Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction

The free energy landscape for the folding of large, multidomain RNAs is rug ged, and kinetically trapped, misfolded intermediates are a hallmark of RNA folding reactions. Here, we examine the role of a native loop-receptor int eraction in determining the ruggedness of the energy landscape for folding of the Tetrahymena ribozyme. We demonstrate a progressive smoothing of the energy landscape for ribozyme folding as the strength of the loop-receptor interaction is reduced. Remarkably, with the most severe mutation, global f olding is more rapid than for the wildtype ribozyme and proceeds in a conce rted fashion without the accumulation of long-lived kinetic intermediates. The results demonstrate that a complex interplay between native tertiary in teractions, divalent ion concentration, and Iron-native secondary structure determines the rugged ness of the energy landscape. Furthermore, the resul ts suggest that kinetic folding transitions involving large regions of high ly structured RNAs can proceed in a concerted fashion, in the absence of si gnificant stable, preorganized tertiary structure. (C) 2001 Academic Press.