MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICAL/MOLECULAR MECHANICAL METHODS FOR PROTON AND HYDRIDE TRANSFER IN THE ENZYME DIHYDROOROTATE DEHYDROGENASE
Open Access
Author:
Small, Yolanda A.
Graduate Program:
Chemistry
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
December 14, 2006
Committee Members:
Associate Professor Juliette T J Lecomte, Committee Member Albert Welford Castleman Jr., Committee Member Professor Sharon Hammes Schiffer, Committee Chair/Co-Chair Kristen Ann Fichthorn, Committee Member
Inhibiting the enzyme Dihydroorotate Dehydrogenase (DHOD) has the effect of interrupting the pyrimidine biosynthetic pathway responsible for the generation of precursors for DNA and RNA synthesis. Given this impact, therapeutic drugs for cancer and arthritis have been designed to target DHOD, but it is not clearly understood how the drugs function because details about the enzyme’s mechanism still remain elusive. Experimental researchers have contributed structural and kinetic results in an attempt to elucidate the mechanism in DHOD. Their proposals for a proton and hydride transfer reaction form the basis for our computational contributions to the ongoing dialogue about catalysis in DHOD. In this study, three methods have been applied to the DHOD system. Quantum mechanical calculations were performed to determine transition states for proton and hydride transfer in DHOD. Molecular dynamics simulations were conducted to study proton relay pathways that facilitate proton transfer in the weakly basic active site environment. Finally, combined quantum mechanical/molecular mechanical methods were used to quantify the likelihood of a sequential or concerted mechanism for proton and hydride transfer.
In this thesis, Chapter 1 provides the framework and general motivation for studying enzymes with computational methods. Chapter 2 provides background on the DHOD system, including discussions about the experimental techniques used, relevant data obtained and how useful this data will be for comparison to computational methods. Chapter 3 discusses the computational methods applied to DHOD. Chapter 4 reports the results of molecular dynamics simulations that were done to investigate proton relay pathways at the active site of DHOD. Chapter 5 reports the results of QM/MM calculations that were done to investigate the proton and hydride transfer mechanism. Chapter 6 concludes the study with perspectives on what has been gained by this study and what future directions can be taken.
