{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:05:47Z","timestamp":1789477547417,"version":"build-2803163510"},"reference-count":54,"publisher":"American Chemical Society (ACS)","issue":"18","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM139449"],"award-info":[{"award-number":["R35GM139449"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides, utilizing a \u223c32 \u00c5 chain of proton-coupled electron transfer (PCET) reactions spanning two protein subunits to generate a catalytic cysteine radical. Two cryogenic electron microscopy structures of the active complex of E. coli RNR are currently available. One structure was trapped in the preturnover state, prior to radical translocation, and the other structure was trapped in the midturnover state, with the radical in the active site. Herein, we use molecular dynamics simulations to investigate the differences in hydrogen-bonding interactions and conformational motions between the preturnover and midturnover states. Our simulations show that Y731, an interfacial tyrosine that participates in the PCET pathway, samples multiple conformations in both states, allowing it to participate in forward and reverse PCET between subunits. We also observe interfacial water channels between the protein subunits in both states. Moreover, our simulations show that E623, which is near Y730 in the preturnover structure and was shown by previous simulations to mediate PCET between Y731 and Y730, can also sample conformations distal to Y730 in the preturnover state, similar to its position in the midturnover structure. Our mixed quantum mechanical\/molecular mechanical free energy simulations indicate that forward radical transfer from Y731 to Y730 is thermodynamically favorable with a reasonable free energy barrier, even in the absence of mediation by E623. These results provide insights into the critical role of conformational motions and flexibility in regulating PCET reactions at and near the protein subunit interface of RNR.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00487","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T23:08:28Z","timestamp":1788217708000},"page":"2896-2904","source":"Crossref","is-referenced-by-count":0,"title":["Comparative\nSimulations of Conformational Flexibility\nduring Radical Transport in Ribonucleotide Reductase"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6378-2685","authenticated-orcid":true,"given":"Matthew","family":"Tremblay","sequence":"first","affiliation":[{"name":"Princeton University , , , ,","place":["Princeton, New Jersey, United States, 08540"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3782-6995","authenticated-orcid":true,"given":"Sharon","family":"Hammes-Schiffer","sequence":"additional","affiliation":[{"name":"Princeton University , , , ,","place":["Princeton, New Jersey, United States, 08540"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,25]]},"reference":[{"key":"2026091508070252000_cit1","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1146\/annurev-biochem-013118-111843","article-title":"Ribonucleotide Reductases: Structure,\nChemistry, and Metabolism Suggest New Therapeutic Targets","volume":"89","author":"Greene","year":"2020","journal-title":"Annu. Rev. Biochem."},{"key":"2026091508070252000_cit2","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1038\/onc.2014.155","article-title":"Ribonucleotide reductase and cancer:\nbiological mechanisms and targeted therapies","volume":"34","author":"Aye","year":"2015","journal-title":"Oncogene"},{"key":"2026091508070252000_cit3","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.67447","article-title":"Ribonucleotide reductase,\na novel drug target for gonorrhea","volume":"11","author":"Narasimhan","year":"2022","journal-title":"eLife"},{"key":"2026091508070252000_cit4","doi-asserted-by":"publisher","first-page":"3381","DOI":"10.1021\/cr4006654","article-title":"Biochemistry\nand\nTheory of Proton-Coupled Electron Transfer","volume":"114","author":"Migliore","year":"2014","journal-title":"Chem. Rev."},{"key":"2026091508070252000_cit5","doi-asserted-by":"publisher","first-page":"7062","DOI":"10.1021\/cr1002003","article-title":"Proton-Coupled\nElectron Transfer in Cytochrome Oxidase","volume":"110","author":"Kaila","year":"2010","journal-title":"Chem.\nRev."