The analysis of enzymic free energy relationships using kinetic and computational models.

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Chemical Society Reviews

• Publication date

  2010-05-25

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1039/b902741fPMID 20419174
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mechanism of general acid-base catalysis in transesterification of an RNA model phosphodiester studied with strongly basic catalysts.

  2010cited by this paper
• Valence bond modelling and density functional theory calculations of reactivity and mechanism of cytochrome P450 enzymes: thioether sulfoxidation

  2010cited by this paper
• Efficient intramolecular general-acid catalysis of the reactions of alpha-effect nucleophiles and ammonia oxide with a phosphate triester.

  2009cited by this paper
• Dissociative solvolytic cleavage of methyl (ortho-carboxymethyl)aryl phosphate diesters mediated by Yb3+ in methanol gives a 10(12)-fold rate acceleration attributable to leaving group assistance.

  2009cited by this paper
• Transition-state geometry measurements from (13)c isotope effects. The experimental transition state for the epoxidation of alkenes with oxaziridines.

  2009cited by this paper
• An immobilized ortho-palladated dimethylbenzylamine complex as an efficient catalyst for the methanolysis of phosphorothionate pesticides.

  2009cited by this paper
• Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships.

  2009cited by this paper
• Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome

  2009cited by this paper
• Toward accurate screening in computer-aided enzyme design.

  2009cited by this paper
• Dinuclear Zn(II) complex promotes cleavage and isomerization of 2-hydroxypropyl alkyl phosphates by a common cyclic phosphate intermediate.

  2009cited by this paper
• Computational approach for ranking mutant enzymes according to catalytic reaction rates.

  2009cited by this paper
• A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.

  2009cited by this paper
• Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures.

  2009cited by this paper
• Altered transition state for the reaction of an RNA model catalyzed by a dinuclear zinc(II) catalyst.

  2008cited by this paper
• Ligand field stabilization and activation energies revisited: molecular modeling of the thermodynamic and kinetic properties of divalent, first-row aqua complexes.

  2008cited by this paper
• Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

  2008cited by this paper
• Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion.

  2008cited by this paper
• Cold adaptation of enzyme reaction rates.

  2008cited by this paper
• De Novo Computational Design of Retro-Aldol Enzymes

  2008cited by this paper
• The Rap–RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues

  2008cited by this paper
• Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase.

  2008cited by this paper
• A universal approach to solvation modeling.

  2008cited by this paper
• Mechanistic study of protein phosphatase-1 (PP1), a catalytically promiscuous enzyme.

  2008cited by this paper
• DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state.

  2008cited by this paper
• The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

  2008cited by this paper
• Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

  2008cited by this paper
• Mechanistic insights into glycosidase chemistry.

  2008cited by this paper
• On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution.

  2008cited by this paper
• Transition-state analysis of the DNA repair enzyme MutY.

  2008cited by this paper
• Direct Evidence for ArOS Bond Cleavage upon Inactivation of Pseudomonas aeruginosa Arylsulfatase by Aryl Sulfamates

  2008cited by this paper
• Kemp elimination catalysts by computational enzyme design

  2008cited by this paper
• A minimalist approach to understanding the efficiency of mononuclear Zn(II) complexes as catalysts of cleavage of an RNA analog.

  2007cited by this paper
• Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction.

  2007cited by this paper
• Empirical valence bond models for reactive potential energy surfaces. II. Intramolecular proton transfer in pyridone and the Claisen reaction of allyl vinyl ether

  2007cited by this paper
• The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases.

  2007cited by this paper
• Theoretical evaluation of the substrate-assisted catalysis mechanism for the hydrolysis of phosphate monoester dianions.

  2007cited by this paper
• Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta.

  2007cited by this paper
• A Marcus treatment of rate constants for protonation of ring-substituted alpha-methoxystyrenes: intrinsic reaction barriers and the shape of the reaction coordinate.

  2007cited by this paper
• Formation and stability of mononuclear and dinuclear Eu(III) complexes and their catalytic reactivity toward cleavage of an RNA analog.

  2007cited by this paper
• Enzymatic Reaction Mechanisms

  2007cited by this paper
• Working tools for theoretical chemistry: Polanyi, eyring, and debates over the “semiempirical method”

  2007cited by this paper
• Synthesis of 2‘-C-α-(Hydroxyalkyl) and 2‘-C-α-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA

  2007cited by this paper
• Transition state analysis of acid-catalyzed dAMP hydrolysis.

