Table 2.
Expulsion parameters, routes, and structural changes for the REMD pathways in P450eryF
| Traj # | Pw # | k*, kJ/mol⋅nm | Traj length, ps | Global RMSD†, Å | Max. CαRMSF‡, Å | Res #§ |
|---|---|---|---|---|---|---|
| 1 | 2a | 800 | 590 | 3.2 (3.0) | 2.7 (74) | 35, 37, 59, 72, 73, 177, 292, 391 |
| 2 | 850 | 2.8 (2.7) | 2.6 (74) | 35, 74, 75, 76, 174, 175, 177 | ||
| 3 | 1,190 | 4.4 (4.3) | 4.9 (179) | 72, 73, 86, 174, 176, 177, 185, 292 | ||
| 4 | 510 | 3.1 (2.9) | 2.8 (75) | 37, 73, 74, 75, 78, 83, 86, 174, 292, 391, 392 | ||
| 5 | 700 | 700 | 2.8 (2.6) | 3.1 (77) | 74, 75, 76, 77, 78, 174, 175, 177, 182, 185, 389 | |
| 6 | 2b | 600 | 1,440 | 2.9 (2.7) | 2.4 (72) | 34, 37, 68, 72, 73, 75, 78, 86, 288, 292, 391 |
| 7 | 2e | 800 | 550 | 2.2 (2.1) | 2.1 (76) | 58, 59, 64, 72, 75, 84, 91, 92, 292 |
| 8 | 730 | 2.5 (2.2) | 2.5 (66) | 64, 69, 70, 71, 72, 80, 83, 86, 87, 292 | ||
| 9 | 220 | 2.3 (2.1) | 4.0 (74) | 59, 69, 72, 74, 75, 76, 174, 175 | ||
| 10 | 3 | 700 | 570 | 2.7 (2.7) | 5.7 (193) | 78, 83, 86, 170, 174, 188, 192, 193, 195, 290, 292, 391 |
*
k is the force constant of the random expulsion force acting on the center of mass of the ligand. The other parameters defining this expulsion force were constant for all trajectories (rmin = 0.03 Å, N = 300).
†
The maximum global rms deviation of nonhydrogen atoms from their crystal structure positions and (in parentheses) from their positions in the initial structure of the trajectory.
‡
The number of the residue with the highest Cα RMSF is given in brackets.
§
Residues lining the expulsion trajectories are calculated as described in ref. 14, table 3. The five residues with the highest RMSF (averaged over the whole REMD trajectory) are given in bold type.