An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide.

A method is described which extends the structural resolution of the usual hydrogen-exchange experiment by quantifying the exchange kinetics from known regions of a protein. In the usual out-exchange experiment with tritium-labeled protein, all exchange events are simultaneously monitored by measuring total protein-bound radioactivity at various specified times. In the present procedure, the protein is adjusted from the out-exchange conditions to pH 2.8 at 8 °C, immediately digested with an acid protease and the digest run on a high pressure column at the same temperature and pH. The specific activities of the individual peptide peaks are then determined. The entire analytical process requires 20 to 30 minutes depending on the position of the peptide in the chromatogram. Since the peptides are fully exposed to solvent during the analysis, this time corresponds to several half-lives of exchange. However, with sufficient isotope in the starting material large amounts of radioactivity remain associated with each peptide fragment allowing accurate analyses. With care, the digestion and separation can be made very reproducible.The procedure was tested on the ribonuclease S system using labeled S-peptide (providing an extension of the observations of Schreier &; Baldwin, 1976). At pH 2.8 and pH 4.2 free S-peptide exchanges at rates which agree quite well with the values predicted by the data of Molday et al. (1972). In complex with S-protein, the S-peptide protons are not all protected to the same extent. For residues 7 through 13, 7 and 8 are more highly protected than 13, while 10 and 11 are essentially unaffected by complex formation. The model based on the X-ray structure determination indicates that all of these residues are part of an α-helical segment in the chain.