Structure and Dynamics of Ribonucleic Acids

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The ribosome is a small particle composed of molecules of proteins and ribonucleic acid which is responsible for the synthesis of proteins in the cell. A wide variety of experimental methods are providing information on the structure of this particle. Dr. Harvey is developing computer modeling methods for integrating that information into models for the ribosome and for other ribonucleoprotein complexes. The procedures are capable of producing low or high resolution models, depending on the available data. The lowest resolution "succinct" models identify only the locations of the principal substructures, such as individual proteins and RNA stems, but no more detailed information; at the other extreme are all-atom models. Models of mixed resolution are also produced, with succinct models for most of the structure and all-atom detail only where sufficient information exists. These procedures produce a range of models, all consistent with the experimental data and provide quantitative statements about the uncertainties in various parts of the structure, which should be useful in guiding future experimental studies. The study will involve extensions and improvements to the methodology, including more powerful algorithms for energy minimization, Monte Carlo, and molecular dynamics simulations on all-atom models. It also describes applications to the E. coli ribosome, eukaryotic small nuclear ribonucleoproteins, RNase P, and the Tetrahymena ribozyme.