},{"key":"2026091508070252000_cit6","doi-asserted-by":"publisher","first-page":"7171","DOI":"10.1021\/jacs.1c13041","article-title":"Molecular Principles\nof Redox-Coupled Protonation Dynamics in Photosystem II","volume":"144","author":"Allgo\u0308wer","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit7","doi-asserted-by":"publisher","first-page":"e2535102123","DOI":"10.1073\/pnas.2535102123","article-title":"Conformationally gated multisite proton-coupled electron\ntransfer in the ribonucleotide reductase \u03b2 subunit","volume":"123","author":"Deng","year":"2026","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026091508070252000_cit8","doi-asserted-by":"publisher","first-page":"13768","DOI":"10.1021\/jacs.0c04325","article-title":"Conformational\nMotions and Water Networks at the \u03b1\/\u03b2 Interface in E. coli Ribonucleotide Reductase","volume":"142","author":"Reinhardt","year":"2020","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit9","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1038\/s41570-024-00646-7","article-title":"Conformational control over proton-coupled electron\ntransfer in metalloenzymes","volume":"8","author":"Fatima","year":"2024","journal-title":"Nat. Rev. Chem."},{"key":"2026091508070252000_cit10","doi-asserted-by":"publisher","first-page":"2458","DOI":"10.1038\/s41467-025-57735-4","article-title":"Conformational landscapes\nof a class I ribonucleotide reductase complex during turnover reveal\nintrinsic dynamics and asymmetry","volume":"16","author":"Xu","year":"2025","journal-title":"Nat. Commun."},{"key":"2026091508070252000_cit11","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1126\/science.aba6794","article-title":"Structure\nof a trapped\nradical transfer pathway within a ribonucleotide reductase holocomplex","volume":"368","author":"Kang","year":"2020","journal-title":"Science"},{"key":"2026091508070252000_cit12","doi-asserted-by":"publisher","first-page":"9229","DOI":"10.1074\/jbc.M117.783092","article-title":"Glutamate\n52-\u03b2 at the \u03b1\/\u03b2 subunit interface of Escherichia coli class Ia ribonucleotide\nreductase is essential for conformational gating of radical transfer","volume":"292","author":"Lin","year":"2017","journal-title":"J. Biol. Chem."},{"key":"2026091508070252000_cit13","doi-asserted-by":"publisher","first-page":"4784","DOI":"10.1021\/jacs.2c13615","article-title":"Direct Proton-Coupled Electron Transfer\nbetween Interfacial Tyrosines in Ribonucleotide Reductase","volume":"145","author":"Zhong","year":"2023","journal-title":"J. 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Chem."},{"key":"2026091508070252000_cit32","doi-asserted-by":"crossref","DOI":"10.25080\/Majora-629e541a-00e","article-title":"MDAnalysis: A Python Package for the Rapid Analysis\nof Molecular Dynamics Simulations","volume-title":"Proceedings\nOf The 15th Python In Science Conference","author":"Gowers","year":"2016"},{"key":"2026091508070252000_cit33","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/0021-9991(77)90121-8","article-title":"Nonphysical sampling distributions in Monte Carlo free-energy\nestimation: Umbrella sampling","volume":"23","author":"Torrie","year":"1977","journal-title":"J. Comput. Phys."},{"key":"2026091508070252000_cit34","unstructured":"Grossfield, A.\n          \n          WHAM: an\nimplementation of the weighted histogram analysis method, version\n2.1.0, 2000."},{"key":"2026091508070252000_cit35","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.1002\/jcc.540130812","article-title":"THE weighted\nhistogram analysis method for free-energy calculations on biomolecules.\nI. The method","volume":"13","author":"Kumar","year":"1992","journal-title":"J. Comput. Chem."},{"key":"2026091508070252000_cit36","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1515\/crll.1908.134.198","article-title":"Nouvelles\napplications des parame\u0300tres continus a\u0300 la the\u0301orie\ndes formes quadratiques. Deuxie\u0300me me\u0301moire. Recherches\nsur les paralle\u0301lloe\u0300dres primitifs","volume":"1908","author":"Voronoi","year":"1908","journal-title":"J. Reine Angew. Math."},{"key":"2026091508070252000_cit37","doi-asserted-by":"publisher","first-page":"1404","DOI":"10.1021\/acscentsci.2c00702","article-title":"Detecting the First Hydration Shell\nStructure around\nBiomolecules at Interfaces","volume":"8","author":"Konstantinovsky","year":"2022","journal-title":"ACS Cent. Sci."},{"key":"2026091508070252000_cit38","doi-asserted-by":"publisher","first-page":"5260","DOI":"10.1021\/acs.jpclett.3c01159","article-title":"Characterizing\nInterfaces by Voronoi\nTessellation","volume":"14","author":"Konstantinovsky","year":"2023","journal-title":"J. Phys. Chem. Lett."},{"key":"2026091508070252000_cit39","doi-asserted-by":"publisher","first-page":"107275","DOI":"10.1016\/j.cpc.2020.107275","article-title":"freud: A software\nsuite for high\nthroughput analysis of particle simulation data","volume":"254","author":"Ramasubramani","year":"2020","journal-title":"Comput. Phys. Commun."