{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:02:52Z","timestamp":1790254972215,"version":"4.1.0"},"reference-count":50,"publisher":"American Chemical Society (ACS)","issue":"38","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI166050"],"award-info":[{"award-number":["R01AI166050"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>SARS-CoV-2 nonstructural protein 13 (nsp13) is a highly conserved helicase that couples ATP hydrolysis to RNA translocation through long-range allosteric communication between its ATPase and RNA-binding domains. In prior work, we identified L405 as a key regulator of interdomain motions and proposed that the L405D mutation would disrupt this coupling by perturbing conformational transitions required for translocation [J. Phys. Chem. B2024, v128, 492\u2013503. ]. Subsequent experiments confirmed that L405D attenuates helicase activity and ATPase activity, implicating the potential formation of a new salt bridge, D405-R560, for both effects [ J. Biol. Chem.2026, v302, 111198.]. Here, we provide a data-driven explanation for both effects by combining Gaussian accelerated molecular dynamics (GaMD) simulations with Shape-GMM clustering and linear discriminant analysis. Whereas wild-type nsp13 exhibits both conformational selection and induction, L405D collapses the conformational landscape to operate predominantly through selection, with ATP-induced structural transitions observed in the wild-type ensemble no longer sampled by the mutant. This loss of induction likely impairs ATP turnover while simultaneously disrupting coordinated motif\u2013RNA interactions required for inchworm translocation. These findings demonstrate how mutation-induced reshaping of conformational ensembles can modulate access to reaction-competent states, providing a general framework for understanding how targeted mutations disrupt catalytic function through allosteric ensemble remodeling in motor proteins.<\/jats:p>","DOI":"10.1021\/acs.jpcb.6c03935","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T12:02:04Z","timestamp":1788955324000},"page":"9851-9861","source":"Crossref","is-referenced-by-count":0,"title":["Mechanochemical\nDecoupling of ATP Hydrolysis and RNA\nTranslocation in SARS-CoV-2 nsp13 by the L405D Mutation"],"prefix":"10.1021","volume":"130","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-0307-1609","authenticated-orcid":true,"given":"Elham","family":"Fazelpour","sequence":"first","affiliation":[{"name":"Oklahoma State University , , , ,","place":["Stillwater, Oklahoma, United States, 74078"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priti","family":"Roy","sequence":"additional","affiliation":[{"name":"Oklahoma State University , , , ,","place":["Stillwater, Oklahoma, United States, 74078"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kole J.","family":"Frederick","sequence":"additional","affiliation":[{"name":"Oklahoma State University , , , ,","place":["Stillwater, Oklahoma, United States, 74078"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8603-4388","authenticated-orcid":true,"given":"Martin","family":"McCullagh","sequence":"additional","affiliation":[{"name":"Oklahoma State University , , , ,","place":["Stillwater, Oklahoma, United States, 74078"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092408095862500_cit1","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1146\/annurev.bi.65.070196.001125","article-title":"Mechanisms of Helicase-Catalyzed DNA Unwinding","volume":"65","author":"Lohman","year":"1996","journal-title":"Annu. Rev. Biochem."},{"key":"2026092408095862500_cit2","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1146\/annurev.biochem.76.052305.115300","article-title":"Structure and Mechanism of Helicases\nand Nucleic Acid Translocases","volume":"76","author":"Singleton","year":"2007","journal-title":"Annu. Rev. Biochem."},{"key":"2026092408095862500_cit3","doi-asserted-by":"publisher","first-page":"5619","DOI":"10.1128\/JVI.78.11.5619-5632.2004","article-title":"Multiple enzymatic\nactivities associated\nwith severe acute respiratory syndrome coronavirus helicase","volume":"78","author":"Ivanov","year":"2004","journal-title":"J. Virol."},{"key":"2026092408095862500_cit4","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1016\/j.cell.2020.07.033","article-title":"Structural\nbasis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription\ncomplex","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"2026092408095862500_cit5","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/bs.enz.2021.09.005","article-title":"RNA helicases required\nfor viral propagation in humans","volume":"50","author":"Marecki","year":"2021","journal-title":"Enzymes"},{"key":"2026092408095862500_cit6","doi-asserted-by":"publisher","first-page":"9144","DOI":"10.1021\/acs.jpclett.0c02421","article-title":"Discovery\nof COVID-19 inhibitors targeting the SARS-CoV-2\nNsp13 helicase.","volume":"11","author":"White","year":"2020","journal-title":"J. Phys. Chem. Lett."},{"key":"2026092408095862500_cit7","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abj4526","article-title":"Toward wide-spectrum\nantivirals against coronaviruses:\nMolecular characterization of SARS-CoV-2 NSP13 helicase inhibitors","volume":"8","author":"Perez-Lemus","year":"2022","journal-title":"Sci. Adv."},{"key":"2026092408095862500_cit8","doi-asserted-by":"publisher","first-page":"1819","DOI":"10.1128\/JB.184.7.1819-1826.2002","article-title":"Modularity and specialization in superfamily 1 and\n2 helicases","volume":"184","author":"Singleton","year":"2002","journal-title":"J. Bacteriol."},{"key":"2026092408095862500_cit9","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1016\/0968-0004(92)90338-A","article-title":"A new group\nof putative RNA helicases","volume":"17","author":"Koonin","year":"1992","journal-title":"Trends Biochem. Sci."},{"key":"2026092408095862500_cit10","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.sbi.2010.03.011","article-title":"SF1 and SF2\nhelicases: family matters","volume":"20","author":"Fairman-Williams","year":"2010","journal-title":"Curr. Opin. Struct.\nBiol."},{"key":"2026092408095862500_cit11","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.virusres.2014.12.001","article-title":"What we\nknow but do not understand about nidovirus helicases","volume":"202","author":"Lehmann","year":"2015","journal-title":"Virus Res."},{"key":"2026092408095862500_cit12","doi-asserted-by":"publisher","first-page":"2737","DOI":"10.1007\/s00705-020-04752-x","article-title":"Changes to virus\ntaxonomy and the Statutes ratified\nby the International Committee on Taxonomy of Viruses (2020)","volume":"165","author":"Walker","year":"2020","journal-title":"Arch. Virol."},{"key":"2026092408095862500_cit13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25166-6","article-title":"Structure, mechanism and crystallographic fragment\nscreening of the SARS-CoV-2 NSP13 helicase","volume":"12","author":"Newman","year":"2021","journal-title":"Nat. Commun."},{"key":"2026092408095862500_cit14","doi-asserted-by":"publisher","first-page":"8787","DOI":"10.1021\/acs.jpcb.1c04528","article-title":"Role of ATP\nin the RNA translocation mechanism of SARS-CoV-2\nNSP13 helicase","volume":"125","author":"Weber","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2026092408095862500_cit15","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.1002\/prot.70113","article-title":"Allosteric\nRegulation of RNA Affinity by Motif V-VI\nCoupling in West Nile Virus NS3 Helicase","volume":"94","author":"Roy","year":"2026","journal-title":"Proteins"},{"key":"2026092408095862500_cit16","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1021\/acs.jpcb.3c06714","article-title":"Role of ATP hydrolysis and product release in the translocation\nmechanism of SARS-CoV-2 NSP13","volume":"128","author":"Lawal","year":"2024","journal-title":"J. Phys. Chem.\nB"},{"key":"2026092408095862500_cit17","doi-asserted-by":"publisher","first-page":"6516","DOI":"10.1021\/acs.chemrev.5b00562","article-title":"Protein ensembles: how does nature\nharness thermodynamic fluctuations for life? The diverse functional\nroles of conformational ensembles in the cell","volume":"116","author":"Wei","year":"2016","journal-title":"Chem. Rev."},{"key":"2026092408095862500_cit18","doi-asserted-by":"publisher","first-page":"2375","DOI":"10.1002\/anie.199423751","article-title":"The key-lock theory and the induced fit theory","volume":"33","author":"Koshland","year":"1995","journal-title":"Angew. Chem., Int. Ed. Engl."},{"key":"2026092408095862500_cit19","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.bpc.2017.01.004","article-title":"Conformational selection\nand induced fit as a useful\nframework for molecular motor mechanisms","volume":"223","author":"Galburt","year":"2017","journal-title":"Biophys.\nChem."},{"key":"2026092408095862500_cit20","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/nchembio.232","article-title":"The role of dynamic conformational\nensembles in biomolecular recognition","volume":"5","author":"Boehr","year":"2009","journal-title":"Nat.\nChem. Biol."},{"key":"2026092408095862500_cit21","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.tibs.2010.04.009","article-title":"Induced fit, conformational selection\nand independent dynamic segments: an extended view of binding events","volume":"35","author":"Csermely","year":"2010","journal-title":"Trends Biochem. Sci."},{"key":"2026092408095862500_cit22","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","article-title":"On the nature of\nallosteric transitions:\na plausible model","volume":"12","author":"Monod","year":"1965","journal-title":"J. Mol. Biol."},{"key":"2026092408095862500_cit23","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/nature04331","article-title":"RNA translocation\nand unwinding mechanism of HCV NS3 helicase and its coordination by\nATP","volume":"439","author":"Dumont","year":"2006","journal-title":"Nature"},{"key":"2026092408095862500_cit24","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1016\/j.jmb.2010.11.034","article-title":"Visualizing ATP-Dependent RNA Translocation\nby the NS3 Helicase from HCV","volume":"405","author":"Appleby","year":"2011","journal-title":"J. Mol. Biol."},{"key":"2026092408095862500_cit25","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/S0092-8674(00)80716-3","article-title":"Crystal structures\nof complexes of PcrA DNA helicase\nwith a DNA substrate indicate an inchworm mechanism","volume":"97","author":"Velankar","year":"1999","journal-title":"Cell"},{"key":"2026092408095862500_cit26","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/S0968-0004(00)01734-5","article-title":"Unwinding the Gordian knot\u2019of helicase action","volume":"26","author":"Soultanas","year":"2001","journal-title":"Trends Biochem. Sci."},{"key":"2026092408095862500_cit27","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2026.111198","article-title":"Motif V\nis an allosteric\ncouple between the SARS-CoV-2 nsp13 nucleotide triphosphatase and\nhelicase active sites","volume":"302","author":"Mingroni","year":"2026","journal-title":"J. Biol. Chem."},{"key":"2026092408095862500_cit28","doi-asserted-by":"publisher","first-page":"445a","DOI":"10.1016\/j.bpj.2022.11.2400","article-title":"Predicting\nthe locations of cryptic pockets from single protein structures using\nthe PocketMiner graph neural network","volume":"122","author":"Meller","year":"2023","journal-title":"Biophys.\nJ."},{"key":"2026092408095862500_cit29","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1016\/j.molcel.2011.02.010","article-title":"Molecular\nmechanisms\nfor the RNA-dependent ATPase activity of Upf1 and its regulation by\nUpf2","volume":"41","author":"Chakrabarti","year":"2011","journal-title":"Mol. Cell"},{"key":"2026092408095862500_cit30","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: improving\nthe accuracy of\nprotein side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"2026092408095862500_cit31","doi-asserted-by":"publisher","first-page":"3836","DOI":"10.1021\/ct100481h","article-title":"Performance\nof molecular mechanics force fields for RNA simulations: stability\nof UUCG and GNRA hairpins","volume":"6","author":"Bana\u0301s\u030c","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"2026092408095862500_cit32","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1002\/jcc.10262","article-title":"Development\nof polyphosphate parameters\nfor use with the AMBER force field","volume":"24","author":"Meagher","year":"2003","journal-title":"J. Comput.\nChem."},{"key":"2026092408095862500_cit33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006103","article-title":"Allostery\nin the dengue virus NS3 helicase: Insights into the NTPase cycle from\nmolecular simulations","volume":"14","author":"Davidson","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"2026092408095862500_cit34","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1021\/acs.jcim.5b00674","article-title":"MCPB.py: A python based metal center\nparameter builder","volume":"56","author":"Li","year":"2016","journal-title":"J. Chem. Inf. Model"},{"key":"2026092408095862500_cit35","doi-asserted-by":"publisher","DOI":"10.64898\/2026.01.26.701677","article-title":"Multifaceted Functional\nComplexity of SARS-CoV-2 Helicase Nsp13 Underlies Its Integrated Motor\nand Remodeling Activities","volume":"15","author":"Li","year":"2026","journal-title":"eLife"},{"key":"2026092408095862500_cit36","doi-asserted-by":"publisher","first-page":"2043","DOI":"10.1021\/acs.jcim.8b00462","article-title":"GPU-accelerated molecular dynamics\nand free energy\nmethods in Amber18: performance enhancements and new features","volume":"58","author":"Lee","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"2026092408095862500_cit37","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical\nintegration of the cartesian\nequations of motion of a system with constraints: molecular dynamics\nof n-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. Phys."