2021 Student Research Conference:
34th Annual Student Research Conference

Investigating Deprotonation of DNA Base Pairs by DNA Polymerase I in G. stearothermophilus Using QM/MM

Jake A. Collins
Dr. Bill Miller, Faculty Mentor

DNA replication is a vital process to the growth and reproduction of cells. During DNA replication, DNA Polymerase I is the main enzyme responsible for deleting RNA primers and adding correct Watson-Crick Base Pairs. Much of the DNA polymerase mechanism has been well studied, but the removal of the terminal proton on the 3' alcohol of the primer strand that initiates catalysis remains uncharacterized in Geobacillus stearothermophilus DNA polymerase I. In particular, it is unknown what molecule/residue accepts the 3'-OH proton. Using Quantum Mechanics/Molecular Mechanics, the reaction chemistry that occurs in the closed conformation of G. stearothermophilus DNA polymerase I can be studied. Our preliminary results show that the proton can be successfully transferred to another site, but further work is needed to determine the relative energy needed to transfer the proton to multiple acceptors.

Keywords: Computational Chemistry, DNA Polymerase I, DNA, Quantum Mechanics

Topic(s):Biochemistry and Molecular Biology

Presentation Type: Asynchronous Virtual Oral Presentation

Session: 3-14
Location: https://flipgrid.com/f86d186b
Time: 0:00

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