Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain

Abstract

The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg 2+-dependent folded states, which we suggest lie along the folding pathway of the RNA. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome.

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles

“…Although we cannot further characterize these compact conformations, we do have some insight into their role in the biology of the GAC. We note that recent measurements ( 39 ) showed that, in the absence of Mg 2 + , GAC RNA has negligible affinity for the L11 protein. In prokaryotes, L11 protein binding to the GAC rRNA in the large ribosomal subunit is necessary for efficient translation.…”

“…All systems were prepared from the available crystal structure of GAC in its folded state (PDB ID: 1HC8 [38], see Figure 2) after removing the bound protein. We notice that a recent RNA-only crystal structure is virtually identical [39]. The system was described using the AMBER force field for nucleic acids [40,41,42], the 4-point optimal-point-charge (OPC) model for water [43], and compatible ion parameters [44,45].…”

Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures

“…Finally, our findings here highlight how protein binding can contribute to RNA structural changes. In a recent study, we showed that proteins partners can help stabilize RNA structure (55). Work by other groups also showed the generality of mechanisms in which proteins help fold RNA.…”

Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations

“…In particular, the experiments suggested that K + favored more extended conformations of GAC, while Mg 2+ favored the folded state. Notably, our systems were constructed with the RNA molecule in its folded conformation, as found in crystal structures [21,45]. Nevertheless, it is interesting to note that none of the solvent conditions that we examined found agreement with neither of the experimental SAXS spectra.…”