Neurotransmitter receptors in vivo are linked to intracellular adaptor proteins and signalling molecules driving downstream pathways. Methods for physical isolation are essential to answer fundamental questions about the size, structure and composition of in vivo complexes and complement the widely used yeast 2-hybrid method. The N-methyl-D-aspartate receptor (NMDAR) binds postsynaptic density 95 (PSD-95) protein; both are required for synaptic plasticity and learning and participate in other important pathophysiological functions. Here we describe the development and optimization of novel methods for large-scale isolation of NMDAR±PSD-95 complexes from mouse brain including immunoaf®nity, immunoprecipitation, ligand-af®nity and immobilized PSD-95 binding peptides. Short PDZ binding peptides modelled on NMDAR subunits were shown to isolate NMDAR complexes. Gel ®ltration indicated the native NMDAR±PSD-95 complexes were 2000 kDa, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed a complexity suggesting a huge network of both structural components and signalling enzymes. These methods can be used to de®ne the structure of the complexes at different synapses and in mice carrying gene mutations as well as new tools for drug discovery. Keywords: hebbosome, immunoaf®nity, NMDA receptor, peptide af®nity, postsynaptic density 95, signalling complexes.Large multiprotein complexes linking receptors to intracellular proteins are emerging as a general mechanism for conducting a variety of cellular functions. The synapse also appears to contain a number of important presynaptic and postsynaptic complexes regulating synaptic transmission and synaptic plasticity. At the presynaptic terminal, the traf®cking, docking and exocytosis of synaptic vesicles involves complexes of proteins including snare complexes (reviewed by Catterall 1999). On the postsynaptic side, most neurotransmitter receptors and channels are now known to bind to intracellular proteins that are involved with signal transduction. A neurotransmitter receptor, for which a vast body of pharmacological literature demonstrates its importance in the physiology of stroke, pain and other conditions, is the N-methyl-d-aspartate receptor (NMDAR). Despite the importance of this receptor, there have been no reports of general methods for its physical isolation as a large complex with its associated proteins from intact brain. These methods are essential for characterization of these in vivo complexes and will provide a basis for proteomic characterization, structural studies as well as new approaches to drug screening for agents modifying the pathological conditions involving the NMDAR.The ®rst described NMDAR interacting protein was postsynaptic density 95 (PSD-95) (Kornau et al. 1995), an intracellular protein found in postsynaptic density (PSD) preparations. The physiological role of PSD-95 was revealed by mouse gene targeting experiments where it was shown to regulate the coupling of the NMDAR to downstream pathways that regulate ...