2017 Student Research Conference:
30th Annual Student Research Conference

Investigation of Product Dissociation Mechanism for DNA Polymerase I of B. stearothermophilus


Gene R. Cline
Dr. Bill R. Miller, Faculty Mentor

DNA polymerase is a vital enzyme involved in the replication of an organism’s genome. A nucleotide and magnesium ion travel into the active site while the polymerase is in the open conformation. Catalysis occurs upon the transition to the closed conformation when the incoming nucleotide forms a Watson-crick base pair, with pyrophosphate (PPi) as a byproduct of the reaction. However, the detailed mechanism of byproduct release is currently unknown. The structures of B. stearothermophilus DNA polymerase I in the open, closed, and ajar conformation have been obtained from the Protein Data Bank and modified to simulate product release of the post-catalytic state. Molecular dynamics (MD) simulations starting from each of these conformations were performed using Amber 14. All trajectories were visually analyzed using the VMD program and thermodynamic properties were calculated using MD analysis tools in Amber 14  Preliminary results suggests that a conformational change causes byproduct release.

Keywords: Molecular Biology, Computational Chemistry, Biochemistry

Topic(s):Biology
Chemistry

Presentation Type: Oral Paper

Session: 103-1
Location: MG 1096
Time: 8:00

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