QM/MM study of thymidylate synthase: enzymatic motions and the temperature dependence of the rate limiting step
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Otros documentos de la autoría: Kanaan Izquierdo, Natalia; Martí Forés, Sergio; Moliner, Vicent; Kohen, Amnon
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Título
QM/MM study of thymidylate synthase: enzymatic motions and the temperature dependence of the rate limiting stepFecha de publicación
2009Editor
American Chemical SocietyISSN
1089-5639Tipo de documento
info:eu-repo/semantics/articleVersión de la editorial
http://pubs.acs.org/doi/abs/10.1021/jp810548dVersión
info:eu-repo/semantics/publishedVersionPalabras clave / Materias
Resumen
Thymidylate synthase (TS) is an enzyme that catalyzes a complex cascade of reactions. A theoretical study of the reduction of an exocyclic methylene intermediate by hydride transfer from the 6S position of 5,6,7,8-t ... [+]
Thymidylate synthase (TS) is an enzyme that catalyzes a complex cascade of reactions. A theoretical study of the reduction of an exocyclic methylene intermediate by hydride transfer from the 6S position of 5,6,7,8-tetrahydrofolate (H4folate), to form 2′-deoxyuridine 5′-monophosphate (dTMP) and 7,8-dihydrofolate (H2folate), has been carried out using hybrid quantum mechanics/molecular mechanics methods. This step is of special interest because it is the rate-limiting step of the reaction catalyzed by TS. The acceptor of this hydride is an intermediate that is covalently bound to the enzyme via a thioether bond to an overall conserved active site cysteine residue (Cys146 in Escherichia coli). Heretofore, whether the hydride transfer precedes the thiol abstraction that releases the product from the enzyme or whether these two processes are concerted has been an open question. We have examined this step in terms of free energy surfaces obtained at the same temperatures we previously used in experimental studies of this mechanistic step (273−313 K). Analysis of the results reveals that substantial features of the reaction and the nature of the H-transfer seem to be temperature independent, in agreement with our experimental data. The findings also indicate that the hydride transfer and the scission of Cys146 take place in a concerted but asynchronous fashion. This 1,3-SN2 substitution is assisted by arginine 166 and several other arginine residues in the active site that polarize the carbon−sulfur bond and stabilize the charge transferred from cofactor to substrate. Finally, the simulation elucidates the molecular details of the enzyme’s motion that brings the system to its transition state and, in accordance with the experimental data, indicates that this “tunneling ready” conformation is temperature independent. [-]
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Journal of Physical Chemistry A, 113, 10, p. 2176–2182Derechos de acceso
Copyright © 2009 American Chemical Society
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