List of works - Carmen Domene

13C-Carbamylation as a mechanistic probe for the inhibition of class D β-lactamases by avibactam and halide ions

scientific article published on 5 July 2017

2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2.

scientific article published on 9 March 2018

A Unified Orbital Model of Delocalised and Localised Currents in Monocycles, from Annulenes to Azabora-heterocycles

scientific article published on 01 February 2005

A perspective on structural and computational work on collagen

scientific article

An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species

scientific article published on 03 September 2021

Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase

scientific article

Antibiotic resistance and host immune evasion in mediated by a metabolic adaptation

scientific article published on 11 February 2019

Antimicrobial peptide dendrimer interacts with phosphocholine membranes in a fluidity dependent manner: A neutron reflection study combined with molecular dynamics simulations

scientific article published on 27 May 2015

Aromaticity of anthranil and its isomers, 1,2-benzisoxazole and benzoxazole

Atypical mechanism of conduction in potassium channels.

scholarly article

Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels

scientific article published in April 2015

Binding of Capsaicin to the TRPV1 Ion Channel.

scientific article

Blocking the Passage: C60 Geometrically Clogs K+ Channels

Calculation of dipole-shielding polarizabilities (sigma(alphabetagamma)I): the influence of uniform electric field effects on the shielding of backbone nuclei in proteins

scientific article published in August 2003

Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1alpha

scientific article published on August 2010

Cholesterol-dependent membrane fusion induced by the gp41 membrane-proximal external region-transmembrane domain connection suggests a mechanism for broad HIV-1 neutralization.

scientific article

Combining Structural Data with Computational Methodologies to Investigate Structure-Function Relationships in TRP Channels

scientific article published on 01 January 2019

Computational studies of transport in ion channels using metadynamics.

scientific article published on 13 February 2016

Computational studies on the interactions of inhalational anesthetics with proteins.

scientific article published on January 2010

Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields

scientific article published on 09 December 2020

Conformational changes and gating at the selectivity filter of potassium channels.

scientific article published on 28 June 2008

Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.

scientific article published in November 2005

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

scientific article

Critical Assessment of Common Force Fields for Molecular Dynamics Simulations of Potassium Channels

scientific article published on 15 October 2020

DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations.

scientific article published on 6 November 2014

Development of GoSlo-SR-5-69, a potent activator of large conductance Ca2+-activated K+ (BK) channels

scientific article published on 03 February 2014

Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure.

scientific article published on 23 April 2009

Effects of point mutations in pVHL on the binding of HIF-1α.

scientific article published on 22 November 2011

Effects of the protonation state of the EEEE motif of a bacterial Na(+)-channel on conduction and pore structure

scientific article

Energetics of Ion Permeation in an Open-Activated TRPV1 Channel

scientific article published on September 2016

Examining ion channel properties using free-energy methods

scientific article

Exploring the Dynamics of the TWIK-1 Channel.

scientific article published on August 2016

Exposure of the HIV-1 broadly neutralizing antibody 10E8 MPER epitope on the membrane surface by gp41 transmembrane domain scaffolds

article

Functional mapping of the N-terminal arginine cluster and C-terminal acidic residues of Kir6.2 channel fused to a G protein-coupled receptor

scientific article published on 27 July 2017

Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions.

scientific article published on October 2011

In silico identification of PAP-1 binding sites in the Kv1.2 potassium channel.

scientific article published on 16 March 2015

Influence of Cholesterol and Its Stereoisomers on Members of the Serotonin Receptor Family

scientific article published on 08 March 2019

Insights into the Mechanisms of K+ Permeation in K+ Channels from Computer Simulations

scientific article published on 20 December 2019

Insights into the sliding movement of the lac repressor nonspecifically bound to DNA.

scientific article published in February 2010

Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis

scientific article published on 29 February 2008

Ion channel gating: insights via molecular simulations.

