Ribosome density mapping

Detecting Ribosomal Association with the 5 Leader of mRNAs by Ribosome Density Mapping (RDM)... 

Arava, Y., Boas, F. E., Brown, P. O., and Herschlag, D. (2005). Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res. 33, 2421-2432. 

Ban et al 7 Courtesy of T. A. Steitz. The peptidyltransferase center is marked by the green image of the transition state inhibitor shown in Fig. 29-13. (F) Model of three tRNAs bound to a ribosome from Thermus thermophilus in the A (a mi noacyl), P (pepti-dyl), and E (exit) sites. These are based on 0.75-nm X-ray data and a number of difference electron density maps. The 3-CCA end of the A-site tRNA is not modeled hut is... 

With the exception of true 3D crystals, which must be sectioned to make them thin enough to study by transmission electron mi-croscopy,the resolutions obtained with biological specimens are generally dictated by the preservation of periodic order, and the symmetry and complexity of the object. Hence, studies of the helical acetylcholine receptor tubes (36), the icosahedral hepatitis B virus capsid (44), the SOS ribosome (45), and the centriole (26) have yielded 3D density maps at resolutions of 4.6, 7.4, 15, and 280 A, respectively. 

Although the locations of many proteins and thousands of nucleotides must still be teased out of the electron density maps, stmctural features of specihc regions of the ribosome have already provided mechanistic clues. A more detailed understanding of the mechanism of protein synthesis will emerge from these stmctural studies. 

On the interface side of the 308 subunit (where it interacts with the 508 subunit), a large region of rRNA is visible which lacks any protein density. This observation supports the theory that a primitive ribosome was composed only of RNA. Localization of the proteins of known stmc-ture revealed that 85 makes close contacts with 84 these were previously known to be near each other based on cross-linking and neutron diffraction data. Mutations in 84 and 85 produce error-prone ribosomes, and in fact these mutations are mapped to the area of contact between the two proteins. It seems likely, therefore, that inaccuracy results from a dismption of this protein-protein interaction. 

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