ARPE 19 and ARPE-19/EMP2 cells were plated in 10-cm dishes (Corning, Corning, NY). Cells were washed twice with PBS, lysed (1% Nonidet P-40 containing 10 μg/mL aprotinin, 2 μg/mL pepstatin, 0.1 mM EDTA, 10 mM HEPES, and 10 mM KCl with Complete Mini Protease Inhibitor Cocktail Tablet [Roche Applied Sciences, Mannheim, Germany]) for 30 minutes at 4°C and then sonicated for 15 seconds. Cell lysates were precleared by incubation with Protein A agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA) and then incubated overnight with agarose beads and either anti–FAK polyclonal antibody (Santa Cruz Biotechnology, Santa Cruz, CA) or anti–EMP2 rabbit polyclonal antibody. The beads were washed four times in the lysis solution and twice in 62.5 mM Tris, pH 6.8. Immune complexes were eluted from the beads by boiling in Laemmli sample buffer (62.5 mM Tris-Cl, pH 6.8, 10% glycerol, 2% SDS, 0.01% bromophenol blue, 2% β-mercaptoethanol) for 5 minutes. Samples were analyzed with Western blot analysis. For EMP2 detection, N-linked glycans were cleaved using PNgase (New England Biolabs). Eluates were treated according to the manufacturer’s instructions at 37°C for 2 hours.
The stoichiometry of FAK and EMP2 in coimmunoprecipitation experiments was determined in the following manner. First, titrations of whole cell lysate and cognate immunoprecipitates were quantitated by densitometry. Using these data, we calculated the percentage of each protein (per input cell equivalents) in the cognate immunoprecipitate. Second, the coimmunoprecipitates were similarly analyzed to determine the percentage of each protein captured in the coimmunoprecipitate. Finally, we calculated the ratio of these two values (percentage cognate and percentage coimmunoprecipitate), representing the stoichiometry of the coimmunoprecipitated proteins.