期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2022
卷号：119
期号：32
DOI：10.1073/pnas.2202239119
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance
Hexametric helicase is a central component in DNA replication and many replicative helicases have been proposed as drug targets for disease treatment. Knowledge of both the structures of replicative helicases and their mechanisms of translocation is essential for a better understanding of DNA replication and replication stress response, as well as for therapeutic targeting of helicases. The very large size of the helicase and the large-scale conformational changes that occur during helicase translocation have hindered investigations of helicase structure and dynamics. Simulations with our newly developed coarse-grained protein–single-stranded DNA force field recapitulated the large-scale translocation of the gp4 subunit with limited computational cost and revealed numerous mechanistic details about gp4 helicase translocation.
Bacteriophage T7 gp4 helicase has served as a model system for understanding mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how nucleoside 5′-triphosphate hydrolysis and translocation of gp4 helicase are coupled is not fully resolved. Here, we used a thermodynamically benchmarked coarse-grained protein force field, Associative memory, Water mediated, Structure and Energy Model (AWSEM), with the single-stranded DNA (ssDNA) force field 3SPN.2C to investigate gp4 translocation. We found that the adenosine 5′-triphosphate (ATP) at the subunit interface stabilizes the subunit–subunit interaction and inhibits subunit translocation. Hydrolysis of ATP to adenosine 5′-diphosphate enables the translocation of one subunit, and new ATP binding at the new subunit interface finalizes the subunit translocation. The LoopD2 and the N-terminal primase domain provide transient protein–protein and protein–DNA interactions that facilitate the large-scale subunit movement. The simulations of gp4 helicase both validate our coarse-grained protein–ssDNA force field and elucidate the molecular basis of replicative helicase translocation.
关键词：enhelicasegp4motor proteinscoarse-grained model
