Literature DB >> 17571875

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase.

Hanbin Liu1, Arieh Warshel.   

Abstract

The origin of the temperature dependence of kinetic isotope effects (KIEs) in enzyme reactions is a problem of general interest and a major challenge for computational chemistry. The present work simulates the nuclear quantum mechanical (NQM) effects and the corresponding KIE in dihydrofolate reductase (DHFR) and two of its mutants by using the empirical valence bond (EVB) and the quantum classical path (QCP) centroid path integral approach. Our simulations reproduce the overall observed trend while using a fully microscopic rather than a phenomenological picture and provide an interesting insight. It appears that the KIE increases when the distance between the donor and acceptor increases, in a somewhat counter intuitive way. The temperature dependence of the KIE appears to reflect mainly the temperature dependence of the distance between the donor and acceptor. This trend is also obtained from a simplified vibronic treatment, but as demonstrated here, the vibronic treatment is not valid at short and medium distances, where it is essential to use the path integral or other approaches capable of moving seamlessly from the adiabatic to the diabatic limits. It is pointed out that although the NQM effects do not contribute to catalysis in DHFR, the observed temperature dependence can be used to refine the potential of mean force for the donor and acceptor distance and its change due to distanced mutations.

Entities:  

Mesh:

Substances:

Year:  2007        PMID: 17571875     DOI: 10.1021/jp070938f

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  60 in total

1.  Probing quantum and dynamic effects in concerted proton-electron transfer reactions of phenol-base compounds.

Authors:  Todd F Markle; Adam L Tenderholt; James M Mayer
Journal:  J Phys Chem B       Date:  2011-12-23       Impact factor: 2.991

2.  Taking Ockham's razor to enzyme dynamics and catalysis.

Authors:  David R Glowacki; Jeremy N Harvey; Adrian J Mulholland
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

3.  Good vibrations in enzyme-catalysed reactions.

Authors:  Sam Hay; Nigel S Scrutton
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

4.  Evidence that a 'dynamic knockout' in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis.

Authors:  E Joel Loveridge; Enas M Behiry; Jiannan Guo; Rudolf K Allemann
Journal:  Nat Chem       Date:  2012-03-11       Impact factor: 24.427

5.  Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.

Authors:  Tomáš Zimmermann; Jiří Vaníček
Journal:  J Mol Model       Date:  2010-04-30       Impact factor: 1.810

Review 6.  Coupled motions in enzyme catalysis.

Authors:  Vishal C Nashine; Sharon Hammes-Schiffer; Stephen J Benkovic
Journal:  Curr Opin Chem Biol       Date:  2010-08-20       Impact factor: 8.822

7.  Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.

Authors:  Jerônimo Lameira; Ilya Kupchencko; Arieh Warshel
Journal:  J Phys Chem B       Date:  2016-02-29       Impact factor: 2.991

8.  A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.

Authors:  Zhen Wang; Thelma Abeysinghe; Janet S Finer-Moore; Robert M Stroud; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2012-10-15       Impact factor: 15.419

9.  Kinetic isotope effects on aromatic and benzylic hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase as probes of chemical mechanism and reactivity.

Authors:  Aram J Panay; Paul F Fitzpatrick
Journal:  Biochemistry       Date:  2008-09-26       Impact factor: 3.162

10.  The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.

Authors:  Sonja Braun-Sand; Pankaz K Sharma; Zhen T Chu; Andrei V Pisliakov; Arieh Warshel
Journal:  Biochim Biophys Acta       Date:  2008-03-14
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.