The PSD-95/SAP90 family of PDZ-containing proteins is directly involve
d in the clustering of specific ion channels at synapses. We report th
at channel clustering depends on a conserved N-terminal domain of PSD-
95 that mediates multimerization and disulfide linkage of PSD-95 proto
mers. This N-terminal multimerization domain confers channel clusterin
g activity on a single PDZ domain. Thus, channel clustering depends on
aggregation of PDZ domains achieved by head-to-head multimerization o
f PSD-95, rather than by concatenation of PDZ domains in PSD-95 monome
rs. This mechanism predicts that PSD-95 can organize heterogeneous mem
brane protein clusters via differential binding specificities of its t
hree PDZ domains. PSD-95 and its relative chapsyn-110 exist as disulfi
de-linked complexes in rat brain, consistent with head-to-head multime
rization of these proteins in vivo.