The enzyme trypsin is a serine protease. It uses serine residue at the active site to hydrolyze peptide bonds in the target protein. Chymosin of the cattle is an aspartic protease. It also uses aspartic residues at the active site to hydrolyze the target protein. Serine and aspartic acid are closely similar with only OH group in serine replaced with COOH in aspartic acid. Based on this, will trypsin inhibitor be able to cross-inhibit chymsoin?
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It is unlikely. Inhibition of trypsin by trypsin inhibitory proteins involves protein-protein recognition, not just recognition of the active site nucleophilic serine residue. Inhibition of serine proteases such as trypsin by chemical serine protease inhibitors, such as PMSF, involves chemistry that is different between serine and aspartate site residues.
PMSF was shown not to inhibit chymosin from Rhizopus microsporus:
https://www.brenda-enzymes.org/literature.php?e=3.4.23.4&r=731169
The difference between aspartate (acid) and serine (alcohol) side chain chemistries is actually very substantial.
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