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Architecture of basic building blocks in protein and domain structural interaction networks

Architecture of basic building blocks in protein and domain structural interaction networks,10.1093/bioinformatics/bti240,Bioinformatics/computer Appl

Architecture of basic building blocks in protein and domain structural interaction networks   (Citations: 13)
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Motivation: The structural interaction of proteins and their domains in networks is one of the most basic molecular mechanisms for biological cells. Topological analysis of such networks can provide an understanding of and solutions for predicting properties of proteins and their evolution in terms of domains. A single paradigm for the analysis of interacti- ons at different layers, such as domain and protein layers, is needed. Results: Applying a colored vertex graph model, we integra- ted two basic interaction layers under a unified model: (1) structural domains, and (2) their protein/complex networks. We identified four basic and distinct elements in the model that explains protein interactions at the domain level. We searched for motifs in the networks to detect their topologi- cal characteristics using a pruning strategy and a hash table for rapid detection. We obtained the following results: First, compared with a random distribution, a substantial part of the protein interactions could be explained by domain-level struc- tural interaction information. Second, there were distinct kinds of protein interaction patterns classified by specific and distin- guishable numbers of domains. The intermolecular domain interaction was the most dominant protein interaction pattern. Third, despite the coverage of the protein interaction informa- tion differing among species, the similarity of their networks indicated shared architectures of protein interaction network in living organisms. Remarkably, there were only a few basic architectures in the model (fewer than ten for a four-node network topology), and we propose that most biological com- binations of domains into proteins and complexes can be explained by a small number of key topological motifs.
Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 21, no. 8, pp. 1479-1486, 2005
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