Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations.

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Biophysical Journal

• Publication date

  2006-06-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1529/BIOPHYSJ.105.074633PMID 16533834PMCID PMC1459526
• 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.

• Molecular Models of Water: Derivation and Description

  2007influential reference
• Role of protein flexibility in ion permeation: a case study in gramicidin A.

  2006cited by this paper
• Epilepsy surgery

  2005cited by this paper
• Theoretical and computational models of biological ion channels

  2004cited by this paper
• Computer simulations of membrane proteins.

  2004cited by this paper
• Ionic permeation free energy in gramicidin: a semimicroscopic perspective.

  2004influential reference
• Gramicidin A channel as a test ground for molecular dynamics force fields.

  2003cited by this paper
• Energetics of ion conduction through the gramicidin channel

  2003influential reference
• Molecular dynamics simulations of biomolecules

  2002cited by this paper
• Trial by ordeal: ionic free energies in gramicidin.

  2002cited by this paper
• Molecular dynamics simulations of biomolecules.

  2002cited by this paper
• Continuum electrostatics fails to describe ion permeation in the gramicidin channel.

  2002influential reference
• Computational studies of the gramicidin channel.

  2002cited by this paper
• Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles.

  2001influential reference
• Mechanisms of permeation and selectivity in calcium channels.

  2001cited by this paper
• Models of permeation in ion channels

  2001cited by this paper
• Simulation approaches to ion channel structure–function relationships

  2001cited by this paper
• Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations

  2001cited by this paper
• Structure of lipid bilayers.

  2000cited by this paper
• NAMD2: Greater Scalability for Parallel Molecular Dynamics

  1999influential reference
• Modeling of Ion Channels

  1999cited by this paper
• Structural, electronic, and bonding properties of liquid water from first principles

  1999cited by this paper
• Cation transport: an example of structural based selectivity.

  1999cited by this paper
• Comparison of Selectively Polarizable Force Fields for Ion−Water−Peptide Interactions: Ion Translocation in a Gramicidin-like Channel

  1998cited by this paper
• The structure of the potassium channel: molecular basis of K+ conduction and selectivity.

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998influential reference
• High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints.

  1997cited by this paper
• Monovalent cation transport: lack of structural deformation upon cation binding.

  1996cited by this paper
• A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity.

  1996cited by this paper
• VMD: visual molecular dynamics.

  1996cited by this paper
• Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study.

  1996cited by this paper
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

  1995cited by this paper
• Ion pair binding of Ca2+ and Cl- ions in micellar-packaged gramicidin A.

  1995influential reference
• The determination of binding constants of micellar-packaged gramicidin A by 13C-and 23Na-NMR.

  1995cited by this paper
• GROMACS: A message-passing parallel molecular dynamics implementation

  1995cited by this paper
• Constant pressure molecular dynamics simulation: The Langevin piston method

  1995cited by this paper
• Molecular dynamics simulations of the gramicidin channel.

  1994cited by this paper
• The use of physical methods in determining gramicidin channel structure and function.

  1993cited by this paper
• Molecular determinants of channel function.

  1992cited by this paper
• Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches

  1992cited by this paper
• THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

  1992cited by this paper
• Location of ion-binding sites in the gramicidin channel by X-ray diffraction.

  1991influential reference
• The divalent cation‐binding sites of gramicidin A transmembrane ion‐channel

  1991cited by this paper
• Numerical recipes

  1990cited by this paper
• MOLECULAR SIMULATION: Applications to Chemical and Biomolecular Systems

  1989cited by this paper
• Interpretation of biological ion channel flux data--reaction-rate versus continuum theory.

  1986cited by this paper
• Equilibrium binding constants for the group I metal cations with gramicidin-A determined by competition studies and T1+-205 nuclear magnetic resonance spectroscopy.

  1986influential reference
• Ionic channels of excitable membranes

  1984cited by this paper
• Structure and dynamics of ion transport through gramicidin A.

  1984cited by this paper
• Ca2+-gramicidin A interactions and blocking effects on the ionic channel.

  1983cited by this paper
• Blocking of the gramicidin channel by divalent cations

  1977influential reference
• Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

  1977cited by this paper
• The Gramicidin A Transmembrane Channel: A Proposed π(L,D) Helix

  1971cited by this paper
• The gramicidin A transmembrane channel: a proposed pi(L,D) helix.

  1971cited by this paper

• Design space exploration in ion channels using fine grained brownian dynamics

  2020cites this paper
• Thermodynamics of Transition Metal Ion Binding to Proteins.

  2020cites this paper
• Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140.

  2019cites this paper
• Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits

  2018cites this paper
• Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A

  2016cites this paper
• Force fields for simulating the interaction of surfaces with biological molecules

  2016cites this paper
• Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

  2016cites this paper
• Molecular Modeling and Its Applications in Protein Engineering

  2016cites this paper
• Numerical methods for a Poisson-Nernst-Planck-Fermi model of biological ion channels.

  2015cites this paper
• New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations.

  2015cites this paper
• Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels

  2015cites this paper
• Molecular Dynamics Study of Binding of µ-Conotoxin GIIIA to the Voltage-Gated Sodium Channel Nav1.4

  2014cites this paper
• Computational studies of glutamate transporters and receptors

  2014cites this paper
• The permeation of potassium and chloride ions through nanotubes: a molecular simulation study

  2014cites this paper
• Systematic Study of Binding of µ-Conotoxins to the Sodium Channel NaV1.4

  2014cites this paper
• Computational Studies of Marine Toxins Targeting Ion Channels

  2013cites this paper
• Force fields for divalent cations based on single-ion and ion-pair properties.

  2013cites this paper
• Density-functional theory study of gramicidin A ion channel geometry and electronic properties

  2013cites this paper
• Mechanism and energetics of ligand release in the aspartate transporter GltPh.

  2013cites this paper
• Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex.

  2013cites this paper
• Molecular Dynamics Simulations using Advanced Sampling and Polarizable Force Fields

  2013cites this paper
• Temperature Dependence of Gramicidin Channel Transport and Structure

  2013cites this paper
• Position of the Third Na+ Site in the Aspartate Transporter GltPh and the Human Glutamate Transporter, EAAT1

  2012cites this paper
• Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

  2012cites this paper
• Molecular dynamics simulations of membrane proteins

  2012cites this paper
• The preferential permeation of ions across carbon and boron nitride nanotubes

  2012cites this paper
• Estudo da dinâmica de íons em canais iônicos

  2012cites this paper
• Computational modeling of ion transport through nanopores.

  2012cites this paper
• Polarizable molecular dynamics simulations of aqueous dipeptides.

  2012cites this paper
• Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl.

  2011cites this paper
• Free energy simulations of ligand binding to the aspartate transporter Glt(Ph).

  2011cites this paper
• Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.

  2011cites this paper
• Carbon nanotube as a gramicidin analogue

  2011cites this paper
• Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy.

  2011cites this paper
• Dissociation of NaCl in water from ab initio molecular dynamics simulations.

  2010cites this paper
• Molecular simulations of ion channels: a quantum chemist’s perspective

  2010cites this paper
• Importance of the peptide backbone description in modeling the selectivity filter in potassium channels.

  2009cites this paper
• Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites.

  2009cites this paper
• Developing Improved Charge Sets for the Modeling of the KcsA K(+) Channel Using QM/MM Electrostatic Potentials.

  2009cites this paper
• The gramicidin channel ion permeation free-energy profile: Direct and indirect effects of CHARMM force field improvements

  2009cites this paper
• Low free energy barrier for ion permeation through double-helical gramicidin.

  2009cites this paper
• Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling.

  2008cites this paper
• Response to “Comment on ‘Free energy simulations of single and double ion occupancy in gramicidin A’ ” [J. Chem. Phys.128, 227101 (2008)]

  2008cites this paper
• Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].

  2008cites this paper
• Electric field effects on membranes: gramicidin A as a test ground.

  2007cites this paper
• Application of Jarzynski's equality in simple versus complex systems

  2007cites this paper
• Free energy simulations of single and double ion occupancy in gramicidin A.

  2007cites this paper
• Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations.

  2007cites this paper
• Finite system and periodicity effects in free energy simulations of membrane proteins

  2006cites this paper