Models of conformational selection of DNA polymerase X in the presence of oxoG lesions help interpret kinetics data

Abstract

DNA polymerase X (pol X) from the African swine fever virus (ASFV) is a 174‐amino‐acid repair polymerase that participates in a viral Base Excision Repair (BER) pathway. Pol X is a member of the X‐family of polymerases, which includes the homologous human DNA polymerase β (pol β). In contrast to pol β, pol X lacks the fingers subdomain and exhibits substantially lower fidelity. Molecular dynamic studies of polX/DNA complexes suggest a hybrid conformational selection, whereby polX/DNA complexes sample low‐energy conformations, which are stabilized by the correct incoming dNTP. Here we present molecular dynamic simulations of pol X/DNA complexes in which the template base opposite to the incoming dNTP contains the damaged base 7,8‐ Dihydro‐8‐oxoguanine (oxoG). OxoG is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetics data reveals that pol X accommodates A opposite to oxoG with efficiency even higher than the non‐damaged G:C base pair. The goal of this molecular dynamic study is to help interpret, at an atomistic level, previously published kinetics data. The simulations presented in this study reveal that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson‐Crick ternary complexes. Comparisons with other polX/DNA systems with oxoG on the templating strand will also be presented.