Fig. 3

BD simulation of lipid scrambling. a Distribution of lipid head groups at the beginning (0 µs) and after 48 µs of BD simulation. Black and yellow spheres represent lipid head groups initially located in the upper and lower bilayer leaflets, respectively. The cyan semi-transparent surface schematically illustrates the volume accessible to lipid head groups during the simulation; L denotes the size of the lipid patch (here L = 12 nm). b Z coordinates of two representative lipid head groups. Horizontal dashed lines (at Z = ±1.75 nm) indicate approximate boundaries of upper and lower leaflets. The traces feature five inter-leaflet transfer events; τ defines the interval between two consecutive events. Head group trajectories were sampled every 2.4 ns. c Normalized probability of observing an inter-leaflet transfer event within time interval τ. An exponential fit (red line) yields the average transfer rate 1 / τ₀ = 23.0 ± 1.03 µs⁻¹. Data were obtained from a 500 µs trajectory of the L = 24 nm system sampled every 2.4 ns. d Fraction of lipid head groups remaining in the upper bilayer leaflet vs. time elapsed from the beginning of the simulation. Data are shown for two systems differing by the size of the lipid patch. Lipids reentering the leaflet were not included in the fraction calculation. The black dashed line shows an exponential fit to the curves; the fitting parameter k is the scrambling rate. Dashed lines plot the same quantity for randomly chosen lipids mimicking experimental conditions where only a small amount of fluorescently labeled lipids is used to assess lipid scrambling. e Simulated transfer rate (left axis) and scrambling rate (right axis) vs. pore-to-lipid ratio. Data were derived from BD simulations of systems of different lipid patch size (L = 12, 16, 20, 24, and 36 nm). Scrambling rate extracted directly from the simulation is plotted using squares. Dashed line plots k = r / 〈 τ₀ 〉 curve; transparent triangles indicate k = r / τ₀, where 1 / 〈 τ₀ 〉 and 1 / τ₀ are system-size-averaged and system-size-specific lipid transfer rates, respectively. Error bars indicate standard deviation