We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).

• MeSH
• algoritmy * MeSH
• buněčná membrána * chemie   metabolismus   MeSH
• metoda Monte Carlo MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Mammalian and Drosophila melanogaster model mitochondrial membrane compositions are constructed from experimental data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation, and pH. We draw the conclusion that cardiolipin-negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid.

• MeSH
• Drosophila melanogaster MeSH
• kardiolipiny * chemie   MeSH
• mitochondriální membrány * MeSH
• savci MeSH
• simulace molekulární dynamiky MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kardiolipiny * MeSH

Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.

• Klíčová slova
• Laurdan, anionic lipids, calcium, headgroup mobility, headgroup organization, lipid hydration, molecular dynamics, phospholipid bilayer, proton, time dependent fluorescence shift,
• MeSH
• fosfatidylseriny MeSH
• ionty MeSH
• lipidové dvojvrstvy * chemie   MeSH
• protony * MeSH
• simulace molekulární dynamiky MeSH
• vápník chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fosfatidylseriny MeSH
• ionty MeSH
• lipidové dvojvrstvy * MeSH
• protony * MeSH
• vápník MeSH