Literature DB >> 11972016

Quantum mechanical methods for enzyme kinetics.

Jiali Gao1, Donald G Truhlar.   

Abstract

This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

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Year:  2001        PMID: 11972016     DOI: 10.1146/annurev.physchem.53.091301.150114

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  115 in total

1.  Electronic continuum model for molecular dynamics simulations of biological molecules.

Authors:  I V Leontyev; A A Stuchebrukhov
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

2.  Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes.

Authors:  Mats H M Olsson; Per E M Siegbahn; Arieh Warshel
Journal:  J Biol Inorg Chem       Date:  2003-12-09       Impact factor: 3.358

3.  How an enzyme surmounts the activation energy barrier.

Authors:  Richard L Schowen
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-06       Impact factor: 11.205

4.  Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction.

Authors:  Mireia Garcia-Viloca; Tina D Poulsen; Donald G Truhlar; Jiali Gao
Journal:  Protein Sci       Date:  2004-09       Impact factor: 6.725

5.  Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship.

Authors:  N Arul Murugan; Jacob Kongsted; Zilvinas Rinkevicius; Hans Agren
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-07       Impact factor: 11.205

6.  Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors:  Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal:  J Comput Chem       Date:  2015-08-27       Impact factor: 3.376

7.  QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.

Authors:  Hao Hu; Zhenyu Lu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

8.  On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions.

Authors:  Edina Rosta; Arieh Warshel
Journal:  J Chem Theory Comput       Date:  2012-03-29       Impact factor: 6.006

9.  Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol.

Authors:  Yang Yang; Qiang Cui
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

10.  The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2).

Authors:  Alessandro Cembran; Makenzie R Provorse; Changwei Wang; Wei Wu; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2012-09-04       Impact factor: 6.006

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