Impact of System Size on the Biophysical Properties of Multicomponent Lipid Bilayers: A Systematic Study Using Molecular Dynamics Simulations

Understanding how membrane lipids interact with small-molecule drugs is crucial for applications in anesthetics, antibacterial agents, surfactants, and biopesticides. Key questions include identifying the factors that modulate drug affinity for target membranes and elucidating the mechanisms underlying their interactions and translocations across lipid bilayers. Molecular dynamics simulations are a widely used tool to characterize these interactions at a high resolution. Given the finely tuned lipid composition of different cell types and subcellular compartments, membrane models must account for this diversity to accurately represent the chemical, structural, and dynamic environments of the membrane of interest. Nonetheless, most simulation studies model drug-bilayer interactions using small patches of pure or binary lipid mixtures, with about 20-120 lipids per leaflet. In this study, we systematically investigate the effect of the model membrane patch size on the biophysical properties of symmetric bilayers composed of complex lipid mixtures. We used a mixture of POPC, SOPS, SOPE, PSM, SAPI, and cholesterol to model eukaryotic cell membranes and determine the minimum bilayer patch size required to accurately reproduce key biophysical properties. Systems were constructed in six sizes, ranging from 50 to 300 lipids per leaflet, at two cholesterol concentrations, resulting in 36 trajectories totaling 11.6 μs of simulation trajectories. Each system was simulated for at least four times longer than the time required to reach thermal equilibrium, ensuring sufficient sampling for analysis. Using metrics such as area per lipid, bilayer thickness, lipid headgroup tilt, 2D radial distribution functions, lipid tail splay angle, lipid packing defects, area compressibility, and lateral pressure profiles, we determined that a bilayer patch of approximately 8 × 8 nm, containing at least 150 lipids per leaflet, provides robust and efficient sampling of membrane structure and dynamics as well as sufficient surface area to capture interactions between membrane lipids and small molecules.