Molecular dynamics simulation using coarse-grained model to study protein function and beyond

To make an inquiry into the mechanisms of biomolecular functions, particularly of protein molecule's, we conducted molecular dynamics (MD) simulations of protein molecules using coarse-grained models that preserve 3-dimensional native structure information, together with the hope of inquiring dynamical aspect of design principle of not only molecular machines but also biomolecular computing systems. In this preliminary report, we address to what extent the coarse-grained models, which reduce computational load dramatically, can reproduce collective, large-scale molecular motions essential for molecular functions. Complex structural dynamics were characterized through principal component analysis, and we showed that coarse-grained models can well reproduce collective, large-scale movements that were observed in more precise «all-atom» model simulations. An application of the coarse-grained model to a molecular motor system and a possible role for biomolecular computing will also be discussed.