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The past two decades have seen an immense increase in our appreciation of the vast range of signalling processes and supporting machinery that occur in cells. Pivotal to this is the notion of signal compartmentalization (compartmentation). Targeting by protein domains is critical in allowing signalling complexes to be assembled at defined intracellular locales so as to confer correct function. This issue of the BJP contains two intriguing articles that address functional protein–protein interactions involving PDZ domains [Post-synaptic density protein-95 (PSD95), Drosophila disc large tumour suppressor (DlgA) and Zonula occludens-1 protein (zo-1)] and their implications for signalling. One involves targeting of neuronal nitric oxide synthase to the N-methyl D-aspartic acid (NMDA) receptor via the PDZ-containing signal scaffold, PSD95. The other involves controlling multiple receptor inputs into regulation of epithelial Na+K+-ATPase through the PDZ-containing signal scaffold Pals-associated tight junction. Highlighted is not only the use of dominant-negative strategies to identify the importance of targeting at specific types of PDZ domains but also the exciting notion that small molecule disruptors of interaction at specific PDZ domains can be generated for potential therapeutic application.