},{"key":"2026091508070252000_cit40","doi-asserted-by":"publisher","first-page":"041111","DOI":"10.1063\/1.3215722","article-title":"VORO++:\nA three-dimensional Voronoi cell library in C++","volume":"19","author":"Rycroft","year":"2009","journal-title":"Chaos"},{"key":"2026091508070252000_cit41","doi-asserted-by":"publisher","first-page":"8934","DOI":"10.1021\/ja200173a","article-title":"Catalytic Mechanism\nof RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics\/Molecular\nMechanics Simulations","volume":"133","author":"Rosta","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit42","doi-asserted-by":"publisher","first-page":"1483","DOI":"10.1021\/ja4104217","article-title":"Quantum Mechanical\/Molecular Mechanical\nFree Energy\nSimulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus\nRibozyme","volume":"136","author":"Ganguly","year":"2014","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit43","doi-asserted-by":"publisher","first-page":"2257","DOI":"10.1063\/1.1677527","article-title":"Self\u2500Consistent Molecular\nOrbital Methods. XII. Further Extensions of Gaussian\u2500Type Basis\nSets for Use in Molecular Orbital Studies of Organic Molecules","volume":"56","author":"Hehre","year":"1972","journal-title":"J. Chem. Phys."},{"key":"2026091508070252000_cit44","doi-asserted-by":"publisher","first-page":"6615","DOI":"10.1039\/b810189b","article-title":"Long-range corrected hybrid density functionals with\ndamped atom\u2013atom dispersion corrections","volume":"10","author":"Chai","year":"2008","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026091508070252000_cit45","doi-asserted-by":"publisher","first-page":"084801","DOI":"10.1063\/5.0055522","article-title":"Software for the frontiers of quantum chemistry:\nAn overview of developments in the Q-Chem 5 package","volume":"155","author":"Epifanovsky","year":"2021","journal-title":"J. Chem. Phys."},{"key":"2026091508070252000_cit46","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1002\/jcc.23444","article-title":"An extensible\ninterface for QM\/MM\nmolecular dynamics simulations with AMBER","volume":"35","author":"Go\u0308tz","year":"2014","journal-title":"J.\nComput. Chem."},{"key":"2026091508070252000_cit47","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/S0010-4655(00)00215-0","article-title":"Extension to the weighted\nhistogram analysis method: combining umbrella\nsampling with free energy calculations","volume":"135","author":"Souaille","year":"2001","journal-title":"Comput.\nPhys. Commun."},{"key":"2026091508070252000_cit48","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.1039\/C5SC03460D","article-title":"Radical transfer in\nE. coli ribonucleotide reductase: a NH2Y731\/R411A-\u03b1 mutant unmasks\na new conformation of the pathway residue 731","volume":"7","author":"Kasanmascheff","year":"2016","journal-title":"Chem. Sci."},{"key":"2026091508070252000_cit49","doi-asserted-by":"publisher","first-page":"16657","DOI":"10.1021\/jacs.7b08192","article-title":"Conformationally\nDynamic Radical Transfer within Ribonucleotide Reductase","volume":"139","author":"Greene","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit50","doi-asserted-by":"publisher","first-page":"11270","DOI":"10.1021\/jacs.2c02906","article-title":"19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active\nTyrosines across the \u03b1\/\u03b2 Interface of E. coli Ribonucleotide Reductase","volume":"144","author":"Meyer","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit51","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: Improving the Accuracy of\nProtein Side Chain and Backbone Parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"2026091508070252000_cit52","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison\nof simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2026091508070252000_cit53","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1021\/jacs.0c07879","article-title":"Gated Proton Release during Radical Transfer at the\nSubunit Interface of Ribonucleotide Reductase","volume":"143","author":"Cui","year":"2021","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508070252000_cit54","doi-asserted-by":"publisher","first-page":"5145","DOI":"10.1021\/jacs.2c11483","article-title":"Radical\nTransport Facilitated by a Proton Transfer Network at the Subunit\nInterface of Ribonucleotide Reductase","volume":"145","author":"Cui","year":"2023","journal-title":"J. Am.\nChem. Soc."}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00487","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/18\/2896\/67401774\/acs.biochem.6c00487.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/18\/2896\/67401774\/acs.biochem.6c00487.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:26:58Z","timestamp":1789475218000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/18\/2896\/5328659\/Comparative-Simulations-of-Conformational"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,25]]},"references-count":54,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,8,25]]},"published-print":{"date-parts":[[2026,9,15]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00487","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,25]]}}}