Fig. 4: Coarse-grained MD simulations of scrambling by a specific VDAC1 dimer.

a Structure of VDAC1 dimer-1. The β-strands at the interface are indicated, and the E73 residue on the β4-strand is marked. Dimer-1* and dimer-3 are shown in Fig. S8. b Surface representation (white, hydrophobic; yellow, backbone; green, hydrophilic; blue, positive; red, negative) showing each protomer, rotated 90^o to expose the interface, with the contact region marked with a shaded ellipse; polar residues flanking the interface are indicated. Residues with side-chains oriented towards the pore, are colored yellow. c Percentage of lipids scrambled as a function of simulation time. The graphs show the scrambling activity of dimer-1, monomer (M) and protein-free membrane (L) (average over 200 ns time intervals, shading = 68% confidence interval; the inner full line shows the running average of the average scrambling rate measured in 3 independent replicas). Unless constrained during the simulation, dimer-1 reorients to form dimer-1*. Three individual runs of unconstrained dimer-1 are shown (dimer-1 (relaxed)), with the change in scrambling rate occurring between 2 and 4 µs coinciding with reorientation. d Bar chart showing scrambling rate for dimer-1, dimer-1*, dimer-3 and monomer (M) (mean ± SD, n = 3). e Snapshot of dimer-1 from the simulation showing phospholipids (multiple colors) transiting between bilayer leaflets along the interface. Membrane phospholipids surrounding the dimer are gray. f Top view snapshot of dimer-1 showing representative phospholipids transiting across the bilayer on both sides of the interface. g Bilayer thinning at the dimer-1 interface and near E73 in monomeric VDAC1 (thickness indicated by the color scale at right). Top views are shown, β-strands at the interface are indicated as colored dots (same color scheme as in a); the red dot indicates the β4-strand where E73 is located (arrowheads); the N-terminal helix is shown as a gray oblong within the VDAC1 pore. h Snapshot side-view of VDAC dimer-1, with one protomer removed, demonstrating membrane thinning at the interface. The ochre surface indicates the average positions of lipid phosphates from both membrane leaflets. The protein is shown in surface representation. i Water penetration into the membrane (water defect, color scale shown at right) in the vicinity of the dimer-1 interface and monomeric VDAC1, as indicated.