The proteasome's active sites sit deep within its core, far removed from its regulatory particles, which cap the ends of the proteolytic tunnel. Nonetheless, proteasome inhibitors that bind to the core's active site, such as epoxomicin, make it more likely that the core and regulatory units coprecipitate, suggesting that inhibitors may stabilize the interface between the two despite their distance.
To test this theory, the authors treated purified proteasome constituents with apyrase, which destabilizes and inactivates the proteasome by hydrolyzing its bound ATP and ADP cofactors to AMP. With apyrase alone, the two complexes separated readily. But if the authors also added increasing concentrations of epoxomicin, the proportion of linked and active units increased. “No one had noticed this before,” Finley says. “Only by following both the assembly state and the activity state at the same time can you see this effect.”
It is not yet clear whether the protein substrates normally degraded by the proteasome exert the same linking–activating effect, although Finley expects they will. The group is also not sure how a conformational change in the buried active site alters the binding of core and regulatory particles. Experiments to answer both questions are in progress. But it would make sense that protein substrates prevent subunit dissociation, Finley says, since once degradation of a protein begins, its stabilizing effect on the proteasome will both ensure the job gets finished and prevent harmful intermediaries from lingering in the cell.