Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study
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Title
Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study
Authors
Keywords
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Journal
Frontiers in Chemistry
Volume 7, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2019-04-10
DOI
10.3389/fchem.2019.00200
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- (2017) Benoit David et al. ACS Catalysis
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- A Trapped Covalent Intermediate of a Glycoside Hydrolase on the Pathway to Transglycosylation. Insights from Experiments and Quantum Mechanics/Molecular Mechanics Simulations
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- (2015) Bastien Bissaro et al. BIOCHEMICAL JOURNAL
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- Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism
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- ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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- Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations
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- PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
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- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
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- Substrate-Assisted and Nucleophilically Assisted Catalysis in Bovine α1,3-Galactosyltransferase. Mechanistic Implications for Retaining Glycosyltransferases
- (2013) Hansel Gómez et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Semi-rational approach for converting a GH1 -glycosidase into a -transglycosidase
- (2013) D. Teze et al. PROTEIN ENGINEERING DESIGN & SELECTION
- ChemShell-a modular software package for QM/MM simulations
- (2013) Sebastian Metz et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- High-resolution structures ofNeotermes koshunensisβ-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates
- (2012) Wen-Yih Jeng et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Probing the Active Site Chemistry of β-Glucosidases along the Hydrolysis Reaction Pathway
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- Alkoxyamino glycoside acceptors for the regioselective synthesis of oligosaccharides using glycosynthases and transglycosidases
- (2012) David Teze et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Theoretical study on the deglycosylation mechanism of rice BGlu1 β-glucosidase
- (2012) Jinhu Wang et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
- (2012) Andreas W. Götz et al. Journal of Chemical Theory and Computation
- Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State
- (2012) Hansel Gómez et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Glycosynthases as tools for the production of glycan analogs of natural products
- (2012) Beatrice Cobucci-Ponzano et al. NATURAL PRODUCT REPORTS
- Conformational Analyses of the Reaction Coordinate of Glycosidases
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- Challenging reaction equilibria
- (2011) Robert A Field Nature Chemical Biology
- Chemical Approaches to Glycobiology
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- (2010) Gerald W. Hart et al. CELL
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- The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
- (2008) B. L. Cantarel et al. NUCLEIC ACIDS RESEARCH
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