TABLE 3.
Effect of cyt f rotation rate on the number of complexes formed and the interaction rates with PC and cyt c6
| Interactions with PC
|
Interactions with cyt c6
|
|||
|---|---|---|---|---|
| Number of complexes/10,000 trajectories† | ka† (×108) M−1 s−1 | Number of complexes/10,000 trajectories† | ka† (×108) M−1 s−1 | |
| cyt f (a)* | 137 ± 4 | 4.5 ± 0.3 | 91 ± 3 | 3.0 ± 0.3 |
| cyt f (b)* | 127 ± 2 | 4.2 ± 0.5 | 72 ± 1 | 2.4 ± 0.3 |
Cyt f (a) is the molecule with the rotational diffusion coefficient of 0.33 × 10−4 ps−1, which is the value computed by the MacroDox program for the cyt f molecule alone and has been used for cyt f in the simulations listed in Tables 1 and 2. Cyt f (b) is also cyt f alone but with its rotational diffusional coefficient replaced by that calculated by MacroDox for the cyt f+Rieske subcomplex-far (i.e., a value of 0.80 × 10−5 ps−1).
The complexes formed were those with Cu-Fe distances ≤17 Å for PC interactions and those with heme-heme distances ≤14.5 Å for cyt c6 interactions. These complexes are considered electron transfer-active. The second-order association rate constants, ka, were calculated for the formation of these complexes, as described in the Methods section. Five sets of 10,000 trajectories each were carried out to obtain the error values.