Table 1.
Summary of CG–MD and mesoscale simulations performed
| CG–MD simulations | ||||||
|---|---|---|---|---|---|---|
| Simulation | Proteins | Lipids | Temperature (K) | Duration (µs) |
Box dimensions at 20 µs (nm3) | Total number of particles |
| BtuB313 | 144 BtuB | 28,888 | 313 | 20 | 109 × 109 × 12 | 1,331,636 |
| BtuB323 | 144 BtuB | 28,888 | 323 | 20 | 109 × 109 × 12 | 1,331,636 |
| OmpF313 | 100 OmpF | 26,832 | 313 | 20 | 112 × 112 × 12 | 1,370,636 |
| OmpF323 | 100 OmpF | 26,832 | 323 | 20 | 110 × 110 × 12 | 1,370,636 |
| Mixed313 | 72 BtuB + 72 OmpF | 25,448 | 313 | 20 | 112 × 112 × 12 | 1,377,536 |
| Mixed323 | 72 BtuB + 72 OmpF | 25,448 | 323 | 20 | 112 × 112 × 12 | 1,377,536 |
| vBig | 1152 BtuB + 1152 OmpF | 407,168 | 323 | 2.5 | 446 × 446 × 12 | 22,040,576 |
| Mesoscale simulations | ||||
|---|---|---|---|---|
| Simulation | Proteins | Duration (ms) | Box dimensions (µm2) | CG–MD simulation used for parameterisation |
| BtuB_interfaces | 4900 BtuB | 24 | 1 × 1 | BtuB313 BtuB313 |
| No_specific_interfaces | 4900 BtuBa | 24 | 1 × 1 | BtuB313a |
| BtuB_1ms | 2500 BtuB | 1 | 0.5 × 0.5 | BtuB313 |
| Insert_25 | 2525 BtuB | 1 | 0.5 × 0.5 | BtuB313 |
aIn this simulation, no specific interfaces were present, i.e. a pair of proteins upon encounter would interact regardless of their relative orientation