Literature DB >> 22857146

Hydrogen donor-acceptor fluctuations from kinetic isotope effects: a phenomenological model.

Daniel Roston1, Christopher M Cheatum, Amnon Kohen.   

Abstract

Kinetic isotope effects (KIEs) and their temperature dependence can probe the structural and dynamic nature of enzyme-catalyzed proton or hydride transfers. The molecular interpretation of their temperature dependence requires expensive and specialized quantum mechanics/molecular mechanics (QM/MM) calculations to provide a quantitative molecular understanding. Currently available phenomenological models use a nonadiabatic assumption that is not appropriate for most hydride and proton-transfer reactions, while others require more parameters than the experimental data justify. Here we propose a phenomenological interpretation of KIEs based on a simple method to quantitatively link the size and temperature dependence of KIEs to a conformational distribution of the catalyzed reaction. This model assumes adiabatic hydrogen tunneling, and by fitting experimental KIE data, the model yields a population distribution for fluctuations of the distance between donor and acceptor atoms. Fits to data from a variety of proton and hydride transfers catalyzed by enzymes and their mutants, as well as nonenzymatic reactions, reveal that steeply temperature-dependent KIEs indicate the presence of at least two distinct conformational populations, each with different kinetic behaviors. We present the results of these calculations for several published cases and discuss how the predictions of the calculations might be experimentally tested. This analysis does not replace molecular QM/MM investigations, but it provides a fast and accessible way to quantitatively interpret KIEs in the context of a Marcus-like model.

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Year:  2012        PMID: 22857146      PMCID: PMC3448806          DOI: 10.1021/bi300613e

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  39 in total

1.  Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis.

Authors:  R Steven Sikorski; Lin Wang; Kelli A Markham; P T Ravi Rajagopalan; Stephen J Benkovic; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2004-04-21       Impact factor: 15.419

2.  Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.

Authors:  Mats H M Olsson; Janez Mavri; Arieh Warshel
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

Review 3.  Electrostatic basis for enzyme catalysis.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; Yun Xiang; Hanbin Liu; Mats H M Olsson
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

4.  Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase.

Authors:  Lin Wang; Nina M Goodey; Stephen J Benkovic; Amnon Kohen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

5.  The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer.

Authors:  Vanja Stojković; Laura L Perissinotti; Jeeyeon Lee; Stephen J Benkovic; Amnon Kohen
Journal:  Chem Commun (Camb)       Date:  2010-10-25       Impact factor: 6.222

6.  Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence.

Authors:  Aurélien de la Lande; Jan Řezáč; Bernard Lévy; Barry C Sanders; Dennis R Salahub
Journal:  J Am Chem Soc       Date:  2011-02-23       Impact factor: 15.419

7.  Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase.

Authors:  A Kohen; R Cannio; S Bartolucci; J P Klinman
Journal:  Nature       Date:  1999-06-03       Impact factor: 49.962

8.  Examination of enzymatic H-tunneling through kinetics and dynamics.

Authors:  Jigar N Bandaria; Christopher M Cheatum; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2009-07-29       Impact factor: 15.419

Review 9.  Hydrogen tunneling and protein motion in enzyme reactions.

Authors:  Sharon Hammes-Schiffer
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

10.  Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms.

Authors:  Christopher R Pudney; Sam Hay; Jiayun Pang; Claire Costello; David Leys; Michael J Sutcliffe; Nigel S Scrutton
Journal:  J Am Chem Soc       Date:  2007-10-16       Impact factor: 15.419

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  36 in total

1.  Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion.

Authors:  Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Chem Phys       Date:  2015-11-21       Impact factor: 3.488

2.  A critical test of the "tunneling and coupled motion" concept in enzymatic alcohol oxidation.

Authors:  Daniel Roston; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2013-09-10       Impact factor: 15.419

3.  Unraveling the role of protein dynamics in dihydrofolate reductase catalysis.

Authors:  Louis Y P Luk; J Javier Ruiz-Pernía; William M Dawson; Maite Roca; E Joel Loveridge; David R Glowacki; Jeremy N Harvey; Adrian J Mulholland; Iñaki Tuñón; Vicent Moliner; Rudolf K Allemann
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-24       Impact factor: 11.205

4.  Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase.

Authors:  Jiayue Li; Gabriel Fortunato; Jennifer Lin; Pratul K Agarwal; Amnon Kohen; Priyanka Singh; Christopher M Cheatum
Journal:  Biochemistry       Date:  2019-08-30       Impact factor: 3.162

5.  Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

Authors:  J Gao
Journal:  Methods Enzymol       Date:  2016-07-22       Impact factor: 1.600

6.  Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer.

Authors:  Daniel Roston; Amnon Kohen; Dvir Doron; Dan T Major
Journal:  J Comput Chem       Date:  2014-05-02       Impact factor: 3.376

Review 7.  Hydrogen tunneling in enzymes and biomimetic models.

Authors:  Joshua P Layfield; Sharon Hammes-Schiffer
Journal:  Chem Rev       Date:  2013-12-20       Impact factor: 60.622

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.  The general base in the thymidylate synthase catalyzed proton abstraction.

Authors:  Ananda K Ghosh; Zahidul Islam; Jonathan Krueger; Thelma Abeysinghe; Amnon Kohen
Journal:  Phys Chem Chem Phys       Date:  2015-12-14       Impact factor: 3.676

10.  Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction.

Authors:  Zahidul Islam; Timothy S Strutzenberg; Ananda K Ghosh; Amnon Kohen
Journal:  ACS Catal       Date:  2015-09-02       Impact factor: 13.084

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