Date of Award

8-2011

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Legacy Department

Physical Chemistry

Advisor

Dominy, Brian N.

Committee Member

Stuart , Steve J.

Committee Member

Arya , Dev P.

Committee Member

McNeill , Jason

Abstract

Glycosylase enzymes initiate the process of base excision repair (BER) in order to prevent the irreversible modification of the genome. In the BER process a damaged DNA base is recognized, removed from the DNA sequence, and then the remaining abasic site is repaired. Glycosylase enzymes are responsible for the base recognition mechanism and catalysis of the base excision. One of the most studied glycosylase superfamilies is uracil DNA glycosylase (UDG). The UDG superfamily has demonstrated specificity for excising uracil, which is the deamination product of cytosine, from DNA sequences of prokaryotes and eukaryotes. Mismatch-specific uracil DNA glycosylase (MUG) is a member of the UDG superfamily, and interestingly has shown specificity for both uracil and xanthine bases.
The following dissertation provides an anlaysis on the recognition mechanism of E. coli MUG for deaminated DNA bases. Glycosylase enzymes require the damaged base to be flipped out of the base stack, and into an active site for catalysis of the N-glycosidic cleavage. Typically, recognition of substrates by enzymes is characterized by binding affinities, but in the following work the binding of E.Coli MUG is broken down into contributions from the base flipping and enzyme binding equilibria.
Since DNA conformational changes play a large role in UDG systems, the robustness of molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy method was evaluated for a DNA conformational change. The A-form to B-form DNA conformational free energy differences were calculated using MM/PBSA, and compared with free energy differences determined with a more rigorous umbrella sampling method. MM/PBSA calculations of the free energy difference between A-form and B-form DNA are shown to be in very close agreement with the PMF result determined using an umbrella sampling approach. The sensitivity to solvent model and force field used during conformational sampling was also established for the MM/PBSA free energies.
In order to determine the influence of base flipping conformational changes on the MUG recognition process, PMF profiles were generated for each of the damaged bases (uracil, xanthine, oxanine, inosine). Agreement was displayed between the base pair stability trends from the umbrella sampling, and the enzyme activities from experiment. Interaction energies and structural analyses were used to examine the MUG enzyme, which revealed regions of the active site critical for binding xanthine and uracil substrates. Site-directed mutagenesis experiments were performed on MUG to determine the role of specific amino acids in the recognition mechanism. Mutations were studied further through modeling and molecular dynamics (MD) simulations of the unbound and bound proteins.

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