Predicting enzyme–substrate specificity with qm/mm methods: a case study of the stereospecificity ofd-glucarate dehydratase
Eriksson, Leif A.
Jacobson, Matthew P.
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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
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.