Computer Simulations Of Enzymes

Author:

Hanoian, Philip

Graduate Program:

Chemistry

Degree:

Doctor of Philosophy

Document Type:

Dissertation

Date of Defense:

May 09, 2014

Committee Members:

William George Noid, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Mark Maroncelli, Committee Member
James David Kubicki, Committee Member
Sharon Hammes Schiffer, Special Member

Keywords:

molecular dynamics simulations
enzymes
computational
ketosteroid isomerase
dihydrfolate reductase
empirical valence bond

Abstract:

Enzymes are proteins that perform the essential function of facilitating chemical reactions within living organisms, and the rate enhancements provided by enzymes are so significant that they remain a marvel for chemists today. The study of enzymes is thus pervaded by attempts to understand the precise mechanisms by which enzymes achieve these rate enhancements, with additional focus on the impressive level of specificity and selectivity these protein catalysts display as well. In this thesis, four studies on enzymatic systems are presented with the goal of further elucidating the mechanisms by which enzymes confer enormous rate enhancements to chemical reactions. In the first study, mixed quantum mechanical/molecular mechanical calculations are applied to study a series of phenolate inhibitors of increasing pKa bound to ketosteroid isomerase to explore the catalytically relevant hydrogen bonds in the enzyme active site. The second study uses molecular dynamics simulations to explore the use of water in the active site in lieu of the native enzymatic hydrogen bonds. The third study focuses on the positioning of the catalytic base in ketosteroid isomerase using molecular dynamics simulations, and this positioning is suggested to arise from non-local contributions involving nearby hydrophobic residues and an active site loop. In the final study, an additional enzyme, dihydrofolate reductase is examined, and empirical valence bond molecular dynamics simulations are applied to evaluate the free energy barriers of the wild-type enzyme and several evolutionarily motivated mutants. Overall, these studies help to further our understanding of enzymes and the roles of individual factors in enzyme catalysis.