The ribosome is a well-known target for antibiotics, genetic diseases, and anti-cancer drugs, but its actual mechanism of action is not yet understood in detail. The availability of a number of structures of the ribosome in different states now presents an important opportunity to achieve the overall goals to unravel the steps involved in the translocation of the tRNAs and mRNA, protein elongation, and the assembly of the 30S subunit protein components onto the 16S RNA scaffold. The project is built upon previous successes in 1) experimental foot printing experiments for identifying intermediates in the assembly process and 2) computing the important large domain motions of proteins and RNAs by coarse-graining the structures, represented as an elastic network, revealing the structural motions through normal mode analysis. Thus it becomes feasible to compute the motions of the entire ribosome structure, yielding information about how the various components engage together or in opposition, as well as visualizing the motions. By adopting a mixed coarse-grained approach, the large domain motions and at the same time the intricate atomic details at binding sites, active sites, and hinges are revealed within the structure. Validation of the predicted changes in conformation and suggested mechanisms of function will come from experimental data such as FRET and single molecule experiments. For the 30S ribosomal subunit assembly, molecular models will be developed for assembly intermediates by utilizing these robust computations to generate structures consistent with new modification experiments indicating conformational changes. This innovative coordination of experiments and computations will enhance the utility of both groups of studies. Extensive simulations of the structural dynamics of the ribosome, combined with the various known structural, biochemical, and sequence conservation data are expected to yield important new molecular details of how this ribonucleo-protein machine functions, opening prospects for new therapeutic approaches.
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