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Allostery of the flavivirus NS3 helicase and bacterial IGPS studied with molecular dynamics simulations




Davidson, Russell Bruce, author
McCullagh, Martin, advisor
Bernstein, Elliot, committee member
Barisas, George, committee member
Geiss, Brian, committee member

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Allostery is a biochemical phenomenon where the binding of a molecule at one site in a biological macromolecule (e.g. a protein) results in a perturbation of activity or function at another distinct active site in the macromolecule's structure. Allosteric mechanisms are seen throughout biology and play important functions during cell signaling, enzyme activation, and metabolism regulation as well as genome transcription and replication processes. Biochemical studies have identified allosteric effects for numerous proteins, yet our understanding of the molecular mechanisms underlying allostery is still lacking. Molecular-level insights obtained from all-atom molecular dynamics simulations can drive our understanding and further experimentation on the allosteric mechanisms at play in a protein. This dissertation reports three such studies of allostery using molecular dynamics simulations in conjunction with other methods. Specifically, the first chapter introduces allostery and how computational simulation of proteins can provide insight into the mechanisms of allosteric enzymes. The second and third chapters are foundational studies of the flavivirus non-structural 3 (NS3) helicase. This enzyme hydrolyzes nucleoside triphosphate molecules to power the translocation of the enzyme along single-stranded RNA as well as the unwinding of double-stranded RNA; both the hydrolysis and helicase functions (translocation and unwinding) have allosteric mechanisms where the hydrolysis active site's ligand affects the protein-RNA interactions and bound RNA enhances the hydrolysis activity. Specifically, a bound RNA oligomer is seen to affect the behavior and positioning of waters within the hydrolysis active site, which is hypothesized to originate, in part, from the RNA-dependent conformational states of the RNA-binding loop. Additionally, the substrate states of the NTP hydrolysis reaction cycle are seen to affect protein-RNA interactions, which is hypothesized to drive unidirectional translocation of the enzyme along the RNA polymer. Finally, chapter four introduces a novel method to study the biophysical coupling between two active sites in a protein. The short-ranged residue-residue interactions within the protein's three dimensional structure are used to identify paths that connect the two active sites. This method is used to highlight the paths and residue-residue interactions that are important to the allosteric enhancement observed for the Thermatoga maritima imidazole glycerol phosphate synthase (IGPS) protein. Results from this new quantitative analysis have provided novel insights into the allosteric paths of IGPS. For both the NS3 and IGPS proteins, results presented in this dissertation have highlighted structural regions that may be targeted for small-molecule inhibition or mutagenesis studies. Towards this end, the future studies of both allosteric proteins as well as broader impacts of the presented research are discussed in the final chapter.


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molecular dynamics


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