A theoretical study of the catalytic mechanism of formate dehydrogenase
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Scholar |
Otros documentos de la autoría: Castillo, Raquel; Oliva, Mónica; Martí Forés, Sergio; Moliner, Vicent
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Mostrar el registro completo del ítemcomunitat-uji-handle:10234/9
comunitat-uji-handle2:10234/7013
comunitat-uji-handle3:10234/8638
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http://dx.doi.org/10.1021/jp8025896 |
Metadatos
Título
A theoretical study of the catalytic mechanism of formate dehydrogenaseFecha de publicación
2008-07Editor
American Chemical SocietyISSN
1520-6106Cita bibliográfica
The Journal of Physical Chemistry B, 112, 32, p. 10012–10022Tipo de documento
info:eu-repo/semantics/articleVersión de la editorial
http://pubs.acs.org/doi/abs/10.1021/jp8025896Versión
info:eu-repo/semantics/publishedVersionPalabras clave / Materias
Resumen
A theoretical study of the hydride transfer between formate anion and nicotinamide adenine dinucleotide (NAD+) catalyzed by the enzyme formate dehydrogenase (FDH) has been carried out by a combination of two hybrid ... [+]
A theoretical study of the hydride transfer between formate anion and nicotinamide adenine dinucleotide (NAD+) catalyzed by the enzyme formate dehydrogenase (FDH) has been carried out by a combination of two hybrid quantum mechanics/molecular mechanics techniques: statistical simulation methods and internal energy minimizations. Free energy profiles, obtained for the reaction in the enzyme active site and in solution, allow obtaining a comparative analysis of the behavior of both condensed media. Moreover, calculations of the reaction in aqueous media can be used to probe the dramatic differences between reactants state in the enzyme active site and in solution. The results suggest that the enzyme compresses the substrate and the cofactor into a conformation close to the transition structure by means of favorable interactions with the amino acid residues of the active site, thus facilitating the relative orientation of donor and acceptor atoms to favor the hydride transfer. Moreover, a permanent field created by the protein reduces the work required to reach the transition state (TS) with a concomitant polarization of the cofactor that would favor the hydride transfer. In contrast, in water the TS is destabilized with respect to the reactant species because the polarity of the solute diminishes as the reaction proceeds, and consequently the reaction field, which is created as a response to the change in the solute polarity, is also decreased. Therefore protein structure is responsible of both effects; substrate preorganization and TS stabilization thus diminishing the activation barrier. Because of the electrostatic features of the catalyzed reaction, both media preferentially stabilize the ground-state, thus explaining the small rate constant enhancement of this enzyme, but FDH does so to a much lower extent than aqueous solution. Finally, a good agreement between experimental and theoretical kinetic isotope effects is found, thus giving some credit to our results. [-]
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Copyright © 2008 American Chemical Society
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