Genomewide conserved epitope profiles of HIV-1 predicted by biophysical properties of MHC binding peptides

Journal of Computational Biology

Volumn 11, Issue 1, 2004, Pages 125-145

  Sung, Myong Hee ^a   Simon, Richard ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Bioinformatics; Epitope prediction; HIV 1; MHC binding; Peptide property model; Vaccine design

Indexed keywords

AMINO ACID; EPITOPE; HLA A2 ANTIGEN; HLA DR1 ANTIGEN; HLA DR4 ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; PEPTIDE; VACCINE;

ARTICLE; BIOINFORMATICS; BIOPHYSICS; DRUG DESIGN; EPITOPE PREDICTION; GENETIC CONSERVATION; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERMETHOD COMPARISON; MAJOR HISTOCOMPATIBILITY COMPLEX; MODEL; NONHUMAN; PEPTIDE PROPERTY MODEL; PERFORMANCE; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; STATISTICAL ANALYSIS; STATISTICAL DISTANCE; VALIDATION PROCESS; VIRUS GENOME;

COMPUTER SIMULATION; EPITOPE MAPPING; GENOME, VIRAL; HIV-1; MAJOR HISTOCOMPATIBILITY COMPLEX; OLIGOPEPTIDES; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 1842555217     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652704773416920     Document Type: Article

References (39)

