Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway

Large, structured RNAs traverse folding landscapes in which intermediates a nd long-lived misfolded states are common. To obtain a comprehensive descri ption of the folding landscape for a structured RNA, it is necessary to und erstand the connections between productive folding pathways and pathways to these misfolded states. The Tetrahymena group I ribozyme partitions betwee n folding to the native state and to a long-lived misfolded conformation. H ere, we show that the observed rate constant for commitment to fold to the native or misfolded states is 1.9 min(-1) (37 degreesC, 10 mM Mg2+), the sa me within error as the rate constant for overall folding to the native stat e. Thus, the commitment to alternative folding pathways is made late in the folding process, concomitant with or after the rate-limiting step for over all folding. The ribozyme forms much of its tertiary structure significantl y faster than it reaches this commitment point and the tertiary structure i s expected to be stable, suggesting that the commitment to fold along pathw ays to the native or misfolded states is made from a partially structured i ntermediate. These results allow the misfolded conformation to be incorpora ted into a folding framework that reconciles previous data and gives quanti tative information about the energetic topology of the folding landscape fo r this RNA. (C) 2001 Academic Press.