A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.

ABSTRACT: DNA polymerase beta (pol beta) is a small eukaryotic enzyme with the ability to repair short single-stranded DNA gaps that has found use as a model system for larger replicative DNA polymerases. For all DNA polymerases, the factors determining their catalytic power and fidelity are the interactions between the bases of the base pair, amino acids near the active site, and the two magnesium ions. In this report, we study effects of all three aspects on human pol beta transition state (TS) binding free energies by reproducing a consistent set of experimentally determined data for different structures. Our calculations comprise the combination of four different base pairs (incoming pyrimidine nucleotides incorporated opposite both matched and mismatched purines) with four different pol beta st

SUBMITTER: Rucker R 

PROVIDER: S-EPMC2966340 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature