{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T17:16:51Z","timestamp":1788455811879,"version":"build-2803163510"},"reference-count":60,"publisher":"American Chemical Society (ACS)","issue":"34","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["PID2024-157213NB-I00"],"award-info":[{"award-number":["PID2024-157213NB-I00"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011033","name":"Agencia Estatal de Investigaci?n","doi-asserted-by":"publisher","award":["PID2024-157213NB-I00"],"award-info":[{"award-number":["PID2024-157213NB-I00"]}],"id":[{"id":"10.13039\/501100011033","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014849","name":"Conselleria de Cultura, Educaci?n y Ciencia, Generalitat Valenciana","doi-asserted-by":"publisher","award":["PROMETEO CIPROM\/2021\/079"],"award-info":[{"award-number":["PROMETEO CIPROM\/2021\/079"]}],"id":[{"id":"10.13039\/501100014849","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Viral NS3 helicases convert the chemical energy of ATP hydrolysis into directional motion along nucleic acids, but the molecular basis of this coupling remains unclear. Here, we combine AI-based structural modeling, molecular dynamics simulations, and hybrid QM\/MM free energy calculations to investigate ATP hydrolysis in the Zika virus NS3 helicase (ZIKV NS3h). We first address the structural limitations of the available ternary crystallographic structure, which displays a noncanonical ATP-Mg2+ coordination mode and an RNA-binding arrangement inconsistent with the expected ATP-bound state. Our simulations show that alternative ATP-Mg2+ coordination modes can form stable but less favorable local minima, potentially associated with the secondary pyrophosphatase activity reported for this enzyme. Instead, the AlphaFold-predicted ternary complex provides a catalytically competent model with canonical coordination and the expected two-nucleotide separation between conserved \u201cpincer\u201d residues. We then use this model to explain the origin of RNA-stimulated ATPase activity. In the absence of ssRNA, the ATPase active site samples a broad conformational ensemble dominated by open, catalytically impaired states. Binding of ssRNA restricts this landscape and stabilizes a closed conformation in which the catalytic motifs are properly aligned. QM\/MM free energy profiles show that the open state is effectively inactive, whereas the closed state lowers the activation barrier for ATP hydrolysis by optimizing active-site interactions with ATP and the nucleophilic water molecule. These results rationalize RNA-stimulated ATPase activity as an allosteric conformational selection mechanism that links RNA binding to optimal organization of the ATPase active site.<\/jats:p>","DOI":"10.1021\/jacs.6c11584","type":"journal-article","created":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T23:29:18Z","timestamp":1788132558000},"page":"37154-37166","source":"Crossref","is-referenced-by-count":0,"title":["Tuning the ZIKV NS3\nHelicase Motor Activity through\nMagnesium Coordination and RNA-Driven Allostery"],"prefix":"10.1021","volume":"148","author":[{"given":"Adria\u0301n","family":"Garci\u0301a-Marti\u0301nez","sequence":"first","affiliation":[{"name":"Universitat de Vale\u0300ncia , , ,","place":["Burjassot, Spain, 46100"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4640-0419","authenticated-orcid":true,"given":"J. Javier","family":"Ruiz-Perni\u0301a","sequence":"additional","affiliation":[{"name":"Universitat de Vale\u0300ncia , , ,","place":["Burjassot, Spain, 46100"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6995-1838","authenticated-orcid":true,"given":"In\u0303aki","family":"Tun\u0303o\u0301n","sequence":"additional","affiliation":[{"name":"Universitat de Vale\u0300ncia , , ,","place":["Burjassot, Spain, 46100"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"issue":"1","key":"2026090312093269800_cit1","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.physa.2006.05.014","article-title":"Helicases as Molecular Motors: An Insight","volume":"372","author":"Tuteja","year":"2006","journal-title":"Phys. 