Coarse-graining the nano-machine ribosome to elucidate its functional dynamics

Coarse-grained computational techniques can provide information on conformational dynamics of the supramolecule ribosome, for which full-atom approaches become computationally demanding. Elastic network models and coarse-grained molecular dynamics simulations are the most commonly used methods for simple descriptions of the biomolecular structure. Usually, an amino acid or a nucleotide residue is represented by a single node, and simplified potential energy functions are used for interacting nodes. These approaches have been successful in reproducing the micro-to-milliseconds dynamics information, such as the experimentally observed ratchet-like rotation of the ribosomal subunits. Furthermore, they have provided insights on the structure-dynamicsfunction relationship of the ribosomal complex. This review summarizes various coarsegraining approaches on the nano-machine and recent studies that focus on its different functional sites.