TABLE 1.
Summary of simulated systems
| ID | Content | No. of water molecules | Box* size (Å) | Concentration (mM) | No. of simulations | Length of each |
|---|---|---|---|---|---|---|
| 1 | Protofibril1+PR† | 7165 | 67.4 | 7.0 | 2 | 20 ns |
| 2 | Protofibril2+PR | 7165 | 67.4 | 7.0 | 2 | 20 ns |
| 3 | Protofibril3+PR | 7165 | 67.4 | 7.0 | 2 | 20 ns |
| 4 | Protofibril 1 | 2965 | 50.8 | 16.5 | 1 | 10 ns |
| 5 | Protofibril 2 | 2965 | 50.8 | 16.5 | 1 | 10 ns |
| 6 | Protofibril 3 | 2965 | 50.8 | 16.5 | 1 | 10 ns |
| 7 | PR, acidic | 788 | 31.9 | 42.0 | 1 | 10 ns |
| 8 | PR, basic | 788 | 31.9 | 42.0 | 1 | 10 ns |
*
Triclinic box equivalent to the true truncated octahedral box.
†
PR, phenol red.
Na+ is added to neutralize the charge of basic form (Fig. 4).