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Multiple native states reveal persistent ruggedness of an RNA folding landscape


According to the ‘thermodynamic hypothesis’, the sequence of a biological macromolecule defines its folded, active (or ‘native’) structure as a global energy minimum in the folding landscape1,2. However, the enormous complexity of folding landscapes of large macromolecules raises the question of whether there is in fact a unique global minimum corresponding to a unique native conformation or whether there are deep local minima corresponding to alternative active conformations3. The folding of many proteins is well described by two-state models, leading to highly simplified representations of protein folding landscapes with a single native conformation4,5. Nevertheless, accumulating experimental evidence suggests a more complex topology of folding landscapes with multiple active conformations that can take seconds or longer to interconvert6,7,8. Here we demonstrate, using single-molecule experiments, that an RNA enzyme folds into multiple distinct native states that interconvert on a timescale much longer than that of catalysis. These data demonstrate that severe ruggedness of RNA folding landscapes extends into conformational space occupied by native conformations.

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Figure 1: Docking and cleavage of the oligonucleotide substrate by the Tetrahymena ribozyme, observed using single-molecule FRET.
Figure 2: Distribution of docking behaviours of individual ribozyme molecules.
Figure 3: Catalytic activities of molecules from different parts of docking distribution are the same.
Figure 4: Interconversion of docking behaviours.

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We thank T. H. Lee, B. Cui, H. Kim, W. Zhao and other current and former members of the Chu laboratory, and the Mabuchi laboratory, for technical assistance. We thank members of the Herschlag laboratory for discussions and comments on the manuscript. Financial support for this work was provided by US National Institutes of Health (NIH) programme project grant P01-GM-66275 and NIH grant GM49243, to D.H. We thank the Stanford Bio-X Program for fellowship support to S.V.S.

Author Contributions All authors contributed to the experimental design and writing of the manuscript. S.V.S. performed the experiments and M.G. and S.V.S. carried out data analysis.

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Correspondence to Daniel Herschlag.

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The authors declare no competing financial interests.

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Solomatin, S., Greenfeld, M., Chu, S. et al. Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature 463, 681–684 (2010).

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