Anharmonic Effects of Small Clusters of Molecules and Ranking Activity of Protein Mutants

Open Access
Author:
Kumarasiri, Malika Dhananjaya
Graduate Program:
Chemistry
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
December 03, 2008
Committee Members:
  • Prof Sharon Hammes Schiffer, Dissertation Advisor
  • Sharon Hammes Schiffer, Committee Chair
  • Will Castleman, Committee Member
  • Philip C. Bevilacqua, Committee Member
  • James David Kubicki, Committee Member
Keywords:
  • Molecular Dynamics
  • Mutant Studies
Abstract:
This thesis is presented in two parts. In part 1, anharmonic effects of small molecules are investigated using theoretical methods. In part 2, mutants of enzymes are ranked according to their activation energy barriers. Anharmonic effects are required to describe vital processes such as bond breaking or bond forming, and they significantly affect properties such as geometries and vibrational frequencies. Despite their importance, anharmonic effects are typically overlooked due to the high computational cost associated with calculating them. In part 1 of this thesis, anharmonic effects of small clusters of ammonium nitrate and hydroxylammonium nitrate are investigated. We compare the structures and vibrational modes against their harmonic counterparts using a vibrational perturbation theory approach within the density functional theory framework. Anharmonic effects significantly alter the structures and vibrational frequencies of ammonium nitrate and hydroxylammonium nitrate clusters. In part 2 of the thesis, we implement an efficient procedure to rank many mutants of enzymes or protein designs according to the free energy barrier of the catalyzed reaction. Escherichia coli dihydrofolate reductase (DHFR) and its mutants are used in this study, and the mutant structures are generated based on the wild type enzyme structure. Different methods are investigated to calculate the free energy barrier of hydride transfer in DHFR. The hydride transfer reaction is investigated using empirical valence bond molecular dynamics simulations followed by a weighted histogram analysis or umbrella integration to generate the free energy distribution along the reaction coordinate. Fifteen single mutants of DHFR are used in this study. Our results indicate a promising correlation between experimentally determined reaction rates and calculated free energy barriers. The procedures are mostly automated and can easily be adapted for other enzymatic mutants or designs.