ArticlePLoS computational biology2014
Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 34 citations in OpenAlex.
- Structure-function analysis of the lithium-ion selectivity of the voltage-gated sodium channel.The Journal of general physiology · 2026Article
- Ion channel selectivity through ion-modulated changes of selectivity filter pProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels.Journal of chemical theory and computation · 2023Article
- A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.The Journal of general physiology · 2023Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Determinants of conductance of a bacterial voltage-gated sodium channel.Biophysical journal · 2021Article
- The regulatory function of mixed lineage kinase 3 in tumor and host immunity.Pharmacology & therapeutics · 2021Review
- IR Spectroscopy Can Reveal the Mechanism of KBiophysical journal · 2020Article
- Bases of Bacterial Sodium Channel Selectivity Among Organic Cations.Scientific reports · 2019Article
- Comparison of permeation mechanisms in sodium-selective ion channels.Neuroscience letters · 2019Review
- Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel.Biophysical journal · 2018Article
- Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaThe journal of physical chemistry. B · 2018Article
- Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel.PLoS computational biology · 2018Article
- Ion-triggered selectivity in bacterial sodium channels.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na(v) Channels.PLoS computational biology · 2016Article
- Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels.Current topics in membranes · 2016Article
- The hitchhiker's guide to the voltage-gated sodium channel galaxy.The Journal of general physiology · 2016Review
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms. Here, we use molecular dynamics (MD) simulations with an applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs. 5.9 µs simulations with 500 mM NaCl suggest different mechanisms for inward and outward flux. The predicted inward conductance rate of ∼27±3 pS, agrees with experiment. The estimated outward conductance rate is 15±3 pS, which is considerably lower. Comparing inward and outward flux, the mean ion dwell time in the selectivity filter (SF) is prolonged from 13.5±0.6 ns to 20.1±1.1 ns. Analysis of the Na+ distribution revealed distinct patterns for influx and efflux events. In 32.0±5.9% of the simulation time, the E53 side chains adopted a flipped conformation during outward conduction, whereas this conformational change was rarely observed (2.7±0.5%) during influx. Further, simulations with dihedral restraints revealed that influx is less affected by the E53 conformational flexibility. In contrast, during outward conduction, our simulations indicate that the flipped E53 conformation provides direct coordination for Na+. The free energy profile (potential of mean force calculations) indicates that this conformational change lowers the putative barriers between sites SCEN and SHFS during outward conduction. We hypothesize that during an action potential, the increased Na+ outward transition propensities at depolarizing potentials might increase the probability of E53 conformational changes in the SF. Subsequently, this might be a first step towards initiating slow inactivation.
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