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PEDS Advance Access originally published online on September 29, 2008
Protein Engineering Design and Selection 2008 21(12):689-698; doi:10.1093/protein/gzn051
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

Sarah E. Hart1, Christopher J. Howe1, Kenji Mizuguchi1,2,3,5 and Juan Fernandez-Recio4,5

1Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW 2Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK 3 National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan 4Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain

5 To whom correspondence should be addressed. E-mail: kenji{at}nibio.go.jp (K.M.); juan.fernandez{at}bsc.es, juanf{at}bsc.es (J.F-R.)

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 aa3-type cytochrome c oxidase of the cyanobacterium Phormidium laminosum and its redox partners plastocyanin and cytochrome c6 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 ba3-type cytochrome c oxidase and its redox partner cytochrome c552 from Thermus thermophilus. The docking between cytochrome c oxidase and its redox partners plastocyanin and cytochrome c6 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 c6 with cytochrome f and photosystem I).

Keywords: aa3-cytochrome c oxidase/electron transfer/homology modelling/protein–protein docking/redox proteins

Received June 10, 2008; revised August 18, 2008; accepted September 4, 2008.


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