I am trying to sequence amyloid peptides (in this case chaplins/rodlins from streptomyces) by mass spectrometry but this is hampered by lack of trypsin cleavage sites. We have also tried chymotrypsin and elastase .
Try Achromobacter lysyl endopeptidase or Achromobacter protease I (API). The protease is specific for the cleavage of lysyl bonds, including the lysylproline bond. In addition to lysine specificity, the protease has distinctive properties, such as a high peptidase activity, a wide pH optimum, and stability against denaturants. These favorable properties as a lysine-specific protease makes it useful as a tool for peptide fragmentation in protein sequence analysis. API consists of a single chain of 268 amino acid residues and three disulfide bonds. API also holds an extension composed of several amino acid residues at the N terminus and a long extension (about 26 residues) at the C terminus.
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