Two complementary methods for predicting peptides binding major histocompatibility complex molecules

Journal of Molecular Biology

Volumn 267, Issue 5, 1997, Pages 1258-1267

  Gulukota, Kamalakar ^a   Sidney, John ^b   Sette, Alessandro ^b   DeLisi, Charles ^a  

^a Boston University   (United States)

^b CYTEL CORPORATION   (United States)

Author keywords

Binary decision; Independent binding of side chains; Neural networks; Polynomial method

Indexed keywords

HLA A2 ANTIGEN; PEPTIDE;

ALLELE; AMINO ACID SEQUENCE; ANTIGEN BINDING; ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING AFFINITY; CONTROLLED STUDY; DATA BASE; DRUG STRUCTURE; INTERMETHOD COMPARISON; MAJOR HISTOCOMPATIBILITY COMPLEX; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL;

EID: 0031576987     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0937     Document Type: Article

References (26)

1. Adams H. P., Koziol J. A. Prediction of binding to MHC class I molecules. J. Immunol. Methods. 185:1995;181-190.
2. Alegretta M., Nicklas J. A., Sriram S., Albertini R. J. T cells responsive to myelin basic protein in patients with multiple sclerosis. Science. 247:1990;718-721.
3. Bisset L. R., Fierz W. Using a neural network to identify potential HLA-DR1 binding sites within proteins. J. Mol. Recognit. 6:1993;41-48.
4. Brusic V., Rudy G., Harrison L. C. Prediction of MHC binding peptides using artificial neural networks. Complex Systems: Mechanism of Adaptation. 1994;IOS Press, Amsterdam.
5. Buus S., Sette A., Colon S. M., Miles C., Grey H. M. The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenic peptides. Science. 235:1987;1353-1358.
6. Gulukota K., DeLisi C. HLA allele selection for designing peptide vaccines. Genet. Anal: Biomol. Eng. 13:1996;81-86.
7. Gulukota K., Vajda S., DeLisi C. Peptide docking using dynamic programming. J. Comput. Chem. 17:1996;418-428.
8. Hammer J. New methods to predict MHC-binding sequences within protein antigens. Curr. Opin. Immunol. 7:1995;263-269.
9. Hammer J. E., Bono E., Gallazzi F., Belunis C., Nagy Z., Sinigaglia F. Precise prediction of major histocompatibility comlex class II-peptide interaction based on peptide side chain scanning. J. Exp. Med. 180:1994;2353-2358.
10. Herrington D. A., Clyde D. F., Losonsky G. Safety and immunogenicity in man of a synthetic peptide malaria vaccine against Plasmodium falciparum sporozoites. Nature. 328:1987;257-259.
11. Kane K. P., Vitiello A., Sherman L. A., Mescher M. F. Cytotoxic T-lymphocyte response to isolated class I H-2 proteins and influenza peptides. Nature. 340:1989;157-159.
12. Kast W. M., Brandt R. M. P., Sidney J., Drijfhout J.-W., Kubo R. T., Grey H. M., Melief C. J. M., Sette A. Role of HLA-A motifs in identification of potential CTL epitopes in human papilloma virus type 16 E6 and E7 proteins. J. Immunol. 152:1994;3904-3912.
13. Madden D. R., Garboczi D. N., Wiley D. C. The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell. 75:1993;693-708.
14. Marshall K. W., Wilson K. J., Liang J., Woods A., Zaller D., Rothbard J. B. Prediction of peptide affinity to HLA DRB1*0401. J. Immunol. 154:1995;5927-5933.
15. Naruse H., Ogasawara K., Kaneda R. A potential peptide vaccine against two different strains of influenza virus isolated at intervals of about 10 years. Proc. Natl Acad. Sci. USA. 91:1994;9588-9592.
16. Nijman H. W., Houbiers J. G., Vierboom M. P., van der Burg S. H., Drijfhout J. W., D'Amaro J., Kenemans P., Melief C. J., Kast W. M. Identification of peptide sequences that potentially trigger HLA-A2.1 restricted cytoxic T lymphocytes. Eur. J. Immunol. 23(6):1993;1215-1219.
17. 2-microglobulin dissociation rate is an accurate measure of the stability of MHC class I heterotrimers and depends on which peptide is bound. J. Immunol. 149:1992;1896-1904.
18. Parker K. C., Bednarek M. A., Coligan J. E. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide sidechains. J. Immunol. 152:1994;163-175.
19. Protti M. P., Manfredi A. A., Horton R. M., Bellone M., Conti-Tronconi B. M. Myasthenia gravis: recognition of a human autoantigen at the molecular level. Immunol. Today. 14:1993;363-368.
20. Rammensee H.-G., Friede T., Stevanovic S. MHC ligands and peptide motifs: first listing. Immunogenetics. 41:1995;178-228.
21. Rumelhart D. E., Hinton G. E., Williams R. J. Learning internal representation by error propagation. Parallel Distributed Processing: Explorations in the Microstructures of Cognition. 1986;MIT Press, Cambridge.
22. 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-A2.1 molecules. Cell. 74:1993;929.
23. Sette A., Vitiello A., Reherman B., Fowler P., Nayersina R., Kast W. M., Melief C. J., Oseroff C., Yuan L., Ruppert J., Sidney J., del Guercio M.-F., Southwood S., Kubo R. T., Chestnut R. W., Grey H. M., Chisari F. V. The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J. Immunol. 153:1994;5586-5592.
24. Sezerman O. U., Vajda S., DeLisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci. 5(7):1996;1272-1281.
25. Toffoli T. Neural networks. Encycl. Appl. Phys. 11:1994;275-296.
26. Vajda S., Weng Z., Rosenfeld R., DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 33:1994;13977-13988.