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Wolynes, Peter G. Shoemaker, Benjamin Allen 2015-09-25T22:14:41Z 2015-09-25T22:14:41Z 10000-01-01 2000 2000 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. Made available in DSpace on 2015-09-25T22:14:41Z (GMT). No. of bitstreams: 2 license.txt: 4848 bytes, checksum: 96035ab3f5e1c23cc7138a224ce498bd (MD5) 9971191.pdf: 7908864 bytes, checksum: 863114432218688d4ce39daa17f0a2f3 (MD5) Previous issue date: 2000 Embargo set by: Seth Robbins for item 85755 Lift date: Forever Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs U of I Only 148 p. Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2000. http://hdl.handle.net/2142/84474 (MiAaPQ)AAI9971191 eng Chemistry, Biochemistry Applications of Funneled Landscapes: Protein Folding and Molecular Recognition text Chemistry Chemistry University of Illinois at Urbana-Champaign Dissertation Ph.D.