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Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate ReductaseTuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational StudiesCritical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution.Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects.Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant.Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an intermediate?Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State.Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.QM/MM study of l-lactate oxidation by flavocytochrome b2.Minimization of dynamic effects in the evolution of dihydrofolate reductase† †Electronic supplementary information (ESI) available: Full experimental procedures; mass spectra of purified proteins; circular dichroism spectra, tabulated experimental dLinking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-MethyltransferaseActivation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditionsComparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reactionHybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processesEnzymatic effects on reactant and transition states. The case of chalcone isomeraseAnalysis of the decarboxylation step in mammalian histidine decarboxylase. A computational studyQM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effectsEnsemble-averaged QM/MM kinetic isotope effects for the S(N)2 reaction of cyanide anions with chloroethane in DMSO solutionA Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael AdditionA QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical DescriptionsHeavy enzymes--experimental and computational insights in enzyme dynamicsWhy are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase
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description
researcher ORCID ID=0000-0002-4640-0419
@en
name
J Javier Ruiz-Pernía
@en
J Javier Ruiz-Pernía
@nl
type
label
J Javier Ruiz-Pernía
@en
J Javier Ruiz-Pernía
@nl
prefLabel
J Javier Ruiz-Pernía
@en
J Javier Ruiz-Pernía
@nl
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0000-0002-4640-0419