Structure studies of the human class II major histocompatibility complex protein HLA-DR1
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56571175-MIT.pdf
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Author(s)
Zavala-Ruiz, Zarixia, 1977-
Advisor(s)
Lawrence J. Stern.
Date Issued
2004
Publisher
Massachusetts Institute of Technology
Abstract
Major Histocompatibility Complex (MHC) proteins are heterodimeric membrane glycoproteins that bind antigens in the form of short peptides within the cell and present them to the T cell receptors on the surface T cells. In this thesis work, the structural aspects of the human class II MHC protein HLA-DR1 in complex with different peptides and also in the peptide-free form were investigated. Biochemical, crystallographic, and immunological analyses of an unusually long peptide antigen derived from HIV-gag (p24) and its interaction with HLA-DR1 and a HIV-specific CD4+ T cell clone were studied. The HIV-gag (p24) peptide binds in an unexpected conformation, with its C- terminal region making a hairpin turn that bends back over the groove. The residues at the C-terminus are critical for T-cell recognition, and disruption of the hairpin turn abrogates the immune response. The results suggest a new mode of MHC-peptide-TCR interaction. A set of viral peptide analogs designed to increase binding affinity for HLA-DR while maintaining antigenic interactions with a virus-specific T cell receptor were designed, tested and analyzed. Ultimately, a N-methyl substitution at position 7 is shown to increase binding affinity by displacement of one of three water molecules bound between the MHC and peptide. The results have implications for design of peptido-mimetic vaccines, and are discussed in the broad context of other attempts to increase protein-ligand interaction through displacement of tightly bound water molecules. The role for the P10 shelf in peptide binding site was investigated. Crystallographic studies confirm the formation of a P10 shelf that is lined with highly polymorphic residues. Biochemical studies were conducted
(cont.) on a series of peptides different at the P10 position on four HLA-DRl(P10) mutants showing that this shelf has some specificity and can be involved in the discrimination of peptides that bind to class II MHC proteins. Studies of the empty, peptide-free form of HLA-DR1 were conducted by NMR spectroscopy showing that the conformation of this empty form is not in a molten globule-like state and that in general is similar to that of the peptide-loaded form but with several differences. Preliminary characterization of the peptide-receptive and peptide-averse forms of the empty HLA-DR1 is described.
Description
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004.
Vita.
Includes bibliographical references (leaves 149-162).
Subjects
Chemistry.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
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