Table 1.
Free energy barriers and the local minima after the first revolution for all four topoisomerase systems, and the effect of adding a constant torque Γc in Eq. 3, corresponding to a free energy change of 5.8 kcal/mol/supercoil released (for a tension of 0.2 pN, see text)
| Torque-free system |
Tilted system |
|||||
|---|---|---|---|---|---|---|
| System | Barrier 1 | Minimum 1 | Barrier 2 | Barrier 1 | Minimum 1 | Barrier 2 |
| Topo/DNA (+) | 8.9 ± 0.27 | 1.7 ± 0.35 | 7.4 ± 0.29 | 6.8 ± 0.27 | −3.9 ± 0.35 | 4.57 ± 0.29 |
| Topo/DNA/TPT (+) | 12.6 ± 0.23 | 4.0 ± 0.35 | 9.6 ± 0.25 | 10.2 ± 0.23 | −1.3 ± 0.35 | 6.7 ± 0.25 |
| Topo/DNA (−) | 8.3 ± 0.28 | 2.6 ± 0.37 | 5.1 ± 0.24 | 5.6 ± 0.28 | −3.5 ± 0.37 | 3.1 ± 0.24 |
| Topo/DNA/TPT (−) | 6.2 ± 0.25 | 1.5 ± 0.37 | 6.1 ± 0.27 | 4.7 ± 0.25 | −4.2 ± 0.37 | 4.0 ± 0.25 |
Although the semiopen and deformed states are unfavorable in relaxed systems, the energy provided by the release of supercoils makes them favorable and also reduces the second energy barriers to the range of 3–7 kcal/mol.