Table 1.
Average interaction energies between POUs and HMG-DNA complex
| Model complex | With DNA |
With HMG |
With HMG-DNA |
||||||
|---|---|---|---|---|---|---|---|---|---|
| elec | vdw | IE | elec | vdw | IE | elec | vdw | IE | |
| WT | −570 (20) | −36 (2) | −600 (20) | −80 (10) | −25 (1) | −100 (10) | −640 (20) | −61 (2) | −700 (20) |
| HMG-POUSM···DNA | −180 (20) | −23 (2) | −200 (20) | −70 (10) | −32 (1) | −100 (10) | −250 (30) | −56 (2) | −306 (30) |
| HMGM···POUS-DNA | −540 (20) | −37 (2) | −580 (20) | −70 (8) | −17 (1) | −86 (8) | −610 (20) | −54 (2) | −670 (20) |
Average interaction energies and standard deviations (in parentheses) between the POUS domain and the HMG-DNA complex over the last 1 ns MD simulation of the association reaction. The energies are in unit kcal/mol. The columns list the electrostatic energy (elec), van der Waals energy (vdw), and interaction energy (IE) between the POUS domain with DNA, HMG domain, and the HMG-DNA binary complex. The columns from left to right correspond to panels A, D, G, B, E, H, C, F, and I of Fig. S6.