29th Annual Student Research Conference
Investigation of Product Dissociation Pathways for DNA Polymerase
Gene R. Cline
Dr. Bill R. Miller, Faculty Mentor
DNA polymerase is a vital enzyme involved in the replication of the genome of an organism. Upon catalysis, the triphosphate of the newly added dinucleotide is cleaved, forming diphosphate as a byproduct. It has been accepted that diphosphate and two magnesium atoms leave the active site after catalysis, but the exact pathway of product release is currently unknown. We are utilizing GPU-accelerated computer simulations from the Amber 14 Molecular Dynamics package to determine how and when the byproducts egress from the active site. The structures of B. stearothermophilus DNA polymerase in the open, closed, and ajar conformation have been obtained from the Protein Data Bank and modified to simulate product release of post-catalytic state. Modified forms of each conformation have resulted in a total of 15 different simulations (~250 ns per simulation); however, details are still not clearly known, suggesting the necessity for extending simulation times further.
Keywords: DNA Polymerase, Biochemistry, Computational Chemistry
Topic(s):Biology
Chemistry
Computer Science
Presentation Type: Poster
Session: 4-10
Location: GEO-SUB
Time: 3:30