Literature DB >> 25388538

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.

Jeronimo Lameira1, Ram Prasad Bora, Zhen T Chu, Arieh Warshel.   

Abstract

The enzyme catechol O-methyltransferase (COMT) catalyzes the transfer of a methyl group from S-adenosylmethionine to dopamine and related catechols. The search for the origin of COMT catalysis has led to different proposals and hypothesis, including the entropic, the NAC, and the compression proposals as well as the more reasonable electrostatic idea. Thus, it is important to understand the catalytic power of this enzyme and to examine the validity of different proposals and in particular the repeated recent implication of the compression idea. The corresponding analysis should be done by well-defined physically-based considerations that involve computations rather than circular interpretations of experimental results. Thus, we explore here the origin of the catalytic efficiency of COMT by using the empirical valence bond and the linear response approximation approaches. The results demonstrate that the catalytic effect of COMT is mainly due to electrostatic preorganization effects. It is also shown that the compression, NAC and entropic proposals do not account for the catalytic effect.
© 2014 Wiley Periodicals, Inc.

Entities:  

Keywords:  NAC; compression; electrostatic; methyltransferase; preorganization

Mesh:

Substances:

Year:  2015        PMID: 25388538      PMCID: PMC4300294          DOI: 10.1002/prot.24717

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  37 in total

1.  Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution.

Authors:  P A Kollman; B Kuhn; O Donini; M Perakyla; R Stanton; D Bakowies
Journal:  Acc Chem Res       Date:  2001-01       Impact factor: 22.384

Review 2.  A view at the millennium: the efficiency of enzymatic catalysis.

Authors:  Thomas C Bruice
Journal:  Acc Chem Res       Date:  2002-03       Impact factor: 22.384

3.  Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase.

Authors:  Marek Strajbl; Avital Shurki; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-01       Impact factor: 11.205

Review 4.  Enzymes that catalyse SN2 reaction mechanisms.

Authors:  David O'Hagan; Jason W Schmidberger
Journal:  Nat Prod Rep       Date:  2010-04-07       Impact factor: 13.423

5.  Enzymatic methyl transfer: role of an active site residue in generating active site compaction that correlates with catalytic efficiency.

Authors:  Jianyu Zhang; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2011-10-10       Impact factor: 15.419

6.  Linking electrostatic effects and protein motions in enzymatic catalysis. A theoretical analysis of catechol o-methyltransferase.

Authors:  Rafael García-Meseguer; Kirill Zinovjev; Maite Roca; Javier J Ruiz-Pernía; Iñaki Tuñón
Journal:  J Phys Chem B       Date:  2014-09-10       Impact factor: 2.991

Review 7.  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

8.  QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects.

Authors:  Natalia Kanaan; J Javier Ruiz Pernía; Ian H Williams
Journal:  Chem Commun (Camb)       Date:  2008-10-29       Impact factor: 6.222

9.  A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.

Authors:  Nidhi Singh; Arieh Warshel
Journal:  Proteins       Date:  2010-05-15

10.  Inhibition of rat liver and duodenum soluble catechol-O-methyltransferase by a tight-binding inhibitor OR-462.

Authors:  E Schultz; E Nissinen
Journal:  Biochem Pharmacol       Date:  1989-11-15       Impact factor: 5.858

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  23 in total

1.  Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36.

Authors:  Myles B Poulin; Jessica L Schneck; Rosalie E Matico; Patrick J McDevitt; Michael J Huddleston; Wangfang Hou; Neil W Johnson; Sara H Thrall; Thomas D Meek; Vern L Schramm
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

2.  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

3.  Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.

Authors:  Subhendu Roy; Patrick Schopf; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-07-05       Impact factor: 2.991

4.  Human DNMT1 transition state structure.

Authors:  Quan Du; Zhen Wang; Vern L Schramm
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-29       Impact factor: 11.205

Review 5.  Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.

Authors:  Arieh Warshel; Ram Prasad Bora
Journal:  J Chem Phys       Date:  2016-05-14       Impact factor: 3.488

6.  Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.

Authors:  Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W Qi; Adam H Steeves; Heather J Kulik
Journal:  React Chem Eng       Date:  2018-11-29       Impact factor: 4.239

7.  Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer.

Authors:  Heather J Kulik
Journal:  Phys Chem Chem Phys       Date:  2018-08-08       Impact factor: 3.676

8.  Kinetic Isotope Effects and Transition State Structure for Human Phenylethanolamine N-Methyltransferase.

Authors:  Christopher F Stratton; Myles B Poulin; Quan Du; Vern L Schramm
Journal:  ACS Chem Biol       Date:  2016-12-28       Impact factor: 5.100

9.  Mediation of donor-acceptor distance in an enzymatic methyl transfer reaction.

Authors:  Jianyu Zhang; Heather J Kulik; Todd J Martinez; Judith P Klinman
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-15       Impact factor: 11.205

10.  Examining the Origin of Catalytic Power of Catechol O-Methyltransferase.

Authors:  Xi Chen; Steven D Schwartz
Journal:  ACS Catal       Date:  2019-09-17       Impact factor: 13.084

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