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Predicting enzyme–substrate specificity with qm/mm methods: a case study of the stereospecificity ofd-glucarate dehydratase

Tian, Boxue
; 
Wallrapp, Frank
; 
Kalyanaraman, Chakrapani
; 
Zhao, Suwen
; 
Eriksson, Leif A.
; 
Jacobson, Matthew P.
Repository DOI
Publication Date
2013-08-20
Keywords
mandelate racemase enzyme, d-galactonate dehydratase, general acid catalyst, enolase superfamily, escherichia-coli, active-site, computer-simulations, pseudomonas-putida, molecular-dynamics, unknown function
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Article
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Citation
Tian, Boxue; Wallrapp, Frank; Kalyanaraman, Chakrapani; Zhao, Suwen; Eriksson, Leif A. Jacobson, Matthew P. (2013). Predicting enzyme–substrate specificity with qm/mm methods: a case study of the stereospecificity ofd-glucarate dehydratase. Biochemistry 52 (33), 5511-5513
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.
Funder
Publisher
American Chemical Society (ACS)
Publisher DOI
10.1021/bi400546j
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Attribution-NonCommercial-NoDerivs 3.0 Ireland
cbn
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Externally hosted open access publications with University of Galway authors (2)