ArticleJournal of computational chemistry2020
Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Molecular basis for the regulation of membrane proteins through preferential lipid solvation.Nature chemical biology · 2026Article
- Elucidating the mechanical properties of asymmetric membranes by direct derivation of their energetics.Faraday discussions · 2025Article
- Lipid-mediated hydrophobic gating in the BK potassium channel.Nature communications · 2025Article
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- On the function of TRAP substrate-binding proteins: Conformational variation of the sialic acid binding protein SiaP.The Journal of biological chemistry · 2024Article
- Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A.eLife · 2024Article
- Mesoscopic elasticity controls dynamin-driven fission of lipid tubules.Scientific reports · 2024Article
- The local variation of the Gaussian modulus enables different pathways for fluid lipid vesicle fusion.Scientific reports · 2024Article
- Nonuniversal impact of cholesterol on membranes mobility, curvature sensing and elasticity.Nature communications · 2023Article
- Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening.PNAS nexus · 2023Article
- Mesoscale simulations: An indispensable approach to understand biomembranes.Biophysical journal · 2023Review
- Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening.bioRxiv : the preprint server for biology · 2023Article
- Article
- LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems.Biomolecules · 2023Article
- Determination of Elastic Parameters of Lipid Membranes with Molecular Dynamics: A Review of Approaches and Theoretical Aspects.Membranes · 2022Review
- Molecular Dynamics Simulations of Curved Lipid Membranes.International journal of molecular sciences · 2022Review
- Activation energy and force fields during topological transitions of fluid lipid vesicles.Communications physics · 2022Article
- Cholesterol Hinders the Passive Uptake of Amphiphilic Nanoparticles into Fluid Lipid Membranes.The journal of physical chemistry letters · 2021Article
- The Role of the Membrane in Transporter Folding and Activity.Journal of molecular biology · 2021Review
- Data-guided Multi-Map variables for ensemble refinement of molecular movies.The Journal of chemical physics · 2020Article
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3 authors.
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Abstract
We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this "Multi-Map" variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich-Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
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