Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.
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ABSTRACT:
SUBMITTER: Tian B
PROVIDER: S-EPMC3964877 | biostudies-literature | 2013 Aug
REPOSITORIES: biostudies-literature
Publications
Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.
Tian Boxue B Wallrapp Frank F Kalyanaraman Chakrapani C Zhao Suwen S Eriksson Leif A LA Jacobson Matthew P MP
Biochemistry 20130809 33
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. ...[more]
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