Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases

Fungal Cellulases

(2015) Christina M. Payne et al.   CHEMICAL REVIEWS

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study

(2015) Manju Kumari et al.   JOURNAL OF PHYSICAL CHEMISTRY B

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases

(2014) Gregg T Beckham et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational tools for designing and engineering enzymes

(2014) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Dissecting conformational contributions to glycosidase catalysis and inhibition

(2014) Gaetano Speciale et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Carbohydrate–Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity

(2014) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Highly reduced mass loss rates and increased litter layer in radioactively contaminated areas

(2014) Timothy A. Mousseau et al.   OECOLOGIA

Computational Investigation of the pH Dependence of Loop Flexibility and Catalytic Function in Glycoside Hydrolases

(2013) Lintao Bu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Loop Motions Important to Product Expulsion in theThermobifida fuscaGlycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies

(2013) Miao Wu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Binding Site Dynamics and Aromatic–Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases

(2013) Courtney B. Taylor et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biocatalysis in Organic Chemistry and Biotechnology: Past, Present, and Future

(2013) Manfred T. Reetz   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies

(2013) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy

(2013) Christina M. Payne et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis

(2013) Heather B. Mayes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Identification of Tyr241 as a Key Catalytic Base in the Family 4 Glycoside Hydrolase BglT from Thermotoga maritima

(2012) Vivian L. Y. Yip et al.   BIOCHEMISTRY

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes

(2012) Lintao Bu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of theSerratia marcescensChitinases

(2012) Christina M. Payne et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

α-1-C-Butyl-1,4-dideoxy-1,4-imino-l-arabinitol as a Second-Generation Iminosugar-Based Oral α-Glucosidase Inhibitor for Improving Postprandial Hyperglycemia

(2012) Atsushi Kato et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Structure of a Bacterial Cellobiohydrolase: The Catalytic Core of the Thermobifida fusca Family GH6 Cellobiohydrolase Cel6B

(2012) Mats Sandgren et al.   JOURNAL OF MOLECULAR BIOLOGY

Unraveling the Reactions that Unravel Cellulose

(2012) Heather B. Mayes et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Engineering the third wave of biocatalysis

(2012) U. T. Bornscheuer et al.   NATURE

The case of the missing base

(2012) Stephen G Withers et al.   Nature Chemical Biology

Structural snapshots of the reaction coordinate for O-GlcNAc transferase

(2012) Michael B Lazarus et al.   Nature Chemical Biology

O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis

(2012) Marianne Schimpl et al.   Nature Chemical Biology

Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation

(2011) Christina M. Payne et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods

(2011) Lintao Bu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

(2011) J. L. A. Bras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Traffic Jams Reduce Hydrolytic Efficiency of Cellulase on Cellulose Surface

(2011) K. Igarashi et al.   SCIENCE

Quantum Mechanical Modeling of Catalytic Processes

(2011) Alexis T. Bell et al.   Annual Review of Chemical and Biomolecular Engineering

Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals

(2011) Shishir P.S. Chundawat et al.   Annual Review of Chemical and Biomolecular Engineering

Glycoside hydrolases: Catalytic base/nucleophile diversity

(2010) Thu V. Vuong et al.   BIOTECHNOLOGY AND BIOENGINEERING

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Applications of computational science for understanding enzymatic deconstruction of cellulose

(2010) Gregg T Beckham et al.   CURRENT OPINION IN BIOTECHNOLOGY

Transition-State Theory, Dynamics, and Narrow Time Scale Separation in the Rate-Promoting Vibrations Model of Enzyme Catalysis

(2010) Baron Peters   Journal of Chemical Theory and Computation

Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase

(2010) Ian J. Barker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Visualizing the Reaction Coordinate of an O-GlcNAc Hydrolase

(2010) Yuan He et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The absence of an identifiable single catalytic base residue inThermobifida fuscaexocellulase Cel6B

(2009) Thu V. Vuong et al.   FEBS Journal

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software

(2009) Michael F. Crowley et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

(2009) Olgun Guvench et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hybrid Quantum Mechanical/Molecular Mechanical Investigation of the β-1,4-Galactosyltransferase-I Mechanism

(2009) Martin Krupička et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

(2009) Luis Petersen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor†

(2008) Demian Riccardi et al.   BIOCHEMISTRY

Carbohydrate Polymers at the Center of Life’s Origins: The Importance of Molecular Processivity

(2008) Robert Stern et al.   CHEMICAL REVIEWS

Additive empirical force field for hexopyranose monosaccharides

(2008) Olgun Guvench et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism

(2008) Baron Peters et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Long-Range Proton Transfer in Aqueous Acid−Base Reactions†

(2007) B. J. Siwick et al.   JOURNAL OF PHYSICAL CHEMISTRY B