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Predicting Enzyme-Substrate Specificity with QM/MM Methods: A Case Study of the Stereospecificity of D-Glucarate Dehydratase

Journal article
Authors B. X. Tian
F. Wallrapp
C. Kalyanaraman
S. W. Zhao
Leif A Eriksson
M. P. Jacobson
Published in Biochemistry
Volume 52
Issue 33
Pages 5511-5513
ISSN 0006-2960
Publication year 2013
Published at Department of Chemistry and Molecular Biology
Pages 5511-5513
Language en
Links dx.doi.org/10.1021/bi400546j
Keywords MANDELATE RACEMASE ENZYME, D-GALACTONATE DEHYDRATASE, GENERAL ACID, CATALYST, ENOLASE SUPERFAMILY, ESCHERICHIA-COLI, ACTIVE-SITE, COMPUTER-SIMULATIONS, PSEUDOMONAS-PUTIDA, MOLECULAR-DYNAMICS, UNKNOWN, FUNCTION
Subject categories Cell and Molecular Biology

Abstract

The stereospecificity of D-glucarate dehydratase (GlucD) is explored by QM/MM calculations. Both the substrate binding and the chemical steps of GlucD contribute to substrate specificity. Although the identification of transition states remains computationally intensive, we suggest that QM/MM computations on ground states or intermediates can capture aspects of specificity that cannot be obtained using docking or molecular mechanics methods.

Page Manager: Webmaster|Last update: 9/11/2012
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