Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase

Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase Tsuyoshi Terakawa, Fritz Nagae, Yutaka Murata, Masataka Yamauchi, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6598384/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Faithful replication of eukaryotic chromatin requires the CMG helicase to translocate directionally along single-stranded DNA (ssDNA) while unwinding double-stranded DNA (dsDNA) and navigating nucleosomes. However, the mechanism by which CMG achieves processive translocation and deals with nucleosomal barriers remains incompletely understood. Here, using coarse-grained molecular dynamics simulations with ATP-driven conformational switching, we showed that asymmetric rotational transitions among four distinct ssDNA-binding states enable CMG to achieve directional translocation and DNA unwinding. We further demonstrated that the fork protection complex (Csm3/Tof1) and RPA enhance processivity through distinct mechanisms: Csm3/Tof1 grips the parental duplex to suppress backtracking, while RPA alleviates lagging-strand clogging. Upon nucleosome encounter, Csm3/Tof1 promoted partial unwrapping of the entry DNA, but further progression was energetically restricted near the nucleosomal dyad. The histone chaperone FACT lowered this barrier and simultaneously prevented inappropriate histone transfer to the lagging strand. Our results provide mechanistic insights into how the eukaryotic replisome coordinates helicase activity, nucleosome navigation, histone chaperon function, and histone recycling during eukaryotic DNA replication. Biological sciences/Biophysics/Computational biophysics Biological sciences/Biophysics/Molecular biophysics/Molecular conformation Biological sciences/Molecular biology/DNA replication/Replisome Full Text Additional Declarations There is NO Competing Interest. Supplementary Files MovieS1.mp4 Supplementary Movie 1 MovieS2.mp4 Supplementary Movie 2 MovieS3.mp4 Supplementary Movie 3 MovieS4.mp4 Supplementary Movie 4 MovieS5.mp4 Supplementary Movie 5 MovieS6.mp4 Supplementary Movie 6 MovieS7.mp4 Supplementary Movie 7 MovieS8.mp4 Supplementary Movie 8 MovieS9.mp4 Supplementary Movie 9 MovieS10.mp4 Supplementary Movie 10 MovieS11.mp4 Supplementary Movie 11 MovieS12.mp4 Supplementary Movie 12 MovieS13.mp4 Supplementary Movie 13 RS.pdf Reporting Summary softwarepolicy.pdf Software Policy Checklist Cite Share Download PDF Status: Published Journal Publication published 21 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6598384","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":453447311,"identity":"482fa025-2d6a-4cdb-8a17-ee53af446ae6","order_by":0,"name":"Tsuyoshi 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