Protein complexes take the bait.

o appropriate a quote from John Donne, " no protein is an island entire of itself " — or at least, very few proteins are. Most seem to function within complicated cellular pathways, interacting with other proteins either in pairs or as components of larger complexes. A comprehensive understanding of these interactions will be needed before we can appreciate the mechanisms by which cellular pathways function and interlink. On pages 141 and 180 of this issue, Gavin et al. 1 and Ho et al. 2 describe significant advances towards this goal. Each group has characterized hundreds of distinct multiprotein complexes in the budding yeast Saccharomyces cerevisiae, using approaches in which individual proteins are tagged and used to pull down associated proteins, which are then analysed by mass spectrometry. These studies 1,2 exemplify an emerging paradigm in protein biology: the systematic analysis of an organism's complete complement of proteins (its 'proteome'). Protein interactions on a proteome-wide scale have already been analysed in several ways. In a pair of landmark papers, Uetz et al. 3 and Ito et al. 4 adapted the yeast 'two-hybrid' assay — a means of assessing whether two single proteins interact — into a high-throughput method of mapping pair-wise protein interactions on a large scale. The authors collectively identified over 4,000 protein–protein interactions in S. cerevisiae. Our own group 5 has developed a microarray technology in which purified, active proteins from almost the entire yeast proteome are printed onto a microscope slide at high density, such that thousands of protein interactions (and other protein functions) can be assayed simultaneously. Gavin et al. 1 and Ho et al. 2 take a different approach — one that is particularly effective at identifying protein complexes that contain three or more components. Large-scale efforts to characterize protein complexes are generally rate-limited by the need for a nearly pure preparation of each complex. In the new studies 1,2 , protein complexes were purified as follows (Fig. 1). First, the authors attached tags to hundreds of different proteins (to create 'bait' proteins). They then introduced DNA encoding these bait proteins into yeast cells, allowing the modified proteins to be expressed in the cells and to form physiological complexes with other proteins. Then, using the tag, each bait protein was pulled out, often fishing out the entire complex with it (hence the term 'bait'). The proteins extracted with the tagged bait were identified using standard …