Literature DB >> 24742825

Protein motions and the activation of the CH bond catalyzed by dihydrofolate reductase.

Kevin Francis1, Amnon Kohen2.   

Abstract

The role of protein motions in enzymatic CH→C transfer is an area of great contemporary debate. An effective tool in probing such a role is the temperature dependence of the intrinsic kinetic isotope effects for the enzyme-catalyzed reaction. The outcome of those experiments is interpreted within the context of phenomenological Marcus-like models of hydrogen tunneling. The current review focuses on recent studies of dihydrofolate reductase (DHFR) and how the role of protein motions in the catalyzed reaction has been demonstrated. The motions in DHFR are controlled by local effects of active site residues, global effects involving remote residues across the enzyme and appear to be preserved during the evolution of the enzyme from bacteria to human.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 24742825      PMCID: PMC4149937          DOI: 10.1016/j.cbpa.2014.03.009

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  37 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.  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

Review 3.  Relating protein motion to catalysis.

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

4.  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

5.  The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer.

Authors:  Vanja Stojković; Laura L Perissinotti; Jeeyeon Lee; Stephen J Benkovic; Amnon Kohen
Journal:  Chem Commun (Camb)       Date:  2010-10-25       Impact factor: 6.222

6.  Preservation of protein dynamics in dihydrofolate reductase evolution.

Authors:  Kevin Francis; Vanja Stojkovic; Amnon Kohen
Journal:  J Biol Chem       Date:  2013-10-24       Impact factor: 5.157

7.  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

Review 8.  Hydrogen tunneling and protein motion in enzyme reactions.

Authors:  Sharon Hammes-Schiffer
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

9.  Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes.

Authors:  T D Colby; B J Bahnson; J K Chin; J P Klinman; B M Goldstein
Journal:  Biochemistry       Date:  1998-06-30       Impact factor: 3.162

10.  Extension and limits of the network of coupled motions correlated to hydride transfer in dihydrofolate reductase.

Authors:  Priyanka Singh; Arundhuti Sen; Kevin Francis; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2014-01-31       Impact factor: 15.419

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  11 in total

1.  The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism.

Authors:  Katarzyna Swiderek; Amnon Kohen; Vicent Moliner
Journal:  Phys Chem Chem Phys       Date:  2015-12-14       Impact factor: 3.676

2.  Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase.

Authors:  Katarzyna Świderek; Iñaki Tuñón; Sergio Martí; Vicent Moliner
Journal:  ACS Catal       Date:  2015-01-07       Impact factor: 13.084

3.  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

4.  Network of remote and local protein dynamics in dihydrofolate reductase catalysis.

Authors:  Priyanka Singh; Kevin Francis; Amnon Kohen
Journal:  ACS Catal       Date:  2015-04-08       Impact factor: 13.084

5.  Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase.

Authors:  Amrinder Singh; R Bryn Fenwick; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2021-08-24       Impact factor: 3.321

Review 6.  The importance of ensemble averaging in enzyme kinetics.

Authors:  Laura Masgrau; Donald G Truhlar
Journal:  Acc Chem Res       Date:  2014-12-24       Impact factor: 22.384

7.  Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway.

Authors:  David Oyen; R Bryn Fenwick; Robyn L Stanfield; H Jane Dyson; Peter E Wright
Journal:  J Am Chem Soc       Date:  2015-07-14       Impact factor: 15.419

8.  The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture.

Authors:  Archie C Reyes; Xiang Zhai; Kelsey T Morgan; Christopher J Reinhardt; Tina L Amyes; John P Richard
Journal:  J Am Chem Soc       Date:  2015-01-20       Impact factor: 15.419

9.  Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer.

Authors:  Archie C Reyes; Tina L Amyes; John P Richard
Journal:  J Am Chem Soc       Date:  2016-11-10       Impact factor: 15.419

10.  Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations.

Authors:  Anil R Mhashal; Dan Thomas Major
Journal:  J Phys Chem B       Date:  2021-02-01       Impact factor: 2.991

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