Literature DB >> 15884923

Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase.

Alejandro Crespo1, Marcelo A Martí, Darío A Estrin, Adrian E Roitberg.   

Abstract

A novel technique for computing free energy profiles in enzymatic reactions using the multiple steering molecular dynamics approach in the context of an efficient QM-MM density functional scheme is presented. The conversion reaction of chorismate to prephenate catalyzed by the Bacillus subtilis enzyme chorismate mutase has been chosen as an illustrative example.

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Year:  2005        PMID: 15884923     DOI: 10.1021/ja0452830

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  28 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.  Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

Authors:  Shenglong Wang; Po Hu; Yingkai Zhang
Journal:  J Phys Chem B       Date:  2007-03-22       Impact factor: 2.991

Review 3.  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 4.  Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Authors:  Hao Hu; Weitao Yang
Journal:  Annu Rev Phys Chem       Date:  2008       Impact factor: 12.703

5.  Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Authors:  Edina Rosta; Maciej Haranczyk; Zhen T Chu; Arieh Warshel
Journal:  J Phys Chem B       Date:  2008-04-16       Impact factor: 2.991

Review 6.  Thiol redox biochemistry: insights from computer simulations.

Authors:  Ari Zeida; Carlos M Guardia; Pablo Lichtig; Laura L Perissinotti; Lucas A Defelipe; Adrián Turjanski; Rafael Radi; Madia Trujillo; Darío A Estrin
Journal:  Biophys Rev       Date:  2014-01-09

7.  Catalytic mechanism of aromatic prenylation by NphB.

Authors:  Yue Yang; Yipu Miao; Bing Wang; Guanglei Cui; Kenneth M Merz
Journal:  Biochemistry       Date:  2012-03-12       Impact factor: 3.162

8.  Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Authors:  Nikolay V Plotnikov; Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

Review 9.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

10.  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

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