ArticleThe Journal of chemical physics2020
Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint.
Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 22 citations in OpenAlex.
- Molecular Insights into End-Group Cluster Formation in Natural Rubber Induced by l-Quebrachitol, a Major Component of Natural Rubber Serum Waste.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- Micelle and Inverse Micelle Structure Driven Viscoelasticity and Phase Separation in 2‑Isobutoxyethanol-Water Mixtures: Insights from All-Atom Simulations.Precision chemistry · 2026Article
- Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Exploring the Role of Hydroxy- and Phosphate-TerminatedACS polymers Au · 2024Article
- Effect of Impurities on the Formation of End-Group Clusters in Natural Rubber: Phenylalanine Dipeptide as an Impurity Protein.Macromolecules · 2024Article
- Initiation and evolution of pores formed by influenza fusion peptides probed by lysolipid inclusion.Biophysical journal · 2023Article
- Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration.Nature communications · 2022Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The free energy of pore formation in lipid bilayers has been previously calculated using a variety of reaction coordinates. Here, we use free energy perturbation of a cylindrical lipid exclusion restraint to compute the free energy profile as a function of pore radius in dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) bilayers. Additionally restraining the headgroups to lie on the membrane surface allows us to also calculate the free energy profile of hydrophobic pores, i.e., cylindrical pores lined by acyl chains. For certain pore radii, the free energy of wetting of hydrophobic pores is calculated using the density bias method. It is found that wetting of hydrophobic pores becomes thermodynamically favorable at 5.0 Å for DMPC and 6.5 Å for DOPC, although significant barriers prevent spontaneous wetting of the latter on a nanosecond time scale. The free energy of transformation of hydrophilic pores to hydrophobic ones is also calculated using free energy perturbation of headgroup restraints along the bilayer normal. This quantity, along with wetting and pore growth free energies, provides complete free energy profiles as a function of radius. Pore line tension values for the hydrophilic pores obtained from the slope of the free energy profiles are 37.6 pN for DMPC and 53.7 pN for DOPC. The free energy profiles for the hydrophobic pores are analyzed in terms of elementary interfacial tensions. It is found that a positive three-phase line tension is required to explain the results. The estimated value for this three-phase line tension (51.2 pN) lies within the expected range.
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