Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.

@article{Tian2013PredictingES,
  title={Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.},
  author={Boxue Tian and Frank Wallrapp and Chakrapani Kalyanaraman and Suwen Zhao and Leif A. Eriksson and Matthew P. Jacobson},
  journal={Biochemistry},
  year={2013},
  volume={52 33},
  pages={5511-3}
}
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.