Literature DB >> 22354429

Good vibrations in enzyme-catalysed reactions.

Sam Hay1, Nigel S Scrutton.   

Abstract

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

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Year:  2012        PMID: 22354429     DOI: 10.1038/nchem.1223

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


  61 in total

1.  Role of conformation transitions in adenylate kinase.

Authors:  Martin Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-27       Impact factor: 11.205

2.  Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase.

Authors:  Lin Wang; Nina M Goodey; Stephen J Benkovic; Amnon Kohen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

3.  Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase.

Authors:  Jigar N Bandaria; Samrat Dutta; Michael W Nydegger; William Rock; Amnon Kohen; Christopher M Cheatum
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

4.  Parallel pathways and free-energy landscapes for enzymatic hydride transfer probed by hydrostatic pressure.

Authors:  Christopher R Pudney; Tom McGrory; Pierre Lafite; Jiayun Pang; Sam Hay; David Leys; Michael J Sutcliffe; Nigel S Scrutton
Journal:  Chembiochem       Date:  2009-05-25       Impact factor: 3.164

5.  Solvent-slaved protein motions accompany proton but not hydride tunneling in light-activated protochlorophyllide oxidoreductase.

Authors:  Derren J Heyes; Michiyo Sakuma; Nigel S Scrutton
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

Review 6.  Structural and mechanistic aspects of flavoproteins: probes of hydrogen tunnelling.

Authors:  Sam Hay; Christopher R Pudney; Nigel S Scrutton
Journal:  FEBS J       Date:  2009-07-03       Impact factor: 5.542

7.  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

8.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Authors:  Gira Bhabha; Jeeyeon Lee; Damian C Ekiert; Jongsik Gam; Ian A Wilson; H Jane Dyson; Stephen J Benkovic; Peter E Wright
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

9.  Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms.

Authors:  Christopher R Pudney; Sam Hay; Jiayun Pang; Claire Costello; David Leys; Michael J Sutcliffe; Nigel S Scrutton
Journal:  J Am Chem Soc       Date:  2007-10-16       Impact factor: 15.419

10.  Probing active site geometry using high pressure and secondary isotope effects in an enzyme-catalysed 'deep' H-tunnelling reaction.

Authors:  Sam Hay; Christopher R Pudney; Michael J Sutcliffe; Nigel S Scrutton
Journal:  J Phys Org Chem       Date:  2010-07-01       Impact factor: 2.391

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  91 in total

1.  Of polemics and progress.

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

2.  A Biophysical Perspective on Enzyme Catalysis.

Authors:  Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

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.  Proton transfer through the water gossamer.

Authors:  Ali Hassanali; Federico Giberti; Jérôme Cuny; Thomas D Kühne; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-18       Impact factor: 11.205

5.  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

6.  Coherent neutron scattering and collective dynamics in the protein, GFP.

Authors:  Jonathan D Nickels; Stefania Perticaroli; Hugh O'Neill; Qiu Zhang; Georg Ehlers; Alexei P Sokolov
Journal:  Biophys J       Date:  2013-11-05       Impact factor: 4.033

7.  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

8.  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

9.  Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change.

Authors:  Xi Chen; Steven D Schwartz
Journal:  Biochemistry       Date:  2018-03-22       Impact factor: 3.162

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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