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 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.
Highlights
Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs and a number of proteins
As a prelude toward undertaking computational studies in the early events in the assembly of the 30S particle, here we report our investigations of the Mg2+-induced folding of the central domain of the 16S ribosomal RNAs (rRNAs) using an accurate simulation model
From equilibrium simulations of the rRNA fragment at various Mg2+ ion concentrations, we calculated the average radius of gyration (Rg) as a function of [Mg2+] (Fig. 2A). rRNA undergoes an apparent two-state folding transition, as indicated by the order parameter Rg, as Mg2+ concentration increases from 0 to 30 mM
Summary
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. To solve the assembly problem, many elegant experiments have been systematically performed initially by investigating how the various domains of the rRNA fold and subsequently by the effect of ribosomal proteins in reshaping the assembly landscape Along the way it has been pointed out [10] that some of the principles of ribozyme folding might form a useful framework for producing a quantitative theoretical model for ribosome assembly. Previous simulation studies, focusing on the nuances of the protein-induced structural transitions in the 5 domain [14,15,16], have been most insightful, especially when combined with experiments [16] These studies showed that S4-guided assembly results in the 5 domain reaching the folded state by navigating through multiple metastable states, revealing the rugged nature of the folding landscape of RNA [17, 18]. In the central domain of the small subunit, in vitro studies have shown that a three-way junction (3WJ) (Fig. 1) is in dynamic equilibrium between an open and a closed conformation, whose
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