DNA polymerases are crucial to DNA replication and repair. Various cancers and premature aging have been related to malfunction of DNA polymerases. Experiments and computations have revealed a common three-step nucleotide insertion pathway, involving a closing conformational transition following nucleotide insertion, a chemical reaction of nucleotidyl transfer, and a reverse conformational change to the open form of the product complex. Modeling and simulations, with full-atom details and long-range electrostatics via particle mesh Ewald methods, can help dissect details of these mechanisms. We will describe recent work providing recent insights into the reduced activity of DNA polymerase beta (pol beta) mutant E295K. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol beta in terms of the individual transition states along the pathway, associate denergies, and the active site conformation in the final closed form of the mutant. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Ongoing work also aims to study the effects of site specific mutations of another pol beta mutant, R283K, and the crucial role of ions in the enzyme's conformational pathway. Together, these studies underscore how the differences in conformational pathway affect the activity of DNA polymerases on atomic and energetic levels. Our analysis also suggests further experiments for pol beta mutants.

Atomistic dynamics simulations of DNA polymerase conformational pathways help unravel mechanistic aspects of enzyme repair

246th National Meeting (2013)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.