ArticleJournal of chemical theory and computation2012
Theory and simulation of ion conduction in the pentameric GLIC channel.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Water-Mediated Ion Selectivity in 2D MXene Channels.Journal of the American Chemical Society · 2026Article
- Molecular permeation through large pore channels: computational approaches and insights.The Journal of physiology · 2025Review
- A multiscale predictive digital twin for neurocardiac modulation.The Journal of physiology · 2023Article
- Fast prediction of antibiotic permeability through membrane channels using Brownian dynamics.Biophysical journal · 2023Article
- Interplay of Hydropathy and Heterogeneous Diffusion in the Molecular Transport within Lamellar Lipid Mesophases.Pharmaceutics · 2023Article
- Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal KeLife · 2022Article
- Unifying Single-Channel Permeability From Rare-Event Sampling and Steady-State Flux.Frontiers in molecular biosciences · 2022Article
- Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel.eLife · 2021Article
- Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations.Entropy (Basel, Switzerland) · 2021Article
- In Silico Prediction of Permeability Coefficients.Methods in molecular biology (Clifton, N.J.) · 2021Article
- In Silico Prediction of Permeability Coefficients.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels.The journal of physical chemistry. B · 2017Article
- Article
- A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip.The Journal of general physiology · 2017Article
- Pore size matters for potassium channel conductance.The Journal of general physiology · 2016Review
- Computational Studies of Molecular Permeation through Connexin26 Channels.Biophysical journal · 2016Article
- Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.Journal of chemical theory and computation · 2015Article
- Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.The journal of physical chemistry. B · 2014Article
- Pentameric Ligand-gated Ion Channels : Insights from Computation.Molecular simulation · 2014Article
- Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF.Biochimica et biophysica acta · 2013Article
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Authors and funding
2 authors.
Funding
Abstract
GLIC is a bacterial member of the large family of pentameric ligand-gated ion channels. To study ion conduction through GLIC and other membrane channels, we combine the one-dimensional potential of mean force for ion passage with a Smoluchowski diffusion model, making it possible to calculate single-channel conductance in the regime of low ion concentrations from all-atom molecular dynamics (MD) simulations. We then perform MD simulations to examine sodium ion conduction through the GLIC transmembrane pore in two systems with different bulk ion concentrations. The ion potentials of mean force, calculated from umbrella sampling simulations with Hamiltonian replica exchange, reveal a major barrier at the hydrophobic constriction of the pore. The relevance of this barrier for ion transport is confirmed by a committor function that rises sharply in the barrier region. From the free evolution of Na(+) ions starting at the barrier top, we estimate the effective diffusion coefficient in the barrier region, and subsequently calculate the conductance of the pore. The resulting diffusivity compares well with the position-dependent ion diffusion coefficient obtained from restrained simulations. The ion conductance obtained from the diffusion model agrees with the value determined via a reactive-flux rate calculation. Our results show that the conformation in the GLIC crystal structure, with an estimated conductance of ~1 picosiemens at 140 mM ion concentration, is consistent with a physiologically open state of the channel.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.