Table 1.
Summary of molecular dynamics simulations.
Simulation Systems | Sampling Method | The Initial Conformation | Two Collective Variables (CVs) | Acronym | Simulation Length (ns) |
---|---|---|---|---|---|
Tetramer AapA1-28/POPE/POPG (3:1) | CMD simulation | Figure 1A | CMD_T1 | 5000 ns | |
Figure 1B | CMD_T2 | 5000 ns | |||
AapA1-28/POPE/POPG (3:1) | 2D-MetaD simulation | Figure 3C | CV1: Contact number between K-23 and the top phosphate group. CV2: Contact number between K-23 and the bottom phosphate group. |
WT1 | 2 replica× 1000 ns |
AapA1-28/POPE/POPG (3:1) | 2D-MetaD simulation | Figure 3D | The same CVs | WT2 | 2 replica ×1000 ns |
AapA1-28/POPE/POPG (3:1) | CMD simulation | Figure 5A (representative conformation of region A in Figure 4) | CMD_M1 | 1000 ns | |
Figure 5B (representative conformation of region B in Figure 4) | CMD_M2 | 1000 ns | |||
Figure 5C (representative conformation of region A’ in Figure 4) | CMD_M3 | 1000 ns | |||
Figure 5D (representative conformation of region B’ in Figure 4) | CMD_M4 | 1000 ns | |||
Figure 5E (representative conformation of region C’ in Figure 4) | CMD_M5 | 1000 ns |