Large-scale simulations of ribosomal decoding

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 DESCRIPTION (provided by applicant): The advent of higher resolution cryo electron microscopy and structures of eukaryotic ribosomes has opened the field of ribosome mechanism to a vast array of possibilities. Together with the Christian Spahn cryo-EM lab, we recently published one of the first all-atom models of the human ribosome in various functional states related to decoding. Using our MDfit method, we produced models highly consistent with cryo-EM density. The study revealed a new conformational change specific to eukaryotes: subunit rolling. We have also performed extensive studies on tRNA accommodation into the bacterial ribosome. Here, we will investigate the effect of subunit rolling on accommodation during decoding by the mammalian ribosome. We will also study conformational changes occurring prior to decoding and after accommodation. By comparing human and bacterial ribosome mechanism, we hope to gain insight into antibiotic action mechanism. We will use a combination of explicit solvent and all-atom reduced description techniques based on our previous publications. We will also extend our MDfit technique for higher resolution cryo-EM density.