ArticleBiophysical journal2014
Atomistic simulations of pore formation and closure in lipid bilayers.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- A nanoscale Jitterbug transformer from DNA.Nature communications · 2026Article
- Understanding cell-penetrating peptide mechanisms using computational electrophysiology simulations.Protein science : a publication of the Protein Society · 2026Article
- AI-guided transition path sampling of lipid flip-flop and membrane nanoporation.Nature communications · 2025Article
- Electroporation in lipid vesicles by varying PEG-grafted lipids in their membranes: an experimental and simulation study.RSC advances · 2025Article
- Structural pores not required: Antimicrobial peptides induce ion permeabilization of lipid membranes through transient water channels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- How pore formation in complex biological membranes is governed by lipid composition, mechanics, and lateral sorting.PNAS nexus · 2025Article
- Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths.Computational and structural biotechnology journal · 2024Article
- Molecular and energetic analysis of the interaction and specificity of Maximin 3 with lipid membranes: In vitro and in silico assessments.Protein science : a publication of the Protein Society · 2024Article
- Nanoparticle induced fusion of lipid membranes.Nanoscale · 2024Article
- Molecular Dynamics Simulations of Drug-Conjugated Cell-Penetrating Peptides.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Accelerating Lipid Flip-Flop at Low Concentrations: A General Mechanism for Membrane Binding Peptides.The journal of physical chemistry letters · 2023Article
- Review
- Molecular Dynamics Simulation of Antimicrobial Peptide CM15 inIranian journal of biotechnology · 2023Article
- Initiation and evolution of pores formed by influenza fusion peptides probed by lysolipid inclusion.Biophysical journal · 2023Article
- Passive transport of CaBiophysical journal · 2023Article
- Translocation of a single Arg[Formula: see text] peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method.Scientific reports · 2023Article
- Biophysics of Membrane Stiffening by Cholesterol and Phosphatidylinositol 4,5-bisphosphate (PIP2).Advances in experimental medicine and biology · 2023Article
- Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration.Nature communications · 2022Article
- Advances of Electroporation-Related Therapies and the Synergy with Immunotherapy in Cancer Treatment.Vaccines · 2022Review
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No grant is acknowledged in the PubMed record.
Abstract
Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes.
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