Strategy for trapping intermediates in the folding of ribonuclease and for using 1H‐NMR to determine their structures

The major unfolded form of ribonuclease A is known to show well‐populated structural intermediates transiently during folding at 0°–10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H‐nmr after folding is complete. The feasibility of using 1H‐nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7–14 are in the 1H‐form. All eight of these protected peptide protons are H‐bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H‐form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H‐bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3–13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α‐helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.