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

Autor:	Suwen Zhao, Chakrapani Kalyanaraman, Boxue Tian, Matthew P. Jacobson, Leif A. Eriksson, Frank H. Wallrapp
Rok vydání:	2013
Předmět:	Models Molecular Protein Structure Biochemistry & Molecular Biology Stereochemistry Adipates molecular-dynamics Chemical Medical Biochemistry and Metabolomics Molecular Dynamics Simulation Biochemistry Molecular mechanics active-site Article Substrate Specificity QM/MM Medicinal and Biomolecular Chemistry Glucaric Acid Stereospecificity Models enolase superfamily Glucarate dehydratase Hydro-Lyases chemistry.chemical_classification Molecular Structure Molecular general acid catalyst Stereoisomerism d-galactonate dehydratase computer-simulations Transition state Protein Structure Tertiary mandelate racemase enzyme Enzyme chemistry Models Chemical Docking (molecular) Dehydratase escherichia-coli Biocatalysis Quantum Theory Thermodynamics Generic health relevance Biochemistry and Cell Biology unknown function Tertiary pseudomonas-putida Protein Binding
Zdroj:	Biochemistry, vol 52, iss 33
ISSN:	1520-4995
Popis:	The stereo-specificity 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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8e2282303531afb2dfc6bfbf505c9d9f https://pubmed.ncbi.nlm.nih.gov/23901785 Zobrazit plný text záznamu