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Biochem"},{"issue":"1","key":"2026090312093269800_cit3","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/S0969-2126(98)00010-0","article-title":"Hepatitis C Virus\nNS3 RNA Helicase Domain with a Bound Oligonucleotide: The Crystal\nStructure Provides Insights into the Mode of Unwinding","volume":"6","author":"Kim","year":"1998","journal-title":"Structure"},{"issue":"16","key":"2026090312093269800_cit4","doi-asserted-by":"publisher","first-page":"10278","DOI":"10.1128\/JVI.79.16.10278-10288.2005","article-title":"Structure of the Dengue\nVirus Helicase\/Nucleoside Triphosphatase Catalytic Domain at a Resolution\nof 2.4 \u00c5","volume":"79","author":"Xu","year":"2005","journal-title":"J. Virol"},{"issue":"8","key":"2026090312093269800_cit5","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1007\/s13238-016-0293-2","article-title":"Structural\nBasis of Zika Virus Helicase in Recognizing Its Substrates","volume":"7","author":"Tian","year":"2016","journal-title":"Protein Cell"},{"issue":"2","key":"2026090312093269800_cit6","doi-asserted-by":"publisher","DOI":"10.1002\/wrna.1688","article-title":"Conserved Motifs\nin the Flavivirus NS3 RNA Helicase Enzyme","volume":"13","author":"Du Pont","year":"2022","journal-title":"WIREs\nRNA"},{"issue":"5055","key":"2026090312093269800_cit7","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1126\/science.256.5055.350","article-title":"Allosteric Effects of Nucleotide Cofactors on Escherichia Coli Rep Helicase&DNA Binding","volume":"256","author":"Wong","year":"1992","journal-title":"Science"},{"issue":"2","key":"2026090312093269800_cit8","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1073\/pnas.0913380107","article-title":"Three Conformational\nSnapshots of the Hepatitis C Virus\nNS3 Helicase Reveal a Ratchet Translocation Mechanism","volume":"107","author":"Gu","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"issue":"33","key":"2026090312093269800_cit9","doi-asserted-by":"publisher","first-page":"29377","DOI":"10.1074\/jbc.M112315200","article-title":"Helicase from Hepatitis\nC Virus, Energetics of DNA\nBinding","volume":"277","author":"Levin","year":"2002","journal-title":"J. Biol. Chem"},{"issue":"26","key":"2026090312093269800_cit10","doi-asserted-by":"publisher","first-page":"23311","DOI":"10.1074\/jbc.M301283200","article-title":"ATP Binding\nModulates the Nucleic\nAcid Affinity of Hepatitis C Virus Helicase","volume":"278","author":"Levin","year":"2003","journal-title":"J. Biol. Chem"},{"issue":"1","key":"2026090312093269800_cit11","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1146\/annurev.biophys.37.032807.125908","article-title":"Translocation\nand Unwinding Mechanisms of RNA and DNA Helicases","volume":"37","author":"Pyle","year":"2008","journal-title":"Annu. Rev. 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Biol"},{"issue":"5","key":"2026090312093269800_cit14","doi-asserted-by":"publisher","first-page":"2769","DOI":"10.1021\/acscatal.0c04500","article-title":"Octahedral\nTrifluoromagnesate, an Anomalous Metal Fluoride\nSpecies, Stabilizes the Transition State in a Biological Motor","volume":"11","author":"Ge","year":"2021","journal-title":"ACS Catal"},{"issue":"45","key":"2026090312093269800_cit15","doi-asserted-by":"publisher","first-page":"24809","DOI":"10.1021\/jacs.3c09015","article-title":"Conformational\nChanges and ATP Hydrolysis in Zika Helicase: The Molecular Basis of\na Biomolecular Motor Unveiled by Multiscale Simulations","volume":"145","author":"Garci\u0301a-Marti\u0301nez","year":"2023","journal-title":"J. Am. Chem. 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Nucleic Acids Force Field Based on Reference\nQuantum Chemical Calculations of Glycosidic Torsion Profiles","volume":"7","author":"Zgarbova\u0301","year":"2011","journal-title":"J. Chem. Theory Comput"},{"issue":"9","key":"2026090312093269800_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"},{"issue":"4","key":"2026090312093269800_cit33","doi-asserted-by":"publisher","first-page":"1645","DOI":"10.1021\/ct500918t","article-title":"Systematic Parameterization of Monovalent\nIons Employing the Nonbonded Model","volume":"11","author":"Li","year":"2015","journal-title":"J. Chem.\nTheory Comput"},{"key":"2026090312093269800_cit34","unstructured":"Case, D. A.; Aktulga, H. M.; Belfon, K.; Ben-Shalom, I. Y.; Berryman, J. T.; Brozell, S. R.; Cerutti, D. S.; Cheatham, T. E., III; Cisneros, G. A.; Cruzeiro, V. W. D.; et al., AMBER 2024; University of California: San Francisco, 2024."},{"issue":"12","key":"2026090312093269800_cit35","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh\nEwald: An N \u00b7log(N) Method\nfor Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys"},{"issue":"19","key":"2026090312093269800_cit36","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A Smooth Particle\nMesh Ewald Method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. 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