Literature DB >> 19805169

Enzyme millisecond conformational dynamics do not catalyze the chemical step.

Andrei V Pisliakov1, Jie Cao, Shina C L Kamerlin, Arieh Warshel.   

Abstract

The idea that enzymes catalyze reactions by dynamical coupling between the conformational motions and the chemical coordinates has recently attracted major experimental and theoretical interest. However, experimental studies have not directly established that the conformational motions transfer energy to the chemical coordinate, and simulating enzyme catalysis on the relevant timescales has been impractical. Here, we introduce a renormalization approach that transforms the energetics and dynamics of the enzyme to an equivalent low-dimensional system, and allows us to simulate the dynamical coupling on a ms timescale. The simulations establish, by means of several independent approaches, that the conformational dynamics is not remembered during the chemical step and does not contribute significantly to catalysis. Nevertheless, the precise nature of this coupling is a question of great importance.

Mesh:

Substances:

Year:  2009        PMID: 19805169      PMCID: PMC2762662          DOI: 10.1073/pnas.0909150106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  19 in total

1.  Computer simulation of protein folding.

Authors:  M Levitt; A Warshel
Journal:  Nature       Date:  1975-02-27       Impact factor: 49.962

Review 2.  NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis.

Authors:  Mikael Akke
Journal:  Curr Opin Struct Biol       Date:  2002-10       Impact factor: 6.809

3.  Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair.

Authors:  Magnus Wolf-Watz; Vu Thai; Katherine Henzler-Wildman; Georgia Hadjipavlou; Elan Z Eisenmesser; Dorothee Kern
Journal:  Nat Struct Mol Biol       Date:  2004-08-29       Impact factor: 15.369

4.  Out of hot water.

Authors:  Mikael Akke
Journal:  Nat Struct Mol Biol       Date:  2004-10       Impact factor: 15.369

Review 5.  Electrostatic basis for enzyme catalysis.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; Yun Xiang; Hanbin Liu; Mats H M Olsson
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

Review 6.  Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis.

Authors:  Mats H M Olsson; William W Parson; Arieh Warshel
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  Structural biology. Dynamic visions of enzymatic reactions.

Authors:  Michele Vendruscolo; Christopher M Dobson
Journal:  Science       Date:  2006-09-15       Impact factor: 47.728

8.  On the relationship between folding and chemical landscapes in enzyme catalysis.

Authors:  Maite Roca; Benjamin Messer; Donald Hilvert; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-08       Impact factor: 11.205

9.  Energetics of nucleophile activation in a protein tyrosine phosphatase.

Authors:  T Hansson; P Nordlund; J Aqvist
Journal:  J Mol Biol       Date:  1997-01-17       Impact factor: 5.469

10.  Intrinsic dynamics of an enzyme underlies catalysis.

Authors:  Elan Z Eisenmesser; Oscar Millet; Wladimir Labeikovsky; Dmitry M Korzhnev; Magnus Wolf-Watz; Daryl A Bosco; Jack J Skalicky; Lewis E Kay; Dorothee Kern
Journal:  Nature       Date:  2005-11-03       Impact factor: 49.962

View more
  86 in total

1.  Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase.

Authors:  Shayantani Mukherjee; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-05       Impact factor: 11.205

2.  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

3.  Good vibrations in enzyme-catalysed reactions.

Authors:  Sam Hay; Nigel S Scrutton
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

4.  Realistic simulation of the activation of voltage-gated ion channels.

Authors:  Anatoly Dryga; Suman Chakrabarty; Spyridon Vicatos; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-13       Impact factor: 11.205

5.  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

6.  Resolving the complex role of enzyme conformational dynamics in catalytic function.

Authors:  Urmi Doshi; Lauren C McGowan; Safieh Tork Ladani; Donald Hamelberg
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-26       Impact factor: 11.205

Review 7.  Capturing the essence of folding and functions of biomolecules using coarse-grained models.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Nat Commun       Date:  2011-09-27       Impact factor: 14.919

8.  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

9.  Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility.

Authors:  Xiaogang Niu; Lei Bruschweiler-Li; Omar Davulcu; Jack J Skalicky; Rafael Brüschweiler; Michael S Chapman
Journal:  J Mol Biol       Date:  2010-11-12       Impact factor: 5.469

Review 10.  Computer aided enzyme design and catalytic concepts.

Authors:  Maria P Frushicheva; Matthew J L Mills; Patrick Schopf; Manoj K Singh; Ram B Prasad; Arieh Warshel
Journal:  Curr Opin Chem Biol       Date:  2014-05-08       Impact factor: 8.822

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.