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Department of Biochemistry & Molecular Biology

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These digital collections include theses, dissertations, and datasets from the Department of Biochemistry & Molecular Biology.

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Browsing Department of Biochemistry & Molecular Biology by Subject "allostery"

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    Adenosine triphosphate is an allosteric inhibitor of coxsackievirus B3 3Dpol
    (Colorado State University. Libraries, 2016) Karr, Jonathan Paul, author; Peersen, Olve, advisor; Cohen, Robert, committee member; Perera, Rushika, committee member
    Picornaviruses pose a significant threat to human and animal health, but at present there are no drugs to prevent or treat picornaviral infections. However, intensive study of the picornaviral lifecycle has revealed several promising pharmacological targets, including the RNA-dependent RNA polymerase, 3Dpol, that is responsible for replicating the viral genome. 3Dpol is central in the virus lifecycle, determines the distribution of mutants in viral progeny, and is a very highly conserved protein across picornavirus species. As such, it is an attractive target for antiviral research. The only 3Dpol inhibitors that have been found to date are nucleoside analogues that act directly on the active site, even though global dynamics of the protein that are sensitive to allosteric effects of various mutations have been shown to be important determinants of fidelity. The research presented in this thesis provides the first direct evidence of allosteric regulation of 3Dpol by a small molecule. Inhibition assays investigating the relative affinities of a stalled coxsackievirus elongation complex for non-cognate nucleotides uncovered a mixed inhibition profile of ATP. Among the six picornavirus species tested, this mode of inhibition seems specific to coxsackievirus B3 (CVB3). Engineered mutations in CVB3 3Dpol, including two that were previously found to lower polymerase fidelity, diminish the uncompetitive component of ATP inhibition. ATP inhibition was found to be dependent on the β- and γ-phosphates. The potential role of ATP’s allosteric effect in the virus lifecycle as well as the importance of a biochemically confirmed allosteric site on the polymerase are discussed.