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• W3117708478 abstract "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 Mg 2+ ions or by interaction with ribosomal proteins. In order to provide a quantitative description of ion-induced folding of the ~350 nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg 2+ concentration between 0−30 mM. The Mg 2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg 2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg 2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg 2+ -dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg 2+ -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." @default.
• W3117708478 created "2021-01-05" @default.
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• W3117708478 date "2020-04-09" @default.
• W3117708478 modified "2023-10-16" @default.
• W3117708478 title "Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA" @default.
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• W3117708478 doi "https://doi.org/10.1101/2020.04.08.032474" @default.
• W3117708478 hasPublicationYear "2020" @default.
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