ArticleJournal of chemical theory and computation2021
Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- The Role of Architectural Forces in Ion Selectivity.Advances in experimental medicine and biology · 2026Article
- Deciphering CaProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Preorganized Electric Fields in Voltage-Gated Sodium Channels.Chembiochem : a European journal of chemical biology · 2025Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClJournal of chemical theory and computation · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClbioRxiv : the preprint server for biology · 2024Article
- Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer.The journal of physical chemistry. B · 2024Article
- A non-B DNA binding peptidomimetic channel alters cellular functions.Nature communications · 2024Article
- Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Computational drug development for membrane protein targets.Nature biotechnology · 2024Review
- Thermodynamics of Metal-Acetate Interactions.The journal of physical chemistry. B · 2024Article
- Metadynamics simulations reveal mechanisms of Na+ and Ca2+ transport in two open states of the channelrhodopsin chimera, C1C2.PloS one · 2024Article
- Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel.Journal of chemical information and modeling · 2023Article
- The voltage-sensing domain of a hERG1 mutant is a cation-selective channel.Biophysical journal · 2022Article
- Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces.Biophysical journal · 2022Article
- Influence of effective polarization on ion and water interactions within a biomimetic nanopore.Biophysical journal · 2022Article
- Ion permeation, selectivity, and electronic polarization in fluoride channels.Biophysical journal · 2022Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Despite the progress in modeling complex molecular systems of ever-increasing complexity, a quantitatively accurate computational treatment of ion permeation through narrow membrane channels remains challenging. An important factor to reach this goal is induced electronic polarization, which is likely to impact the permeation rate of small ions through narrow molecular pores. In this work, we extended the recently developed polarizable force field based on the classical Drude oscillators to assess the role of induced polarization effects on the energetics of sodium and potassium ion transport across the gramicidin A (gA) ion channel. The inclusion of induced polarization lowers barriers present in 1D potential of mean force (PMF) for cation permeation by ∼50% compared to those obtained with the additive force field. Conductance properties calculated with 1D PMFs from Drude simulations are in better agreement with experimental results. Polarization of single-file water molecules and protein atoms forming the narrow pore has a direct impact on the free-energy barriers and cation-specific solid-state NMR chemical shifts. Sensitivity analysis indicates that small changes to water-channel interactions can alter the free energy barrier for ion permeation. These results, illustrating polarization effects present in the complex electrostatic environment of the gA channel, have broad implications for revising proposed mechanisms of ion permeation and selectivity in a variety of ion channels.
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.