Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007.

Bibliographic Details
Main Author: Joughin, Brian Alan
Other Authors: Bruce Tidor and Michael B. Yaffe.
Format: Thesis
Language:eng
Published: Massachusetts Institute of Technology 2007
Subjects:
Online Access:http://hdl.handle.net/1721.1/38630
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author Joughin, Brian Alan
author2 Bruce Tidor and Michael B. Yaffe.
author_facet Bruce Tidor and Michael B. Yaffe.
Joughin, Brian Alan
author_sort Joughin, Brian Alan
collection MIT
description Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007.
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spelling mit-1721.1/386302019-04-12T23:39:14Z Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions Joughin, Brian Alan Bruce Tidor and Michael B. Yaffe. Massachusetts Institute of Technology. Dept. of Biology. Massachusetts Institute of Technology. Dept. of Biology. Biology. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007. Includes bibliographical references (p. 107-130). This thesis presents a number of novel computational methods for the analysis and design of protein-protein complexes, and their application to the study of the interactions of phosphopeptides with phosphopeptide-binding domain interactions. A novel protein-protein interaction type, the action-at-a-distance interaction, is described in the complex of the TEM1 P-lactamase with the 3-lactamase inhibitor protein (BLIP). New action-at-a-distance interactions were designed on the surface of BLIP and computed to enhance the affinity of that complex. A new method is described for the characterization and prediction of protein ligand-binding sites. This method was used to analyze the phosphoresidue-contacting sites of known phosphopeptide-binding domains, and to predict the sites of phosphoresidue-contact on some protein domains for which the correct site was not known. The design of a library of variant WW domains that is predicted to be enriched in domains that might have specificity for "pS/pT-Q" peptide ligands is detailed. General methods for designing libraries of degenerate oligonucleotides for expressing protein libraries as accurately as possible are given, and applied to the described WW domain variant library. by Brian Alan Joughin. Ph.D. 2007-08-29T20:37:35Z 2007-08-29T20:37:35Z 2007 2007 Thesis http://hdl.handle.net/1721.1/38630 156998703 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 130 leaves application/pdf Massachusetts Institute of Technology
spellingShingle Biology.
Joughin, Brian Alan
Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title_full Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title_fullStr Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title_full_unstemmed Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title_short Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
title_sort novel methods in computational analysis and design of protein protein interactions applications to phosphoregulated interactions
topic Biology.
url http://hdl.handle.net/1721.1/38630
work_keys_str_mv AT joughinbrianalan novelmethodsincomputationalanalysisanddesignofproteinproteininteractionsapplicationstophosphoregulatedinteractions