Control of peptide product sizes by the energy-dependent protease ClpAP

Processive proteases can unfold proteins and cleave them into fragments of a characteristic size. The detailed mechanism by which product sizes are controlled is still in question. One possible mechanism for the control of product sizes would be translocation of unfolded polypeptides to the protease active sites in units of defined length. We have investigated the mechanism by which ClpAP, an energy-dependent protease from Escherichia coli, controls the sizes of its peptide products. We show that ClpAP generates peptide products with a distribution of sizes that has a pronounced peak at a peptide length of 6-8 amino acid residues. This product size distribution, which is similar to that observed previously for the proteasome, is robust to perturbations that interfere with translocation or proteolysis. To explain these results, we propose a mechanism in which translocation alternates with proteolysis, allowing peptides of more or less uniform length to be cleaved processively from a translocating substrate. To estimate the rate and energy efficiency of ClpAP-catalyzed measurements of product sizes, we apply information theory to quantify how precisely the product sizes are controlled. This analysis may also prove to be useful in characterizing the mechanisms of other proteases and nucleases, such as the proteasome and Dicer, which control the sizes of their products.