Applications of Funneled Landscapes: Protein Folding and Molecular Recognition
Shoemaker, Benjamin Allen
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https://hdl.handle.net/2142/84474
Description
Title
Applications of Funneled Landscapes: Protein Folding and Molecular Recognition
Author(s)
Shoemaker, Benjamin Allen
Issue Date
2000
Doctoral Committee Chair(s)
Wolynes, Peter G.
Department of Study
Chemistry
Discipline
Chemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Chemistry, Biochemistry
Language
eng
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.
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