Fig. 1. Molecular system. (A) Bovine cytochrome bc1 (CIII) and cytochrome c oxidase (CIV). The models of CIII and CIV are identical to the ones used in our previous studies.23,24 Briefly, CIII’s dimer was built from a combination of four experimental structures (PDB entries: 1 l0l,53; 1sqb/; 1sqq 54 and ; 2a06 (ref. 55)), excluding the six hemes and two iron-sulfur clusters. CIV's monomer was built from the PDB entries ; 1occ and ; 2occ,56 also excluding two deeply buried hemes. Details are given in the ESI† Methods section. (B) Matrix view of the membrane-exposed CL binding sites on both complexes.23,24 The detail of the CIII and CIV subunits, their nomenclature (Fig. S1†) and the comparison of predicted CL binding sites to experimental data have been described previously.23,24 The location of the non-CL-binding surface on CIV is indicated by a star. In the simulated system the complexes are embedded in a POPC bilayer containing CL at a 1:15 CL:POPC molar ratio; side (C) and top (D) views. The system shown contains 9 CIII dimers, 27 CIV, 17 462 POPCs, 1175 CLs (∼32 000 beads) and the aqueous phase (∼1 116 000 water beads and ∼2600 sodium ions), thus a total of slightly less than 1 400 000 CG beads. To ease visualization, the aqueous phase is omitted and to emphasize the relative orientation of the complexes two subunits of each complex are highlighted (A and B in red for CIII and D and G in yellow for CIV). CL topology and parameters were taken from the work of Dahlberg et al.57 (E) View of the CL-containing system after 20 μs of self-assembly simulation.
