Literature DB >> 11913389

Simulating enzyme reactions: challenges and perspectives.

Martin J Field1.   

Abstract

Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.

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Year:  2002        PMID: 11913389     DOI: 10.1002/jcc.1156

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  23 in total

1.  Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.

Authors:  Mats H M Olsson; Janez Mavri; Arieh Warshel
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

2.  On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.

Authors:  Marco Klähn; Sonja Braun-Sand; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2005-08-18       Impact factor: 2.991

3.  A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes.

Authors:  Pankaz K Sharma; Zhen T Chu; Mats H M Olsson; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-21       Impact factor: 11.205

4.  Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.

Authors:  Chuanyun Xiao; Yingkai Zhang
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

5.  GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

Authors:  José Fernando R Bachega; Luís Fernando S M Timmers; Lucas Assirati; Leonardo R Bachega; Martin J Field; Troy Wymore
Journal:  J Comput Chem       Date:  2013-09-30       Impact factor: 3.376

6.  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

7.  The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.

Authors:  Patrick Schopf; Matthew J L Mills; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-24       Impact factor: 11.205

8.  Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs.

Authors:  Robin Chaudret; Jerry M Parks; Weitao Yang
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

9.  Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.

Authors:  Joanna Trylska; Piotr Bała; Maciej Geller; Paweł Grochowski
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

Review 10.  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

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