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How do metal ions direct ribozyme folding?

Nature Chemistry volume 7, pages 793–801 (2015)Cite this article

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Abstract

Ribozymes, which carry out phosphoryl-transfer reactions, often require Mg2+ ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner that is not fully understood. Here we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg2+ concentrations, and are transiently stabilized by the coordination of Mg2+ ions to specific nucleotides. However, competition for scarce Mg2+ and topological constraints that arise from chain connectivity prevent the complete folding of the ribozyme. A much higher Mg2+ concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg2+ is replaced by Ca2+ the ribozyme folds, but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.

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Figure 1: Secondary and tertiary structure of the Azoarcus group I intron studied in this work.
Figure 2: Mg2+ promotes folding and function of the Azoarcus ribozyme.
Figure 3: Mg2+ fingerprints in 50 mM KCl.
Figure 4: Site-specific Mg2+–RNA interactions stabilize principal tertiary structure motifs.
Figure 5: Conformational states of the Azoarcus ribozyme at intermediate-to-high concentrations of divalent ion.

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Acknowledgements

This work was supported by a grant from the National Science Foundation (CHE 13-61946).

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Authors and Affiliations

  1. Institute for Physical Science and Technology, University of Maryland, College Park, 20742, Maryland, USA

    Natalia A. Denesyuk & D. Thirumalai

  2. Department of Chemistry and Biochemistry and Biophysics Program, University of Maryland, College Park, 20742, Maryland, USA

    D. Thirumalai

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Contributions

N.A.D. and D.T. conceived and designed the project, analysed the simulation data and co-wrote the paper. N.A.D. performed the simulations.

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Correspondence to D. Thirumalai.

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Denesyuk, N., Thirumalai, D. How do metal ions direct ribozyme folding?. Nature Chem 7, 793–801 (2015). https://doi.org/10.1038/nchem.2330

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