Bioinformatics studies on sequence, structure and functional relationships of proteins involved in the complement system

The complement system consists of -30 proteins involved in a series of cascading reactions ultimately resulting in the destruction of invading pathogens. Central to the pathway are three paralogous proteins, C3, C4 and C5. Furthermore, pivotal to the successful functioning of this system are five proteins belonging to the regulators of complement activation (RCA) family they ensure that a complement-mediated immune response is proportionate and targeted against infection. RCA proteins are characterised by numerous occurrences of a single module-type; the complement control protein (CCP) module. In this work, comprehensive bioinformatics analyses of sequence and structure of CCP modules was undertaken. Through extensive database and literature searches CCP module sequences and structures were retrieved and large-scale all-against-all sequence and structure comparisons performed; analysis of intermodular orientations for pairs of modules and larger fragments was performed. These analyses revealed interesting consensus and novel trends. Based upon optimal use of experimentally determined CCP module structures as templates, an automated large-scale protein structure comparative modelling procedure was implemented for a set of 203 CCPmodule sequences. The accuracies of models produced were validated, and the models are publicly available online at "The CCP module model database" (http://www.bru.ed.ac.uk/—dinesh/ccp-db.html), which also serves as a comprehensive resource for information on CCP modules. By way of example, surface electrostatic analyses were undertaken for the first 28 CCP module models of complement receptor type 1 (CR1). This revealed a striking case of adaptive evolution assignments to clusters based on surfaces differ from assignments to clusters based on sequences and sheds light on mutagenesis studies. Overall, the models provide a rich vein of information for design of mutants, interpretation of phenotypic consequences of polymorphisms, and prediction of function. This wider utility of models is discussed in relation to inferring consequences of several disease-associated sequence variations for complement proteins CR1, factor H, MCP, and another CCP-containing protein, SRPX2. Finally, homology models of CS and C5b were created on the basis of the recent landmark publication of C3 and C3b structures. This revealed presence of a novel