Lista de obras - Iñaki Tuñón - Dominio Público Uruguay

A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases

artículo científico publicado en 2012

A 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 Addition

scientific article published on 10 April 2012

A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

artículo científico publicado en 2005

A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone

scientific article published in 1997

A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity.

artículo científico publicado en 2006

A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules

artículo científico publicado en 2019

A hybrid potential reaction path and free energy study of the chorismate mutase reaction

artículo científico publicado en 2001

A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

artículo científico publicado en 2007

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

scientific article published on 01 January 2007

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline

artículo científico publicado en 2008

A simple model for barrier frequencies for enzymatic reactions

artículo científico publicado en 2010

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

artículo científico publicado en 2006

Activation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†

artículo científico publicado en 2006

Adaptive Finite Temperature String Method in Collective Variables

artículo científico publicado en 2017

Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study

artículo científico publicado en 2008

Application of Grote−Hynes Theory to the Reaction Catalyzed by Thymidylate Synthase

artículo científico publicado en 2010

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step

artículo científico publicado en 2015

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues

scientific article published on 13 March 2007

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis

artículo científico publicado en 2006

Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis

scientific article published on 12 September 2018

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase

artículo científico publicado en 2015

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction

artículo científico publicado en 2006

Computational design of biological catalysts.

artículo científico publicado en 2008

Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an intermediate?

artículo científico publicado en 2010

Computational strategies for the design of new enzymatic functions

artículo científico publicado en 2015

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

artículo científico publicado en 2012

Computer-aided rational design of catalytic antibodies: The 1F7 case

artículo científico publicado en 2007

Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy

artículo científico publicado en 2005

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

artículo científico publicado en 2017

Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase

artículo científico publicado en 2006

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

artículo científico publicado en 2008

Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.

artículo científico publicado en 2009

DFT Study on the Interaction of Tris(benzene-1,2-dithiolato)molybdenum Complex with Water. A Hydrolysis Mechanism Involving a Feasible Seven-Coordinate Aquomolybdenum Intermediate

artículo científico publicado en 2016

Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study.

artículo científico publicado en 2015

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

artículo científico publicado en 2005

Digitalis purpurea P5 beta R2, encoding steroid 5 beta-reductase, is a novel defense-related gene involved in cardenolide biosynthesis

artículo científico publicado en 2009

Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase

artículo científico publicado en 2010

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

artículo científico publicado en 2012

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase

artículo científico publicado en 2005

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

artículo científico publicado en 2008

Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase

artículo científico publicado en 2014

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

scientific article published on 18 September 2018

Enzymatic effects on reactant and transition states. The case of chalcone isomerase

artículo científico publicado en 2007

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

artículo científico publicado en 2015

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase

artículo científico publicado en 2011

Exploring chemical reactivity of complex systems with path-based coordinates: role of the distance metric

scientific article published on 01 July 2014

Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA.

artículo científico publicado en 2017

Heavy enzymes--experimental and computational insights in enzyme dynamics

artículo científico publicado en 2014

Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes

artículo científico publicado en 2006

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

artículo científico

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

artículo científico publicado en 2012

Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment

artículo científico publicado en 2019

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

artículo científico publicado en 2005

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

artículo científico publicado en 2013

Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling.

artículo científico publicado en 2018

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

artículo científico publicado en 2018

Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase

artículo científico publicado en 2014

Mechanism and plasticity of isochorismate pyruvate lyase: a computational study

artículo científico publicado en 2009

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 d

artículo científico publicado en 2016

Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design

scientific article published on 27 February 2019

Modeling methods for studying post-translational and transcriptional modifying enzymes.

artículo científico publicado en 2012

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

artículo científico publicado en 2005

Peptide Bond Formation Mechanism Catalyzed by Ribosome

artículo científico publicado en 2015

Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design.

artículo científico publicado en 2008

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

artículo científico publicado en 2003

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

artículo científico publicado en 2011

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

artículo científico publicado en 2015

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant

artículo científico publicado en 2014

Publisher's Note: "Transition state ensemble optimization for reactions of arbitrary complexity" [J. Chem. Phys. 143, 134111 (2015)].

artículo científico publicado en 2015

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site

artículo científico publicado en 2003

QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis

artículo científico publicado en 2004

Quantifying the limits of transition state theory in enzymatic catalysis

artículo científico publicado en 2017

Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of CpNagJ in complex with PUGNAc.

artículo científico publicado en 2010

Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

artículo científico publicado en 2017

Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3.

