A native-like intermediate on the ribonuclease A folding pathway. 2. Comparison of its properties to native ribonuclease A.

Abstract

A folded intermediate IN has been detected in the slow refolding reaction of ribonuclease A, US→N, where US is an unfolded species which contains non‐native isomers of X‐Pro peptide bonds and N is the native enzyme. IN has been characterized previously as a structured folding intermediate: it shows a tyrosine absorbance like native ribonuclease, but it still contains at least one non‐native proline peptide bond and its tyrosine fluorescence differs from the native enzyme.Here we have used three probes to characterize further the structure of IN in comparison to native ribonuclease A. (1) The accessibility of the tyrosine hydroxyl groups to ionization has been investigated in IN. (2) The binding of the specific inhibitor cytidine 2′‐phosphate (2′CMP) to IN was measured. (3) The regain of enzymatic activity during folding was monitored to decide whether IN is an enzymatically active intermediate.The results indicate that IN possesses a compact folded structure which shields part of the tyrosine residues from the aqueous environment like native ribonuclease A. The active‐site region of IN has folded to the native conformation. IN binds 2′CMP as well as native ribonuclease A does and it shows enzymatic activity similar to the native enzyme.We conclude that unfolded molecules, which have only proline‐93 in the non‐native trans configuration, can refold to the native‐like intermediate IN before proline isomerization takes place. Proline‐93 is located far away from the active‐site region in an external bend and therefore does not block folding. It isomerizes in the folded molecule to the native cis configuration.