ArticlePloS one2015
A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 57 citations in OpenAlex.
- Lipid Disorder and PIP2-Regulated Clustering of Syntaxin-1 JMD-TMD Regions Govern Membrane Fusion Competence.International journal of molecular sciences · 2026Article
- Electrostatics and Local Aromatic Residues Govern Lipid Binding and Membrane Penetration of Synaptotagmin C2 Domains.bioRxiv : the preprint server for biology · 2026Article
- Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release.Quarterly reviews of biophysics · 2025Review
- Exploring the structural dynamics of the vesicle priming machinery.Biochemical Society transactions · 2024Review
- Self-Assembly of Lipid Molecules under Shear Flows: A Dissipative Particle Dynamics Simulation Study.Biomolecules · 2023Article
- Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?Membranes · 2023Review
- Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties.Membranes · 2022Article
- Asymmetric Lipid Membranes under Shear Flows: A Dissipative Particle Dynamics Study.Membranes · 2021Article
- Fusion pores with low conductance are cation selective.Cell reports · 2021Article
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- Finite-size transitions in complex membranes.Biophysical journal · 2021Article
- Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier.Biochemistry and biophysics reports · 2020Article
- Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms.Biophysical journal · 2020Article
- Predicting asymmetric phospholipid microstructures in solutions.RSC advances · 2020Article
- Twisting and tilting of a mechanosensitive molecular probe detects order in membranes.Chemical science · 2020Article
- Shear-induced microstructures and dynamics processes of phospholipid cylinders in solutions.Scientific reports · 2019Article
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.
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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.