Unlike phosphorylation and ubiquitinylation, which are reversible, the activation or inactivation of protein function by proteolytic cleavage is an irreversible mechanism for regulating protein activity. For example, many polypeptide hormones, such as insulin, are synthesized as longer precursors, and prior to secretion from cells some of their peptide bonds must be hydrolyzed for them to fold properly. In some cases, a single long precursor prohormone polypeptide is cleaved into several distinct active hormones. To prevent the pancreatic serine proteases from inappropriately digesting proteins before they reach the small intestine, they are synthesized as zymogens, inactive precursor enzymes. Cleavage of a peptide bond near the N-terminus of trypsinogen (the zymogen of trypsin) by a highly specific protease in the small intestine generates a new N-terminal residue (Ile-16), whose amino group can form an ionic bond with the carboxylic acid side chain of an internal aspartic acid. This binding causes a conformational change that opens the substrate-binding site, activating the enzyme. The active trypsin can then activate trypsinogen, chymotrypsinogen, and other zymogens. Similar but more elaborate protease cascades (with one protease activating inactive precursors of others) that can amplify an initial signal play important roles in several systems, such as the blood-clotting cascade and the complement system (see Chapter 23). The importance of carefully regulating such systems is clear—inappropriate clotting, for example, could fatally clog the circulatory system, while insufficient clotting could lead to uncontrolled bleeding.
An unusual and rare type of proteolytic processing, termed protein self-splicing, takes place in bacteria and some eukaryotes. This process is analogous to editing film: an internal segment of a polypeptide is removed and the ends of the polypeptide are rejoined (ligated). Unlike other forms of proteolytic processing, protein self-splicing is an autocatalytic process, which proceeds by itself without the participation of other enzymes. The excised peptide appears to eliminate itself from the protein by a mechanism similar to that used in the processing of some RNA molecules (see Chapter 10). In vertebrate cells, the processing of some proteins includes self-cleavage, but the subsequent ligation step is absent. One such protein is Hedgehog, a membrane-bound signaling molecule that is critical to a number of developmental processes (see Chapter 16).