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Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate
Boxue Tian1, Frank Wallrapp, Chakrapani Kalyanaraman
1School of Chemistry, National University of Ireland, Galway, Galway, Ireland.
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.
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