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Title:Applications of Funneled Landscapes: Protein Folding and Molecular Recognition
Author(s):Shoemaker, Benjamin Allen
Doctoral Committee Chair(s):Wolynes, Peter G.
Department / Program:Chemistry
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):Chemistry, Biochemistry
Abstract:Energy landscape theory provides a general framework in which models can be used to describe complex macromolecular processes. A free energy functional model is formulated to describe protein folding which includes a specific potential, a polymer chain entropy, and explicit physically motivated cooperativities. The functional is applied to a range of protein systems in order to characterize their folding funnels. General features of folding are explored and specific results compared to experimental data. I then address the problem of molecular recognition, examining the interplay of binding and folding in a protein/operator DNA complex. Extending the free energy functional formalism, a distance dependent binding free energy is included to treat the intermolecular interactions. A kinetic advantage is found for partially folded protein binding and a speedup mechanism proposed in the spirit of earlier dimensionality reduction mechanisms.
Issue Date:2000
Description:148 p.
Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2000.
Other Identifier(s):(MiAaPQ)AAI9971191
Date Available in IDEALS:2015-09-25
Date Deposited:2000

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