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Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase

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Google Scholar Scholar | Other documents of the author: Roca Moliner, María Teresa; Oliva, Mónica; Castillo Solsona, Raquel; Moliner, Vicent; Tuñón, IñakiMicrosoft Academico
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comunitat-uji-handle:10234/9

comunitat-uji-handle2:10234/7013

comunitat-uji-handle3:10234/8638

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http://dx.doi.org/10.1002/chem.201000635

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Title
Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase
Author (s)
Roca Moliner, María Teresa;
Oliva, MónicaOrcidScopusResearcherID;
Castillo Solsona, Raquel;
Moliner, Vicent;
Tuñón, Iñaki
Date
2010
URI
http://hdl.handle.net/10234/51339
Publisher version
http://onlinelibrary.wiley.com/doi/10.1002/chem.201000635/abstract
DOI
http://dx.doi.org/10.1002/chem.201000635
ISSN
0947-6539
Publisher
Wiley-VCH
Abstract
A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD+), catalyzed by formate dehydrogenase (FDH), is presented in this paper. ... [+]
A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD+), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme and in solution were 0.46±0.04 and 0.20±0.03, respectively. These values represent a contribution to catalysis of 0.5 kcal mol−1, which, although small, is not negligible keeping in mind the low efficiency of FDH. The analysis of the reactive trajectories also reveals how the relative movements of some amino acids, mainly His332 and Arg284, precede and promote the chemical reaction. In spite of these movements, the time-dependent evolution of the electric field created by the enzyme on the key atoms of the reaction reveals a permanent field, which reduces the work required to reach the transition state, with a concomitant polarization of the cofactor. Finally, application of Grote–Hynes theory has allowed the identification of the modes responsible for the substrate–environment coupling, showing how some protein motions take place simultaneously with the reaction. Thus, the equilibrium approach would provide, in this case, an overestimation of the catalyzed rate constant. [-]
Subject
dynamic effects | enzyme catalysis | FDH | Grote–Hynes theory | molecular dynamics | rare-event trajectories
Bibliographic citation
Chemistry - A European Journal (2010), 16, 37, p. 11399-11411
Type
info:eu-repo/semantics/article
Rights
Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
info:eu-repo/semantics/closedAccess
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Our content is published in:

HispanaEuropeanaRePEc: Research Papers in EconomicsTesis Doctorals en XarxaGoogle ScholarRecolectaOpenDOARRevistes Catalanes d'Accés ObertOpenAIREMaterials Docents en Xarxa

Ministerio This project has received a grant from the Dirección General del Libro, Archivos y Bibliotecas of the Spanish Ministry of Culture.
DSpace
Metadata subject to:Public Domain | Information and queries:biblioteca@uji.es | Security and privacy center | Legal Advice
Universitat Jaume I - Av. de Vicent Sos Baynat, s/n 12071 Castelló de la Plana, Spain - Phone: +34 964 72 87 61 Fax: +34 964 72 87 78