  2007cited by this paper
• The role of metal ions in phosphate ester hydrolysis.

  2007cited by this paper
• Efficient synthesis of methyl 3,5-di-O-benzyl-alpha-D-ribofuranoside and application to the synthesis of 2'-C-beta-alkoxymethyluridines.

  2007cited by this paper
• The mechanism of RNA strand scission: an experimental measure of the Brønsted coefficient, beta nuc.

  2007cited by this paper
• Analysis of PUGNAc and NAG-thiazoline as transition state analogues for human O-GlcNAcase: mechanistic and structural insights into inhibitor selectivity and transition state poise.

  2007cited by this paper
• Empirical Valence-Bond Models for Reactive Potential Energy Surfaces Using Distributed Gaussians.

  2006cited by this paper
• Electrostatic basis for enzyme catalysis.

  2006cited by this paper
• Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases.

  2006cited by this paper
• Efficient synthesis of 2'-C-beta-methylguanosine.

  2006cited by this paper
• Degrees of difficulty of water-consuming reactions in the absence of enzymes.

  2006cited by this paper
• Structure and mechanism of a bacterial β-glucosaminidase having O-GlcNAcase activity

  2006cited by this paper
• The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA.

  2006cited by this paper
• Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.

  2006cited by this paper
• Phase I Study of STX 64 (667 Coumate) in Breast Cancer Patients: The First Study of a Steroid Sulfatase Inhibitor

  2006cited by this paper
• Identification of Asp174 and Asp175 as the key catalytic residues of human O-GlcNAcase by functional analysis of site-directed mutants.

  2006cited by this paper
• gamma-Glutamyl transpeptidase acylation with peptidic substrates: free energy relationships measured by an HPLC kinetic assay.

  2006cited by this paper
• Catalysis and linear free energy relationships in aspartic proteases.

  2006cited by this paper
• On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins.

  2006cited by this paper
• Efficient Synthesis of 2‘-C-β-Methylguanosine

  2006cited by this paper
• Mechanistic studies of La3+- and Zn2+-catalyzed methanolysis of aryl phosphate and phosphorothioate triesters. Development of artificial phosphotriesterase systems.

  2005cited by this paper
• O-GlcNAcase catalyzes cleavage of thioglycosides without general acid catalysis.

  2005cited by this paper
• Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides.

  2005cited by this paper
• Studies on the transglucosylation reactions of cassava and Thai rosewood beta-glucosidases using 2-deoxy-2-fluoro-glycosyl-enzyme intermediates.

  2005cited by this paper
• Altered mechanisms of reactions of phosphate esters bridging a dinuclear metal center.

  2004cited by this paper
• Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark.

  2004cited by this paper
• Sulfatases: structure, mechanism, biological activity, inhibition, and synthetic utility.

  2004cited by this paper
• Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited

  2004cited by this paper
• Why does the Ras switch “break” by oncogenic mutations?

  2004cited by this paper
• Mononuclear Co(III)-complex promoted phosphate diester hydrolysis: dependence of reactivity on the leaving group†

  2004cited by this paper
• Compelling evidence for a stepwise mechanism of the alkaline cyclisation of uridine 3'-phosphate esters.

  2004cited by this paper
• Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm

  2004cited by this paper
• Guanidinium groups act as general-acid catalysts in phosphoryl transfer reactions: a two-proton inventory on a model system.

  2004cited by this paper
• Nucleophilic participation in the transition state for human thymidine phosphorylase.

  2004cited by this paper
• Kinetic studies of rat kidney gamma-glutamyltranspeptidase deacylation reveal a general base-catalyzed mechanism.

  2003cited by this paper
• Synthesis of 2'-C-beta-fluoromethyluridine.

  2003cited by this paper
• Transition State Analysis Using Multiple Kinetic Isotope Effects: Mechanisms of Enzymatic and Non-Enzymatic Glycoside Hydrolysis and Transfer

  2003cited by this paper
• Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta- and gamma-class.

  2002cited by this paper
• The Catalytic Mechanism of Cdc25A Phosphatase*

  2002cited by this paper
• Chemical Rescue of Proton Transfer in Catalysis by Carbonic Anhydrases in the β- and γ-Class†

  2002cited by this paper
• Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.

