Sequential exoproteolysis is not valid as a structural probe

Beynon, R.J. (2004) Sequential exoproteolysis as a structural probe: a cautionary note. J. Mass. Spec. 39, 188-192. [PUBMED] [PDF]

In a recent paper, Villaneuva et al. (J. Mass Spectrom. 2002; 37: 974) described the use of exoproteases as probes of higher order structure in proteins. Their model assumes that the proteins are attacked sequentially from either the N-terminus or the C-terminus, depending on the type of exoprotease (aminopeptidase or carboxypeptidase) used. The products of this presumed exoproteolysis were then analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The pattern of fragments obtained was mapped on to the primary sequence of the protein, and the exoproteolysis was interpreted as comprising a series of fast and slow phases, the rates of the different phases being directly related to the higher order structure of particular segments of the protein. Here, it is shown that this explanation is unlikely, that both kinetic and practical considerations suggest that alternative explanations for the data should be sought, and that exoproteolysis will perhaps not be as valuable as a conformational probe as the authors suggest.