TABLE 1.
Structural properties in the crystal and time averaged structural properties calculated over the last 2.5 ns for the native system at 300 K and over the last nanosecond for the three unfolding trajectories at 550 K (D-1, D-2, D-3)
| Properties* | Crystal | Native | D-1 | D-2 | D-3 | Avg |
|---|---|---|---|---|---|---|
| RMSD (nm) | 0.13 (0.02) | 0.31 (0.02) | 0.39 (0.02) | 0.57 (0.02) | 0.42 (0.02) | |
| RG (nm) | 1.26 | 1.27 (0.01) | 1.30 (0.01) | 1.28 (0.01) | 1.28 (0.02) | 1.29 (0.01) |
| (%) of α-helix | 41 | 43 (4) | 27 (4) | 33 (4) | 27 (4) | 29 (4) |
| Contacts | 732† | 694† | 79‡ | 80‡ | 72‡ | 77‡ |
| H-bonds | 83§ | 93§ (4) | 56¶ (5) | 57¶ (4) | 41¶ (4) | 51¶ (4) |
| SASAPho (nm2) | 25.6 | 24.3 (0.8) | 22.8 (0.9) | 22.7 (1.1) | 22.8 (1.1) | 22.8 (1.0) |
| SASAPhi (nm2) | 38.9 | 41.0 (1.2) | 42.0 (1.3) | 42.0 (1.4) | 42.0 (1.4) | 42.0 (1.4) |
In the last column (Avg), the values of the partial denatured ensemble, obtained averaging the three high temperature simulations over the last nanosecond, are reported. Standard deviations are given in parentheses.
*
The solvent-accessible surface area (SASA) is given for the hydrophobic residues (SASAPho) and for the hydrophilic ones (SASAPhi).
†
Number of contacts.
‡
Percentage of native contacts (with respect to the 300-K simulation).
§
Number of H-bonds.
¶
Percentage of native H-bonds (with respect to the 300-K simulation).