrane. J. Virol. 2007, 81:800-812.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 2000, 28:235-242.
3. Bettahi I., Nesburn A.B., Yoon S., Zhang X., Mohebbi A., Sue V., Vanderberg A., Wechsler S.L., BenMohamed L. Protective immunity against ocular herpes infection and disease induced by highly immunogenic self-adjuvanting glycoprotein D lipopeptide vaccines. Invest. Ophthalmol. Visual Sci. 2007, 48:4643-4653.
4. Bi J., Song R., Yang H., Fan J., Liu Z., Long C. Stepwise identification of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus type 1 genome boosted by a StepRank scheme. Biopolymers (Pept. Sci.) 2011, Epub ahead of print. 10.1002/bip.21564.
5. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003, 31:365-370.
6. Brown S.M., MacLean A.R., McKie E.A., Harland J. The herpes simplex virus virulence factor ICP34.5 and the cellular protein MyD116 complex with proliferating cell nuclear antigen through the 63-amino-acid domain conserved in ICP34.5, MyD116, and GADD34. J. Virol 1997, 71:9442-9449.
7. Campadelli-Fiume G., Amasio M., Avitabile E., Cerretani A., Forghieri C., Gianni T., Menotti L. The multipartite system that mediates entry of herpes simplex virus into the cell. Rev. Med. Virol. 2007, 17:313-326.
8. Chentoufi A.A., Zhang X., Lamberth K., Dasgupta G., Bettahi I., Nguyen A., Wu M., Zhu X., Mohebbi A., Buus S., Wechsler S.L., Nesburn A.B., BenMohamed L. HLA-A*0201-restricted CD8+ vytotoxic T lymphocyte epitopes identified from herpes simplex virus glycoprotein D. J. Immunol. 2008, 180:426-437.
9. Chou K.C., Wei D.Q., Zhong W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun. 2003, 308:148-151.
10. Chou K.C. Review: structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 2004, 11:2105-2134.
11. Chou K.C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res 2005, 4:1681-1686.
12. Chou K.C. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol. 2011, 273:236-247.
13. Doytchinova I.A., Flower D.R. Toward the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201. J. Med. Chem. 2001, 44:3572-3581.
14. Du Q.S., Wang S.Q., Chou K.C. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem. Biophys. Res. Commun. 2007, 362:525-531.
15. Du Q.S., Huang R.B., Wang S.Q., Chou K.C. Designing inhibitors of M2 proton channel against H1N1 swine influenza virus. PLoS ONE 2010, 5:e9388.
16. Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G., Zhang W., Yang R., Cieplak P., Luo R., Lee T.A. Point-charge force field for molecular mechanics simulations of proteins. J. Comput. Chem. 2003, 24:1999-2012.
17. Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature 1986, 319:199-203.
18. Falk K., Rotzschke O., Stefanovic S., Jung G., Rammensee H.G. Allele specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991, 351:290-296.
19. Hou T., McLaughlin W., Lu B., Chen K., Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J. Proteome Res. 2006, 5:32-43.
20. Hou T., Chen C., McLaughlin W.A., Lu B., Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput. Biol. 2006, 2:e1.
21. Hou T., Zhang W., Case D.A., Wang W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. J. Mol. Biol. 2008, 376:1201-1214.
22. Koelle D.M., Corey L. Herpes simplex: insights on pathogenesis and possible vaccines. Ann. Rev. Med 2008, 59:381-395.
23. Krivov G.G., Shapovalov M.V., Dunbrack R.L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77:778-795.
24. Lafuente E.M., Reche P.A. Prediction of MHC-peptide binding: a systematic and comprehensive overview. Curr. Pharm. Des 2009, 15:3209-3220.
25. Li Y., Yang Y., He P., Yang Q. QM/MM study of epitope peptides binding to HLA-A*0201: the roles of anchor residues and water. Chem. Biol. Drug Des. 2009, 74:611-618.
26. Madden D.R. The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 1995, 13:587-622.
27. Mott K.R., Chentoufi A.A., Carpenter D., BenMohamed L., Wechsler S.L., Ghiasi H. The role of a glycoprotein K (gK) CD8+ T-cell epitope of herpes simplex virus on virus replication and pathogenicity. Invest. Ophthalmol. Visual Sci. 2009, 50:2903-2912.
28. Nesburn A.B., Slanina S., Burke R.L., Ghiasi H., Bahri S., Wechsler S.L. Therapeutic periocular vaccination with a subunit vaccine induces higher levels of herpes simplex virus-specific tear secretory immunoglobulin A than systemic vaccination and provides protection against recurrent spontaneous ocular shedding of virus in latently infected rabbits. J. Virol. 1998, 72:7715-7721.
29. Papavassiliou A.G., Wilcox K.W., Silverstein S.J. The interaction of ICP4 with cell/infected-cell factors and its state of phosphorylation modulate differential recognition of leader sequences in herpes simplex virus DNA. EMBO J 1991, 10:397-406.
30. Parker K.C., Bednarek M.A., Coligan J.E. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chain. J. Immunol. 1994, 152:163-175.
31. Rajcáni J., Andrea V., Ingeborg R. Peculiarities of herpes simplex virus (HSV) transcription: an overview. Virus Genes 2004, 28:293-310.
32. Ruppert J., Sidney J., Celis E., Kubo R.T., Grey H.M., Sette A. Prominent role of secondary anchor residues in peptide binding to HLA-A*0201s. Cell 1993, 74:929-937.
33. Ryckaert J., Ciccotti G., Berendsen H.J.C. Numerical-integration of Cartesian equations of motion of a system with constraints molecular-dynamics of n-alkanes. J. Comput. Phys. 1977, 23:327-341.
34. Sette A., Sidney J., del Guercio M.F., Southwood S., Ruppert J., Dalberg C., Grey H.M., Kubo R.T. Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays. Mol. Immunol. 1994, 31:813-822.
35. Sheridan B.S., Cherpes T.L., Urban J., Kalinski P., Hendricks R.L. Reevaluating the CD8 T-cell response to herpes simplex virus type 1: involvement of CD8 T cells reactive to subdominant epitopes. J. Virol. 2009, 83:2237-2245.
36. Sylvester-Hvid C., Nielsenm M., Lamberth K., Røder G., Justesen S., Lundegaard C., Worning P., Thomadsen H., Lund O., Brunak S., Buus S. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation. Tissue Antigens 2004, 63:395-400.
37. Toseland C.P., Clayton D.J., McSparron H., Hemsley S.L., Blythe M.J., Paine K., Doytchinova I.A., Guan P., Hattotuwagama C.K., Flower D.R. AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res. 2005, 1:4.
38. Vita R., Zarebski L., Greenbaum J.A., Emami H., Hoof I., Salimi N., Damle R., Sette A., Peters B. The immune epitope database 2.0. Nucleic Acids Res. 2010, 38:D854-D862.