Literature DB >> 25285029

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

Shina C L Kamerlin1, Arieh Warshel1.   

Abstract

Recent years have seen dramatic improvements in computer power, allowing ever more challenging problems to be approached. In light of this, it is imperative to have a quantitative model for examining chemical reactivity, both in the condensed phase and in solution, as well as to accurately quantify physical organic chemistry (particularly as experimental approaches can often be inconclusive). Similarly, computational approaches allow for great progress in studying enzyme catalysis, as they allow for the separation of the relevant energy contributions to catalysis. Due to the complexity of the problems that need addressing, there is a need for an approach that can combine reliability with an ability to capture complex systems in order to resolve long-standing controversies in a unique way. Herein, we will demonstrate that the empirical valence bond (EVB) approach provides a powerful way to connect the classical concepts of physical organic chemistry to the actual energies of enzymatic reactions by means of computation. Additionally, we will discuss the proliferation of this approach, as well as attempts to capture its basic chemistry and repackage it under different names. We believe that the EVB approach is the most powerful tool that is currently available for studies of chemical processes in the condensed phase in general and enzymes in particular, particularly when trying to explore the different proposals about the origin of the catalytic power of enzymes.

Entities:  

Year:  2010        PMID: 25285029      PMCID: PMC4184467          DOI: 10.1039/B907354J

Source DB:  PubMed          Journal:  Faraday Discuss        ISSN: 1359-6640            Impact factor:   4.008


  125 in total

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Journal:  Biophys J       Date:  2002-03       Impact factor: 4.033

Review 2.  NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis.

Authors:  Mikael Akke
Journal:  Curr Opin Struct Biol       Date:  2002-10       Impact factor: 6.809

3.  Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

Authors:  Navin Pokala; Tracy M Handel
Journal:  J Mol Biol       Date:  2005-01-20       Impact factor: 5.469

Review 4.  The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations.

Authors:  Mitsunori Kato; Andrei V Pisliakov; Arieh Warshel
Journal:  Proteins       Date:  2006-09-01

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.  Dispersed polaron simulations of electron transfer in photosynthetic reaction centers.

Authors:  A Warshel; Z T Chu; W W Parson
Journal:  Science       Date:  1989-10-06       Impact factor: 47.728

8.  Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

Authors:  S R Billeter; S P Webb; P K Agarwal; T Iordanov; S Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2001-11-14       Impact factor: 15.419

9.  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

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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  30 in total

1.  Exploring the Drug Resistance of HCV Protease.

Authors:  Garima Jindal; Dibyendu Mondal; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-07-05       Impact factor: 2.991

2.  Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases.

Authors:  Garima Jindal; Balajee Ramachandran; Ram Prasad Bora; Arieh Warshel
Journal:  ACS Catal       Date:  2017-03-30       Impact factor: 13.084

3.  Simulating the dynamics of the mechanochemical cycle of myosin-V.

Authors:  Shayantani Mukherjee; Raphael Alhadeff; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-13       Impact factor: 11.205

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase.

Authors:  Garima Jindal; Katerina Slanska; Veselin Kolev; Jiri Damborsky; Zbynek Prokop; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-26       Impact factor: 11.205

6.  Exploring the Proteolysis Mechanism of the Proteasomes.

Authors:  Arjun Saha; Gabriel Oanca; Dibyendu Mondal; Arieh Warshel
Journal:  J Phys Chem B       Date:  2020-06-25       Impact factor: 2.991

7.  Quantum-chemical approach to determining the high potency of clorgyline as an irreversible acetylenic monoamine oxidase inhibitor.

Authors:  Matic Pavlin; Janez Mavri; Matej Repič; Robert Vianello
Journal:  J Neural Transm (Vienna)       Date:  2013-04-02       Impact factor: 3.575

8.  Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII.

Authors:  Hanwool Yoon; Li Na Zhao; Arieh Warshel
Journal:  ACS Catal       Date:  2018-12-28       Impact factor: 13.084

9.  Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.

Authors:  Michael R Duff; Jose M Borreguero; Matthew J Cuneo; Arvind Ramanathan; Junhong He; Ganesh Kamath; S Chakra Chennubhotla; Flora Meilleur; Elizabeth E Howell; Kenneth W Herwig; Dean A A Myles; Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-07-06       Impact factor: 3.162

10.  Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis.

Authors:  Garima Jindal; Arieh Warshel
Journal:  Proteins       Date:  2017-09-30
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