Abstract
Large-scale conformational rearrangements in biomolecular assemblies can be crucial to their functional dynamics. We investigate the functional rearrangements in a massive nucleoprotein assembly present in all living cells, the ribosome. It is responsible for protein synthesis, which requires several large-scale structural rearrangements in the ribosome bound tRNA molecules. To probe the energetics of the ribosome, we employ all-atom structure-based models and molecular dynamics simulations. Structure-based models provide simplified energetic descriptions, where experimentally obtained atomic structures are defined to be potential energy minima.
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