Jin, ShikaiBueno, CarlosLu, WeiWang, QianChen, MingchenChen, XunWolynes, Peter G.Gao, Yang2022-09-012022-09-012022Jin, Shikai, Bueno, Carlos, Lu, Wei, et al.. "Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA." <i>Proceedings of the National Academy of Sciences,</i> 119, no. 32 (2022) National Academy of Sciences: https://doi.org/10.1073/pnas.2202239119.https://hdl.handle.net/1911/113171Bacteriophage 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.engThis open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).Journal articlepnas-2202239119https://doi.org/10.1073/pnas.2202239119