The importance of G center dot A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA

Ben Turner, David M. J. Lilley

    Research output: Contribution to journalArticle

    34 Citations (Scopus)

    Abstract

    The kink turn (K-turn) is a common motif in RNA structure, found in many RNA species important in translation, RNA modification and splicing, and the control of gene expression. In general the K-turn comprises a three nucleotide bulge followed by trans sugar-Hoogsteen G center dot A pairs. The RNA adopts a tightly kinked conformation, and is a common target for binding proteins, exemplified by the L7Ae family. We have measured the rates of association and dissociation for the binding of L7Ae to the Kt-7 kink turn, from which we calculate an affinity of K-D=10 pM. This high affinity is consistent with the role of this binding as the first stage in the assembly of key functional nucleoproteins such as box C/D snoRNP. Kink-turn RNA undergoes a two-state transition between the kinked conformation, and a more extended structure, and folding into the kinked form is induced by divalent metal ions, or by binding of proteins of the L7Ae class. The K-turn provides an excellent, simple model for RNA folding, which can be dissected at the atomic level. We have analyzed the contributions of the hydrogen bonds that form the G-A pairs to the ion- and protein-induced folding of the K-turn. We find that all four hydrogen bonds are important to the stability of the kinked form of the RNA, and we can now define all the important hydrogen bonding interactions that stabilize the K-turn. The high affinity of L7Ae binding is coupled to the induced folding of the K-turn, allowing some sub-optimal variants to adopt the kinked geometry. However, in all such cases the affinity is lowered, and the results underline the importance of both G-A pairs to the stability of the K-turn. (c) 2008 Elsevier Ltd. All rights reserved.

    Original languageEnglish
    Pages (from-to)431-442
    Number of pages12
    JournalJournal of Molecular Biology
    Volume381
    Issue number2
    DOIs
    Publication statusPublished - 2008

    Keywords

    • Archaeal Proteins
    • Archaeoglobus fulgidus
    • Base Sequence
    • Fluorescence Resonance Energy Transfer
    • Humans
    • Hydrogen Bonding
    • Ions
    • Magnesium
    • Metals
    • Models, Biological
    • Molecular Structure
    • Nucleic Acid Conformation
    • Protein Binding
    • Protein Structure, Secondary
    • RNA, Archaeal
    • Ribonucleoproteins, Small Nucleolar

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