Characterization of the unfolding of ribonuclease A by a pulsed hydrogen exchange study: evidence for competing pathways for unfolding

Abstract

The unfolding of ribonuclease A was studied in 5.2 M guanidine hydrochloride at pH 8 and 10°C using multiple optical probes, native-state hydrogen exchange (HX), and pulse labeling by hydrogen exchange. First, native-state HX studies were used to demonstrate that the protein exists in two slowly interconverting forms under equilibrium native conditions: a predominant exchange-incompetent N form and an alternative ensemble of conformations, N^∗_I, in which some amide hydrogens are fully exposed to exchange. Pulsed HX studies indicated that, during unfolding, the rates of exposure to exchange with solvent protons were similar for all backbone NH probe protons. It is shown that two parallel routes of unfolding are available to the predominant N conformation as soon as it encounters strong unfolding conditions. A fraction of molecules appears to rapidly form N^∗_I on one route. On the other route an exchange-incompetent intermediate state ensemble, I²_U, is formed. The kinetics of unfolding measured by far-UV circular dichroism (CD) were faster than those measured by near-UV CD and intrinsic tyrosine fluorescence of the protein. The logarithms of the rate constants of the unfolding reaction measured by all three optical probes also showed a nonlinear dependence on GdnHCl concentration. All of the data suggest that N^∗_I and I²_U are nativelike in their secondary and tertiary structures. While N^∗_I unfolds directly to the fully exchange-competent unfolded state (U), I_U² forms another intermediate I_U³ which then unfolds to U. I_U³ is devoid of all native α-helical secondary structure and has only 30% of the tertiary interactions still intact. Since the rates of global unfolding measured by near-UV CD and fluorescence agree well with the rates of exposure determined for all of the backbone NH probe protons, it appears that the rate-limiting step for the unfolding of RNase A is the dissolution of the entire native tertiary structure and penetration of water into the hydrophobic core.