HYBRID QUANTUM/CLASSICAL MOLECULAR DYNAMICS SIMULATIONS OF HYDROGEN TRANSFER REACTIONS IN ENZYMES

Open Access
Author:
Chakravorty, Dhruva Kumar
Graduate Program:
Chemistry
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
March 15, 2010
Committee Members:
  • Prof Sharon Hammes Schiffer, Dissertation Advisor
  • Prof Sharon Hammes Schiffer, Committee Chair
  • James Bernhard Anderson, Committee Member
  • Philip C. Bevilacqua, Committee Member
  • James David Kubicki, Committee Member
Keywords:
  • DLPROTEIN
  • EVB
  • DHFR
  • ketosteroid isomerase
  • KSI
  • WHAM
  • Umbrella Integration
  • hydrogen transfer
Abstract:
This thesis describes the study of hydrogen transfer reactions in enzymes. For this purpose the thesis is divided into two parts. The first part is work undertaken in the development of new methods for the study of such reactions, while the second part of the thesis focuses on the study of the isomerization reaction in ketosteroid isomerase (KSI). In part one of this thesis, the implementation of the umbrella integration method for calculating the potential of mean force (PMF) for a chemical reaction within the empirical valence bond (EVB) framework is presented. The umbrella integration method is based on the derivative of the PMF with respect to the reaction coordinate. An analytical expression for this derivative applicable to certain types of EVB potentials is presented. The umbrella integration method reduces the statistical errors, converges efficiently, and does not require significantly overlapping windows compared to the Weighted Histogram Analysis method. A modified version of the weighted histogram analysis method that shares these advantages is also proposed and implemented. The second part of this thesis presents the study of proton transfer reactions in ketosteroid isomerase (KSI) using hybrid quantum/classical methodologies. The reaction requires two proton transfer reactions. Tyr14 and Asp99 form catalytically important hydrogen bonds that help stabilize the dienolate intermediate in these reactions. Chapter 3 describes the study of these proton transfer reactions in wild-type KSI. Chapter 4 extends this analysis to the Tyr14Phe, Asp99Leu and Tyr14Phe/Asp99Leu mutant varieties of KSI. Our simulations suggest a pre-organized active site in which relatively small changes occur to strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions.