Systems Biology

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Science  22 Aug 2008:
Vol. 321, Issue 5892, pp. 1020
DOI: 10.1126/science.321.5892.1020c

Although evolutionary pressures may alter the spatial and temporal aspects of gene expression and thus dictate whether the proteins encoded by these genes have the opportunity to recognize each other, protein-protein interactions may in fact be mediated through largely independent modular domains. To date, most network mapping studies have been based on the whole protein as the unit. Boxem et al. have begun a long-term project to build interactome maps derived from protein domains. They describe a resource of 800 early-embryogenesis proteins that are present after the first two cell divisions in Caenorhabditis elegans. They systematically fragmented the open reading frames to create a library of yeast two-hybrid fusions; multiple fragments of each protein were generated to minimize the possibility of missing an interaction because the fusion products had not folded properly. Taking the fragment out of its native protein context did not result in promiscuous liaisons but increased the ability to detect interactions, which confirmed those already reported in the literature via other means. New interactions were also identified, and because they tended to connect proteins with similar phenotypes and functional annotations, will probably be functionally relevant. Minimum regions of interaction (defined as the smallest region shared by all interacting fragments) were studied in 200 proteins, and interaction maps within two molecular complexes—the nuclear pore and the centrosome—were assembled. — BJ

Cell 134, 534 (2008).

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