We will develop and apply widely applicable, methods, based on advanced computational techniques, to the problems involved in elucidating the structural basis of receptor-ligand interactions. Although we expect the methods to be generally useful, the proposed project will focus specifically on early events in the activation of cytotoxic T cells, and to some extent on helper T cells. Both cell types play major roles in normal and pathological responses. The cytotoxic response is central to destroying host cells that have been infected by virus. Common to the early phases of both responses is recognition of foreign peptides (e.g., the remnants of proteins from an invading organism) by host major histocompatibility complex (MHC) products on the infected cell- called class I for the cytotoxic response and class II for the helper response. A given individual has very few MHC structures, but must be able to recognize a wide range of peptides. Developing a predictive understanding of the structural basis of recognition i.e., being able to predict which peptides will and which will not form stable complexes with a given MHC allele, is central to a wide range of fundamental and applied problems including manipulation of the immune response by vaccination or other means. Class I structures will be predicted using the known crystal structure of a human class I molecule. The method for computationally determining unknown structures from a closely homologous sequence of known structure will be validated using a structural database of highly homologous molecules. Similarly structural data from other systems is available to test the docking algorithm that will predict where and how stably a given peptide sequence binds to class I. The methods will be further validated against a large and rapidly growing database of peptides and their analogues known to bind particular effects of site specific changes in either peptide or MHC can quickly be made and evaluated. This will be done and the predictions tested experimentally.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI030535-05
Application #
2065685
Study Section
Special Emphasis Panel (SSS (E))
Project Start
1991-01-01
Project End
1996-06-30
Budget Start
1995-01-01
Budget End
1996-06-30
Support Year
5
Fiscal Year
1995
Total Cost
Indirect Cost
Name
Boston University
Department
Biomedical Engineering
Type
Schools of Engineering
DUNS #
604483045
City
Boston
State
MA
Country
United States
Zip Code
02118
Gulukota, K; Sidney, J; Sette, A et al. (1997) Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J Mol Biol 267:1258-67
Zhang, C; Vasmatzis, G; Cornette, J L et al. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 267:707-26
Zhang, C; Cornette, J L; Berzofsky, J A et al. (1997) The organization of human leucocyte antigen class I epitopes in HIV genome products: implications for HIV evolution and vaccine design. Vaccine 15:1291-302
Zhang, C; Cornette, J L; Delisi, C (1997) Consistency in structural energetics of protein folding and peptide recognition. Protein Sci 6:1057-64
Weng, Z; Vajda, S; Delisi, C (1996) Prediction of protein complexes using empirical free energy functions. Protein Sci 5:614-26
Luidens, M K; Figge, J; Breese, K et al. (1996) Predicted and trifluoroethanol-induced alpha-helicity of polypeptides. Biopolymers 39:367-76
Vasmatzis, G; Zhang, C; Cornette, J L et al. (1996) Computational determination of side chain specificity for pockets in class I MHC molecules. Mol Immunol 33:1231-9
Sezerman, U; Vajda, S; DeLisi, C (1996) Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci 5:1272-81
Gulukota, K; DeLisi, C (1996) HLA allele selection for designing peptide vaccines. Genet Anal 13:81-6
Rosenbach, D; Rosenfeld, R (1995) Simultaneous modeling of multiple loops in proteins. Protein Sci 4:496-505

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