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.

核糖体的小亚基和大亚基，即合成蛋白质的分子机器，都是核糖体 RNA (rRNA) 和许多蛋白质的复合物。在细菌中，小亚基具有单个 16S rRNA，其折叠是其组装的第一步。16S rRNA 的中央结构域独立折叠，由 Mg ²⁺离子或与核糖体蛋白的相互作用驱动。为了提供~350 个核苷酸的 rRNA 的离子诱导折叠的定量描述，我们进行了广泛的粗粒度分子模拟，Mg ²⁺浓度介于 0 和 30 mM 之间。回转半径的 Mg ²⁺依赖性表明 rRNA 整体上协同折叠。令人惊讶的是，各种结构元素在不同的 Mg ²⁺浓度，表明即使在 rRNA 的单个域内也存在异质组装。Mg ²⁺离子的结合是高度特异性的，连续的离子凝聚导致三级结构的成核。我们还预测了 Mg ²⁺依赖性保护因子，可在羟基自由基足迹实验中测量，这证实了 Mg ²⁺诱导折叠的特异性。模拟与关于三路连接折叠的几个实验在数量上一致，表明其折叠之前在中心连接中形成了其他三级接触。我们的工作为模拟核糖体小亚基组装的早期事件提供了一个起点。