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Type II transmembrane serine proteases are an emerging class of proteo-lytic enzymes involved in tissue homeostasis and a number of human disor-ders such as cancer. To better define the biochemical functions of a subset of these proteases, we compared the enzymatic properties of matriptase, matriptase-2, hepsin and DESC1 using a series of internally quenched fluorogenic peptide substrates containingo-aminobenzoyl and 3-nitro-tyro-sine. | ỊFEBS Journal Probing the substrate specificities of matriptase matriptase-2 hepsin and DESC1 with internally quenched fluorescent peptides Francois Beliveau Antoine Desilets and Richard Leduc Department of Pharmacology Universite de Sherbrooke Canada Keywords DESC1 enzyme kinetics hepsin internally quenched fluorogenic peptides matriptase Correspondence R. Leduc Department of Pharmacology Faculty of Medicine and Health Sciences Universite de Sherbrooke Sherbrooke Quebec J1H 5N4 Canada Fax 1 819 564 5400 Tel 1 819 564 5413 E-mail Richard.Leduc@USherbrooke.ca Received 28 November 2008 revised 3 February 2009 accepted 5 February 2009 doi 10.1111 j.1742-4658.2009.06950.x Type II transmembrane serine proteases are an emerging class of proteolytic enzymes involved in tissue homeostasis and a number of human disorders such as cancer. To better define the biochemical functions of a subset of these proteases we compared the enzymatic properties of matriptase matriptase-2 hepsin and DESC1 using a series of internally quenched fluorogenic peptide substrates containing o-aminobenzoyl and 3-nitro-tyro-sine. We based the sequence of the peptides on the P4 to P4 activation sequence of matriptase RQAR-VVGG . Positions P4 P3 P2 and PT were substituted with nonpolar Ala Leu aromatic Tyr acid Glu and basic Arg amino acids whereas P1 was fixed to Arg. Of the four type II transmembrane serine proteases studied matriptase-2 was the most promiscuous and matriptase was the most discriminating with a distinct specificity for Arg residues at P4 P3 and P2. DESC1 had a preference similar to that of matriptase but with a propensity for small nonpolar amino acids Ala at PT. Hepsin shared similarities with matriptase and DESC1 but was markedly more permissive at P2. Matriptase-2 manifested broader specificities as well as substrate inhibition for selective internally quenched fluorescent substrates. Lastly we found that antithrombin III has robust inhibitory properties toward matriptase .