Endoproteases

Endoproteases are proteolytic enzymes that hydrolyze peptide bonds within polypeptide chains, in contrast to exopeptidases that remove amino acids from chain ends. They act on internal sites and generate smaller fragments, often in regulated biological processes such as digestion, maturation of proteins, and antigen processing. Endoproteases can be broadly classified by their catalytic mechanism into serine proteases, cysteine proteases, aspartic proteases, and metalloproteases, among others.

Serine proteases such as trypsin and chymotrypsin use a catalytic triad of histidine, serine, and aspartate to perform nucleophilic attack on the peptide bond. Cysteine proteases employ a catalytic cysteine, aided by histidine. Aspartic proteases rely on two aspartate residues in the active site. Metalloproteases coordinate a metal ion, usually zinc, to activate a water molecule for hydrolysis. Substrate specificity varies: trypsin cleaves after lysine/arginine; chymotrypsin after aromatic residues; pepsin in acidic environments cleaves mostly hydrophobic residues.

Endoproteases participate in digestion (pancreatic proteases in the gut), protein maturation (zymogen activation), immune functions (antigen processing), and extracellular matrix remodeling (matrix metalloproteinases). They are found in digestive tracts, lysosomes, secreted fluids, and cell interiors, and their activity is tightly regulated by pH, compartmentalization, and endogenous inhibitors.

In research and industry, endoproteases are used for protein sequencing and sample preparation; their specificity is exploited to generate defined peptide fragments. Inhibition or aberrant activity of endoproteases is implicated in diseases such as cancer, inflammation, and neurodegeneration. Common laboratory endoproteases include trypsin, chymotrypsin, pepsin, papain, subtilisin, and TEV protease.