Schematic showing the range of protein interactions that occur in different physiological environments, together with examples of the complementary techniques that can be use to investigate binary protein interactions in each location. While conventional yeast two hybrid (Y2H) methods can be used to investigate many forms of intracellular interactions (1–3), analysis of interactions involving transmembrane or extracellular proteins requires different experimental strategies. In particular, the split ubiquitin system (Split-UBQ) is proving to be a versatile and reliable method of investigating interactions between integral membrane proteins within the same membrane (5) or between the intracellular domains of transmembrane proteins and cytoplasmic proteins (4). In contrast, the AVEXIS and DSCAM assay systems provide important new tools to investigate large numbers of extracellular protein interactions (6–8). Therefore, the combination of these technologies will facilitate the construction of more comprehensive protein interaction networks which link intracellular and extracellular processes.
