Lista de obras - Cláudio M. Soares - Dominio Público Uruguay

A LysM Domain Intervenes in Sequential Protein-Protein and Protein-Peptidoglycan Interactions Important for Spore Coat Assembly in Bacillus subtilis

artículo científico publicado en 2019

A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies ⬇️

artículo científico publicado el 18 de julio de 2013

A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus

artículo científico publicado en 2007

Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin

artículo científico publicado en 1995

An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation

artículo científico publicado en 2018

An iterative structure-assisted approach to sequence alignment and comparative modeling

Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations ⬇️

artículo científico publicado el 30 de enero de 2012

Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1

artículo científico publicado en 2015

Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: putative correlation toward receptor docking

artículo científico publicado en 2006

Conformational changes induced by ATP‐hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter ⬇️

artículo científico publicado el 12 de abril de 2011

Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome

artículo científico publicado en 2001

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations.

artículo científico publicado en 2016

Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding.

artículo científico publicado en 2005

Design of a peptidic turn with high affinity for Hg(II)

scientific article published on 17 October 2012

Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas

artículo científico publicado en 2009

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study

artículo científico publicado en 2017

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

artículo científico publicado en 1999

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies

artículo científico publicado en 2005

Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site

artículo científico publicado en 2014

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space

artículo científico publicado en 2014

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

scientific article published on 17 July 2019

Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding.

artículo científico publicado en 2006

Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme.

artículo científico publicado en 2008

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

artículo científico publicado en 2016

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase.

artículo científico publicado en 2005

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

artículo científico publicado en 2001

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

artículo científico publicado en 1999

Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases

artículo científico publicado en 2013

Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796

artículo científico publicado en 2010

Insights into the structure of the diiron site of RIC from Escherichia coli.

artículo científico publicado en 2015

Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex

artículo científico publicado en 2011

Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations

artículo científico publicado en 2012

Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase

artículo científico publicado en 2003

Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome c 553 from D. vulgaris

artículo científico publicado en 2000

Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

artículo científico publicado en 2010

Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations

artículo científico publicado en 2010

Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1

artículo científico publicado en 2013

Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3).

artículo científico publicado en 2004

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

artículo científico publicado en 2007

Molecular Dynamics Simulation of Cytochrome c3: Studying the Reduction Processes Using Free Energy Calculations ⬇️

artículo científico publicado el 1 de abril de 1998

Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat.

artículo científico publicado en 2002

Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6

artículo científico publicado en 2004

Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin.

artículo científico publicado en 2007

Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results

artículo científico publicado en 2012

Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2.

artículo científico publicado en 2017

Natural Domain Design: Enhanced Thermal Stability of a Zinc-Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site†

scientific article published on 01 August 2006

Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 : primary sequence determination, crystallographic refinement at 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c 3

artículo científico publicado en 1999

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

scientific article published on 01 August 2005

Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field

artículo científico publicado en 2006

Pathways of H2 toward the active site of [NiFe]-hydrogenase

artículo científico publicado en 2006

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model.

artículo científico publicado en 2013

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon

artículo científico publicado en 2007

Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies.

artículo científico publicado en 2008

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

artículo científico publicado en 2008

Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants

artículo científico publicado en 2008

Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX

artículo científico publicado en 2013

Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies

artículo científico publicado en 2003

Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus

artículo científico publicado en 2018

Reorganization and conformational changes in the reduction of tetraheme cytochromes

artículo científico publicado en 2005

Role of the anti-sigma factor SpoIIAB in regulation of sigmaG during Bacillus subtilis sporulation

artículo científico publicado en 2004

Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion Peptide with a membrane bilayer.

artículo científico publicado en 2015

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

artículo científico publicado en 1999

Simulation of multihaem cytochromes ⬇️

artículo científico publicado el 19 de octubre de 2011

Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae.

artículo científico publicado en 2011

Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases

artículo científico publicado en 2010

Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus ⬇️

artículo científico publicado el 9 de noviembre de 2012

Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking

artículo científico publicado en 2015

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

artículo científico publicado en 2017

Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB.

artículo científico publicado en 2011

Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents ⬇️

artículo científico publicado el 1 de febrero de 2011

Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach

scientific article published on 01 April 2012

Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase

artículo científico publicado en 2016

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

artículo científico publicado en 2001

Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods

artículo científico publicado en 2018

Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview

artículo científico publicado en 2004

Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers.

artículo científico publicado en 2007

The Pathway for O2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family

artículo científico publicado en 2014

The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α-Hemolysin Nanopore

artículo científico publicado en 2012

The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel

artículo científico publicado en 1999

The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis

artículo científico publicado en 2014

The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.

artículo científico publicado en 2017

The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - comparative modeling to probe the molecular basis

artículo científico publicado en 2007

The multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity

artículo científico publicado en 2010

The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs

artículo científico publicado en 2022

The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications

artículo científico publicado en 2017

The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton-transfer mechanism

artículo científico publicado en 2012

The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes

artículo científico publicado en 2008

Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens

artículo científico publicado en 2004

Water dependent properties of cutinase in nonaqueous solvents: a computational study of enantioselectivity

artículo científico publicado en 2005

Lista de obras de Cláudio M. Soares

A LysM Domain Intervenes in Sequential Protein-Protein and Protein-Peptidoglycan Interactions Important for Spore Coat Assembly in Bacillus subtilis

A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies ⬇️

A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus

Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin

An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation

An iterative structure-assisted approach to sequence alignment and comparative modeling

Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations ⬇️

Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1

Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: putative correlation toward receptor docking

Conformational changes induced by ATP‐hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter ⬇️

Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations.

Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding.

Design of a peptidic turn with high affinity for Hg(II)

Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies

Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding.

Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme.

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase.

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases

Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796

Insights into the structure of the diiron site of RIC from Escherichia coli.

Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex

Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations

Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase

Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome c 553 from D. vulgaris

Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations

Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1

Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3).

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

Molecular Dynamics Simulation of Cytochrome c3: Studying the Reduction Processes Using Free Energy Calculations ⬇️

Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat.

Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6

Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin.

Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results

Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2.

Natural Domain Design: Enhanced Thermal Stability of a Zinc-Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site†

Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 : primary sequence determination, crystallographic refinement at 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c 3

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field

Pathways of H2 toward the active site of [NiFe]-hydrogenase

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model.

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon

Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies.

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants

Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX

Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies

Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus

Reorganization and conformational changes in the reduction of tetraheme cytochromes

Role of the anti-sigma factor SpoIIAB in regulation of sigmaG during Bacillus subtilis sporulation

Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion Peptide with a membrane bilayer.

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

Simulation of multihaem cytochromes ⬇️

Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae.

Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases

Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus ⬇️

Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB.

Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents ⬇️

Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach

Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods

Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview

Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers.

The Pathway for O2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family

The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α-Hemolysin Nanopore

The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel