Literature DB >> 15136856

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase.

Kara E Ranaghan1, Adrian J Mulholland.   

Abstract

The controversial 'near attack conformation'(NAC) effect in the important model enzyme chorismate mutase is calculated to be 3.8-4.6 kcal mol(-1) by QM/MM free energy perturbation molecular dynamics methods, showing that the NAC effect by itself does not account for catalysis in this enzyme.

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Year:  2004        PMID： 15136856     DOI： 10.1039/b402388a

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  14 in total

Review 1.  Mechanisms and free energies of enzymatic reactions.

Authors:  Jiali Gao; Shuhua Ma; Dan T Major; Kwangho Nam; Jingzhi Pu; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

2.  Conformational effects in enzyme catalysis: reaction via a high energy conformation in fatty acid amide hydrolase.

Authors:  Alessio Lodola; Marco Mor; Jolanta Zurek; Giorgio Tarzia; Daniele Piomelli; Jeremy N Harvey; Adrian J Mulholland
Journal:  Biophys J       Date:  2006-11-10       Impact factor: 4.033

3.  pH Dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42.

Authors:  Jose Olucha; Andrew N Ouellette; Qianyi Luo; Audrey L Lamb
Journal:  Biochemistry       Date:  2011-07-22       Impact factor: 3.162

Review 4.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 5.  Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues.

Authors:  Shina Caroline Lynn Kamerlin; Janez Mavri; A Warshel
Journal:  FEBS Lett       Date:  2010-04-29       Impact factor: 4.124

6.  Near attack conformers dominate β-phosphoglucomutase complexes where geometry and charge distribution reflect those of substrate.

Authors:  Joanna L Griffin; Matthew W Bowler; Nicola J Baxter; Katherine N Leigh; Hugh R W Dannatt; Andrea M Hounslow; G Michael Blackburn; Charles Edwin Webster; Matthew J Cliff; Jonathan P Waltho
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-13       Impact factor: 11.205

Review 7.  Pericyclic reactions catalyzed by chorismate-utilizing enzymes.

Authors:  Audrey L Lamb
Journal:  Biochemistry       Date:  2011-08-12       Impact factor: 3.162

8.  Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase.

Authors:  Alexandra Choutko; Andreas P Eichenberger; Wilfred F van Gunsteren; Jožica Dolenc
Journal:  Protein Sci       Date:  2013-06       Impact factor: 6.725

9.  Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus.

Authors:  Ivan Tubert-Brohman; Cristiano Ruch Werneck Guimarães; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2005       Impact factor: 6.006

10.  Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

Authors:  Richard Lonsdale; Simon Hoyle; Daniel T Grey; Lars Ridder; Adrian J Mulholland
Journal:  Biochemistry       Date:  2012-02-10       Impact factor: 3.162
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