Mutual Arrangement Of Ribosomal Rna And Proteins Quaternary Structure

8.1. Peripheral Localization of Proteins on RNA Core

In contrast to the RNA present in viral nucleoproteins, the RNA of ribosomal particles is not entirely covered by a protein envelope. As was demonstrated many years ago, extended regions of rRNA in the ribosome are exposed to the environment and are open to the action of various agents, e.g. nucleases. This fundamental difference compared to viral particles is understandable, since the ribosome is a functional structure, where RNA should actively participate in interactions with external factors and is not used for storing genetic information.

At the same time, protein and rRNA are not just "scrambled" in the ribosome. The high-molecular-mass rRNA of each ribosomal subunit is self-folded into a compact structure with a unique shape (see Section 6.4.3), and it appears that proteins do not associate with the "inside" of this structure. Hence, ribosomal proteins are positioned mainly on the compactly folded high-molecular-mass rRNA. This implies that proteins occupy a preferentially outside position on the rRNA core.

This principle of ribosomal organization was first deduced from experiments conducted to measure the radii of gyration (Rg) of ribosomal subunits. The radius of gyration measured by the diffuse small-angle X-ray scattering was found to be markedly lower than expected on the basis of the size of the subunit assuming that it was a uniformly dense body (Serdyuk et al., 1970). It followed from this observation that a more electron-dense component of the particle (e.g., rRNA) lay nearer the center of gravity of the particle, while a less dense component (e.g., protein) tended to be closer to the periphery. Furthermore, measurements of the radii of gyration of ribosomal subunits using different types of radiation, e.g. X-rays, neutrons, and light, demonstrated that the greater the contribution to the total scattering by the protein component compared to RNA (the relative scattering capacity of the protein increases in the series from X-rays to neutrons to light), the greater the value of the particle's radius of gyration (Serdyuk & Grenader, 1975). Finally, neutron-scattering experiments in solvents with a different scattering capacity for neutrons, i.e. with different proportions of H2O and D2O, allowed for direct measurement of the radii of gyration of either the rRNA or the protein components in situ (Stuhrmann et al., 1976). The basis is that H2O and D2O are known to differ greatly in their scattering capacity for neutrons, while the scattering capacities of biological macromolecules are intermediate between those of H2O and D2O. Because of this, a proportion between

H2O and D2O in the medium can be Figure 8.1. Dependence of the radii of gyration of the E. coli 50S selected when the scattering values of ribosomal particles measured by neutron scattering at different a given macromolecule, either protein contrasts on the relative contribution of the protein component into the or RNA, and the solvent are equal, i.e. scattering (I.N. Serdyuk, A.K. Grenader & G. Zaccai, J. Mol. Biol. 135,

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