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

Department of Biochemistry and Biophysics Program, The Ohio State University, Columbus, Ohio

Correspondence: Address reprint requests to Dr. Elizabeth L. Gross, Dept. of Biochemistry, The Ohio State University, 484 W. 12th. Ave., Columbus, OH 43210. E-mail: Gross.3{at}osu.edu.

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 (ß-sheet for PC and -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.

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