ArticleBiophysical journal2006
Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- The voltage-sensing domain of a hERG1 mutant is a cation-selective channel.Biophysical journal · 2022Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
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- Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor.Journal of chemical information and modeling · 2020Article
- A constricted opening in Kir channels does not impede potassium conduction.Nature communications · 2020Article
- Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.Journal of the American Chemical Society · 2019Article
- Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation.The Journal of physiology · 2019Review
- The AT Interstrand Cross-Link: Structure, Electronic Properties, and Influence on Charge Transfer in dsDNA.Molecular therapy. Nucleic acids · 2018Article
- Hydrophobic gating in BK channels.Nature communications · 2018Article
- Article
- Chloride Ion Transport by theFrontiers in chemistry · 2018Article
- A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.Molecules (Basel, Switzerland) · 2017Article
- Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A.Membranes · 2016Article
- Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.Journal of chemical theory and computation · 2015Article
- Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.Journal of chemical theory and computation · 2015Article
- Pore dynamics and conductance of RyR1 transmembrane domain.Biophysical journal · 2014Article
- Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.PloS one · 2014Article
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3 authors.
Funding
Abstract
We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence of the PMF, finite size effects, and lipid hydrocarbon chain polarizability. When comparing the modern all-atom force fields of CHARMM27 and AMBER94, we found that a fairly consistent picture emerges, and that both AMBER94 and CHARMM27 predict observables that are in semiquantitative agreement with both the experimental conductance and dissociation coefficient. Even small changes in the force field, however, result in significant changes in permeation energetics. Furthermore, the full two-dimensional free-energy surface describing permeation reveals the location and magnitude of the central barrier and the location of two binding sites for K(+) ion permeation near the channel entrance--i.e., an inner site on-axis and an outer site off-axis. We conclude that the MD-PMF approach is a powerful tool for understanding and predicting the function of narrow ion channels in a manner that is consistent with the atomic and thermally fluctuating nature of proteins.
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