DNA polymerases are enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates. DNA polymerase β, a member of X family DNA polymerase, is involved in gap-filling DNA synthesis. It has been proposed that during the nucleotidyl transfer reaction two metals are utilized to facilitate the reaction. In recent years a third metal was captured by time-resolved X-ray crystallography. In particular, the occupancy of the third metal increased with the accumulation of the reaction product. Since its first visualization, the role of the third metal has been extensively debated. In this study we have performed molecular dynamics and quantum mechanics calculations to investigate the role of the third metal. Properties such as its binding affinity compared with the other two metal binding sites and moving trajectory during the reaction were explored. The corresponding change of reaction energy barrier and geometry alignments before and after reactions were discussed.

Possible role of the third metal: A QM and MD investigation of DNA synthesis with DNA polymerase β

Where thousands of chemistry professionals meet to share ideas and advance scientific and technical knowledge. Spring 2023 abstracts, posters, and presentations will launch at the end of March.

ACS Spring 2023

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