Another PDZ scaffold, ZO-1 (zona occludens-1) is involved in the stabilization and barrier function of tight junctions ( Stevenson et al., 1986). In Drosophila, Scrib (scribble), Dlg (discs large), Baz (Bazooka), and Sdt (stardust) are all PDZ scaffolds that regulate epithelial polarity ( Woods and Bryant, 1991 Bilder et al., 2003). The PDZ scaffolds par-3 and par-6 are essential for establishment of asymmetry and proper cleavage in the early embryo of Caenorhabditis elegans ( Kemphues et al., 1988 Watts et al., 1996). The scaffold Bem1 coordinates a feedback loop to generate localized activation of Cdc42 to ensure that budding yeast assembles a single bud ( Johnson et al., 2011). Scaffolds also perform critical roles in cell polarity ( Thompson, 2013). Other scaffolds, such as members of the NHERF (Na +-H + exchanger regulatory factor) family and SNX27 (sorting nexin family member 27), are involved in the stabilization, sorting, recycling, and localization of cell surface receptors ( Shenolikar and Weinman, 2001 Lauffer et al., 2010 Ardura and Friedman, 2011 Romero et al., 2011). Some well-studied examples include MAPK signaling during mating in the budding yeast using the scaffold Ste5p (sterile 5 Printen and Sprague, 1994), neuronal synaptic signaling exploiting PSD-95 (postsynaptic density 95 Sampedro et al., 1981), and photosensory reception in Drosophila signaling using InaD (inactivation no after-potential D Shieh and Zhu, 1996). Additionally, scaffolding proteins and their partners generally show highly specific subcellular localizations. They achieve this by being composed of several protein–protein interaction modules, most notably PDZ (postsynaptic density 95/discs large/zona occludens-1) and SH3 (Src homology 3) domains ( Pawson and Nash, 2003 Good et al., 2011). Scaffolding proteins have critical roles in cellular signaling pathways in which they bring multiple binding partners together to facilitate their concerted interactions and functions. We also wish to encourage more studies on the dynamics of “stable” complexes and to provide a word of caution about how functionally important dynamic associations may be missed in biochemical and proteomic studies. The purpose of this Perspective is to draw attention to this phenomenon and discuss why complexes might show regulated dynamics. We became aware of this issue in our studies of a scaffolding protein in microvilli, which forced us to reevaluate its contribution to their structure. These studies are scattered among different biological systems, and so the concept that scaffolding complexes might not always represent stable entities and that their dynamics can be regulated has not garnered general attention.

Over the past decade, examples of scaffolding complexes long thought to be stable have instead been found to be surprisingly dynamic. Numerous scaffolding proteins are found in nature, many having multiple protein–protein interaction modules. The function of scaffolding proteins is to bring together two or more proteins in a relatively stable configuration, hence their name.

Scaffold protein