Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods

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Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods is …
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scholarly articleQ13442814

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P356DOI10.1074/JBC.M110.212076
P932PMC publication ID3093888
P698PubMed publication ID21454590

P50authorMichael R. ShirtsQ56896565
Michael E. HimmelQ64516090
P2093author name stringGregg T Beckham
Michael F Crowley
Lintao Bu
William S Adney
Mark R Nimlos
P2860cites workNonequilibrium Equality for Free Energy DifferencesQ21698763
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The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reeseiQ27730832
High-resolution crystal structures reveal how a cellulose chain is bound in the 50 A long tunnel of cellobiohydrolase I from Trichoderma reeseiQ27748854
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesQ29397708
Kinetics of the enzymatic hydrolysis of celluloseQ46773165
Factors influencing glycosylation of Trichoderma reesei cellulases. II: N-glycosylation of Cel7A core protein isolated from different strainsQ47799607
Homologous domains in Trichoderma reesei cellulolytic enzymes: gene sequence and expression of cellobiohydrolase II.Q48351439
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Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations.Q51616083
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems.Q51989869
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Study of the enzymatic hydrolysis of cellulose for production of fuel ethanol by the simultaneous saccharification and fermentation process.Q52397345
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Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equalityQ57233442
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Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics SimulationsQ58846574
Role of the interdomain linker peptide of Trichoderma reesei cellobiohydrolase I in its interaction with crystalline celluloseQ70500454
Cloning and expression of Trichoderma reesei cellobiohydrolase I in Pichia pastorisQ73066196
Modified glycosylation of cellobiohydrolase I from a high cellulase-producing mutant strain of Trichoderma reeseiQ77327656
Cellulase for commodity products from cellulosic biomassQ78131242
Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surfaceQ80150999
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Factors affecting the enzymatic hydrolysis of cellulose in batch and continuous reactors: computer simulation and experimentQ81515043
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CHARMM Additive All-Atom Force Field for Glycosidic Linkages between HexopyranosesQ33531681
Calculation of absolute protein-ligand binding free energy from computer simulationsQ33784404
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Energetics of glycerol conduction through aquaglyceroporin GlpF.Q34067362
Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bondsQ34131204
Identification of two functionally different classes of exocellulasesQ34370815
The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered proteinQ34388738
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamicsQ34565120
Free energy simulations come of age: protein-ligand recognitionQ34691182
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentialsQ35051978
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integrationQ36104911
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurementsQ36689424
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domainQ36897559
Computations of standard binding free energies with molecular dynamics simulationsQ37335295
Modeling cellulase kinetics on lignocellulosic substratesQ37541196
Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I. Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymesQ37676583
Deconstruction of lignocellulosic biomass to fuels and chemicalsQ37995270
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
On the use of orientational restraints and symmetry corrections in alchemical free energy calculationsQ42106721
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation studyQ42536182
Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complexQ42942958
Identification of amino acids responsible for processivity in a Family 1 carbohydrate-binding module from a fungal cellulaseQ43202111
Characterization of cellobiohydrolase I (Cel7A) glycoforms from extracts of Trichoderma reesei using capillary isoelectric focusing and electrospray mass spectrometry.Q43555108
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulationsQ44694277
Improved treatment of the protein backbone in empirical force fields.Q44735024
Discrimination among eight modified michaelis-menten kinetics models of cellulose hydrolysis with a large range of substrate/enzyme ratios: inhibition by cellobiose.Q44790732
Factors influencing glycosylation of Trichoderma reesei cellulases. I: Postsecretorial changes of the O- and N-glycosylation pattern of Cel7A.Q44834921
Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate.Q44885409
The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds.Q45931546
A mechanistic model of the enzymatic hydrolysis of celluloseQ46199858
Multiple-steering QM-MM calculation of the free energy profile in chorismate mutaseQ46482793
Enzymatic kinetic of cellulose hydrolysis: inhibition by ethanol and cellobiose.Q46598875
P433issue20
P407language of work or nameEnglishQ1860
P304page(s)18161-18169
P577publication date2011-03-24
P1433published inJournal of Biological ChemistryQ867727
P1476titleProbing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods
P478volume286

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cites work (P2860)
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Q38942452Strategies to reduce end-product inhibition in family 48 glycoside hydrolases
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Q27678483Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance.
Q27675853Structural, Biochemical, and Computational Characterization of the Glycoside Hydrolase Family 7 Cellobiohydrolase of the Tree-killing Fungus Heterobasidion irregulare
Q36376289Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12.
Q39893918Substrate dynamics in enzyme action: rotations of monosaccharide subunits in the binding groove are essential for pectin methylesterase processivity
Q41881153Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber

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