Table 1.
Summary of the simulations. The systems are labeled according to the initial orientation a, b, r, i, n, p, s of HAfp (see Fig. 1). The suffix (1, 2 or 3) indicates the replicate number for the respective system. A letter f at the end of the system name indicates the extension of the membrane-bound system fo a full POPC membrane. The simulations in which insertion of the peptide was observed (18 out of 21) are indicated in the left column.
| System name | Simulation time | Membrane insertion | |
|---|---|---|---|
| Helix A |
a1
a2 a3 |
100 ns 100 ns 100 ns |
− + + |
| Helix B |
b1
b2 b3 |
100 ns 100 ns 100 ns |
+ + + |
| Reclined |
r1
r2 r3 r3f |
100 ns 100 ns 100 ns 30ns (POPC) |
− − + already membrane-bound |
| Inclined |
i1
i2 i3 i2f |
100 ns 100 ns 100 ns 30ns (POPC) |
+ + + already membrane-bound |
| Nosedive |
n1
n2 n3 |
100 ns 100 ns 100 ns |
+ + + |
| Parallel |
p1
p2 p3 |
100 ns 100 ns 100 ns |
+ + + |
| Standing |
s1
s2 s3 s1f |
100 ns 100 ns 100 ns 30ns (POPC). |
+ + + already membrane-bound |