ArticleBiophysical journal2009
Understanding ion conductance on a molecular level: an all-atom modeling of the bacterial porin OmpF.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 95 citations in OpenAlex.
- Computational Insights into PB1-F2 Mediated Modulation of VDAC1: An Allosteric Mechanism in Mitochondrial Dysfunction.ACS omega · 2026Article
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
- Comparison among Amber-ff14SB, Amber-ff19SB, and CHARMM36 Force Fields for Ionic and Electroosmotic Flows in Biological Nanopores.Journal of chemical theory and computation · 2025Article
- Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.PLoS computational biology · 2025Article
- Dynamics and Interactions of OmpF Porin in an Asymmetric Bacterial Outer Membrane including LPS, ECA, and CPS.Biomacromolecules · 2025Article
- Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets.International journal of molecular sciences · 2023Review
- Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge.Chemical science · 2021Article
- Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.Biochimica et biophysica acta. Biomembranes · 2021Article
- Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations.Entropy (Basel, Switzerland) · 2021Article
- Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study.Scientific reports · 2019Article
- Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.Journal of chemical theory and computation · 2019Article
- Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.Biophysical journal · 2019Article
- Fosfomycin Permeation through the Outer Membrane Porin OmpF.Biophysical journal · 2019Article
- Lipid binding attenuates channel closure of the outer membrane protein OmpF.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction.Biophysical journal · 2017Article
- Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels.The journal of physical chemistry. B · 2017Article
- Exploring bacterial outer membrane barrier to combat bad bugs.Infection and drug resistance · 2017Review
- In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality.International journal of molecular sciences · 2016Article
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.Biophysical journal · 2016Article
- Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example.Biophysical journal · 2016Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
All-atom molecular dynamics simulations of the ion current through OmpF, the major porin in the outer membrane of Escherichia coli, were performed. Starting from the crystal structure, the all-atom modeling allows us to calculate a parameter-free ion conductance in semiquantitative agreement with experiment. Discrepancies between modeling and experiment occur, e.g., at salt concentrations above 1 M KCl or at high temperatures. At lower salt concentrations, the ions have separate pathways along the channel surface. The constriction zone in the channel contains, on one side, a series of positively charges (R42, R82, R132), and on the opposite side, two negatively charged residues (D113, E117). Mutations generated in the constriction zone by removing cationic residues enhance the otherwise small cation selectivity, whereas removing the anionic residues reverses the selectivity. Reduction of the negatively charged residues decreases the conductance by half, whereas cationic residues enhance the conductance. Experiments on mutants confirm the results of the molecular-level simulations.
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