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 rugged, and kinetically trapped, misfolded intermediates are a hallmark of RNA folding reactions. Here, we examine the role of a native loop-receptor interaction 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 folding is more rapid than for the wild-type ribozyme and proceeds in a concerted fashion without the accumulation of long-lived kinetic intermediates. The results demonstrate that a complex interplay between native tertiary interactions, divalent ion concentration, and non-native secondary structure determines the ruggedness of the energy landscape. Furthermore, the results suggest that kinetic folding transitions involving large regions of highly structured RNAs can proceed in a concerted fashion, in the absence of significant stable, preorganized tertiary structure.
Treiber
D K
DK
Department of Molecular Biology and the Skaggs Institute for Chemical Biology MB33, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Williamson
J R
JR
D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D002413:Cations, Divalent / Q000378:metabolism; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008956:Models, Chemical; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013768:Tetrahymena / Q000235:genetics*; D013816:Thermodynamics
D002413:Cations, Divalent; D009843:Oligoribonucleotides; D016337:RNA, Catalytic; D008274:Magnesium