Size, shape, and flexibility of RNA structures

Abstract

Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of RNA in the Protein Data Bank we find that the size of the folded RNA structures, measured using the radius of gyration R(G), follows the Flory scaling law, namely, R(G)=5.5N(1/3) A, where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity Delta and the shape S parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of Delta, we find that a large fraction of folded RNA structures are aspherical and the distribution of S values shows that RNA molecules are prolate (S>0). The flexibility of folded structures is characterized by the persistence length l(p). By fitting the distance distribution function P(r), that is computed using the coordinates of the folded RNA, to the wormlike chain model we extracted the persistence length l(p). We find that l(p) approximately 1.5N(0.33) A which might reflect the large separation between the free energies that stabilize secondary and tertiary structures. The dependence of l(p) on N implies that the average length of helices should increase as the size of RNA grows. We also analyze packing in the structures of ribosomes (30S, 50S, and 70S) in terms of R(G), Delta, S, and l(p). The 70S and the 50S subunits are more spherical compared to most RNA molecules. The globularity in 50S is due to the presence of an unusually large number (compared to 30S subunit) of small helices that are stitched together by bulges and loops. Comparison of the shapes of the intact 70S ribosome and the constituent particles suggests that folding of the individual molecules might occur prior to assembly.