Applications of Funneled Landscapes: Protein Folding and Molecular Recognition

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• Shoemaker, Benjamin Allen

Contributors dc:contributor

• Wolynes, Peter G.

• Chemistry, Biochemistry

Language dc:language

eng

Identifier

(MiAaPQ)AAI9971191

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/84474