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How enzymes work: analysis by modern rate theory and computer simulations

scientific article (publication date: 9 January 2004)

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How enzymes work: analysis by modern rate theory and computer simulations (English)

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Donald G Truhlar

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Martin Karplus

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3

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Martin Karplus

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Mireia Garcia-Viloca

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Jiali Gao

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2

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English

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publication date

9 January 2004

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Science

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303

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page(s)

186-95

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5655

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cites work

QM−FE and Molecular Dynamics Calculations on CatecholO-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction

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Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

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Enzymatic H-transfer requires vibration-driven extreme tunneling

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The incorporation of quantum effects in enzyme kinetics modeling

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Statistical Time Events in Enzymes: A Physical Assessmen

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Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence

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The development of mechanistic enzymology in the 20th century

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Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase

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Molecular Architecture and Biological Reactions

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Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

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Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution

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Multiple conformational changes in enzyme catalysis

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The role of protein fluctuations in enzyme action: a review

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Toward identification of acid/base catalysts in the active site of enolase: comparison of the properties of K345A, E168Q, and E211Q variants

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The depth of chemical time and the power of enzymes as catalysts.

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Internal-state nonequilibrium effects for a fast, second-order reaction

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Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions

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Impact of enzyme motion on activity

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Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase

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A new conceptual framework for enzyme catalysis

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Understanding the Role of Active‐Site Residues in Chorismate Mutase Catalysis from Molecular‐Dynamics Simulations

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Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

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Quantum Dynamics of Hydride Transfer in Enzyme Catalysis

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Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism

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Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

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The near attack conformation approach to the study of the chorismate to prephenate reaction

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Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase

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Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase

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Free energy requirement for domain movement of an enzyme

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Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase

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Improved canonical variational theory for chemical reaction rates. Classical mechanical theory and applications to collinear reactions

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Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis

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How much do enzymes really gain by restraining their reacting fragments?

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Effect of mutation on enzyme motion in dihydrofolate reductase

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How an enzyme surmounts the activation energy barrier

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Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism

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Triosephosphate isomerase: a theoretical comparison of alternative pathways

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Current Status of Transition-State Theory

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Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant

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Generalized transition state theory. Classical mechanical theory and applications to collinear reactions of hydrogen molecules

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Chemical basis for enzyme catalysis

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Uracil-DNA glycosylase acts by substrate autocatalysis

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Crystal structure of substrate complexes of methylmalonyl-CoA mutase

1 reference

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Steric bulk at cycloartenol synthase position 481 influences cyclization and deprotonation

1 reference

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Crystal structure of bovine low molecular weight phosphotyrosyl phosphatase complexed with the transition state analog vanadate

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Solvation, reorganization energy, and biological catalysis

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Catalysis by entropic guidance from enzymes

1 reference

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Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

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Energetics of nucleophile activation in a protein tyrosine phosphatase

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Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase

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Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction.

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Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction

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Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor

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The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

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Catalytic proficiency: the unusual case of OMP decarboxylase

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Erratum to: “Quantum mechanical tunneling in methylamine dehydrogenase” [Chem. Phys. Lett. 347 (2001) 512–518]

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Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding

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Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization

1 reference

11 October 2022

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Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase

1 reference

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Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2-A resolution

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A perspective on enzyme catalysis.

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Product-assisted catalysis in base-excision DNA repair

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Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

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Recognition in the minor groove of double-stranded DNA by microgonotropens

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Quantum mechanical methods for enzyme kinetics

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Network of coupled promoting motions in enzyme catalysis

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Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

(Q28238088)

How enzymes work: analysis by modern rate theory and computer simulations

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