TABLE 2.
Number of complexes formed with heme-heme distances ≤14.5 Å and the corresponding association rate constants (ka) for the interactions of cyt c6 with cyt f+Rieske subcomplexes from C. reinhardtii
| Number of complexes/10,000 trajectories* | Corrected value† | ka* (×108) M−1 s−1 | Corrected value† | |
|---|---|---|---|---|
| Cyt f-unmodified alone | 91 ± 3 | – | 3.0 ± 0.3 | – |
| Cyt f+Rieske subcomplex-far‡ | 36 ± 2 | 89 ± 4 | 1.0 ± 0.15 | 2.9 ± 0.4 |
| Cyt f+Rieske subcomplex-far no charge§ | 38 ± 2 | – | 1.1 ± 0.2 | – |
| Cyt f-modified¶ alone | 493 ± 6 | – | 16.0 ± 0.7 | – |
| Cyt f-modified+Rieske subcomplex-far | 551 ± 8 | 617 ± 11 | 14.7 ± 0.7 | 19.2 ± 1.1 |
| Cyt f-modified+Rieske subcomplex-far no charge | 427 ± 3 | – | 11.5 ± 0.4 | – |
| Cyt f+Rieske subcomplex-close‡ | 56 ± 3 | 123 ± 3 | 1.6 ± 0.2 | 3.9 ± 0.2 |
| Cyt f+Rieske subcomplex-close no charge | 24 ± 1 | – | 0.68 ± 0.15 | – |
| Cyt f-modified+Rieske subcomplex-close | 408 ± 8 | 653 ± 9 | 11.3 ± 0.5 | 20.4 ± 1.0 |
| Cyt f-modified+Rieske subcomplex-close no charge | 248 ± 7 | – | 6.9 ± 0.4 | – |
The complexes included were those with the heme-heme distances ≤14.5 Å, which 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.
The corrected values for the number of complexes formed for all of the cyt f+Rieske subcomplexes were obtained as follows. First, the number of complexes formed for cyt f+Rieske subcomplexes with all of the Rieske charges set to zero were subtracted from that obtained for the cyt f-unmodified alone. Second, the difference obtained was added to the number of complexes formed for the cyt f+Rieske subcomplexes with all of the Rieske charges in place. In the case of modified cyt f, the subtractions were made from the number of complexes formed by the cyt f-modified alone structure. The values of the interaction rates were corrected in the same way. For an explanation of the corrected values, see the Discussion section.
The cyt f+Rieske subcomplex-far is the structure from the crystal structure of the C. reinhardtii cyt b6f complex. The model of the cyt f+Rieske subcomplex-close was built by moving the extramembrane domain of the Rieske protein closer to the extramembrane domain of cyt f (refer to the Methods section and Fig. 1).
For the cyt f+Rieske-no charge subcomplexes, only the charges on the Rieske protein were set to zero in the charge file used for the MacroDox simulations. Note that the charges were not removed from either cyt f or cyt c6.
In the cyt f-modified structure, the loop of residues 184–191 on the cyt f molecule was replaced by that from the cyt f structure B from PDB code 1CFM (refer to the Methods section).