Dynamic, scaffolded, multi-protein complexes are hallmarks of sophisticated cellular signaling systems. The higher-order architecture of these signaling complexes confers sensitivity, adaptability, control, and crosstalk. Signaling complex architecture is especially notable in the nervous system, where dynamic post-synaptic protein assemblies underlie the molecular origins of learning and memory. Moreover, post-translational modifications within the signaling complexes induce conformational changes to modulate reorganization and retargeting. Understanding the dynamic architecture of these protein assemblies is crucial because disruptions in this system are implicated in neurological disorders such as Parkinson’s disease, autism spectrum disorders, depression, and schizophrenia.