ArticleBiophysical journal2008
Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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
46 citing papers in PubMed, 141 citations in OpenAlex.
- Membrane Topology and Oligomerization of Peptaibols by Solid-State NMR Spectroscopy.Journal of peptide science : an official publication of the European Peptide Society · 2026Review
- Identification and Characterization of an In Silico Designed Membrane-Active Peptide with Antiviral Properties.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterization of Membrane Binding and Protein-Lipid Interactions at the Atomic Level with an Accelerated HMMM Model.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling.Molecules (Basel, Switzerland) · 2024Article
- Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides.Scientific reports · 2024Article
- Structural Phenomena in a Vesicle Membrane Obtained through an Evolution Experiment: A Study Based on MD Simulations.Life (Basel, Switzerland) · 2023Article
- Multi-oligomeric states of alamethicin ion channel: Assemblies and conductance.Biophysical journal · 2023Article
- Pore Formation Mechanism of A-Beta Peptide on the Fluid Membrane: A Combined Coarse-Grained and All-Atomic Model.Molecules (Basel, Switzerland) · 2022Article
- Data-driven discovery of cardiolipin-selective small molecules by computational active learning.Chemical science · 2022Article
- Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration.RSC advances · 2022Article
- Membrane Structure Obtained in an Experimental Evolution Process.Life (Basel, Switzerland) · 2022Article
- Article
- Article
- Twisting and tilting of a mechanosensitive molecular probe detects order in membranes.Chemical science · 2020Article
- Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy.Journal of molecular modeling · 2020Article
- Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1.RSC advances · 2019Article
- Mechanistic Landscape of Membrane-Permeabilizing Peptides.Chemical reviews · 2019Review
- Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel.Biophysical journal · 2019Article
- Computational studies of peptide-induced membrane pore formation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations.Biophysical journal · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-micros CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 micros is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the alpha-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer.
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.