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. 2022 Jun 16;11:e76356. doi: 10.7554/eLife.76356

Figure 3. First MD simulation of primed complexes bridging a vesicle and a flat bilayer.

(A) Overall view of the initial system after equilibration. (B) Close-up view of the four primed complexes in the initial system after equilibration. (C) Snapshot of the system after a 336 ns MD simulation. (D–K) Close-up views of the individual primed complexes (named PC1-PC4) in the initial configuration (D,F,H,J) and after the 336 ns MD simulation (E,G,I,K). In all panels, the primed complexes are illustrated by ribbon diagrams, with the SNAREs in salmon, Cpx1(27-72) in yellow and the Syt1 C2AB fragment in cyan (C2A domain) and violet (C2B domain). The lipids are shown as thin stick models (carbon lime, oxygen red, nitrogen blue, phosphorous orange).

Figure 3.

Figure 3—figure supplement 1. Ribbon diagrams of the four primed complexes generated for the first primed system with one vesicle and a flat bilayer.

Figure 3—figure supplement 1.

The SNAREs are in salmon, Cpx1(27-72) in yellow and the Syt1 C2AB fragment in cyan (C2A domain) and violet (C2B domain).
Figure 3—figure supplement 2. Additional views of the primed complexes bridging a vesicle and a flat bilayer.

Figure 3—figure supplement 2.

(A–E) Close-up views of PC3 in the first MD simulation of primed complexes bridging a vesicle and a flat bilayer in the initial configuration (A) and after 40, 80, 120, and 157 ns (B–E), respectively. PC3 is illustrated by ribbon diagrams, with the SNAREs in salmon, Cpx1(27-72) in yellow and the Syt1 C2AB fragment in cyan (C2A domain) and violet (C2B domain). The lipids are shown as thin stick models (carbon lime, oxygen red, nitrogen blue, phosphorous orange). (F) Close-up view of the region where Cpx1(27-72) remains bound to the SNARE complex in PC4 after 336 ns. The position of the Y70 side chain of Cpx1(27-72), which binds at a hydrophobic pocket of the SNARE complex, is indicated. (G) Close-up view of the region where the Cpx1(27-72) accessory helix interacts with the SNARE motif of synaptobrevin (labeled Syb) and the C-terminal SNARE motif of SNAP-25 (labeled SNC) in PC2 after 336 ns. Cpx1(27-72) and the SNARE complex are illustrated by ribbon diagrams and stick models with oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in light orange and carbon atoms in yellow [for Cpx1(27-72)] or salmon (for the SNAREs).