artículo científico publicado en 2017

Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

artículo científico publicado en 2012

Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases

artículo científico publicado en 2002

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

artículo científico publicado en 2013

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA

artículo científico publicado en 2020

Singlet Oxygen Attack on Guanine: Reactivity and Structural Signature within the B-DNA Helix.

artículo científico publicado en 2016

Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement

scientific article published on 01 January 2006

Structural and vibrational study of the tautomerism of histamine free-base in solution

artículo científico publicado en 2003

Studying the phosphoryl transfer mechanism of the phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations

artículo científico publicado en 2019

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

artículo científico publicado en 2013

Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight

artículo científico publicado en 2012

Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

artículo científico publicado en 2022

Tetraethylorthosilicate as molecular precursor to the formation of amorphous silica networks. A DFT-SCRF study of the base catalyzed hydrolysis

scientific article published on 18 January 2012

The Catalytic Mechanism of Carboxylesterases: A Computational Study

artículo científico publicado en 2014

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach

scientific article published on 01 March 2013

The mechanism of formamide hydrolysis in water from ab initio calculations and simulations

artículo científico publicado en 2005

Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

artículo científico publicado en 2009

Theoretical QM/MM studies of enzymatic pericyclic reactions.

artículo científico publicado en 2010

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

artículo científico publicado en 2003

Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase

artículo científico publicado en 2009

Theoretical rotational constants of MeCnN species

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase.

artículo científico publicado en 2008

Theoretical study of catalytic efficiency of a Diels-Alderase catalytic antibody: an indirect effect produced during the maturation process

scientific article published on 01 January 2008

Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.

artículo científico publicado en 2010

Theoretical study of the catalytic mechanism of DNA-(N4-cytosine)-methyltransferase from the bacterium Proteus vulgaris

artículo científico publicado en 2010

Theoretical study of the temperature dependence of dynamic effects in thymidylate synthase

artículo científico publicado en 2010

Thermal Isomerization Mechanism in Dronpa and Its Mutants.

artículo científico publicado en 2016

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

artículo científico publicado en 2013

Towards a rational design of antibody catalysts through computational chemistry

artículo científico publicado en 2005

Transition state ensemble optimization for reactions of arbitrary complexity

artículo científico publicado en 2015

Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions

artículo científico publicado en 2019

Understanding the different activities of highly promiscuous MbtI by computational methods

artículo científico publicado en 2012

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

scientific article published on 24 September 2013

Using Grote−Hynes Theory To Quantify Dynamical Effects on the Reaction Rate of Enzymatic Processes. The Case of Methyltransferases†

artículo científico publicado en 2008

Water-assisted alkaline hydrolysis of monobactams: a theoretical study

artículo científico publicado en 2002

Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase

scientific article published on 13 May 2019

Lista de obras de Iñaki Tuñón

A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases

A 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 Addition

A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone

A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity.

A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules

A hybrid potential reaction path and free energy study of the chorismate mutase reaction

A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline

A simple model for barrier frequencies for enzymatic reactions

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

Activation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†

Adaptive Finite Temperature String Method in Collective Variables

Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study

Application of Grote−Hynes Theory to the Reaction Catalyzed by Thymidylate Synthase

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis

Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction

Computational design of biological catalysts.

Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an intermediate?

Computational strategies for the design of new enzymatic functions

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

Computer-aided rational design of catalytic antibodies: The 1F7 case

Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.

DFT Study on the Interaction of Tris(benzene-1,2-dithiolato)molybdenum Complex with Water. A Hydrolysis Mechanism Involving a Feasible Seven-Coordinate Aquomolybdenum Intermediate

Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study.

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

Digitalis purpurea P5 beta R2, encoding steroid 5 beta-reductase, is a novel defense-related gene involved in cardenolide biosynthesis

Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

Enzymatic effects on reactant and transition states. The case of chalcone isomerase

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase

Exploring chemical reactivity of complex systems with path-based coordinates: role of the distance metric

Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA.

Heavy enzymes--experimental and computational insights in enzyme dynamics

Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling.

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase

Mechanism and plasticity of isochorismate pyruvate lyase: a computational study

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 d

Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design

Modeling methods for studying post-translational and transcriptional modifying enzymes.

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

Peptide Bond Formation Mechanism Catalyzed by Ribosome

Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design.

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant

Publisher's Note: "Transition state ensemble optimization for reactions of arbitrary complexity" [J. Chem. Phys. 143, 134111 (2015)].

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site

QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis

Quantifying the limits of transition state theory in enzymatic catalysis

Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of CpNagJ in complex with PUGNAc.

Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3.

Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA