ArticleJournal of the American Chemical Society2013
A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed, 28 citations in OpenAlex.
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
- Dynamics and Interactions of OmpF Porin in an Asymmetric Bacterial Outer Membrane including LPS, ECA, and CPS.Biomacromolecules · 2025Article
- Molecular Mechanism of Ciprofloxacin Translocation Through the Major Diffusion Channels of the ESKAPE PathogensThe journal of physical chemistry. B · 2024Article
- Interaction of Tryptophan- and Arginine-Rich Antimicrobial Peptide withInternational journal of molecular sciences · 2023Article
- Design and directed evolution of noncanonical β-stereoselective metalloglycosidases.Nature communications · 2022Article
- What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?Microbiology (Reading, England) · 2022Review
- Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria.Nature reviews. Microbiology · 2020Review
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.Biophysical journal · 2016Article
- Computational modeling of membrane proteins.Proteins · 2015Review
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 at 1 institution in 1 country.
Funding
Abstract
OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.
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.