NHERF ($Na^+/H^+$ exchanger regulatory factor) and E3KARP (NHE3 kinase A regulatory protein) play important roles in membrane targeting, trafficking and sorting of ion channels, transmembrane receptors and signaling proteins in many tissues. Each of these proteins contains two PDZ (PSD-95/Dlg-1/ZO-1) domains, which mediate the assembly of transmembrane and cytosolic proteins into functional signal transduction complexes. The interaction between NHERF and E3KARP was investigated by surface plasmon resonance spectroscopy (BIAcore), fluorescence measurement, His-tagged pull-down experiment, and size-exclusion column (SEC) chromatography. BIAcore experiments revealed that NHERF bound to E3KARP with an apparent $K_D$ of 7 nM. Fluorescence emission spectra of the NHERF-E3KARP complex suggested that the tight interaction between these proteins was accompanied by significant conformational changes in one or both. The CD spectra of NHERF and E3KARP show that the conformational changes of these proteins were dependent on pH and temperature. These results implicate that the NHERF-E3KARP complex allows intracellular signaling complexes to form through PDZ-PDZ interactions.