ArticleThe Journal of general physiology2013
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.
Article in The Journal of general physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Characterization of an open-channel structure and lateral conduction pathway in the cation-selective pentameric ligand-gated ion channel, ELIC.The Journal of general physiology · 2026Article
- Force field sensitivity of ion occupancy in potassium channels.Biophysical journal · 2026Article
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
- Molecular dynamics analyses of CLDN15 pore size and charge selectivity.The Journal of general physiology · 2026Article
- Role of Water Models in Simulations of Ion Conduction in Potassium Channels.Journal of chemical theory and computation · 2026Article
- Characterization of an Open-Channel Structure and Lateral Conduction Pathway in the Cation-Selective Pentameric Ligand-Gated Ion Channel, ELIC.bioRxiv : the preprint server for biology · 2025Article
- Molecular permeation through large pore channels: computational approaches and insights.The Journal of physiology · 2025Review
- Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems.International journal of molecular sciences · 2024Article
- Molecular Dynamics Simulations of Claudin-10a and -10b Ion Channels: With Similar Architecture, Different Pore Linings Determine the Opposite Charge Selectivity.International journal of molecular sciences · 2024Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces.Computational and structural biotechnology journal · 2022Review
- Unifying Single-Channel Permeability From Rare-Event Sampling and Steady-State Flux.Frontiers in molecular biosciences · 2022Article
- Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations.Entropy (Basel, Switzerland) · 2021Article
- Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields.Journal of chemical information and modeling · 2020Article
- Dual Resolution Membrane Simulations Using Virtual Sites.The journal of physical chemistry. B · 2020Article
- Role of Aquaporins in Spermatogenesis and Testicular Steroidogenesis.The Journal of membrane biology · 2020Review
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Molecular determination of claudin-15 organization and channel selectivity.The Journal of general physiology · 2018Article
- Ion-triggered selectivity in bacterial sodium channels.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26-27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K(+) channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K(+) and Na(+) concentration gradients and the electrostatic potential difference of living cells.
Indexed as
Identifiers
What OpenQuestion holds
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.