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PEDS Advance Access published online on June 23, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi039
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received January 18, 2005
Revised May 6, 2005
Accepted May 20, 2005

Article

Large-scale modelling as a route to multiple surface comparisons of the CCP module family

Dinesh C. Soares 1, Dietlind L. Gerloff 2, Neil R. Syme 2, Andrew F. W. Coulson 2, John Parkinson 3, and Paul N. Barlow 4*

1 Biocomputing Research Unit, Michael Swann Building, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK; Biomolecular NMR Unit, Joseph Black Chemistry Building, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
2 Biocomputing Research Unit, Michael Swann Building, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
3 Programs in Genetics and Genomic Biology/Structural Biology and Biochemistry, University of Toronto, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry/Medical Genetics, University of Toronto, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; Department of Microbiology, University of Toronto, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
4 Biomolecular NMR Unit, Joseph Black Chemistry Building, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK

* To whom correspondence should be addressed.
Paul N. Barlow, E-mail: paul.barlow{at}ed.ac.uk


  Abstract

Numerous mammalian proteins are constructed from a limited repertoire of module-types. Proteins belonging to the regulators of complement activation family--crucial for ensuring a complement-mediated immune response is targeted against infectious agents--are composed solely of complement control protein (CCP) modules. In the current study, CCP module sequences were grouped to allow selection of the most appropriate experimentally determined structures to serve as templates in an automated large-scale structure modelling procedure. The resulting 135 individual CCP module models, valuable in their own right, are available at the online database http://www.bru.ed.ac.uk/~dinesh/ccp-db.html. Comparisons of surface properties within a particular family of modules should be more informative than sequence alignments alone. A comparison of surface electrostatic features was undertaken for the first 28 CCP modules of complement receptor type 1 (CR1). Assignments to clusters based on surface properties differ from assignments to clusters based on sequences. This observation might reflect adaptive evolution of surface-exposed residues involved in protein-protein interactions. This illustrative example of a multiple surface-comparison was indeed able to pinpoint functional sites in CR1.

Keywords: CCP modules; comparative modelling; complement system; electrostatic surface analysis; protein function prediction.
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