1. Altfeld, M.A., Livingston, B., et al. 2001. Identification of novel HLA-A2-restricted human immunodeficiency virus type 1-specific cytotoxic T-lymphocyte epitopes predicted by the HLA-A2 supertype peptide-binding motif. J. Virol. 75(3), 1301-1311.
2. Amara, R.R., Villinger, F., et al. 2001. Control of a mucosal challenge and prevention of AIDS by a multiprotein DNA/MVA vaccine. Science 292, 5514, 69-74.
3. Betts, M.R., Ambrozak, D.R., et al. 2001. Analysis of total human immunodeficiency virus (HIV)-specific CD4(+) and CD8(+) T-cell responses: Relationship to viral load in untreated HIV infection. J. Virol. 75(24), 11983-11991.
4. Brander, C., Hartman, K.E., et al. 1998. Lack of strong immune selection pressure by the immunodominant, HLA-A*0201-restricted cytotoxic T lymphocyte response in chronic human immunodeficiency virus-1 infection. J. Clin. Invest. 101(11), 2559-2566.
5. Brusic, V., Rudy, G., et al. 1998a. MHCPEP, a database of MHC-binding peptides: Update 1997. Nucl. Acids Res. 26(1), 368-371.
6. Brusic, V., Rudy, G., et al. 1998b. Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 14(2), 121-130.
7. Chen, Y., Sidney, J., et al. 1994. Naturally processed peptides longer than nine amino acid residues bind to the class I MHC molecule HLA-A2.1 with high affinity and in different conformations. J. Immunol. 152(6), 2874-2881.
8. Collins, E.J., Garboczi, D.N., et al. 1994. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 371(6498), 626-629.
9. De Groot, A.S., Bosma, A., et al. 2001. From genome to vaccine: In silico predictions, ex vivo verification. Vaccine 19(31), 4385-4395.
10. De Groot, A.S., Saint-Aubin, C., et al. 2001. Rapid determination of HLA B*07 ligands from the West Nile virus NY99 genome. Emerg. Infect. Dis. 7(4), 706-713.
11. Doytchinova, I.A., and Flower, D.R. 2001. 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. 44(22), 3572-3581.
12. Dupuis, M., Kundu, S.K., et al. 1995. Characterization of HLA-A 0201-restricted cytotoxic T cell epitopes in conserved regions of the HIV type 1 gp160 protein. J. Immunol. 155(4), 2232-2239.
13. Gaudebout, P., Zeliszewski, D., et al. 1997. Binding analysis of 95 HIV gp120 peptides to HLA-DR1101 and -DR0401 evidenced many HLA-class II binding regions on gp120 and suggested several promiscuous regions. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 14(2), 91-101.
14. Gulukota, K., Sidney, J., et al. 1997. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol. 267(5), 1258-1267.
15. Hanley, J.A., and Hajian-Tilaki, K.O. 1997. Sampling variability of nonparametric estimates of the areas under receiving operating characterstic curves: an update. Acad. Radiol. 4(1), 49-58.
16. Honeyman, M.C., Brusic, V., et al. 1998. Neural network-based prediction of candidate T-cell epitopes. Nat. Biotechnol. 16(10), 966-969.
17. Kidera, A., Konishi, Y., Oka, M., Ooi, T., and Scheraga, H.A. 1985. Statistical Analysis of the Physical Properties of the 20 Naturally Occurring Amino Acids. J. Protein Chem. 4(1), 23-55.
18. Korber, B., Brander, C., Haynes, B., Koup, R., Kuiken, C., Moore, J.P., Walker, B.D., and Watkins, D.I. 2000. HIV Molecular Immunology, Los Alamos National Laboratory, Theoretical Biology and Biophysics.
19. Li, Y., Li, H., et al. 2000. Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins. J. Mol. Biol. 304(2), 177-188.
20. Liang, C., Rong, L., et al. 1999. Mutations within four distinct gag proteins are required to restore replication of human immunodeficiency virus type 1 after deletion mutagenesis within the dimerization initiation site. J. Virol. 73(8), 7014-7020.
21. Liang, C., Rong, L., et al. 2000. Deletion mutagenesis downstream of the 5′ long terminal repeat of human immunodeficiency virus type 1 is compensated for by point mutations in both the U5 region and gag gene. J. Virol. 74(14), 6251-6261.
22. Logean, A., and Rognan, D. 2002. Recovery of known T-cell epitopes by computational scanning of a viral genome. J. Comput. Aided Mol. Des. 16(4), 229-243.
23. Madden, D.R., Garboczi, D.N., et al. 1993. The antigenic identity of peptide-MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75(4), 693-708.
24. Mallios, R.R. 1999. Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm. Bioinformatics 15(6), 432-439.
25. Mamitsuka, H. 1998. Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models. Proteins 33(4), 460-474.
26. Manca, F., Fenoglio, D., et al. 1995. Human CD4+ T cells can discriminate the molecular and structural context of T epitopes of HIV gp120 and HIV p66. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 9(3), 227-237.
27. Milik, M., Sauer, D., et al. 1998. Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nat. Biotechnol. 16(8), 753-756.
28. Nehete, P.N., Schapiro, S.J., et al. 1998. A synthetic peptide from the first conserved region in the envelope protein gp160 is a strong T-cell epitope in HIV-infected chimpanzees and humans. Viral. Immunol. 11(3), 147-158.
29. O'Sullivan, D., Sidney, J., et al. 1990. Characterization of the specificity of peptide binding to four DR haplotypes. J. Immunol. 145(6), 1799-1808.
30. Parker, K.C., Bednarek, M.A., et al. 1994. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J. Immunol. 152(1), 163-175.
31. Pitcher, C.J., Quittner, C., et al. 1999. HIV-1-specific CD4+ T cells are detectable in most individuals with active HIV-1 infection, but decline with prolonged viral suppression. Nat. Med. 5(5), 518-525.
32. Raddrizzani, L., and Hammer, J. 2000. Epitope scanning using virtual matrix-based algorithms. Brief Bioinform. 1(2), 179-189.
33. Schafer, J.R., Jesdale, B.M., et al. 1998. Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix. Vaccine 16(19), 1880-1884.
34. Southwood, S., Sidney, J., et al. 1998. Several common HLA-DR types share largely overlapping peptide binding repertoires. J. Immunol. 160(7), 3363-3373.
35. Sturniolo, T., Bono, E., et al. 1999. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol. 17(6), 555-561.
36. Tang, H., Kuhen, K.L., et al. 1999. Lentivirus replication and regulation. Annu. Rev. Genet. 33, 133-170.
37. van der Burg, S.H., Kwappenberg, K.M., et al. 1999. Identification of a conserved universal Th epitope in HIV-1 reverse transcriptase that is processed and presented to HIV-specific CD4+ T cells by at least four unrelated HLA-DR molecules. J. Immunol. 162(1), 152-160.
38. Walker, B.D., and Korber, B.T. 2001. Immune control of HIV: The obstacles of HLA and viral diversity. Nat. Immunol. 2(6), 473-475.
39. Wilson, C.C., Palmer, B., et al. 2001. Identification and antigenicity of broadly cross-reactive and conserved human immunodeficiency virus type 1-derived helper T-lymphocyte epitopes. J. Virol. 75(9), 4195-4-207.