Date of Award

Spring 2010

Document Type


Degree Name

Doctor of Philosophy (PhD)


Chemistry & Biochemistry

Committee Director

Jennifer Boutsma

Committee Member

Lesley Greene

Committee Member

Craig bayse

Committee Member

Kenneth Brown


The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new conformation. Free energy methods examine the stability of the new loop conformer relative to the others. External perturbation molecular dynamics simulations and normal mode analysis methods examine possible M20 loop pathways occurring either when one loop conformer is forced to change into another or when a ligand is pulled out of its binding site.

On the topological level, conserved residue-residue interaction networks found among three different protein superfamilies (the all α-helix death domains, the α/β-plaits and the all β-sheet immunoglobulins), each of different secondary structure but sharing the Greek-Key topology, are assessed for any inherent stability they might contain relative to randomly selected interaction networks. This assessment is achieved by simulating one protein from each family at different temperatures, ranging from 300 to 600 K, and observing that adding thermal energy to the system causes the random interaction networks to fall apart more easily than the conserved networks.

When considered together, the conformational and topological projects, although very different from each other, both demonstrate the same idea - that regardless of scale, instability causes change and vice versa. This dissertation is divided into five chapters: Introduction, Theoretical Background, M20 Loop Conformers of Dihydrofolate Reductase, Conserved Contact Networks of Greek-Key Proteins and Summary.


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