Literature DB >> 19606825

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it.

Shina C L Kamerlin1, Jie Cao, Edina Rosta, Arieh Warshel.   

Abstract

In recent years, the EVB has become a widely used tool in the QM/MM modeling of reactions in condensed phases and in biological systems, with ever increasing popularity. However, despite the fact that its power and validity have been repeatedly established since 1980, a recent work (Valero, R.; et al. J. Chem. Theory Comput. 2009, 5, 1) has strongly criticized this approach, while not discussing the fact that one of the authors is effectively using it himself for both gas-phase and solution studies. Here, we have responded to the most serious unjustified assertions of that paper, covering both the more problematic aspects of that work and the more complex scientific aspects. Additionally, we have demonstrated that the poor EVB results shown in Valero et al. which where presented as verification of the unreliability of the EVB model were in fact obtained by the use of incorrect parameters, without comparing to the correct surface obtained by our program.

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Year:  2009        PMID: 19606825      PMCID: PMC2736350          DOI: 10.1021/jp901709f

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


  28 in total

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Authors:  D A Cherepanov; L I Krishtalik; A Y Mulkidjanian
Journal:  Biophys J       Date:  2001-03       Impact factor: 4.033

Review 2.  Catalysis by enzyme conformational change as illustrated by orotidine 5'-monophosphate decarboxylase.

Authors:  Jiali Gao
Journal:  Curr Opin Struct Biol       Date:  2003-04       Impact factor: 6.809

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.  Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases.

Authors:  Gongyi Hong; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2006-10-05       Impact factor: 2.991

5.  Empirical valence bond model of an S(N)2 reaction in polar and nonpolar solvents.

Authors:  Ilan Benjamin
Journal:  J Chem Phys       Date:  2008-08-21       Impact factor: 3.488

6.  Cold adaptation of enzyme reaction rates.

Authors:  Sinisa Bjelic; Bjørn O Brandsdal; Johan Aqvist
Journal:  Biochemistry       Date:  2008-08-30       Impact factor: 3.162

7.  Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane.

Authors:  Rosendo Valero; Lingchun Song; Jiali Gao; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2009-01-01       Impact factor: 6.006

8.  Effect of mutation on enzyme motion in dihydrofolate reductase.

Authors:  James B Watney; Pratul K Agarwal; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2003-04-02       Impact factor: 15.419

9.  Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase.

Authors:  Mireia Garcia-Viloca; Donald G Truhlar; Jiali Gao
Journal:  Biochemistry       Date:  2003-11-25       Impact factor: 3.162

10.  Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction.

Authors:  Jochen Blumberger; Leonardo Bernasconi; Ivano Tavernelli; Rodolphe Vuilleumier; Michiel Sprik
Journal:  J Am Chem Soc       Date:  2004-03-31       Impact factor: 15.419

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  8 in total

1.  Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β.

Authors:  Ricardo A Matute; Hanwool Yoon; Arieh Warshel
Journal:  Proteins       Date:  2016-08-24

2.  Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.

Authors:  Maria P Frushicheva; Jie Cao; Arieh Warshel
Journal:  Biochemistry       Date:  2011-04-15       Impact factor: 3.162

3.  On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions.

Authors:  Edina Rosta; Arieh Warshel
Journal:  J Chem Theory Comput       Date:  2012-03-29       Impact factor: 6.006

Review 4.  Proton transport in carbonic anhydrase: Insights from molecular simulation.

Authors:  C Mark Maupin; Gregory A Voth
Journal:  Biochim Biophys Acta       Date:  2009-09-16

Review 5.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01

6.  Recrossing and dynamic matching effects on selectivity in a Diels-Alder reaction.

Authors:  Zhihong Wang; Jennifer S Hirschi; Daniel A Singleton
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

7.  The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions.

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Faraday Discuss       Date:  2010       Impact factor: 4.008

8.  Quantum mechanical modeling: a tool for the understanding of enzyme reactions.

Authors:  Gábor Náray-Szabó; Julianna Oláh; Balázs Krámos
Journal:  Biomolecules       Date:  2013-09-23
  8 in total

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