  2002cited by this paper
• Alkaline Phosphatase Revisited:  Hydrolysis of Alkyl Phosphates †.

  2002cited by this paper
• Dynamics of biochemical and biophysical reactions: insight from computer simulations

  2001cited by this paper
• The catalytic mechanism of protein tyrosine phosphatases revisited

  2001cited by this paper
• Nonlinear free energy relationship in the general-acid-catalyzed acylation of rat kidney gamma-glutamyl transpeptidase by a series of gamma-glutamyl anilide substrate analogues.

  2001cited by this paper
• 2‘-C-Branched Ribonucleosides. 2. Synthesis of 2‘-C-β-Trifluoromethyl Pyrimidine Ribonucleosides1

  2001cited by this paper
• 1.3 A structure of arylsulfatase from Pseudomonas aeruginosa establishes the catalytic mechanism of sulfate ester cleavage in the sulfatase family.

  2001cited by this paper
• Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate

  2001cited by this paper
• 2'-C-branched ribonucleosides. 2. Synthesis of 2'-C-beta-trifluoromethyl pyrimidine ribonucleosides.

  2001cited by this paper
• Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase.

  2001cited by this paper
• Hydration of Carbonyl Compounds, an Analysis in Terms of Multidimensional Marcus Theory

  2000cited by this paper
• 2'-C-Branched Ribonucleosides: Synthesis of the Phosphoramidite Derivatives of 2'-C-beta-Methylcytidine and Their Incorporation into Oligonucleotides.

  1999cited by this paper
• Glycosidase mechanisms: anatomy of a finely tuned catalyst.

  1999cited by this paper
• Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases

  1999cited by this paper
• Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model

  1999cited by this paper
• Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase

  1999cited by this paper
• Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase

  1999cited by this paper
• Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

  1999cited by this paper
• Impaired transition state complementarity in the hydrolysis of O-arylphosphorothioates by protein-tyrosine phosphatases.

  1999cited by this paper

• Micro‐Environment Programmable Quinoline COFs for High‐Performance Photocatalytic H2O2 Generation and Benzylamine Coupling

  2025cites this paper
• Hands-On Approach to Structure Activity Relationships of Substituted MIL-101(Fe)-X Nanozymes: Synthesis, Characterization, and Hammett Analysis

  2023cites this paper
• Mechanistic Inference from Statistical Models at Different Data-Size Regimes

  2022cites this paper
• Mechanistic Insight into the Reactivities of Aqueous-Phase Singlet Oxygen with Organic Compounds.

  2021cites this paper
• A Hammett Study of Clostridium acetobutylicum Alcohol Dehydrogenase (CaADH): An Enzyme with Remarkable Substrate Promiscuity and Utility for Organic Synthesis

  2020cites this paper
• Hammett Relationship in Oxidase‐Mimicking Metal–Organic Frameworks Revealed through a Protein‐Engineering‐Inspired Strategy

  2020cites this paper
• Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.

  2020cites this paper
• Computational physical organic chemistry using the empirical valence bond approach

  2019cites this paper
• Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations.

  2018influential citation
• Remarkable Reactivity Differences between Glucosides with Identical Leaving Groups.

  2017cites this paper
• Biological Chemistry of Hydrogen Selenide

  2016cites this paper
• Enantiodivergent Fluorination of Allylic Alcohols: Data Set Design Reveals Structural Interplay between Achiral Directing Group and Chiral Anion.

  2016cites this paper
• Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.

  2016cites this paper
• Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

  2014cites this paper
• Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues.

  2014cites this paper
• Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer.

  2013cites this paper
• Applications of docking and molecular dynamic studies on the search for new drugs against the biological warfare agents Bacillus anthracis and Yersinia pestis.

  2013cites this paper
• Porphyrin nanochannels reinforced by hydrogen bonding.

  2012cites this paper
• Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide‐promoted cleavages of phosphorothioate and phosphate triesters in water and methanol

  2012cites this paper
• Kinetic and computational evidence for an intermediate in the hydrolysis of sulfonate esters.

  2012cites this paper
• Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation.

  2011cites this paper
• Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase.

  2011cites this paper
• Glucosamine‐6‐sulfamate Analogues of Heparan Sulfate as Inhibitors of Endosulfatases

  2010cites this paper
• The Analysis of Enzymic Free Energy Relationships Using Kinetic and Computational Models

  2010cites this paper