ArticleBMC bioinformatics2016
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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17 citing papers in PubMed.
- A Numerical Implementation to Calculate Elastic Properties of Biological Membrane Simulations.Journal of chemical information and modeling · 2026Article
- Development of Transferable Coarse-Grained Lipid Models with Optimized Structural and Elastic Membrane Properties.Journal of chemical theory and computation · 2025Article
- Cholesterol modulates membrane elasticity via unified biophysical laws.Nature communications · 2025Article
- Mechanisms of SNARE proteins in membrane fusion.Nature reviews. Molecular cell biology · 2024Review
- Mitochondrial membrane model: Lipids, elastic properties, and the changing curvature of cardiolipin.Biophysical journal · 2023Article
- Photomanipulation of Minimal Synthetic Cells: Area Increase, Softening, and Interleaflet Coupling of Membrane Models Doped with Azobenzene-Lipid Photoswitches.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.Biophysical journal · 2023Article
- Capturing Lipid Nanodisc Shape and Properties Using a Continuum Elastic Theory.Journal of chemical theory and computation · 2023Article
- Curvature-based sorting of eight lipid types in asymmetric buckled plasma membrane models.Biophysical journal · 2022Article
- Bending Modulus of Lipid Membranes from Density Correlation Functions.Journal of chemical theory and computation · 2022Article
- Alteration of lipid bilayer mechanics by volatile anesthetics: Insights from μs-long molecular dynamics simulations.iScience · 2022Article
- Multiscale compression-induced restructuring of stacked lipid bilayers: From buckling delamination to molecular packing.PloS one · 2022Article
- Mechanical properties of anionic asymmetric bilayers from atomistic simulations.The Journal of chemical physics · 2021Article
- Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties.The journal of physical chemistry. B · 2020Article
- Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description.Journal of chemical theory and computation · 2019Article
- Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2017Article
- Erratum to: Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.BMC bioinformatics · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influence membrane reshaping and fusion processes as well as the organisation and function of membrane proteins. Determining these properties is therefore key for a mechanistic understanding of how the cell functions.
resultsWe have developed a method to determine the bending rigidity and tilt modulus, for lipidic assemblies of arbitrary lipid composition and shape, from molecular dynamics simulations. The method extracts the elastic moduli from the distributions of microscopic tilts and splays of the lipid components. We present here an open source implementation of the method as a set of Python modules using the computational framework OpenStructure. These modules offer diverse algorithms typically used in the calculatation the elastic moduli, including routines to align MD trajectories of complex lipidic systems, to determine the water/lipid interface, to calculate lipid tilts and splays, as well as to fit the corresponding distributions to extract the elastic properties. We detail the implementation of the method and give several examples of how to use the modules in specific cases.
conclusionsThe method presented here is, to our knowledge, the only available computational approach allowing to quantify the elastic properties of lipidic assemblies of arbitrary shape and composition (including lipid mixtures). The implementation as python modules offers flexibility, which has already allowed the method to be applied to diverse lipid assembly types, ranging from bilayers in the liquid ordered and disordered phases to a study of the inverted-hexagonal phase, and with different force-fields (both all-atom and coarse grained representations). The modules are freely available through GitHub at https://github.com/njohner/ost_pymodules/ while OpenStructure can be obtained at http://www.openstructure.org .
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