Calcium/calmodulin-dependent protein kinase II (CaMKII), a major component of the postsynaptic density (PSD) of excitatory synapses, plays a key role in the regulation of synaptic function in the mammalian brain. Although many postsynaptic substrates for CaMKII have been characterized in vitro, relatively little is known about their phosphorylation in vivo. By tagging synaptic proteins with a peptide substrate specific for CaMKII and expressing them in cultured neurons, we have visualized substrate phosphorylation by CaMKII at intact synapses. All substrates tested were strongly phosphorylated by CaMKII in HEK293 cells. However, activity-dependent phosphorylation of substrates at synapses was highly selective in that the glutamate receptor subunits NR2B and GluR1 were poorly phosphorylated whereas PSD-95 and Stargazin, proteins implicated in the scaffolding and trafficking of AMPA receptors, were robustly phosphorylated. Phosphatase activity limited phosphorylation of Stargazin but not NR2B and GluR1. These results suggest that the unique molecular architecture of the PSD results in highly selective substrate discrimination by CaMKII.Calcium-calmodulin-dependent protein kinase II (CaMKII) 2 is a major effecter for calcium-dependent signaling in neurons. It has been implicated in dendritic filapodial extension (1), presynaptic plasticity (2), retrograde signaling to the presynaptic terminal (3), and most notably, the phenomenon of long-term potentiation (LTP) (4, 5), the leading model for a synaptic mechanism underlying learning and memory (6). Although several candidates have been proposed to mediate the synaptic consequences of activating CaMKII (7), it has been difficult to characterize how synaptic proteins are phosphorylated by CaMKII when incorporated into functioning synapses. This is a particularly important and challenging issue because biochemical and proteomic approaches to identifying CaMKII substrates in the postsynaptic density (PSD), the electron dense postsynaptic specialization that contains glutamate receptors and associated signaling machinery, have found at least 28 potential substrate proteins (8). Furthermore, it is unknown whether stimulus-dependent substrate specificity is an inherent property of the PSD and whether the source of the calcium that activates CaMKII and protein phosphatase activity influence synaptic substrate phosphorylation.Some recent evidence suggests that the intricate scaffolding of proteins within different levels of the PSD may influence CaMKII signal transduction. First, electron microscopy studies on isolated PSDs have revealed both a laminar and heterogeneous distribution of CaMKII on the cytosolic face, suggesting that CaMKII may be specifically positioned to exert its activity on nanodomains within this macromolecular complex (9). Second, CaMKII interactions with the NMDA receptor (NMDAR) subunit NR2B (10) and the Drosophila homolog of CASK, Cmg (11), a member of the MAGUK family of synaptic scaffolding proteins (12), have both been found to influence its state o...