In silico characterization of immunogenic epitopes presented by HLA-Cw*0401

Immunome Research

Volumn 3, Issue 1, 2007, Pages

  Tong, Joo Chuan ^a   Zhang, Zong Hong ^a   August, J Thomas ^c   Brusic, Vladimir ^d   Tan, Tin Wee ^b   Ranganathan, Shoba ^b,e  

^a INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e MACQUARIE UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 35348946351     PISSN: None     EISSN: 17457580     Source Type: Journal    
DOI: 10.1186/1745-7580-3-7     Document Type: Article

References (28)

1. Dill O, Kievits F, Koch S, Ivanyi P, Hämmerling GJ: Immunological function of HLA-C antigens in HLA-Cw3 transgenic mice. Proc Natl Acad Sci USA 1988, 85:5664-5668.
2. + cytotoxic T-lymphocyte clone recognizes a highly conserved epitope on human immunodeficiency virus type I gag. J Virol 1991, 65:4051-4056.
3. Snary D, Barnstable CJ, Bodmer WF, Crumpton MJ: Molecular structure of human histocompatibility antigens: the HLA-C series. Eur J Immunol 1977, 8:580-585.
4. McCutcheon JA, Gumperz J, Smith KD, Lutz CT, Parham P: Low HLA-C expression at cell surfaces correlates with increased turnover of heavy chain mRNA. J Exp Med 1995, 181:2085-2095.
5. Korber BTM, Brander C, Haynes BF, Koup R, Moore JP, Walker BD, Watkind Dl: HIV Molecular Immunology 2005. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico; 2005.
6. Bugawan TL, Klitz W, Blair A, Erlich HA: High-resolution HLA class I typing in the CEPH families: analysis of linkage disequilibrium among HLA loci. Tiss Antigens 2000, 56:392-404.
7. Neefjes JJ, Ploegh HL: Allele and locus-specific differences in cell surface expression and the association of HLA class I heavy chain with β2-microglobulin: differential effects of inhibition of glycosylation on class I subunit association. Eur J Immunol 1988, 18:801-810.
8. Neisig A, Melief CJ, Neefjes J: Reduced cell surface expression of HLA-C molecules correlates with restricted peptide binding and stable TAP interaction. J Immunol 1998, 160:171-179.
9. Brusic V, Bajic VB, Petrovsky N: Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications. Methods 2004, 34:436-443.
10. Buchsbaum S, Barnea E, Dassau L, Beer I, Milner E, Admon A: Large-scale analysis of HLA peptides presented by HLA-Cw4. Immunogenetics 2003, 55:172-176.
11. Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999, 50:213-219.
12. DeLuca DS, Khattab B, Blasczyk R: A modular concept of HLA for comprehensive peptide binding prediction. Immunogenetics 2007, 59:25-35.
13. Tong JC, Tan TW, Ranganathan S: Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci 2004, 13:2523-2532.
14. Tong JC, Bramson J, Kanduc D, Chow S, Sinha AA, Ranganathan S: Modeling the bound conformation of pemphigus vulgaris-associated peptides to MHC class II DR and DQ alleles. Immunome Res 2006, 2:1.
15. Tong JC, Zhang GL, Tan TW, August JT, Brusic V, Ranganathan S: Prediction of HLA-DQ3.2β ligands: Evidence of multiple registers in class II binding peptides. Bioinformatics 2006, 22:1232-1238.
16. Rognan D, Laumøller SL, Holm A, Buus S, Tschinke V: Predicting binding affinities of protein ligands from three-dimensional models: Application to Peptide Binding to Class I Major Histocompatibility Proteins. J Med Chem 1999, 42:4650-4658.
17. Tong JC, Bramson J, Kanduc D, Sinha AA, Ranganathan S: Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris. BMC Bioinformatics 2006, 7(Suppl 5):S7.
18. Johnson RP, Trocha A, Buchanan TM, Walker BD: Recognition of a highly conserved region of human immunodeficiency virus type I gp120 by an HLA-Cw4-restricted cytotoxic T-lymphocyte clone, J Virol 1993, 67:438-445.
19. Sayle RA, Milner-White EJ: RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995, 20:374.
20. Brander C, Goulder PJR: Recent advances in HIV-I CTL epitope characterization. In HIV molecular immunology database. In HIV Molecular Database Edited by: Korber BTM, Brander C, Haynes BF, Koup R, Moore JP, Walker BD, Watkind DI. Los Alamos National Laboratory. Los Alamos, New Mexico; 1999:i1-i19.
21. Buseyne F, Stevanovic S, Rammensee HG, Riviere Y: Characterization of an HIV-1 p24gag epitope recognized by a CD8+ cytotoxic T-cell clone. Immunol Letters 1997, 55:145-149.
22. Fan QR, Wiley DC: Structure of Hla-Cw4, a Ligand for the Kir2D Natural Killer Cell Inhibitory Receptor. J Exp Med 1999, 190:113-124.
23. Abagyan RA, Totrov M: Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. J Comput Phys 1999, 151:402-421.
24. Sidney J, del Guercio MF, Southwood S, Engelhard VH, Appella E, Rammensee HG, Falk K, Rötzschke O, Takiguchi M, Kubo RT, Grey HM, Sette A: Several HLA alleles share overlapping peptide specificities. J Immunol 1995, 154:247-259.
25. Rajagopalan S, Long EO: The direct binding of a p58 killer cell inhibitory receptor to human histocompatibility leukocyte antigen (HLA)-Cw4 exhibits peptide selectivity. J Exp Med 1997, 185:1523-1528.
26. The UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Res 2007, 35:D 193-D197.
27. Srinivasan KN, Zhang GL, Khan AM, August JT, Brusic V: Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. Bioinformatics 2004, 20:i297-i302.
28. Bradley AP: The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognition 1997, 30:1145-1159.