Structural similarity of E. coli 5S rRNA in solution and within the ribosome

Abstract

The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of DT, tauR, and Rg predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.

Eukaryotic 5S rRNA biogenesis

“…Several structural domains of 5S rRNA have been crystallized32 and X‐ray scattering studies in solution have determined that free 5S rRNA is elongated in the absence of bound proteins but becomes more compact when it is in the ribosome33,34 (Figure 4). NMR studies performed on Xenopus laevis 5S rRNA have also shown that while loop E is fully folded in the absence of protein (approximating an A‐formed helix), the junction of helix V and loop A is conformationally heterogenous in the free molecule 1.…”

Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA

“…On the other hand, a bead-and-spring model of 5S rRNA of E. Coli (PDB code IC2X:C) was built according to the structure sketched in Fig. 1 b [ 20 ]. Again, after equilibrating the initial conformation, BD simulations with and without HI were performed.…”

“…a Sketch of the secondary structure of yeast tRNA phe [ 45 ] (note the presence of four helices, three loops and a hinge). b Sketch of the secondary structure of the 5S rRNA [ 20 ] (note the presence of five double helices, four loops, and a hinge). In each case nucleotides are the black points, double helices are the regions with connections between opposite nucleotides and loops are the “circular” regions without connections between opposite nucleotides …”

“…Ribosomal RNAs are structurally quite more complex than tRNAs. For example, the secondary structure of the majority of the 5S rRNAs has five double helices, two hairpin loops, two internal loops, and a hinge region organized into three big domains ( α , β , and γ ) [ 18 – 20 ] as sketched in Fig. 1 b .…”

“…1 b . Combining results from dilute solution experiments with numerical calculations, some models for the tertiary structure of 5S rRNA have been proposed [ 19 , 20 ].…”