Sequencing Peptides and Proteins Lacking Free α-Amino Groups

Abstract

Facing a protein with a blocked α-amino group, even the Automatic Sequenator (133, 134) is powerless, thwarted by a Nature unappreciative of the universal importance of amino-terminal step-wise degradation procedures. In general, these recalcitrant materials fall into two groups: those in which the α-amino groups are acylated — usually with an acetyl group — and those in which the terminal amino acid is a pyrrolidone carboxylyl residue, formed by the cyclization of a terminal glutaminyl or glutamyl residue. In addition, there are a few instances of naturally occurring cyclic peptides which also lack free α-amino groups. The frustrations which accrue when working with these substances include difficulties in finding them, since they do not react with ninhydrin or fluorescamine (unless the peptide contains one or more lysyl ε-amino groups), as well as identifying the terminal residues, since all the traditional end group procedures employing FDNB, DNS-Cl, NCO, etc., also are ineffective. In this article some simple methods for finding peptides with blocked α-amino groups are reviewed, as well as some strategies presented for identifying and/or removing terminal blocked residues.