Brownian Dynamics Simulations of the Interaction of Chlamydomonas Cytochrome f with Plastocyanin and Cytochrome c6

The interaction of Chlamydomonas cytochrome f (cyt f) with either Chlamydomonas plastocyanin (PC) or Chlamydomonas cytochrome c6 (cyt c6) was studied using Brownian dynamics simulations. The two electron acceptors (PC and cyt c6) were found to be essentially interchangeable despite a lack of sequence homology and different secondary structures (β-sheet for PC and α-helix for cyt c6). Simulations using PC and cyt c6 interacting with cyt f showed approximately equal numbers of successful complexes and calculated rates of electron transfer. Cyt f-PC and cyt f-cyt c6 showed the same types of interactions. Hydrophobic residues surrounding the Y1 ligand to the heme on cyt f interacted with hydrophobic residues on PC (surrounding the H87 ligand to the Cu) or cyt c6 (surrounding the heme). Both types of complexes were stabilized by electrostatic interactions between K65, K188, and K189 on cyt f and conserved anionic residues on PC (E43, D44, D53, and E85) or cyt c6 (E2, E70, and E71). Mutations on cyt f had identical effects on its interaction with either PC or cyt c6. K65A, K188A, and K189A showed the largest effects whereas residues such as K217A, R88A, and K110A, which are located far from the positive patch on cyt f, showed very little inhibition. The effect of mutations observed in Brownian dynamics simulations paralleled those observed in experiments.