Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA

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dc.citation.articleNumbere2202239119
dc.citation.issueNumber32
dc.citation.journalTitleProceedings of the National Academy of Sciences
dc.citation.volumeNumber119
dc.contributor.authorJin, Shikai
dc.contributor.authorBueno, Carlos
dc.contributor.authorLu, Wei
dc.contributor.authorWang, Qian
dc.contributor.authorChen, Mingchen
dc.contributor.authorChen, Xun
dc.contributor.authorWolynes, Peter G.
dc.contributor.authorGao, Yang
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2022-09-01T14:18:23Z
dc.date.available2022-09-01T14:18:23Z
dc.date.issued2022
dc.description.abstractBacteriophage 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.
dc.identifier.citationJin, 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.
dc.identifier.digitalpnas-2202239119
dc.identifier.doihttps://doi.org/10.1073/pnas.2202239119
dc.identifier.urihttps://hdl.handle.net/1911/113171
dc.language.isoeng
dc.publisherNational Academy of Sciences
dc.rightsThis open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.titleComputationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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