Table 1.
Summary of RTMD simulations. Residue numbers followed by an atom type indicate that only that atom was included. Residue numbers followed by “BB” indicate that the backbone atoms (N C O CA) were included. CHARMM atom nomenclature is used. “n∕a” indicates that the corresponding simulations were not performed. Important residues in the RS are shown in Figs. 1a, 1b. “RMSD (δ = 0)” is the minimum RMSD value observed after the target RMSD, δ, reaches 0, but before the forces are switched off. “RMSD (relaxed)” is the average RMSD value observed after the forces are switched off. RMSD values are computed using all heavy atoms. The force constant κ is given in units of kcal∕mol∕Å2. Simulation time is quoted in ns. For brevity, “P” denotes the “PPS” state. RMSD values are quoted in Angstroms.
| RMSD (δ = 0) | RMSD (relaxed) | Simulation time | |||
|---|---|---|---|---|---|
| RTMD | Resolving set (number of atoms) | κ | R→P∕P→R | R→P∕P→R | R→P∕P→R |
| 1 | 761–769 CA; 770–773 BB; | 0.5 | 4.2∕3.9 | (n∕a) | 2∕2 |
| 770 SD; 718 766 CG (28) | |||||
| 2 | 762–769 BB; 771–773 BB (44) | 0.5 | 3.8∕(n∕a) | (n∕a) | 2 |
| 3 | 761–769 711–720 774–788 CA; | 1.0 | 3.0∕3.4 | (n∕a) | 2 |
| 770–773 BB; 770 SD; 716 766 CG (38) | |||||
| 4 | 761–769 711–720 774–788 CA; | 1.0 | 1.75∕1.5 | 2.3∕1.65 | 6∕6 |
| 770–773 BB; 770 SD; | |||||
| 718 766 758 749 708 CZ (56) | |||||
| 5 | 761–769 711–720 774–788 CA; | 1.0 | 1.25∕1.26 | 1.60∕1.66 | 6∕10 |
| 770–773 BB; 770 SD; 713 CD; | |||||
| 718 766 758 749 708 739 751 CZ (59) | |||||
| 6 | 761–769 711–720 774–788 CA; | 1.0 | 1.26∕1.26 | 1.75∕1.45 | 6∕6 |
| 770–773 BB; 770 SD; 713 722 CD; | |||||
| 718 766 758 749 708 739 751 CZ (60) |