I came across the NS3 serine protease of HCV (DOI 10.1021/bi980313v). Can you please explain:
(1) Where does the inhibitor peptide product bind, at or remains in the main catalytic site where it was cleaved, and then does the inhibition?
(2) Any examples of proteases whereby the peptide product remains near the site and inhibits the enzyme directly?
(3) How does the inhibition occur... hydroxyls etc?
The technical term for this is product inhibition. It is caused by the enzyme binding to one or both of the products, in competition with the substrate. Here are a few examples:
Article Product Inhibition of the Hepatitis C Virus NS3 Protease
Article Product Inhibition in Native-State Proteolysis
Article The many faces of protease–protein inhibitor Interaction
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