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

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dc.citation.articleNumbere2202239119en_US
dc.citation.issueNumber32en_US
dc.citation.journalTitleProceedings of the National Academy of Sciencesen_US
dc.citation.volumeNumber119en_US
dc.contributor.authorJin, Shikaien_US
dc.contributor.authorBueno, Carlosen_US
dc.contributor.authorLu, Weien_US
dc.contributor.authorWang, Qianen_US
dc.contributor.authorChen, Mingchenen_US
dc.contributor.authorChen, Xunen_US
dc.contributor.authorWolynes, Peter G.en_US
dc.contributor.authorGao, Yangen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2022-09-01T14:18:23Zen_US
dc.date.available2022-09-01T14:18:23Zen_US
dc.date.issued2022en_US
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.en_US
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.en_US
dc.identifier.digitalpnas-2202239119en_US
dc.identifier.doihttps://doi.org/10.1073/pnas.2202239119en_US
dc.identifier.urihttps://hdl.handle.net/1911/113171en_US
dc.language.isoengen_US
dc.publisherNational Academy of Sciencesen_US
dc.rightsThis open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).en_US
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/en_US
dc.titleComputationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNAen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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