title: Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6.
abstract: The interaction of Chlamydomonas cytochrome f (cyt f) with either Chlamydomonas plastocyanin (PC) or Chlamydomonas cytochrome c(6) (cyt c(6)) was studied using Brownian dynamics simulations. The two electron acceptors (PC and cyt c(6)) were found to be essentially interchangeable despite a lack of sequence homology and different secondary structures (beta-sheet for PC and alpha-helix for cyt c(6)). Simulations using PC and cyt c(6) interacting with cyt f showed approximately equal numbers of successful complexes and calculated rates of electron transfer. Cyt f-PC and cyt f-cyt c(6) 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 c(6) (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 c(6) (E2, E70, and E71). Mutations on cyt f had identical effects on its interaction with either PC or cyt c(6). 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.
authors.affiliation: Department of Biochemistry and Biophysics Program, The Ohio State University, Columbus, Ohio 43210, USA. Gross.3@osu.edu
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Gross
authors.forename: Douglas C
authors.initials: DC
authors.lastname: Pearson
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D002696:Chlamydomonas / Q000378:metabolism*; D003198:Computer Simulation; D045365:Cytochromes c6 / Q000737:chemistry*; D045348:Cytochromes f / Q000737:chemistry* / Q000235:genetics; D019992:Databases as Topic; D004579:Electron Transport; D004583:Electrons; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D010970:Plastocyanin / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D055672:Static Electricity
chemical_list: D045365:Cytochromes c6; D008024:Ligands; D010970:Plastocyanin; D045348:Cytochromes f