Table 1.
Table containing all MD simulation sets carried out in this work. For bilayers, we used Slipids forcefield and ff99sb-ildn-NMR for BP100. All sets were simulated at 323 K (above DPPC and DPPG transition temperatures) and 1 bar. L-BP100 indicate constraint-free simulations using random coil BP100 as peptide starting configuration and α-BP100, as alpha helix. Res1–5, res4–8 and res7–11 indicate simulations with BP100 with permanent constraints on the referred residues.
| Simulation sets | ||||
|---|---|---|---|---|
| Simulations | Peptide/Lipid | Waters/Lipid | Time (ns) | |
| Bilayers | DPPC | 0/128 | 54 | 860 |
| DPPG | 53 | 1100 | ||
| PCPG-R | 0/[64/64] | 54 | 1200 | |
| PCPG-NR | 52 | 1200 | ||
| Peptide in water | L-BP100 in water | 1/0 | — | 2000 |
| α-BP100 in water | — | 2850 | ||
| Peptide with bilayers | L-BP100 in DPPC | 1/128 | 54 | 1700 |
| α-BP100 in DPPC | 54 | 2000 | ||
| L-BP100 in DPPG | 1/128 | 53 | 1700 | |
| α-BP100 in DPPG | 53 | 2000 | ||
| L-BP100 in PCPG-R | 1/[64/64] | 54 | 1600 | |
| α-BP100 in PCPG-R | 54 | 2000 | ||
| L-BP100 in PCPG-NR | 1/[64/64] | 52 | 1700 | |
| α-BP100 in PCPG-NR | 52 | 2000 | ||
| Partially constrained peptide in DPPG | α-BP100 (res1–5) in DPPG | 1/128 | 54 | 600 |
| α-BP100 (res4–8) in DPPG | 54 | 600 | ||
| α-BP100 (res7–11) in DPPG | 54 | 600 | ||