Literature DB >> 20729130

Coupled motions in enzyme catalysis.

Vishal C Nashine1, Sharon Hammes-Schiffer, Stephen J Benkovic.   

Abstract

Recently, the hypothesis that protein motions are involved in enzymatic turnover has gained significant attention. We review cases where there is evidence that protein motions are rate-limiting in the overall catalytic cycle and examine experimental and theoretical evidence for how such motions enhance the probability of sampling the transition state configurations relative to the ground state. The impact of tunneling, the possible role of vibrational coupling and the value of conformational chemical landscapes are also scrutinized.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20729130      PMCID: PMC2953590          DOI: 10.1016/j.cbpa.2010.07.020

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


  57 in total

Review 1.  Relating protein motion to catalysis.

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

2.  Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.

Authors:  Yun Xiang; Myron F Goodman; William A Beard; Samuel H Wilson; Arieh Warshel
Journal:  Proteins       Date:  2008-01-01

3.  Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex.

Authors:  Sachin Kale; Gözde Ulas; Jaeyoung Song; Gary W Brudvig; William Furey; Frank Jordan
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-23       Impact factor: 11.205

4.  A unified model of protein dynamics.

Authors:  Hans Frauenfelder; Guo Chen; Joel Berendzen; Paul W Fenimore; Helén Jansson; Benjamin H McMahon; Izabela R Stroe; Jan Swenson; Robert D Young
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-27       Impact factor: 11.205

5.  Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase.

Authors:  Sarah J Edwards; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

6.  Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

Authors:  S R Billeter; S P Webb; P K Agarwal; T Iordanov; S Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2001-11-14       Impact factor: 15.419

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.  Remote mutations alter transition-state structure of human purine nucleoside phosphorylase.

Authors:  Minkui Luo; Lei Li; Vern L Schramm
Journal:  Biochemistry       Date:  2008-02-26       Impact factor: 3.162

Review 9.  Hydrogen tunneling and protein motion in enzyme reactions.

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

10.  Nuclear magnetic resonance study of the role of M42 in the solution dynamics of Escherichia coli dihydrofolate reductase.

Authors:  Randall V Mauldin; Andrew L Lee
Journal:  Biochemistry       Date:  2010-03-02       Impact factor: 3.162

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  66 in total

1.  Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers.

Authors:  Freddie R Salsbury; Ye Yuan; Michael H Knaggs; Leslie B Poole; Jacquelyn S Fetrow
Journal:  J Phys Chem B       Date:  2012-04-04       Impact factor: 2.991

2.  Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.

Authors:  Weina Wang; Eugene Y Wu; Homme W Hellinga; Lorena S Beese
Journal:  J Biol Chem       Date:  2012-05-30       Impact factor: 5.157

3.  Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

Authors:  Tsuyoshi Konuma; Erisa Harada; Kenji Sugase
Journal:  J Biomol NMR       Date:  2015-10-17       Impact factor: 2.835

4.  An intrinsically disordered photosystem II subunit, PsbO, provides a structural template and a sensor of the hydrogen-bonding network in photosynthetic water oxidation.

Authors:  Adam R Offenbacher; Brandon C Polander; Bridgette A Barry
Journal:  J Biol Chem       Date:  2013-08-12       Impact factor: 5.157

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.  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

7.  Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

Authors:  Kate A Stafford; Fabien Ferrage; Jae-Hyun Cho; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2013-11-20       Impact factor: 15.419

8.  Binding of NAD+ and L-threonine induces stepwise structural and flexibility changes in Cupriavidus necator L-threonine dehydrogenase.

Authors:  Shogo Nakano; Seiji Okazaki; Hiroaki Tokiwa; Yasuhisa Asano
Journal:  J Biol Chem       Date:  2014-02-20       Impact factor: 5.157

9.  Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms.

Authors:  Tamar Schlick; Karunesh Arora; William A Beard; Samuel H Wilson
Journal:  Theor Chem Acc       Date:  2012-11-23       Impact factor: 1.702

10.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

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