TABLE 2.

Calculated interaction rates, k₂, and the number of close-distance complexes formed for truncated intact cyt f and its large domain interacting with cyt c₆

	Intact Cyt f		Large domain of Cyt f
	No. of complexes /10,000 trajectories	k2* (108) M−1 S−1	No. of complexes /10,000 trajectories	k2* (108) M−1 S−1
1CFM-A	413±3	13.5±0.8	37±3	1.2±0.2
1CFM-B	467±4	15.1±0.6	41±2	1.3±0.2
1CFM-C	677±10	21.4±0.8	110±2	3.5±0.3
1EWH-A	476±5	15.4±0.6	69±4	2.2±0.2
1EWH-B	61±3	2.0±0.3	1±0.4	0.02±0.01
1EWH-C	1022±11	31.2±0.8	163±7	5.2±0.5
1Q90	39±3	1.3±0.3	24±1	0.8±0.2
1Q90-modified†	366±4	12.0±0.6	–	–
1CFM-C-large‡ domain+K-188 and K-189	1220±4	35.9±3.1	–	–

^*The close-distance complexes were defined as those with Fe-Fe distances 18Å, which are considered electron transfer-active. The second order diffusion-controlled rate constants, k₂, 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 structure of 1Q90 cyt f was altered in its small domain, which does not affect the interactions of its large domain with PC.

^‡Only the large domain of 1CFM-C plus residues K-188 and K-189, but without the rest of the small domain, was used. Since a large number of close-distance complexes were formed, we carried only 1000 trajectories.