Table 1.
Fractional RMS for Cartesian, orthogonalized torsional, and optimized torsional modes
| Protein | PDB ID A | PDB ID B | No. AA | No. of chains | RMS A to B (Å) |
fRMS |
Min. num. modes |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A to B |
B to A |
||||||||||||
| Cart. | Orth. tors. | Opt. tors. | Cart. | Orth. tors. | Opt. tors. | A to B | B to A | ||||||
| Ribose-binding protein | 1BA2_A | 2DRI | 271 | 1 | 6.2 | 0.244 | 0.221 | 0.136 | 0.440 | 0.466 | 0.480 | 2 | 10 |
| Calmodulin | 1CLL | 1CTR | 144 | 1 | 14.8 | 0.561 | 0.580 | 0.194 | 0.655 | 0.709 | 0.133 | 2 | 1 |
| LAO binding protein | 2LAO | 1LST | 238 | 1 | 4.7 | 0.227 | 0.244 | 0.225 | 0.809 | 0.867 | 0.833 | 10 | 10 |
| Ribonuclease III | 1YZ9_AB | 1YYO_AB | 436 | 2 | 7.3 | 0.287 | 0.462 | 0.273 | 0.876 | 0.792 | 0.376 | 10 | 3 |
| Diphtheria toxin | 1DDT | 1MDT_A | 535 | 1 | 15.6 | 0.653 | 0.637 | 0.383 | 0.781 | 0.826 | 0.729 | 3 | 8 |
| Lactoferrin | 1LFH | 1LFG | 691 | 1 | 6.4 | 0.358 | 0.415 | 0.441 | 0.510 | 0.642 | 0.538 | 10 | 10 |
| Aspartate transcarbamoylase | 8ATC | 5AT1 | 912 | 4 | 4.9 | 0.447 | 0.451 | 0.461 | 0.703 | 0.444 | 0.425 | 10 | 4 |
| Aspartate aminotransferase | 9AAT_A | 1AMA | 401 | 1 | 1.7 | 0.502 | 0.495 | 0.470 | 0.519 | 0.496 | 0.519 | 8 | 10 |
| Skeletal muscle Ca2+ ATPase | 1SU4_A | 1IWO_A | 994 | 1 | 14 | 0.546 | 0.544 | 0.472 | 0.778 | 0.861 | 0.732 | 8 | 5 |
| 5′-Nucleotidase | 1HPU_D | 1OID_A | 525 | 1 | 9.3 | 0.663 | 0.661 | 0.529 | 0.676 | 0.758 | 0.615 | 9 | 9 |
| Scallop myosin II | 1QVI_AYZ | 1KK8_ABC | 1079 | 3 | 27.6 | 0.709 | 0.719 | 0.567 | 0.774 | 0.810 | 0.612 | 4 | 4 |
| T7 RNA polymerase | 1MSW_D | 1QLN_A | 883 | 1 | 18.3 | 0.808 | 0.783 | 0.779 | 0.982 | 0.980 | 0.970 | 5 | 9 |
| Nitrogen regulatory protein C | 1DC8_A | 1DC7_A | 123 | 1 | 3.2 | 0.963 | 0.956 | 0.892 | 0.944 | 0.938 | 0.939 | 2 | 10 |
| Average values | 0.536 | 0.551 | 0.448 | 0.727 | 0.738 | 0.608 | 6.4 | 7.2 | |||||
Fractional RMS (fRMS) values of Cartesian normal modes (Cart.), orthogonalized torsional normal modes (Orth. tors.), and optimized torsional normal modes (Opt. tors.). The fRMS values are calculated using the 10 lowest frequency modes. The A and B conformations are named so that the average value of the three methods of calculating normal modes describes A to B better than B to A. The lowest fRMS for each conformational change is highlighted. The minimum number of modes (Min. num. modes) is the number of optimized torsional normal modes required to give a value for fRMS that equals the value for 10 Cartesian normal modes; values ≤5 are highlighted. PDB file names for conformations A and B are as follows: Ribose-binding protein (1BA2 (16), 2DRI (17)), Calmodulin (1CLL (18), 1CTR (19)), LAO binding protein (2LAO (20), 1LST (20)), Ribonuclease III (1YZ9 (21), 1YYO (21)), Diphtheria toxin (1DDT (22), 1MDT (23)), Lactoferrin (1LFH (24), 1LFG (24)), Aspartate transcarbamoylase (8ATC (25), 5AT1 (26)), Aspartate aminotransferase (9AAT (27), 1AMA (28)), Skeletal muscle Ca2+ ATPase (1SU4 (29), 1IWO (30)), 5′-Nucleotidase (1HPU (31), 1OID (32)), Scallop myosin II (1QVI (33), 1KK8 (34)), T7 RNA polymerase (1MSW (35), 1QLN (36)), Nitrogen regulatory protein C (1DC8 (37), 1DC7 (37)).