Molecular Dynamics studies of DNA polymerase kappa, a human protein involved in translesion synthesis

Abstract

Y family DNA polymerases are a class of enzymes characterized by their ability to copy damaged DNA in a process known as translesion synthesis. They do not eliminate the damage per se, but at least they are able to bypass a stalled replication, avoiding cell death. These polymerases bypass a wide variety of DNA damage, including thymine‐thymine dimers, inter‐strand DNA crosslinks, and other damage caused by reactive oxygen species. Unfortunately, they do not replicate the DNA with high fidelity and some polymerases are more error prone than others. In addition, the kinds of lesions that this group of enzymes can bypass are dependent on the enzyme itself, despite the general architectural similarities of all these enzymes. Human DNA polymerase kappa (pol k) is a member of the Y‐family of DNA polymerases involved in translesion synthesis in humans. Kinetics students have shown that this enzyme can bypass minor groove lesions such as O6‐methylated guanine (O‐metG) but not major groove lesions such as N2‐furfuryl‐guanine (N‐fG). Hydrogen exchange experiments have suggested solvent accessibility changes in various systems, hinting at a mechanism of conformational change upon substrate binding. 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 addition, binary systems, comprised of just the DNA and the protein without the incoming nucleotide, were examined. Our results show that pol k does not attain a close, catalytically competent state in both the binary and the O‐metG systems, as evidenced by the few contacts between the protein and the incoming nucleotides. We have also identified key residues important for the stabilization of the incoming nucleotide as well as formulated a hypothesis to why the O‐metG lesion does not get bypassed as efficiently as other damages.Support or Funding InformationThis work was supported in part by the Rose M. Badgeley Residuary Charitable Trust Award and the Colette Mahoney Award to BSB.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.