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Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg²⁺ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg²⁺concentration between 0 and 30 mM. The Mg²⁺dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg²⁺concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg²⁺ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg²⁺-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg²⁺-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.