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Date of Award

Spring 2012

Document Type

Restricted Thesis: Campus only access

Degree Name

Bachelor of Science


Biochemistry & Molecular Biol.

First Advisor

Dr. Ellis Bell

Second Advisor

Dr. Samuel Abrash


Geometry optimization calculations have been used to find the minimum total energy and structure of the transition state for hydride transfer and proton abstraction during the conversion of malate to oxaloacetate catalyzed by glyoxysomal malate dehydrogenase (gMDH). These revealed that the proton abstraction preceded the hydride transfer due to the activity of the arginine residues around the active site. These gas phase simulations tested two truncated models, one including the arginine residues (Arg-124, Arg-130, and Arg-196), whereas the other one did not. The initial transition states were compared to determine the initial catalytic reaction. Molecular dynamics was used with the whole gMDH dimer, in explicit solvent, to simulate the catalytic reaction with the substrate malate and the cofactor NAD. The simulation analysis helps to give insight into the role of specific regions of gMDH that contribute to the mechanism. The relative changes in the position of Asp-193 and His-220 during the simulation were studied to determine their interactions in the proton relay system. The relative flexibility of each residue was measured during the simulation. The experiment gives insight into ways of developing analytical and predictive numerical tools to be used in studying the active site and second sphere mutations of gMDH.