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Project Progress

We have described a method to establish chronologies of ancient ribosomal evolution. This method combines the onion approximation^1^ with our previous methods^2-7 of structural analysis of large RNA complexes. We have combined structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion (Figure 1)

Using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation, combined with a shell-by-shell comparison, captures significant information about ribosomal evolution, suggesting that the conformation and interactions of both RNA and protein are changing over evolutionary time. The tendency of macromolecules (protein and RNA) to assume regular secondary structural elements such as A-form helices with Watson–Crick base pairs (RNA) and α-helices and β-sheets (protein) is low at early time points but increases as time progresses. The non-secondary structures of ribosomal protein segments near the PT-origin suggest that they may be molecular fossils of the peptide ancestors of ribosomal proteins. The rRNA in the inner shells suggests that initial formation of the PTC may have involved Mg²⁺-mediated assembly of at least partially single-stranded RNA oligomers or polymers. As one moves from center to periphery, proteins appear to replace magnesium ions.