Defense Date


Document Type


Degree Name

Doctor of Philosophy



First Advisor

Nicholas Farrell


Zinc is an essential cofactor of several proteins. The roles of zinc in these proteins are classified as catalytic, structural or regulatory. Zinc present in structural sites is considered to be a chemically inert, static structural element. On the contrary, previous studies on a C2H2 type zinc finger model compound and the C3H type HIV-1 NCp7 C-terminal zinc knuckle have shown that zinc at these sites can undergo coordination sphere expansion under the influence of a Pt based electrophile. The pentacoordination observed around zinc in these experiments raises an important question: are the structural zinc motifs found in the proteins susceptible to coordination sphere expansion? Through DFT modeling, the existence and nature of the five coordinate zinc species was investigated. mPW1PW91 was chosen as the DFT method by benchmarking against the experimental parameters of a molecule that closely resembles those to be modeled. The results suggest that the observed coordination sphere expansion is due to the flexible nature of thiolate and chloride ligands that are part of the structure. However, if certain conditions are not met, the same flexibility can lead to the destabilization of these rather fragile structures. Unlike the stable three or four coordinate catalytic and structural zinc sites, at regulatory sites, zinc is typically bound to one or two protein ligands. Zinc inhibition of caspases which are central to the process of apoptosis is one such scenario. Several of the caspases are inhibited by zinc at low micromolar range. Regulation of caspases is a strategy for drug development toward apoptosis related diseases; thus it is important to know the molecular details of zinc inhibition of caspases. Currently, it is speculated that zinc binds to the active site His and Cys residues of caspases thus competing with the substrate. However our studies on caspase-3, using enzyme kinetics and biophysical methods, imply more than one zinc binding sites. Contrary to current beliefs, more than 50% of the inhibition is achieved by zinc without affecting substrate binding. Using DFT models, an alternative inhibitory zinc binding site, which better fits our experimental observations, is predicted.


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Date of Submission

December 2013

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Chemistry Commons