Literature DB >> 22354430

Taking Ockham's razor to enzyme dynamics and catalysis.

David R Glowacki1, Jeremy N Harvey, Adrian J Mulholland.   

Abstract

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

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Year:  2012        PMID: 22354430     DOI: 10.1038/nchem.1244

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  68 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.  From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions.

Authors:  Huan-Xiang Zhou
Journal:  Biophys J       Date:  2010-03-17       Impact factor: 4.033

Review 3.  Protein dynamics and enzyme catalysis: insights from simulations.

Authors:  John D McGeagh; Kara E Ranaghan; Adrian J Mulholland
Journal:  Biochim Biophys Acta       Date:  2010-12-15

4.  First-principles theory for the H + CH4 --> H2 + CH3 reaction.

Authors:  Tao Wu; Hans-Joachim Werner; Uwe Manthe
Journal:  Science       Date:  2004-12-24       Impact factor: 47.728

Review 5.  Relating protein motion to catalysis.

Authors:  Sharon Hammes-Schiffer; Stephen J Benkovic
Journal:  Annu Rev Biochem       Date:  2006       Impact factor: 23.643

Review 6.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

7.  Classical, quantum and statistical simulations of vibrationally excited HOSO(2): IVR, dissociation, and implications for OH + SO(2) kinetics at high pressures.

Authors:  David R Glowacki; Stewart K Reed; Michael J Pilling; Dmitrii V Shalashilin; Emilio Martínez-Núñez
Journal:  Phys Chem Chem Phys       Date:  2008-12-11       Impact factor: 3.676

8.  How does pressure affect barrier compression and isotope effects in an enzymatic hydrogen tunneling reaction?

Authors:  Linus O Johannissen; Nigel S Scrutton; Michael J Sutcliffe
Journal:  Angew Chem Int Ed Engl       Date:  2011-01-25       Impact factor: 15.336

9.  Capture of hydroxymethylene and its fast disappearance through tunnelling.

Authors:  Peter R Schreiner; Hans Peter Reisenauer; Frank C Pickard; Andrew C Simmonett; Wesley D Allen; Edit Mátyus; Attila G Császár
Journal:  Nature       Date:  2008-06-12       Impact factor: 49.962

10.  Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: oxidation of tryptamine by aromatic amine dehydrogenase.

Authors:  Laura Masgrau; Kara E Ranaghan; Nigel S Scrutton; Adrian J Mulholland; Michael J Sutcliffe
Journal:  J Phys Chem B       Date:  2007-03-01       Impact factor: 2.991

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  75 in total

1.  Of polemics and progress.

Authors: 
Journal:  Nat Chem       Date:  2012-02-21       Impact factor: 24.427

2.  Dispelling the effects of a sorceress in enzyme catalysis.

Authors:  Adrian J Mulholland
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-16       Impact factor: 11.205

Review 3.  Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation.

Authors:  Aaron M Appel; John E Bercaw; Andrew B Bocarsly; Holger Dobbek; Daniel L DuBois; Michel Dupuis; James G Ferry; Etsuko Fujita; Russ Hille; Paul J A Kenis; Cheryl A Kerfeld; Robert H Morris; Charles H F Peden; Archie R Portis; Stephen W Ragsdale; Thomas B Rauchfuss; Joost N H Reek; Lance C Seefeldt; Rudolf K Thauer; Grover L Waldrop
Journal:  Chem Rev       Date:  2013-06-14       Impact factor: 60.622

4.  Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates.

Authors:  Rafael García-Meseguer; Sergio Martí; J Javier Ruiz-Pernía; Vicent Moliner; Iñaki Tuñón
Journal:  Nat Chem       Date:  2013-05-26       Impact factor: 24.427

5.  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

6.  Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

Authors:  Katarzyna Świderek; Kemel Arafet; Amnon Kohen; Vicent Moliner
Journal:  J Chem Theory Comput       Date:  2017-02-22       Impact factor: 6.006

7.  Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism.

Authors:  Carlo Camilloni; Aleksandr B Sahakyan; Michael J Holliday; Nancy G Isern; Fengli Zhang; Elan Z Eisenmesser; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-30       Impact factor: 11.205

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.  Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Authors:  Shenshen Hu; Adam R Offenbacher; Erin M Thompson; Christine L Gee; Jarett Wilcoxen; Cody A M Carr; Daniil M Prigozhin; Vanessa Yang; Tom Alber; R David Britt; James S Fraser; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2019-01-15       Impact factor: 15.419

Review 10.  Catalytic efficiency of enzymes: a theoretical analysis.

Authors:  Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2012-12-20       Impact factor: 3.162

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