title: Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum.
abstract: The interactions between redox proteins are transient in nature. Therefore, very few crystal structures are available for the complexes formed between these proteins. Computational docking simulations thus provide a useful alternative method for studying the interactions between electron transfer proteins. In this paper, we have studied the interactions between the aa(3)-type cytochrome c oxidase of the cyanobacterium Phormidium laminosum and its redox partners plastocyanin and cytochrome c(6) using a combination of comparative modelling techniques and docking simulations. Rigid-body docking orientations were scored with a combined energy function that accounts for electrostatics and desolvation. These simulations have identified two plausible docking sites, one of which appears to be unique to the binding of plastocyanin to the oxidase. This unique binding site may be due to the presence of a long loop region in the subunit II of cyanobacterial oxidases. Control simulations were performed with the ba(3)-type cytochrome c oxidase and its redox partner cytochrome c(552) from Thermus thermophilus. The docking between cytochrome c oxidase and its redox partners plastocyanin and cytochrome c(6) is dominated by hydrophobic residues, a feature already observed from kinetic and structural studies in other complexes of P. laminosum (e.g. plastocyanin or cytochrome c(6) with cytochrome f and photosystem I).
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Hart
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Howe
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
authors.forename: Juan
authors.initials: J
authors.lastname: Fernandez-Recio
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D000458:Cyanobacteria / Q000378:metabolism*; D045365:Cytochromes c6 / Q000737:chemistry / Q000378:metabolism*; D003576:Electron Transport Complex IV / Q000737:chemistry / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011487:Protein Conformation; D017385:Sequence Homology; D055672:Static Electricity; D013499:Surface Properties
chemical_list: D045365:Cytochromes c6; D003576:Electron Transport Complex IV