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 translesion synthesis of damaged DNA. Translesion synthesis allows for continued replication past lesions in the DNA that would otherwise stall or halt replication, leading to cell apoptosis. 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. Starting with one of the available crystal structures of pol k, we prepared eight different DNA/protein models and we solvated them in an octahedral water box with counter‐ions to a final ionic strength of 150 MM, using CHARMMgui. Subsequently, 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 nucleotide. All simulations were performed using the program NAMD and were run for 10 ns each. We ran multiple simulations for the same system to ensure reproducibility of the results. Simulation of the binary system (just the protein and DNA without the incoming nucleotide) was also performed as a control system. By analyzing these different structures, we ascertained the residues crucial for fidelity and proposed a mechanism for lesion discrimination.Support or Funding InformationThis work was supported in part by a grant from the Rose M. Badgeley Residuary Charitable Trust.