Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

Alain Laederach, Inna Shcherbakova, Magdalena A. Jonikas, Russ B. Altman, Michael D. Brenowitz

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved "Fast Fenton" hydroxyl radical footprinting and exhaustive kinetic modeling. This integrated approach allows us to define the folding landscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its earliest steps with unprecedented accuracy. Distinct parallel pathways leading the RNA to its native form upon its Mg2+-induced folding are observed. The structures of the intermediates populating the pathways are not affected by variation of the concentration and type of background monovalent ions (electrostatic environment) but are altered by a mutation that destabilizes one domain of the ribozyme. Experiments starting from different conformational ensembles but folding under identical conditions show that whereas the electrostatic environment modulates molecular flux through different pathways, the initial conformational ensemble determines the partitioning of the flux. This study showcases a robust approach for the development of kinetic models from collections of local structural probes.

Original languageEnglish (US)
Pages (from-to)7045-7050
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume104
Issue number17
DOIs
StatePublished - Apr 24 2007

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RNA Folding
Static Electricity
Tetrahymena thermophila
RNA
Catalytic RNA
Hydroxyl Radical
Introns
Ions
Mutation

Keywords

  • Assembly
  • Pathway
  • Ribozyme
  • Salt
  • Topology

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. / Laederach, Alain; Shcherbakova, Inna; Jonikas, Magdalena A.; Altman, Russ B.; Brenowitz, Michael D.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 17, 24.04.2007, p. 7045-7050.

Research output: Contribution to journalArticle

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AU - Brenowitz, Michael D.

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