Table 1.
Structural summary of simulation at 270 K
| Environment | α-Helix, % | β-Strand, % | PPII helix, % | |
|---|---|---|---|---|
| Ala8 | ||||
| Isolated | 30.8 (8.2) | 0.7 (0.2) | 32.1 (5.2) | |
| Near α-helix template | ||||
| 8-Å separation | 65.5 (7.2) | 0.7 (0.7) | 10.0 (2.8) | |
| 9-Å separation | 37.3 (11.3) | 14.5 (3.4) | 13.9 (5.7) | |
| 11-Å separation | 27.4 (10.2) | 2.7 (1.1) | 18.7 (4.0) | |
| Near β-strand template | ||||
| 8-Å separation, 2–8 ns | 16.3 (12.0) | 84.6 (14.0) | 6.7 (1.6) | |
| 8-Å separation, 10–16 ns* | 3.5 (1.4) | 97.1 (1.4) | 4.3 (2.6) | |
| 9-Å separation | 2.8 (1.2) | 92.8 (2.5) | 2.2 (0.7) | |
| 11-Å separation | 9.8 (8.0) | 78.4 (6.2) | 11.4 (0.7) | |
| Isolated, non-GB | ||||
| ε = 1 | 1.3 (0.8) | 46.4 (10.0) | 0.2 (0.1) | |
| ε = 2 | 47.4 (6.0) | 30.8 (8.1) | 1.3 (0.3) | |
| ε = 4 | 65.1 (0.2) | 2.5 (0.4) | 0.06 (0.06) | |
| ε = 10 | 36.2 (1.2) | 0.1 (0.01) | 0.03 (0.03) | |
| ε = 80 | 11.9 (0.6) | 0.1 (0.1) | 0.0 (0.0) | |
| Ala7 | ||||
| Isolated | 3.1 (1.4) | 2.9 (2.7) | 48.6 (3.3) | |
| Near α-helix template | 3.4 (3.4) | 0.0 (0.0) | 19.7 (2.3) | |
| Near β-strand template | 0.0 (0.0) | 96.0 (1.2) | 7.6 (0.3) | |
| Isolated, non-GB | ||||
| ε = 1 | 0.0 (0.0) | 48.8 (4.1) | 0.2 (0.03) | |
| ε = 2 | 25.5 (5.7) | 55.9 (6.4) | 0.4 (0.1) | |
| ε = 4 | 58.5 (1.9) | 2.03 (0.3) | 0.07 (0.03) | |
| ε = 10 | 34.3 (0.9) | 0.07 (0.03) | 0.0 (0.0) | |
| ε = 80 | 18.0 (0.7) | 0.07 (0.03) | 0.0 (0.0) | |
The standard deviations are in parentheses. We note that there exist many disordered conformations that do not have any secondary structures.
*The data are from samples during the 10- to -16-ns step.