Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme

Inna Shcherbakova, Sayan Gupta, Mark R. Chance, Michael D. Brenowitz

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

The time-course of monovalent cation-induced folding of the L-21 Sca1 Tetrahymena thermophila ribozyme and a selected mutant was quantitatively followed using synchrotron X-ray (·OH) footprinting. Initiating folding by increasing the concentration of either Na + or K + to 1.5 M from an initial condition of ∼0.008 M Na + at 42°C resulted in the complete formation of tertiary contacts within the P5abc subdomain and between the peripheral helices within the dead time of our measurements (k>50 s -1). These results contrast with folding rates of 2-0.2 s -1 previously observed for formation of these contacts in 10 mM Mg 2+ from the same initial condition. Thus, the initial formation of native tertiary contacts is inhibited by divalent but not monovalent cations. The native contacts within the catalytic core form without a detectable burst phase at rates of 0.4-1.0 s -1 in a manner reminiscent of the Mg 2+-dependent folding behavior, although tenfold faster. The tertiary interactions stabilizing the catalytic core interaction with P4-P6 and P2.1, as well as one of the protections internal for the P4-P6 domain, display progress curves with appreciable burst amplitudes and a phase comparable in rate to that of the catalytic core. That the slow folding of the ribozyme's core is a consequence of the alt-P3 secondary structure is shown by the 100% burst phase amplitudes that are observed for folding of the U273A mutant ribozyme within which the native secondary structure (P3) is strengthened. Thus, formation of a misfolded intermediate(s) resulting from the alt-P3 secondary structure is independent of ion valency while the rate at which the respective intermediates are resolved is sensitive to ion valency. The overall portrait painted by these results is that ion valency differentially affects steps in the folding process and that folding in monovalent ion alone for the U273A mutant Tetrahymena ribozyme is fast and direct.

Original languageEnglish (US)
Pages (from-to)1431-1442
Number of pages12
JournalJournal of Molecular Biology
Volume342
Issue number5
DOIs
StatePublished - Oct 1 2004

Fingerprint

Tetrahymena thermophila
Catalytic RNA
Ions
Monovalent Cations
Catalytic Domain
Tetrahymena
Synchrotrons
X-Rays

Keywords

  • ions
  • monovalent
  • ribozyme
  • RNA folding
  • Tetrahymena

ASJC Scopus subject areas

  • Virology

Cite this

Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. / Shcherbakova, Inna; Gupta, Sayan; Chance, Mark R.; Brenowitz, Michael D.

In: Journal of Molecular Biology, Vol. 342, No. 5, 01.10.2004, p. 1431-1442.

Research output: Contribution to journalArticle

Shcherbakova, Inna ; Gupta, Sayan ; Chance, Mark R. ; Brenowitz, Michael D. / Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. In: Journal of Molecular Biology. 2004 ; Vol. 342, No. 5. pp. 1431-1442.
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