scientific article published on November 2003

Ion-triggered selectivity in bacterial sodium channels

scientific article published on 07 May 2018

K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations

scientific article published on October 2013

KcsA closed and open: modelling and simulation studies

scientific article published on 22 October 2003

Lateral Fenestrations in K(+)-Channels Explored Using Molecular Dynamics Simulations.

scientific article published on 26 May 2016

Lipid/protein interactions and the membrane/water interfacial region

scientific article published on 01 December 2003

Location and Character of Volatile General Anesthetics Binding Sites in the Transmembrane Domain of TRPV1

scientific article published on 16 August 2018

Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation

scientific article published on 23 January 2020

Membrane Phase-Dependent Occlusion of Intramolecular GLUT1 Cavities Demonstrated by Simulations.

scientific article

Model-based prediction of the alpha-hemolysin structure in the hexameric state.

scientific article published on 23 May 2008

Modeling of an ion channel in its open conformation

scientific article published on July 2005

Modulation of the potassium channel KcsA by anionic phospholipids: Role of arginines at the non-annular lipid binding sites

scientific article published on 24 July 2019

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function.

scientific article published in March 2005

Molecular dynamics simulations and neutron reflectivity as an effective approach to characterize biological membranes and related macromolecular assemblies.

scientific article published on 30 September 2015

Molecular dynamics simulations of the TrkH membrane protein

scientific article published on 14 February 2012

Oxytocin Modulates Nociception as an Agonist of Pain-Sensing TRPV1.

scientific article published in November 2017

Partition coefficients of indoles and betacarbolines

scientific article published on 01 January 1997

Pentagon adjacency as a determinant of fullerene stability

Permeation and dynamics of an open-activated TRPV1 channel.

scientific article published on 3 December 2014

Permeation of water through the KcsA K+channel

scientific article published on 01 February 2009

Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA.

scientific article published on November 2003

Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor.

scientific article

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

scientific article

Role of Zinc and Magnesium Ions in the Modulation of Phosphoryl Transfer in Protein Tyrosine Phosphatase 1B

scientific article published on 19 March 2018

Role of aromatic localization in the gating process of a potassium channel.

scientific article

Selectivity and permeation of alkali metal ions in K+-channels

scientific article published on 22 April 2011

Simulating the pyrolysis of polyazides: a mechanistic case study of the [[P(N3)6]- anion

scientific article published on 28 January 2013

Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential

scientific article published on 30 January 2018

Strong and weak zinc binding sites in human zinc-α2-glycoprotein.

scientific article published in November 2013

Structural and biochemical analyses reveal how ornithine acetyl transferase binds acidic and basic amino acid substrates

scientific article

Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases

scientific article

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.

scientific article

Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope

scientific article

Structure based analysis of K<sub>ATP</sub> channel with a DEND syndrome mutation in murine skeletal muscle

scientific article published on 23 March 2021

Surfactin at the Water/Air Interface and in Solution

scientific article published on 22 September 2015

The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes

scientific article

The role of conformation in ion permeation in a K+ channel

scientific article published on 23 February 2008

Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography.

scientific article published on October 2005

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

scientific article published on 22 October 2018

Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

scientific article

List of works by Carmen Domene

13C-Carbamylation as a mechanistic probe for the inhibition of class D β-lactamases by avibactam and halide ions

2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2.

A Unified Orbital Model of Delocalised and Localised Currents in Monocycles, from Annulenes to Azabora-heterocycles

A perspective on structural and computational work on collagen

An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species

Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase

Antibiotic resistance and host immune evasion in mediated by a metabolic adaptation

Antimicrobial peptide dendrimer interacts with phosphocholine membranes in a fluidity dependent manner: A neutron reflection study combined with molecular dynamics simulations

Aromaticity of anthranil and its isomers, 1,2-benzisoxazole and benzoxazole

Atypical mechanism of conduction in potassium channels.

Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels

Binding of Capsaicin to the TRPV1 Ion Channel.

Blocking the Passage: C60 Geometrically Clogs K+ Channels

Calculation of dipole-shielding polarizabilities (sigma(alphabetagamma)I): the influence of uniform electric field effects on the shielding of backbone nuclei in proteins

Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1alpha

Cholesterol-dependent membrane fusion induced by the gp41 membrane-proximal external region-transmembrane domain connection suggests a mechanism for broad HIV-1 neutralization.

Combining Structural Data with Computational Methodologies to Investigate Structure-Function Relationships in TRP Channels

Computational studies of transport in ion channels using metadynamics.

Computational studies on the interactions of inhalational anesthetics with proteins.

Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields

Conformational changes and gating at the selectivity filter of potassium channels.

Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Critical Assessment of Common Force Fields for Molecular Dynamics Simulations of Potassium Channels

DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations.

Development of GoSlo-SR-5-69, a potent activator of large conductance Ca2+-activated K+ (BK) channels

Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure.

Effects of point mutations in pVHL on the binding of HIF-1α.

Effects of the protonation state of the EEEE motif of a bacterial Na(+)-channel on conduction and pore structure

Energetics of Ion Permeation in an Open-Activated TRPV1 Channel

Examining ion channel properties using free-energy methods

Exploring the Dynamics of the TWIK-1 Channel.

Exposure of the HIV-1 broadly neutralizing antibody 10E8 MPER epitope on the membrane surface by gp41 transmembrane domain scaffolds

Functional mapping of the N-terminal arginine cluster and C-terminal acidic residues of Kir6.2 channel fused to a G protein-coupled receptor

Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions.

In silico identification of PAP-1 binding sites in the Kv1.2 potassium channel.

Influence of Cholesterol and Its Stereoisomers on Members of the Serotonin Receptor Family

Insights into the Mechanisms of K+ Permeation in K+ Channels from Computer Simulations

Insights into the sliding movement of the lac repressor nonspecifically bound to DNA.

Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis

Ion channel gating: insights via molecular simulations.

Ion-triggered selectivity in bacterial sodium channels

K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations

KcsA closed and open: modelling and simulation studies

Lateral Fenestrations in K(+)-Channels Explored Using Molecular Dynamics Simulations.

Lipid/protein interactions and the membrane/water interfacial region

Location and Character of Volatile General Anesthetics Binding Sites in the Transmembrane Domain of TRPV1

Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation

Membrane Phase-Dependent Occlusion of Intramolecular GLUT1 Cavities Demonstrated by Simulations.

Model-based prediction of the alpha-hemolysin structure in the hexameric state.

Modeling of an ion channel in its open conformation

Modulation of the potassium channel KcsA by anionic phospholipids: Role of arginines at the non-annular lipid binding sites

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function.

Molecular dynamics simulations and neutron reflectivity as an effective approach to characterize biological membranes and related macromolecular assemblies.

Molecular dynamics simulations of the TrkH membrane protein

Oxytocin Modulates Nociception as an Agonist of Pain-Sensing TRPV1.

Partition coefficients of indoles and betacarbolines

Pentagon adjacency as a determinant of fullerene stability

Permeation and dynamics of an open-activated TRPV1 channel.

Permeation of water through the KcsA K+channel

Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA.

Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor.

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

Role of Zinc and Magnesium Ions in the Modulation of Phosphoryl Transfer in Protein Tyrosine Phosphatase 1B

Role of aromatic localization in the gating process of a potassium channel.

Selectivity and permeation of alkali metal ions in K+-channels

Simulating the pyrolysis of polyazides: a mechanistic case study of the [[P(N3)6]- anion

Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential

Strong and weak zinc binding sites in human zinc-α2-glycoprotein.

Structural and biochemical analyses reveal how ornithine acetyl transferase binds acidic and basic amino acid substrates

Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.

Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope

Structure based analysis of K<sub>ATP</sub> channel with a DEND syndrome mutation in murine skeletal muscle

Surfactin at the Water/Air Interface and in Solution

The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes

The role of conformation in ion permeation in a K+ channel

Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography.

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology