ArticleJournal of the American Chemical Society2009
Exploring ion permeation energetics in gramicidin A using polarizable charge equilibration force fields.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.Journal of computational biophysics and chemistry · 2022Article
- Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- Ion permeation, selectivity, and electronic polarization in fluoride channels.Biophysical journal · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
- Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation.The Journal of physiology · 2019Review
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Accurate Biomolecular Simulations Account for Electronic Polarization.Frontiers in molecular biosciences · 2019Article
- A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.Molecules (Basel, Switzerland) · 2017Article
- Computational investigation of OChemical science · 2017Article
- Advanced Potential Energy Surfaces for Molecular Simulation.The journal of physical chemistry. B · 2016Review
- CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.The journal of physical chemistry. B · 2015Article
- Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.The journal of physical chemistry. B · 2015Article
- A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers.Journal of chemical theory and computation · 2014Article
- Classical electrostatics for biomolecular simulations.Chemical reviews · 2014Review
- Molecular mechanics.Current pharmaceutical design · 2014Review
- Density-functional theory study of gramicidin A ion channel geometry and electronic properties.Journal of the Royal Society, Interface · 2013Article
- The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
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Authors and funding
3 authors.
Funding
Abstract
All-atom molecular dynamics simulations have been applied in the recent past to explore the free energetics underlying ion transport processes in biological ion channels. Roux and co-workers, Kuyucak and co-workers, Busath and co-workers, and others have performed rather elegant and extended time scale molecular dynamics simulations using current state-of-the-art fixed-charge (nonpolarizable) force fields to calculate the potential of mean force defining the equilibrium flux of ions through prototypical channels such as gramicidin A. An inescapable conclusion of such studies has been the gross overestimation of the equilibrium free energy barrier, generally predicted to be from 10 to 20 kcal/mol depending on the force field and simulation protocol used in the calculation; this translates to an underestimation of experimentally measurable single channel conductances by several orders of magnitude. Next-generation polarizable force fields have been suggested as possible alternatives for more quantitative predictions of the underlying free energy surface in such systems. (1) Presently, we consider ion permeation energetics in the gramicidin A channel using a novel polarizable force field. Our results predict a peak barrier height of 6 kcal/mol relative to the channel entrance; this is significantly lower than the uncorrected value of 12 kcal/mol for nonpolarizable force fields such as GROMOS and CHARMM27 which do not account for electronic polarization. These results provide promising initial indications substantiating the long-conjectured importance of polarization effects in describing ion-protein interactions in narrow biological channels.
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