title: Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.
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.
authors.affiliation: School of Chemistry, National University of Ireland, Galway, Galway, Ireland.
authors.forename: Boxue
authors.initials: B
authors.lastname: Tian
authors.forename: Frank
authors.initials: F
authors.lastname: Wallrapp
authors.forename: Chakrapani
authors.initials: C
authors.lastname: Kalyanaraman
authors.forename: Suwen
authors.initials: S
authors.lastname: Zhao
authors.forename: Leif A
authors.initials: LA
authors.lastname: Eriksson
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
mesh_terms: D000272:Adipates / Q000737:chemistry / Q000378:metabolism; D055162:Biocatalysis; D005937:Glucaric Acid / Q000737:chemistry* / Q000378:metabolism; D006836:Hydro-Lyases / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D013237:Stereoisomerism; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D000272:Adipates; C114809:mannaric acid; D006836:Hydro-Lyases; C020572:glucarate dehydratase; D005937:Glucaric Acid
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