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bioRxiv · 10.64898/2026.08.09.743827

Cholesterol-Dependent Structure and Dynamics of Curved Lipid Vesicles Revealed by Dry MARTINI Simulations

Khodadadi, E.·Moradi, M.
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Abstract

Cholesterol is a key regulator of membrane structure and dynamics, yet its effects on large curved vesicles under implicit-solvent coarse-grained conditions remain incompletely understood. Equilibrating large Dry MARTINI vesicles is challenging because transient membrane deformations can arise during the early stages of equilibration. Here, we developed a leaflet-specific restrained-equilibration protocol that preserves vesicle geometry while allowing local lipid relaxation. All restraints were removed before production simulations, and all reported results were obtained from unbiased trajectories. Using this protocol together with the Dry MARTINI force field and the TS2CG membrane builder, we simulated [~]50 nm DOPC vesicles containing 0-40 mol% cholesterol in three independent 20 {micro}s production simulations for each membrane composition. Increasing cholesterol concentration produced a consistent structural reorganization of the membrane, characterized by increased membrane thickness and lipid-tail ordering, and decreased species-specific Voronoi area per lipid, lipid-tail interdigitation, solvent-accessible surface area, and vesicle shape anisotropy. Cholesterol flip-flop increased progressively with cholesterol concentration, whereas DOPC flip-flop exhibited a reproducible non-monotonic dependence with a maximum near 20 mol% cholesterol. Comparison with our previous explicit-solvent MARTINI simulations showed that the major cholesterol-dependent structural trends were preserved across both solvent representations, whereas species-specific lipid packing, lipid-tail interdigitation, and the absolute magnitude of lipid flip-flop remained sensitive to the solvent representation. Overall, Dry MAR-TINI combined with the restrained-equilibration protocol provides an efficient framework for studying large curved cholesterol-containing vesicles.

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Khodadadi, E., Moradi, M.. 2026-08-11. Cholesterol-Dependent Structure and Dynamics of Curved Lipid Vesicles Revealed by Dry MARTINI Simulations. https://doi.org/10.64898/2026.08.09.743827

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