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Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer
dc.contributor.author | Świderek, Katarzyna | |
dc.contributor.author | Arafet Cruz, Kemel | |
dc.contributor.author | Kohen, Amnon | |
dc.contributor.author | Moliner, Vicent | |
dc.date.accessioned | 2017-06-22T11:47:01Z | |
dc.date.available | 2017-06-22T11:47:01Z | |
dc.date.issued | 2017-02 | |
dc.identifier.citation | ŚWIDEREK, Katarzyna, et al. Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer. Journal of Chemical Theory and Computation, 2017, vol. 13, no 3, p. 1375-1388. | ca_CA |
dc.identifier.uri | http://hdl.handle.net/10234/168073 | |
dc.description.abstract | Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5–40 °C. | ca_CA |
dc.description.sponsorShip | This work was supported by the Spanish Ministerio de Economía y Competitividad for project CTQ2015-66223-C2-1-P, Universitat Jaume I (project P1·1B2014-26), Generalitat Valenciana (No. PROMETEOII/2014/022), the Polish Ministry of Science and Higher Education (“Iuventus Plus” Program Project No. 0478/IP3/2015/73, 2015–2016) and the USA National Institute of Health (Ref No. NIH R01 GM065368). V.M. is grateful to the University of Bath for the award of a David Parkin Visiting Professorship. Authors acknowledge computational resources from the Servei d’Informàtica of Universitat Jaume I. | ca_CA |
dc.format.extent | 13 p. | ca_CA |
dc.format.mimetype | application/pdf | ca_CA |
dc.language.iso | eng | ca_CA |
dc.publisher | American Chemical Society | ca_CA |
dc.relation.isPartOf | J. Chem. Theory Comput., 2017, 13 (3) | ca_CA |
dc.rights | Copyright © 2017 American Chemical Society | ca_CA |
dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | * |
dc.subject | Quantum Mechanics/Molecular Mechanics (QM/MM) | ca_CA |
dc.subject | QM/MM | ca_CA |
dc.subject | hydride-transfer reactions | ca_CA |
dc.subject | enzyme-catalyzed processes | ca_CA |
dc.title | Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer | ca_CA |
dc.type | info:eu-repo/semantics/article | ca_CA |
dc.identifier.doi | http://dx.doi.org/10.1021/acs.jctc.6b01032 | |
dc.rights.accessRights | info:eu-repo/semantics/restrictedAccess | ca_CA |
dc.relation.publisherVersion | http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b01032 | ca_CA |
dc.type.version | info:eu-repo/semantics/publishedVersion | ca_CA |
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