Chemical Cleavage of Proteins at Aspartyl-X Peptide Bonds

Abstract

Some methods for chemically cleaving proteins, such as those described in Chapters 71 and 72, are fairly specific for a particular residue, show good yields, and generate usefully large peptides (as reaction occurs at relatively rare amino acid residues). There may be cases, however, when such peptides (or indeed, proteins) lacking these rarer residues need to be further fragmented, and in such instances cleavage at the more common aspartyl residue may prove useful. The method described in this chapter (and in ref. 1) for cleavage to the carboxy-(C)-terminal side of aspartyl residues is best limited to smaller polypeptides rather than larger proteins because yields are<100% and somewhat variable according to sequence. Partial cleavage of Asp-X bonds in a larger protein leads to a very complex set of peptides that may be difficult to analyze. Partial hydrolysis of smaller peptides yields correspondingly simpler mixtures. This may even be preferable to complete fragmentation for some purposes, such as peptide sequencing or mass spectrometry whereby the series of overlapping peptides may be used to order the peptides in the protein sequence (as in ref. 2 in which partial cleavage at methionyl-X bonds by CNBr was used).