Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme

Takeshi Uchida, Qin He, Corie Y. Ralston, Michael D. Brenowitz, Mark R. Chance

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

We have explored the linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of Tetrahymena thermophila ribozyme by examining the Mg2+-induced folding and the urea-induced denaturation of the folded state as a function of Na+ under equilibrium folding conditions using hydroxyl radical footprinting. These studies allowed a thermodynamic examination of eight discrete protection sites within P4-P6 that are involved in several tertiary structure contacts. Monovalent ions compete with Mg2+ ions in mediating P4-P6 folding. The urea denaturation isotherms demonstrated ΔΔG values of > 2 kcal mol-1 in experiments conducted in 10 versus 200 mM NaCl at a constant 10 mM MgCl2. However, the individual-site isotherms reported by footprinting revealed that larger than average changes in ΔG values were localized to specific sites within the Mg2+-rich A-bulge. The competitive effects of monovalent ions were less when K+ rather than Na+ was the monovalent cation present. This result indicates the importance of the specific K+ binding sites that are associated with AA-platform structures to P4-P6 folding and stability. These site-specific footprinting data provide quantitative and site-specific measurements of the ion-linked stability for P4-P6 that are interpreted with respect to crystallographic data.

Original languageEnglish (US)
Pages (from-to)5799-5806
Number of pages8
JournalBiochemistry
Volume41
Issue number18
DOIs
StatePublished - May 7 2002

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Tetrahymena
Catalytic RNA
Ions
Denaturation
Isotherms
Urea
Tetrahymena thermophila
Monovalent Cations
Magnesium Chloride
Thermodynamics
Hydroxyl Radical
Binding Sites
Experiments

ASJC Scopus subject areas

  • Biochemistry

Cite this

Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme. / Uchida, Takeshi; He, Qin; Ralston, Corie Y.; Brenowitz, Michael D.; Chance, Mark R.

In: Biochemistry, Vol. 41, No. 18, 07.05.2002, p. 5799-5806.

Research output: Contribution to journalArticle

Uchida, Takeshi ; He, Qin ; Ralston, Corie Y. ; Brenowitz, Michael D. ; Chance, Mark R. / Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme. In: Biochemistry. 2002 ; Vol. 41, No. 18. pp. 5799-5806.
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