TABLE 1.
| Molecule | 〈Δx〉(nm) | f* (pN) | ln kf(f)(s−1) | ln ku(f)(s−1) |
|---|---|---|---|---|
| P5ab,Mg+2 | 19 ± 2 | 14.5 ± 1 | 41 ± 1.9 − (2.8 ± 0.1)f | −39 ± 2.3 + (2.9 ± 0.2)f |
| P5ab, by Cocco et al. (2003) | 15.1 | 27.5 − 2.74f | −42.9 + 1.93f | |
| P5ab, EDTA | 18 ± 2 | 13.3 ± 1 | 37 ± 4.0 − (2.7 ± 0.3)f | −32 ± 4.8 + (2.6 ± 0.4)f |
| P5ab, by us | 20.0 | 12.9 ± 0.5 | 36.1 ± 1.4 − (2.7 ± 0.1)f | −31.5 ± 0.7 + (2.6 ± 0.1)f |
| P5ab, fork dynamics | 20.0 | 12.6 ± 0.3 | 16.8 ± 0.2 − (1.1 ± 0.0)f | −26.7 ± 0.2 + (2.3 ± 0.0)f |
| P5abcΔA, Mg+2 | 22 ± 4 | 12.7 ± 0.3 | 58 ± 7.5 − (4.2 ± 0.5)f | −39 ± 9.3 + (2.7 ± 0.7)f |
| P5abcΔA, by Cocco et al. (2003) | 12.9 | 9.4 − 2.05f | −43.8 + 2.06f | |
| P5abcΔA, EDTA | 23 ± 2 | 11.4 ± 0.5 | 31 ± 6.0 − (2.6 ± 0.5)f | −31 ± 11 + (2.5 ± 0.3)f |
| P5abcΔA, by us | 25.0 | 11.3 ± 0.6 | 36.2 ± 1.8 − (3.4 ± 0.2)f | −27.8 ± 0.8 + (2.3 ± 0.1)f |
Simulation results for the P5ab and P5abcΔA compared to the experimental data from Liphardt et al. (2001) (in bold). Cocco et al. (2003) have studied the rate constants of folding and unfolding in the presence of Mg+2. However, they did not give any results in the absence of the ion about which we concern here. We list their results as a comparison. Note in our model the τo value of the P5ab is the same with the value of the P5abcΔA, but it does not equal to the τo in the fork dynamics.