Identification of Gal4 activation domain-binding proteins in the 26S proteasome by periodate-triggered cross-linking

A common occurrence in biology is that a regulatory peptide, protein, or small molecule regulates the activity of a large multi-protein complex through direct interactions with a protein(s) in that complex. To characterize the direct receptor of the regulatory molecule, one would ideally like to study the native system. We report here that periodate-triggered cross-linking of catechol-containing regulatory factors, followed by two-dimensional electrophoresis and Western blotting, is an effective method for the characterization of regulatory factor--protein interactions in the context of large multi-protein complexes. We demonstrate the utility of this methodology by identifying the Rpt6/Sug1 and Rpt4/Sug2 proteins as the direct targets of transcriptional activation domains in the 26S proteasome.