Literature DB >> 19620995

A 21st century revisionist's view at a turning point in enzymology.

Zachary D Nagel1, Judith P Klinman.   

Abstract

Despite the fact that the number of publications associated with the keyword 'enzyme' increases every year, the precise origin of enzyme catalysis has remained unresolved. Because of sustained intensive research efforts from an increasing number of laboratories, detailed information regarding the physics, chemistry and kinetics of enzymes is accumulating rapidly. The growing body of data contains many examples of kinetic behavior that are incompatible with a static view of enzyme catalysis. As a result, numerous laboratories are approaching the consensus that protein motion plays an essential role in enzyme catalysis. A model that incorporates nuclear quantum tunneling together with two classes of protein motion--termed conformational sampling (pre-organization) and reorganization--is recommended as a means of understanding the large body of data for enzyme-catalyzed hydrogen transfers. It should also serve as a vehicle for future efforts in the development of potent enzyme inhibitors and the de novo design of all classifications of enzymes.

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Year:  2009        PMID: 19620995     DOI: 10.1038/nchembio.204

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  52 in total

1.  Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria.

Authors:  Hans-Heinrich Limbach; Juan Miguel Lopez; Amnon Kohen
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

Review 2.  Relating protein motion to catalysis.

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

3.  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

4.  Probes of hydrogen tunneling with horse liver alcohol dehydrogenase at subzero temperatures.

Authors:  S Tsai ; J P Klinman
Journal:  Biochemistry       Date:  2001-02-20       Impact factor: 3.162

5.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

Authors:  R Kaptein; E R Zuiderweg; R M Scheek; R Boelens; W F van Gunsteren
Journal:  J Mol Biol       Date:  1985-03-05       Impact factor: 5.469

6.  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

7.  An internal equilibrium preorganizes the enzyme-substrate complex for hydride tunneling in choline oxidase.

Authors:  Fan Fan; Giovanni Gadda
Journal:  Biochemistry       Date:  2007-05-02       Impact factor: 3.162

8.  Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate.

Authors:  Zhiquan Zhang; P T Ravi Rajagopalan; Tzvia Selzer; Stephen J Benkovic; Gordon G Hammes
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-20       Impact factor: 11.205

9.  Comparison of rates and kinetic isotope effects using PEG-modified variants and glycoforms of glucose oxidase: the relationship of modification of the protein envelope to C-H activation and tunneling.

Authors:  Sean L Seymour; Judith P Klinman
Journal:  Biochemistry       Date:  2002-07-09       Impact factor: 3.162

10.  Driving force analysis of proton tunnelling across a reactivity series for an enzyme-substrate complex.

Authors:  Parvinder Hothi; Sam Hay; Anna Roujeinikova; Michael J Sutcliffe; Michael Lee; David Leys; Paul M Cullis; Nigel S Scrutton
Journal:  Chembiochem       Date:  2008-11-24       Impact factor: 3.164

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  119 in total

1.  Temperature dependence of protein motions in a thermophilic dihydrofolate reductase and its relationship to catalytic efficiency.

Authors:  Olayinka A Oyeyemi; Kevin M Sours; Thomas Lee; Katheryn A Resing; Natalie G Ahn; Judith P Klinman
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-13       Impact factor: 11.205

2.  The promoting vibration in human heart lactate dehydrogenase is a preferred vibrational channel.

Authors:  Ardy Davarifar; Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2011-12-05       Impact factor: 2.991

3.  A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase.

Authors:  John P Richard
Journal:  Biochemistry       Date:  2012-03-20       Impact factor: 3.162

4.  Taking Ockham's razor to enzyme dynamics and catalysis.

Authors:  David R Glowacki; Jeremy N Harvey; Adrian J Mulholland
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

5.  Of polemics and progress.

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

6.  Evidence that a 'dynamic knockout' in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis.

Authors:  E Joel Loveridge; Enas M Behiry; Jiannan Guo; Rudolf K Allemann
Journal:  Nat Chem       Date:  2012-03-11       Impact factor: 24.427

7.  Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase.

Authors:  Maria P Frushicheva; Jie Cao; Zhen T Chu; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-09       Impact factor: 11.205

8.  Impact of oxidation on protein therapeutics: conformational dynamics of intact and oxidized acid-β-glucocerebrosidase at near-physiological pH.

Authors:  Cedric E Bobst; John J Thomas; Paul A Salinas; Philip Savickas; Igor A Kaltashov
Journal:  Protein Sci       Date:  2010-12       Impact factor: 6.725

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.  Specificity in transition state binding: the Pauling model revisited.

Authors:  Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2013-02-04       Impact factor: 3.162

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