endopeptidases

Endopeptidases are proteolytic enzymes that catalyze hydrolysis of peptide bonds within polypeptide chains, thereby cutting proteins at internal sites. This distinguishes them from exopeptidases, which remove amino acids from termini. Endopeptidases play essential roles in digestion, protein maturation, immune response, and activation or inactivation of signaling proteins.

Classification is by catalytic mechanism and site preference. Serine endopeptidases (such as trypsin, chymotrypsin, elastase, and many digestive proteases) use a catalytic triad of serine, histidine, and aspartate. Cysteine endopeptidases (such as papain) employ a catalytic cysteine. Aspartic endopeptidases (such as pepsin) use two aspartate residues. Metalloproteases (including matrix metalloproteases and thermolysin) rely on a metal ion, commonly zinc, in the active site. Substrate specificity reflects the shape and chemistry of the binding pockets; for example, trypsin cleaves after lysine or arginine, chymotrypsin after bulky hydrophobic residues, and elastase after small residues like valine or alanine.

Physiological examples include digestive enzymes such as pepsin in the stomach and pancreatic trypsin and chymotrypsin in the small intestine; thrombin and factor Xa are endopeptidases in the coagulation cascade; some endopeptidases activate prohormones and other zymogens.

Endopeptidases have wide applications in research and industry, including protein sequencing (mass spectrometry), protein digestion for peptide mapping, and various industrial processes. Regulation occurs via inhibitors such as serpins for serine proteases, TIMPs for metalloproteases, pepstatin for aspartic proteases, and E-64 for cysteine proteases.