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 and long-lived misfolded states are common. To obtain a comprehensive description of the folding landscape for a structured RNA, it is necessary to understand the connections between productive folding pathways and pathways to these misfolded states. The Tetrahymena group I ribozyme partitions between folding to the native state and to a long-lived misfolded conformation. Here, we show that the observed rate constant for commitment to fold to the native or misfolded states is 1.9 min(-1) (37 degrees C, 10 mM Mg(2+)), the same within error as the rate constant for overall folding to the native state. Thus, the commitment to alternative folding pathways is made late in the folding process, concomitant with or after the rate-limiting step for overall folding. The ribozyme forms much of its tertiary structure significantly faster than it reaches this commitment point and the tertiary structure is expected to be stable, suggesting that the commitment to fold along pathways to the native or misfolded states is made from a partially structured intermediate. These results allow the misfolded conformation to be incorporated into a folding framework that reconciles previous data and gives quantitative information about the energetic topology of the folding landscape for this RNA.
Russell
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Department of Biochemistry, Stanford University, Stanford, CA 94305-5307, USA.
Herschlag
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D000818:Animals; D001483:Base Sequence; D007438:Introns / Q000235:genetics; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016053:RNA, Protozoan / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013696:Temperature; D013768:Tetrahymena / Q000201:enzymology / Q000235:genetics*
D016337:RNA, Catalytic; D016053:RNA, Protozoan; D008274:Magnesium