Class II HLA-peptide binding prediction using structural principles

Human Immunology

Volumn 70, Issue 3, 2009, Pages 159-169

  Mohanapriya, Arumugam ^a   Lulu, Sajitha ^a   Kayathri, Rajarathinam ^b   Kangueane, Pandjassarame ^a,b  

^a VIT UNIVERSITY   (India)

^b Biomedical Informatics   (India)

Author keywords

Binding; Class II; HLA; Peptide; Prediction; Structural principles

Indexed keywords

AMINO ACID; HLA ANTIGEN CLASS 2;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; IMMUNE RESPONSE; PREDICTION; PREDICTIVE VALIDITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY;

ALLELES; CD4-POSITIVE T-LYMPHOCYTES; DATABASES, PROTEIN; EPITOPES, T-LYMPHOCYTE; FORECASTING; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; IMMUNITY, CELLULAR; MODELS, IMMUNOLOGICAL; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; SENSITIVITY AND SPECIFICITY;

EID: 61349097815     PISSN: 01988859     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.humimm.2008.12.012     Document Type: Article

References (29)

1. James R., Waller M.J., Parham P., Groot N., Bontrop R., Kennedy L.J., et al. IMGT/HLA and IMGT/MHC: Sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 31 (2003) 311-314
2. McNicholl J.M., Whitworth W.C., Oftung F., Fu X., Shinnick T., Jensen P.E., et al. Structural requirements of peptide and MHC for DR(alpha, beta 1*0401)-restricted T cell antigen recognition. J Immunol 155 (1995) 1951-1963
3. Lee C., and McConnell H.M. A general model of invariant chain association with class II major histocompatibility complex proteins. Proc Natl Acad Sci 92 (1995) 8269-8273
4. Penzotti J.E., Doherty D., Lybrand T.P., and Nepom G.T. A structural model for TCR recognition of the HLA class II shared epitope sequence implicated in susceptibility to rheumatoid arthritis. J Autoimmun 9 (1996) 287-293
5. Doherty D.G., Penzotti J.E., Koelle D.M., Kwok W.W., Lybrand T.P., Masewicz S., et al. Structural basis of specificity and degeneracy of T cell recognition: Pluriallelic restriction of T cell responses to a peptide antigen involves both specific and promiscuous interactions between the T cell receptor, peptide, and HLA-DR1. J Immunol 161 (1998) 3527-3535
6. Moustakas A.K., Wal Y., Routsias J., Kooy Y.M.C., Veelen P., Drijfhout J.W., et al. Structure of celiac disease-associated HLA-DQ8 and non-associated HLA-DQ9 alleles in complex with two disease-specific epitopes. Intl Immunol 12 (2000) 1157-1166
7. Sanjeevi C.B., Lybrand T.B., Stevanovic S., and Rammensee H.G. Molecular modeling of eluted peptides from DQ6 molecules (DQB1*0602 and DQB1*0604) negatively and positively associated with type 1 diabetes. Ann N Y Acad Sci 958 (2002) 317-320
8. Díaz G., Amicosante M., Jaraquemada D., Butler R.H., Guillén M.V., and Sánchez M. Functional analysis of HLA-DP polymorphism: A crucial role for DPβ residues 9, 11, 35, 55, 56, 69 and 84-87 in T cell allorecognition and peptide binding. International Immunology 15 (2003) 565-576
9. Schafroth H.D., and Floudas C.A. Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization. Proteins 54 (2004) 534-556
10. Yuan W.H., Chang T.K., and Hou L.T. Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques. J Chem Inform Model 45 (2005) 1343-1351
11. Ettinger R.A., Papadopoulos G.K., Moustakas A.K., Nepom G.T., and Kwok W.W. Allelic variation in key peptide-binding pockets discriminates between closely related diabetes-protective and diabetes-susceptible HLA-DQB1*06 alleles. J Immunol 176 (2006) 1988-1998
12. Tong J.C., Bramson J., Kanduc D., Chow S., Animesh A.S., and Shoba R. Modeling the bound conformation of Pemphigus vulgaris-associated peptides to MHC Class II DR and DQ Alleles. Immunome Res 1186 (2006) 1745-1780
13. Evensen E., McCarthy D.J., Weiss G.A., Schreiber S.L., and Karplus M. Ligand design by a combinatorial approach based on modeling and experiment: Application to HLA-DR4. J Comput Aid Mol Des 21 (2007) 395-418
14. Engelhard V.H. Structure of peptides associated with class I and class II MHC molecules. Annu Rev Immunol 12 (1994) 181-207
15. Samanta U., Bahadur R.P., and Pinak C. Quantifying the accessible surface area of protein residues in their local environment. Protein Eng 15 (2002) 659-667
16. Fraczkiewicz R., and Braun W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comp Chem 19 (1998) 319-333
17. Hammer J., Valsasnini P., Tolba K., Bolin D., Higelin J., Takacs B., et al. Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell 74 (1993) 197-203
18. Schreuder G.M., Hurley C.K., Marsh S.G., Lau M., Fernandez-Vina M., Noreen H.J., et al. The HLA dictionary 2004. Tissue Antigens 65 (2005) 1-55
19. Brown J.H., Jardetzky T.S., Gorga J.C., Stern L.J., Urban R.G., Strominger J.L., et al. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364 (1993) 33-39
20. Hammer J., Nagy Z.A., and Sinigaglia F. Rules governing peptide-class II MHC molecule interactions. Behring Inst Mitt 94 (1994) 124-132
21. Zhao B., Mathura V.S., Rajaseger G., Moochhala S., Sakharkar M.K., and Kangueane P. A novel MHCp binding prediction model. Hum Immunol 64 (2003) 1123-1143
22. Brinda K.V., and Saraswathi V. A network representation of protein structures: Implications for protein stability. Biophys J 89 (2005) 4159-4170
23. Diemand A.V., and Scheib H. iMolTalk: An interactive, Internet-based protein structure analysis server. Nucleic Acids Res 32 (2004) W512-W516
24. Venkatarajan M.S., and Braun W. New quantitative descriptor of amino acids based on multi-dimensional scaling of a large number of physical-chemical properties. J Mol Model 7 (2001) 445-453
25. Bhasin M., Singh H., and Raghava G.P. MHCBN: A comprehensive database of MHC binding and non-binding peptides. Bioinformatics 22 (2003) 665-666
26. Zaitlen N., Reyes-Gomez M., Heckerman D., and Jojic N. Shift-invariant adaptive double threading: Learning MHC II-peptide binding. J Comput Biol 15 (2008) 927-942
27. Wang P., Sidney J., Dow C., Mothé B., Sette A., and Peters B. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 4 (2008) e1000048
28. Kangueane P., Sakharkar M.K., Kolatkar P.R., and Ren E.C. Towards MHC-peptide combinatorics. Hum Immunol 62 (2002) 539-556
29. Gowthaman U., and Agrewala J.N. In silico tools for predicting peptides binding to HLA-class II molecules: More confusion than conclusion. J Proteome Res 7 (2008) 154-163