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. 2022 Nov 14;11:e81432. doi: 10.7554/eLife.81432

Figure 2. Atomistic MD simulations of GSDMDNT 33-mer rings in prepore and pore conformation.

Prepore (A,B; after 3.5 µs of MD) and pore rings (C,D; after 5 µs) are viewed from the top (A,C) and side (B,D). GSDMDNT is shown in blue cartoon representation, lipid headgroup phosphates and glycerol oxygens are shown as orange and green spheres, respectively. Water, ions, and lipid tails are not shown for clarity. The membrane under the prepore ring (A,B) is continuous but visibly bent upwards into the ring (B). In the pore conformation (C,D), lipids are absent from the central pore, which is lined by a continuous, membrane spanning β-barrel.

Figure 2.

Figure 2—figure supplement 1. Snapshots of prepore 33-mer on a larger membrane patch and of prepore 3, 5, and 16-mer on one membrane patch.

Figure 2—figure supplement 1.

Snapshots of 33-mer GSDMDNT prepore ring on 46×46 nm2 membrane after 2.2 µs of MD simulation, viewed from the top (A) and side (B). Snapshots of the system with 3, 5, and 16-mer GSDMDNT in prepore conformation after 1.5 µs of MD simulation, viewed from the top (C) and side (D). The GSDMDNT backbones are shown in blue cartoon representation. Lipid headgroup phosphates and glycerol oxygen atoms are shown as orange and green spheres, respectively. Water, ions, and lipid tails are not shown for clarity. (A) The black triangle indicates where the contacts of the globular domains of two neighboring subunits broke up.