Computer modeling 16 S ribosomal RNA

A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. fitting the RNA to a 3D electron microscopic map at 20 Å 1 1Edited by D. E. Drapper

“…The available data sets include determinations of the spatial distribution of the ribosomal proteins by neutron scattering or immuno-electron microscopy (IEM), analyses of contacts or neighbourhoods between ribosomal proteins and rRNA by cross-linking and foot-printing techniques, analyses of neighbourhoods within or between the rRNA molecules by intra or interrRNA cross-linking, and studies on the location of the rRNA relative to functional ligands such as mRNA and tRNA, again with the help of crosslinking and foot-printing methods (for reviews, see Brimacombe, 1995;Noller et al, 1995). A number of research groups (Expert-Bezanc Ëon & Wollenzien, 1985;Brimacombe et al, 1988;Nagano et al, 1988;Stern et al, 1988;Mitchell et al, 1990;Hubbard & Hearst, 1991;Malhotra & Harvey, 1994;Fink et al, 1996) have made use of these types of data to fold the well-established secondary structures of the 16 S and 23 S rRNA molecules into three dimensions. The resulting 3D models are essentially``cartoon'' structures of the ribosomal subunits, in which the various helical elements of the rRNA have been manoeuvred relative to the ribosomal proteins so as to satisfy as many of the topographical constraints as possible.…”

Three-dimensional Reconstruction of theEscherichia coli30 S Ribosomal Subunit in Ice

“…Since then a considerable amount of work has gone into correlating the cross linking data of RNA-RNA, RNA-protein and protein-protein interactions, neutron scattering and immunoelectron microscopy (Stö ffler-Meilicke & Stö ffler, 1990). Detailed models were built to accommodate the 16 S rRNA within the consensus envelope, and the positions of the 21 different proteins were assigned within the constrained space (Stern et al, 1988;Brimacombe et al, 1988;Hubbard & Hearst, 1991). More recently, a consensus model of 16 S rRNA has been derived by computer modelling (Malhotra & Harvey, 1994) using the 30 S subunit map of Verschoor et al (1984) as a reference envelope.…”

The Structure of Ribosomal RNA: A Three‐Dimensional Jigsaw Puzzle

“…3 [22, 581 were determined with variable precision, in some cases to the exact nucleotide but in others only to within two to five nucleotides; the reader should refer to the original literature for the details of any particular cross-link (or foot-print [4]) site analysis. As another example, the intra-RNA cross-links reported by Wollenzien et al [64], which form the basis for the 16s RNA models of [l] and [5], were localized by electron microscopic measurements on the cross-linked RNA, a method which is only accurate to about k 2 0 nucleotides; in view of this level of uncertainty, as well as the fact (which has been previously discussed in detail [65]) that the cross-links were obtained with isolated 16s RNA rather than complete 30s subunits as substrate, these data are not included in Fig. 3. 23s RNA.…”