Proteases use water molecules and specific amino acid residues to cleave proteins in a site-specific manner. Living cells use proteases in numerous ways. The first function is protein turnover, where old or damaged proteins are replaced and degraded by proteases. The second function is quality control. Incorrectly translated or folded proteins are marked for degradation by ubiquitin molecules, which signal a protein to enter the proteosome, a large complex containing multiple proteases. The proteases work together to break down unwanted proteins into amino acids. The last function of proteases is post-translational protein processing. Both cells and their invaders, such as viruses, employ this mechanism. The HIV virus, for example, uses an aspartic protease to process proteins that are critical to infection. (Not surprisingly, this protease is a possible drug target.) Blood clotting is another process that involves numerous proteases to process the proteins necessary to halt the escape of blood from the circulatory system.
Currently, there are six known classes of proteases. Serine proteases and threonine proteases use similar mechanisms involving histidine and either serine or threonine, respectively. Cysteine proteases are also similar, but they involve a thiol group instead of a hydroxyl group. Aspartic proteases and glutamic proteases use a completely different mechanism, which involves two acidic residues performing acid-base chemistry with a water molecule to process proteins. The last type of protease, the metalloprotease family, uses metal ions to coordinate the active site where amino acid chains are broken.
Proteases usually cleave an amino acid chain before or after specific residues. Three major serine proteases, trypsin, chymotrypsin and elastase, have different specificities because of differing channels at the protein surfaces leading to the three active sites. Trypsin cleaves proteins after lysine or arginine because its channel is narrow and long. Chymotrypsin contains more of a depression, which can facilitate cleavage after large, bulky, aromatic amino acids such as tryptophan and tyrosine. Elastase has a much smaller depression, which can only hold the smallest nonpolar amino acids such as glycine, valine and alanine.
Without proteases, unwanted proteins would aggregate together and fall out of solution, which is detrimental to cellular health. Also, proteins that require proteolysis during processing would never reach full maturity, which would cause a breakdown in cellular functions.
For researchers performing biochemical experiments involving cellular proteins, proteases can cause serious complications. When a cell is ruptured, proteases are released into the solution along with proteins of interest, and so proper protease inhibitors must be added to experimental protocols to limit their activities.