Literature DB >> 31750009

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

Xi Chen1, Steven D Schwartz1.   

Abstract

For decades, there has been debate regarding the origin of the catalytic power of enzymes. In this work, we use the approach of computational chemistry to study the enzyme catechol O-methyltransferase (COMT) and reveal that the two current views on the catalytic mechanism of enzymes, the rate-promoting vibrations and the electric field, may both be viewed as part of the chemical step catalyzed by COMT. However, we show that the rate-promoting vibrations cause the electrostatic effect. This work provides insight into the catalytic mechanism of COMT and resolves a longstanding controversy regarding this enzyme's mechanism.

Entities:  

Keywords:  QM/MM simulation; electric field preorganization; methyltransferase; rate-promoting vibrations; transition path sampling

Year:  2019        PMID: 31750009      PMCID: PMC6865801          DOI: 10.1021/acscatal.9b02657

Source DB:  PubMed          Journal:  ACS Catal            Impact factor:   13.084


  33 in total

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

3.  Structurally Linked Dynamics in Lactate Dehydrogenases of Evolutionarily Distinct Species.

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Journal:  Biochemistry       Date:  2017-05-04       Impact factor: 3.162

4.  POVME 3.0: Software for Mapping Binding Pocket Flexibility.

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Journal:  J Chem Theory Comput       Date:  2017-08-30       Impact factor: 6.006

5.  Triple Isotope Effects Support Concerted Hydride and Proton Transfer and Promoting Vibrations in Human Heart Lactate Dehydrogenase.

Authors:  Zhen Wang; Eric P Chang; Vern L Schramm
Journal:  J Am Chem Soc       Date:  2016-11-04       Impact factor: 15.419

6.  Enzyme homologues have distinct reaction paths through their transition states.

Authors:  Ioanna Zoi; Matthew W Motley; Dimitri Antoniou; Vern L Schramm; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2015-02-18       Impact factor: 2.991

7.  Changes in protein architecture and subpicosecond protein dynamics impact the reaction catalyzed by lactate dehydrogenase.

Authors:  Jean E Masterson; Steven D Schwartz
Journal:  J Phys Chem A       Date:  2013-03-12       Impact factor: 2.781

8.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

9.  Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling.

Authors:  Michael W Dzierlenga; Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem Lett       Date:  2015-03-19       Impact factor: 6.475

10.  How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase.

Authors:  Heather J Kulik; Jianyu Zhang; Judith P Klinman; Todd J Martínez
Journal:  J Phys Chem B       Date:  2016-10-28       Impact factor: 2.991

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  5 in total

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Journal:  ACS Catal       Date:  2020-07-07       Impact factor: 13.084

2.  Mechanochemical Function of Myosin II: Investigation into the Recovery Stroke and ATP Hydrolysis.

Authors:  Anthony P Baldo; Jil C Tardiff; Steven D Schwartz
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3.  Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects.

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Journal:  ACS Catal       Date:  2021-12-30       Impact factor: 13.700

4.  Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study.

Authors:  Thomas J Summers; Qianyi Cheng; Manuel A Palma; Diem-Trang Pham; Dudley K Kelso; Charles Edwin Webster; Nathan J DeYonker
Journal:  Biophys J       Date:  2021-08-04       Impact factor: 3.699

5.  Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer.

Authors:  Maite Roca; Ian H Williams
Journal:  J Am Chem Soc       Date:  2020-08-27       Impact factor: 15.419

  5 in total

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