Table I.
Radii of Gyration (Å) for Various Structural Ensembles Representing Unfolded drkN SH3–MTSL
| Xplor trajectories |
||||
|---|---|---|---|---|
| TraDES/Xplor ensemblea | 700 Kb | 1000 Kb | 1400 Kb | |
| A3C | 18.4 | 13.4 | 16.5 | 21.0 |
| D32C | 18.2 | 13.0 | 17.0 | 20.4 |
| D59C | 18.4 | 13.2 | 18.8 | 22.9 |
The TraDES input parameters as recommended by Marsh et al.61 and used in this work lead to most compact ensembles. If TraDES is used in default configuration, Rg is increased by ca. 1.5 Å. If secondary structure preferences96 are omitted, Rg is further increased by ca. 1 Å.
During the MD simulations, the temperature fluctuated around the target values. The actual readings were 716 ± 39, 681 ± 37, and 702 ± 38 K for three low-temperature trajectories, 963 ± 46, 968 ± 45, and 976 ± 45 K for medium-temperature trajectories, and 1416 ± 54, 1400 ± 57, and 1389 ± 53 K for high-temperature trajectories. Note that comparable degree of protein expansion can be obtained in room-temperature simulations—but only when the solvent is included.