Table 6. Atomistic GSDMDNT simulations.
| Conformation | Subunits | Simulated time [µs] | Membrane size [nm2] | No. of atoms |
|---|---|---|---|---|
| prepore | 1 | 7.0 | 13.4×13.4 | 222740 |
| prepore | 33 | 3.5 | 38.9×38.9 | 1950552 |
| *prepore | 3, 5, 16 | 1.5 | 38.9×38.9 | 1916829 |
| prepore | 33 | 2.2 | 45.8×45.8 | 3113594 |
| pore | 1 | 5.0 | 12.7×12.7 | 216375 |
| pore | 2 | 5.0 | 12.5×12.5 | 213665 |
| pore | 3 | 5.0 | 12.2×12.2 | 208656 |
| pore | 5 | 4.3 | 18.8×18.8 | 481242 |
| pore | 8 | 2.5 | 25.5×31.9 | 1079514 |
| pore | 10 | 3.0 | 25.4×31.7 | 1071088 |
| pore | 16 | 3.5 | 31.3×31.3 | 1329398 |
| †pore | 16 | 1.4 | 34.9×34.9 | 1497819 |
| pore | 27 | 4.1 | 37.2×37.2 | 2226909 |
| pore | 33 | 5.0 | 37.0×37.0 | 2119785 |
| ‡pore | 33 | 1.5 | 37.0×37.0 | 2119785 |
| §pore | 33 | 1.5 | 37.0×37.0 | 1885031 |
*
simulated cut out oligomers of the full 33-mer prepore ring after 200 ns.
†
simulated in pure DOPC membrane.
‡
70°C continuation of the 37°C simulation after 5 µs.
§
simulated with lipid plug inside pore.