Table 1.
Descriptions of performed molecular dynamics simulations
| Simulation | Force field | Composition* | Initial box size (Å) | Run type/Configuration | Time |
|---|---|---|---|---|---|
| PMF analysis of membrane-binding energy | |||||
| CG-pmf-WT | MARTINI | 124 POPC/2439 w/WT | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K8E | MARTINI | 124 POPC/2439 w/K8E | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K15E | MARTINI | 124 POPC/2439 w/K15E | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K20E | MARTINI | 124 POPC/2439 w/K20E | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K22E | MARTINI | 124 POPC/2439 w/K22E | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K25E | MARTINI | 124 POPC/2439 w/K25E | 65×65×110 | z-restrained | 4μs for each z-position |
| CG-pmf-K28E | MARTINI | 124 POPC/2439 w/K28E | 65×65×110 | z-restrained | 4μs for each z-position |
| AT-pmf-WT | Berger/OPLS-AA | 124 POPC /8317 w /WT | 66×66×98 | z-restrained at 1.5–2.8nm | 300ns for each z-position |
| AT-pmf-K15E | Berger/OPLS-AA | 124 POPC /8317 w /K15E | 66×66×98 | z-restrained at 1.5–2.8nm | 300ns for each z-position |
| AT-pmf-K28E | Berger/OPLS-AA | 124 POPC /8317 w /K28E | 66×66×98 | z-restrained at 1.5–2.8nm | 300ns for each z-position |
| AT free run † | |||||
| 60/64-WT | Berger/OPLS-AA | 124 POPC/5696 w/WT | 66×66×80 | free run | 300ns |
| 60/64-K8E | Berger/OPLS-AA | 124 POPC/5696 w/K8E | 66×66×80 | free run | 300ns |
| 60/64-K15E | Berger/OPLS-AA | 124 POPC/5696 w/K15E | 66×66×80 | free run | 300ns |
| 60/64-K20E | Berger/OPLS-AA | 124 POPC/5696 w/K20E | 66×66×80 | free run | 300ns |
| 60/64-K22E | Berger/OPLS-AA | 124 POPC/5696 w/K22E | 66×66×80 | free run | 300ns |
| 60/64-K25E | Berger/OPLS-AA | 124 POPC/5696 w/K25E | 66×66×80 | free run | 300ns |
| 60/64-K28E | Berger/OPLS-AA | 124 POPC/5696 w/K28E | 66×66×80 | free run | 300ns |
| 34/34-WT | Berger/OPLS-AA | 68 POPC/3180 w/WT | 49.5×49.5× 79 | free run | 600ns |
| 34/34-K28E | Berger/OPLS-AA | 68 POPC/3182 w/K28E | 49.5×49.5× 79 | free run | 600ns |
| 30/34-WT | Berger/OPLS-AA | 64 POPC/2560 w/WT | 47×47×76 | free run | 15 × 150ns |
| 30/34-K8E | Berger/OPLS-AA | 64 POPC/2560 w/K8E | 47×47×76 | free run | 15 × 150ns |
| 30/34-K15E | Berger/OPLS-AA | 64 POPC/2560 w/K15E | 47×47×76 | free run | 15 × 150ns |
| 30/34-K20E | Berger/OPLS-AA | 64 POPC/2560 w/K20E | 47×47×76 | free run | 15 × 150ns |
| 30/34-K22E | Berger/OPLS-AA | 64 POPC/2560 w/K22E | 47×47×76 | free run | 15 × 150ns |
| 30/34-K25E | Berger/OPLS-AA | 64 POPC/2560 w/K25E | 47×47×76 | free run | 15 × 150ns |
| 30/34-K28E | Berger/OPLS-AA | 64 POPC/2560 w/K28E | 47×47×76 | free run | 15 × 150ns |
| CG PMF analysis of dimerization in water | |||||
| in-water-2WT | MARTINI | 1684 w/2 WT/13 Na/23 Cl | 59.5×59.5× 59.5 | Umbrella sampling | 3×20μs for each distance1) |
| in-water-2K28E | MARTINI | 1691 w/2 K28E/15 Na/21 Cl | 59.5×59.5× 59.5 | Umbrella sampling | 3×20μs for each distance1) |
| CG run for peptide self-association near membrane | |||||
| 1-to-1-free-WT | MARTINI | 256 POPC/5444 w /2WT/20Na/30Cl | 92×92×118 | free; initially one in water and one on membrane | 100 × 800ns runs |
| 1-to-1-free-K28E | MARTINI | 256 POPC/5444 w/2 K28E/22 Na/28 Cl | 92×92×118 | free; initially one in water and one on membrane | 100 × 800ns runs |
*
For the CG and AT PMF simulations, as well as the AT free runs, chloride ions, but not other ions, were added to adjust the total charge zero.
†
The 30/34 series were performed after knowing the experimental data as described in Text S1.
1)
These analyses based on 3×20μs simulations for each distance were performed after knowing the experimental data as described in Text S1.