Table 2.
Structural effects of equilibrationa
| Contact surface (Å2) | Bond length (Å) | |||
| Monomer A D149:S193 | Monomer B D149:S193 | Monomer A D149O:L128N | Monomer B D149 O:L128N | |
| Operatorb | ||||
| AB dimer | 28.3 | 26.7 | 3.1 | 3.2 |
| Monomer C | 27.0 | 3.2 | ||
| Equil. 1c | 34.9 | 48.0 | 2.8 | 2.8 |
| Equil. 2 | 30.3 | 39.3 | 3.5 | 3.1 |
| Equil. 3 | 49.8 | 30.3 | 2.9 | 3.4 |
| Equil. 4 | 18.3 | 44.0 | 3.3 | 2.9 |
| Inducerd | ||||
| AB dimer | 30.5 | 40.4 | 3.2 | 3.5 |
| CED dimer | 37.0 | 36.5 | 3.4 | 4.0 |
| Equil. 1e | 16.5 | 49.0 | 3.1 | >6 |
| Equil. 2 | 44.4 | 22.7 | 3.0 | >6 |
| Equil. 3 | 39.7 | 35.6 | 3.6 | >6 |
| Equil. 4 | 44.1 | 35.6 | >6 | 3.4 |
| Equil. 5 | 17.7 | 36.4 | 3.3 | >6 |
| Equil. 6 | 41.2 | 25.2 | 3.7 | 3.2 |
| Equil. 7 | 43.3 | 24.2 | 2.9 | 4.6 |
| Equil. 8f | 24.1 | 23.4 | 4.5 | 3.7 |
| Equil. 9 | 19.4 | 46.0 | 4.2 | 3.4 |
| Inducer (proteolytic core)g | ||||
| AB dimer | 31.3 | 34.5 | 3.4 | 3.1 |
| CD dimer | 25.2 | 27.9 | 3.2 | 3.2 |
| Equil. 1 | 32.5 | 42.7 | >6 | 3.4 |
| Equil. 2 | 30.3 | 23.2 | 3.3 | 3.9 |
| Equil. 3 | 41.7 | 27.4 | >6 | 4.2 |
| Equil. 4 | 33.6 | 26.9 | 3.1 | 4.4 |
| Equil. 5 | 34.4 | 20.0 | 2.9 | >6 |
a Values determined by CSU analysis (Sobolev et al. 1999).
b Operator-bound crystal structure (PDB code 1EFA; Bell and Lewis 2000), which has three LacI monomers in the crystallographic unit cell.
c Equilibrated starting structure used for all seven TMD trajectories, generated from AB dimer.
d Inducer-bound crystal structure (PDB code 1LBH; Lewis et al. 1996; ).
e Equilibrated target structure used for TMD trajectories 1–5, generated from AB dimer. Bold values indicate which monomer functioned as the trigger monomer.
f Equilibrated target structure used for TMD trajectories 6 and 7, generated from AB dimer. Bold values indicate which monomer functioned as the trigger monomer.
g Crystal structure of inducer-bound tryptic core (PDB code 1TLF; Friedman et al. 1995; ).