Structural and dynamical effects of phosphorylation on DNA polymerase β studied by molecular dynamics simulations.

Abstract

DNA polymerase β (pol β) is a member of the X-family of DNA polymerases that catalyze the distributive addition of nucleoside triphosphates during base excision DNA repair. Previous studies have shown that the enzyme was phosphorylated in vitro with PKC at two serines (44 and 55), causing the loss of DNA polymerase activity but not DNA binding. Here, we report a comprehensive atomic resolution study of wild-type and phosphorylated DNA polymerase in presence of Mg ions using microsecond-long molecular dynamics (MD) simulations. The results show drastic conformational changes in the structure of DNA polymerase β due to S44 phosphorylation. Phosphorylation-induced conformational changes transform the enzyme from a closed to an open structure. The dynamic cross-correlation calculations show that phosphorylation enhances correlated motions between different domains. Centrality network analysis reveals that the S44 phosphorylation causes structural rearrangements and modulates the information pathway between the Lyase domain and base pair binding domain. Further analysis of our simulations reveals that a critical hydrogen bond (between S44 and E335) disruption and the formation of three additional salt bridges are potential drivers of these conformational changes. In addition, we found that two of these additional salt bridges form in the presence of Mg ions on the active sites of the enzyme. Notably, we have identified phosphorylated-induced allosteric coupling between the inter-domain regions. Collectively, the result provides a mechanistic understating of conformational transitions observed due to the phosphorylation and reveals a putative allosteric site.