},{"key":"2026092408095862500_cit38","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh\nEwald: An N\u00b7log(N) method for\nEwald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"2026092408095862500_cit39","doi-asserted-by":"publisher","first-page":"3218","DOI":"10.1021\/acs.jctc.1c01290","article-title":"Size-and-shape\nspace gaussian mixture\nmodels for structural clustering of molecular dynamics trajectories","volume":"18","author":"Klem","year":"2022","journal-title":"J. Chem. Theory Comput."},{"key":"2026092408095862500_cit40","doi-asserted-by":"publisher","first-page":"3492","DOI":"10.1021\/acs.jctc.4c00223","article-title":"Quantifying\nUnbiased Conformational\nEnsembles from Biased Simulations Using ShapeGMM","volume":"20","author":"Sasmal","year":"2024","journal-title":"J. Chem. Theory Comput."},{"key":"2026092408095862500_cit41","doi-asserted-by":"publisher","DOI":"10.1063\/5.0305455","article-title":"Tutorial on quantifying\nand sampling\nbiomolecular ensembles with ShapeGMM","volume":"163","author":"Sasmal","year":"2025","journal-title":"J. Chem.\nPhys."},{"key":"2026092408095862500_cit42","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1021\/ct500090q","article-title":"Improved reweighting of accelerated molecular dynamics\nsimulations for free energy calculation","volume":"10","author":"Miao","year":"2014","journal-title":"J.\nChem. Theory Comput."},{"key":"2026092408095862500_cit43","doi-asserted-by":"publisher","first-page":"4427","DOI":"10.1021\/acs.jctc.3c00051","article-title":"Reaction coordinates for conformational\ntransitions using linear discriminant analysis on positions","volume":"19","author":"Sasmal","year":"2023","journal-title":"J. Chem. Theory Comput."},{"key":"2026092408095862500_cit44","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"2026092408095862500_cit45","doi-asserted-by":"publisher","first-page":"11009","DOI":"10.1093\/nar\/gks792","article-title":"The Ighmbp2 helicase\nstructure reveals the molecular basis for disease-causing mutations\nin DMSA1","volume":"40","author":"Lim","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2026092408095862500_cit46","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.102980","article-title":"Biochemical\nanalysis of SARS-CoV-2\nNsp13 helicase implicated in COVID-19 and factors that regulate its\ncatalytic functions","volume":"299","author":"Sommers","year":"2023","journal-title":"J. Biol. Chem."},{"key":"2026092408095862500_cit47","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/s41594-022-00734-6","article-title":"Ensemble\ncryo-EM\nreveals conformational states of the nsp13 helicase in the SARS-CoV-2\nhelicase replication-transcription complex","volume":"29","author":"Chen","year":"2022","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026092408095862500_cit48","doi-asserted-by":"publisher","first-page":"9266","DOI":"10.1093\/nar\/gkad660","article-title":"Observing\ninhibition of the SARS-CoV-2 helicase at single-nucleotide resolution","volume":"51","author":"Marx","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2026092408095862500_cit49","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2317747121","article-title":"Ligand-induced protein\ntransition state stabilization switches the binding pathway from conformational\nselection to induced fit","volume":"121","author":"Stenstro\u0308m","year":"2024","journal-title":"Proc. Natl. Acad.\nSci. U.S.A."},{"key":"2026092408095862500_cit50","doi-asserted-by":"publisher","first-page":"1593","DOI":"10.1021\/acschembio.4c00244","article-title":"A Repurposed\nDrug Interferes with Nucleic Acid to Inhibit\nthe Dual Activities of Coronavirus Nsp13","volume":"19","author":"Soper","year":"2024","journal-title":"ACS\nChem. Biol."}],"container-title":["The Journal of Physical\nChemistry B"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jpcb.6c03935","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article-pdf\/130\/38\/9851\/68456677\/acs.jpcb.6c03935.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article-pdf\/130\/38\/9851\/68456677\/acs.jpcb.6c03935.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T12:15:36Z","timestamp":1790252136000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article\/130\/38\/9851\/5426853\/Mechanochemical-Decoupling-of-ATP-Hydrolysis-and"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":50,"journal-issue":{"issue":"38","published-online":{"date-parts":[[2026,9,9]]},"published-print":{"date-parts":[[2026,9,24]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jpcb.6c03935","relation":{},"ISSN":["1520-6106","1520-5207"],"issn-type":[{"value":"1520-6106","type":"print"},{"value":"1520-5207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]}}}