Shape and compactness of the isolated ribosomal 16 S RNA and its complexes with ribosomal proteins

Long range RNA-RNA interactions in the 30 S ribosomal subunit ofE. coli

“…Although studies of isolated ribosomal components are essential, there is no assurance that an isolated protein or RNA molecule has the same structure as in the ribosome, where it interacts with the various macromolecules and cations that make up the biological complex. There is evidence that ribosomal proteins affect the RNA structure (16,17) and are required for the formation of its compact tertiary structure in the ribosome (17,18). Treatments such as unfolding or deproteinizing the ribosome cause large changes in shape and size, as measured by hydrodynamic methods (19).…”

Structure and function of ribosomal RNA

“…The shape of the rRNA within the subunits is beginning to emerge from electron microscopic studies both by negative staining [Knauer et al, 1983 (30S); Oettl et al, 1983 (50S)] and by electron spectroscopic imaging [Korn et al, 1983 (30S)]. Physical techniques have been used to demonstrate that only six proteins need to bind for the 16S RNA to acquire the compactness of a 30S particle (Serdyuk et al, 1983). …”

Computer modeling 16 S ribosomal RNA

“…A decrease in the hypochromicity of 16S RNA during this stepwise reconstitution suggests that there is a decrease in RNA secondary structure despite this compaction. The X-ray scattering profiles indicate that the RNA maintains a similar overall shape under all conditions (Serdyuk, 1983). Inside the assembled 30S particle, 16S rRN A has a radius of gyration of 66 angstroms ) and neutron scattering measurements indicate that the radius of gyration of 16S is 60 to 65 angstroms in the assembled subunit .…”

“…When the all long range crosslinks and relationships are included, DSPACE produces a compacted molecule which resembles the 30S particle, has a longest dimension of -250 angstroms like the 30S particle, and has a radius of gyration (76 angstroms) which is intermediate between that of partially denatured 16S RNA (85 angstroms) and fully folded 16S RNA (66 angstroms) (Serdyuk et al, 1983). It is very gratifying that these physical correspondences were a natural result of the modeling process and not initial modeling assumptions.…”

“…It is well established that the 16S undergoes further compaction upon addition of the ribosomal proteins S4, S7, S8, S15, S16, and S17 (Serdyuk, 1983). As only quantifiable 16S rRNA crosslinks have been used to fold the molecule, the resultant structures may reflect a stage in the assembly process.…”