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Cited by 9Lipid Membrane Structure and BehaviorProtein Structure and DynamicsCaveolin-1 and cellular processes

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations

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Rivel, Timothée, Biriukov, Denys, Kabelka, Ivo, Vácha, Robert·2025·Journal of Chemical Information and Modeling
DOI 10.1021/acs.jcim.4c01960PMC PMC11776052
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Abstract

High Resolution Image Download MS PowerPoint Slide Understanding the molecular mechanisms of pore formation is crucial for elucidating fundamental biological processes and developing therapeutic strategies, such as the design of drug delivery systems and antimicrobial agents. Although experimental methods can provide valuable information, they often lack the temporal and spatial resolution necessary to fully capture the dynamic stages of pore formation. In this study, we present two novel collective variables (CVs) designed to characterize membrane pore behavior, particularly its energetics, through molecular dynamics (MD) simulations. The first CV─termed Full-Path─effectively tracks both the nucleation and expansion phases of pore formation. The second CV─called Rapid─is tailored to accurately assess pore expansion in the limit of large pores, providing quick and reliable method for evaluating membrane line tension under various conditions. Our results clearly demonstrate that the line tension predictions from both our CVs are in excellent agreement. Moreover, these predictions align qualitatively with available experimental data. Specifically, they reflect higher line tension of 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) membranes containing 1-palmitoyl-2-oleoyl- sn -glycero-3-phospho- l -serine (POPS) lipids compared to pure POPC, the decrease in line tension of POPC vesicles as the 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphoglycerol (POPG) content increases, and higher line tension when ionic concentration is increased. Notably, these experimental trends are accurately captured only by the all-atom CHARMM36 and prosECCo75 force fields. In contrast, the all-atom Slipids force field, along with the coarse-grained Martini 2.2, Martini 2.2 polarizable, and Martini 3 models, show varying degrees of agreement with experiments. Our developed CVs can be adapted to various MD simulation engines for studying pore formation, with potential implications in membrane biophysics. They are also applicable to simulations involving external agents, offering an efficient alternative to existing methodologies.

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  • Fusion is initiated by the formation of pores in the opposing membranes stimulated by the electric field.

    “Rather, fusion is initiated by the formation of pores 21 in the opposing membranes stimulated by the electric field.”

    From Fusion of lipid membranes: an alternative pathway (2026) · cites this paper as [21]

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Cited by

Sorted by citations

Authors
Rivel, T., Biriukov, D., Kabelka, I., & Vácha, R.
Affiliations
  • Central European Institute of Technology – Masaryk University (CZ)
  • Masaryk University (CZ)
Corresponding author
Vácha, Robert
ORCID
Venue
Journal of Chemical Information and Modeling
Publisher
American Chemical Society (ACS)
Published
2025-01-10
Volume
65
Issue
2
Pages
908-920
ISSN
  • 1549-9596 (ISSN-L)
  • 1549-960X
DOI
10.1021/acs.jcim.4c01960
PMC
PMC11776052
OpenAlex
W4406235549
Cited by
9
References
1
Citations by year
2026: 7 · 2025: 2
FWCI
2.49
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Chemical Information and Modeling (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Veřejné služby Informačního systému (Masarykiana Brunensis Universitas) (submittedVersion, cc-by)
Funders
  • Ministerstvo ?kolstv?, Ml?de?e a Telov?chovy (CZ.02.01.01/00/22_010/0003229, LX22NPO5103)
  • H2020 European Research Council (101001470)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Caveolin-1 and cellular processes
Keywords
pore formation, collective variables, pore nucleation, pore expansion, POPC membrane, ionic concentration effects, force field comparison, CHARMM36, Martini coarse-grained model, lipid vesicles
MeSH terms
Cell Membrane, Lipid Bilayers, Phosphatidylcholines, Thermodynamics, Porosity, Molecular Dynamics Simulation

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