title: Protease substrate specificity mapping using membrane-bound peptides.
abstract: A method is described for assessing the substrate specificity of proteases by screening for proteolytic activity against large numbers of peptides. All 400 possible peptides derived from the 20 common amino acids were synthesized on small membrane disks in the arrangement FTC-spacer-amino acid P1-amino acid P'1-spacer-membrane, where FTC is a chromophoric group. The disks are incubated simultaneously with the protease, resulting in cleavage of the peptide between the P1 and P'1 amino acids, and the absorbance of the released chromophore is measured as a function of time. As demonstrated for chymotrypsin and papain, plots of the resulting data present a perspective view of the amino acid preferences on both sides of the scissile bond. This technique is fast, requires relatively little enzyme, and can be extended to the systematic screening of longer peptides, including analogs with unnatural amino acids. It has potential use for characterizing the specificity of proteases, assessing the results of site-specific mutagenesis, and searching for optimal substrates and inhibitors.
authors.affiliation: Department of Chemistry, Boston University, Massachusetts 02215.
authors.forename: Y
authors.initials: Y
authors.lastname: Duan
authors.forename: R A
authors.initials: RA
authors.lastname: Laursen
mesh_terms: D000595:Amino Acid Sequence; D002918:Chymotrypsin / Q000378:metabolism*; D004151:Dipeptides / Q000138:chemical synthesis / Q000378:metabolism*; D006868:Hydrolysis; D007700:Kinetics; D008565:Membrane Proteins / Q000378:metabolism; D008567:Membranes, Artificial; D008969:Molecular Sequence Data; D010206:Papain / Q000378:metabolism*; D010449:Peptide Mapping / Q000379:methods*; D013379:Substrate Specificity
chemical_list: D004151:Dipeptides; D008565:Membrane Proteins; D008567:Membranes, Artificial; D002918:Chymotrypsin; D010206:Papain