Investigating the mechanism of trans‐lesion synthesis by human DNA polymerase kappa

Abstract

Our DNA is constantly under attack by both exogenous and endogenous chemicals that have the ability to damage it. If not repaired, these DNA adducts can lead to mutations to the DNA or even worse, they can halt replication, eventually leading to aging and/or cancer. Human DNA polymerase kappa (pol k) is a member of the Y‐family of DNA polymerases, known for their ability to conduct trans‐lesion synthesis of damaged DNA. So far, the mechanism for lesion bypass discrimination by pol k is unclear. Recent studies suggested that similar to other polymerases, pol k might cycle between different open and closed conformations upon binding to DNA and the substrate. Through molecular dynamics simulations, we tested the validity of the conformational change hypothesis by comparing the structural changes undergone by pol k in the presence of different templating lesions and with correct and incorrect incoming nucleotides. In particular, we simulated a binary system, with DNA and protein only, ternary systems with correct and incorrect incoming nucleotides, and a ternary system with with a O6‐methylated guanine (O‐metG) on the templating strand, a damage which pol k cannot bypass. Preliminary results show that pol k does not attain a close, catalytically competent state both in the binary and the O‐metG system, as evidenced by the few contacts between the protein and the incoming nucleotide. We have also identified key residues important for the stabilization of the incoming nucleotide as well as a hypothesis to why the O‐metG does not get bypassed as efficiently as other damages.Support or Funding InformationThis work was funded by the Rose M. Badgeley Residuary Charitable Trust and the Sister Colette Mahoney Science Research Grant.