GAC nucleotides make specific transient contacts with essential ribosome cofactors during translation ( Harms et al. The GAC is also the binding site for the peptide antibiotic thiostrepton ( Blyn et al. In the ribosome, the GAC is bound by the prokaryotic L11 protein (L12 in eukaryotes) L11 binding requires that GAC adopt its tertiary fold ( Blyn et al. 1988 Xing and Draper 1996 Holmberg and Noller 1999 Cameron et al. 1) must adopt an intricate tertiary structure to be functional ( Moazed et al.
The 60 nucleotide (nt) GTPase center RNA (GAC) from 23S rRNA ( Fig. The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.
The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg 2+. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. coli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg 2+, Ca 2+, or Sr 2+ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg 2+ to observe the folding process. To measure how different divalent cations modify folding kinetics of the 60 nucleotide E. Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association).
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