Abstract
What granularity is needed to carry out computer simulations of biomolecular reactions/motions? This is one of the central issues of the in silico biomolecular computing. In this paper, we addressed this issue by studying model granularity dependence of the native structure dynamics of protein molecules. We conducted molecular dynamics simulations employing three different protein models: the model with full atomic details and two coarse-grained models in which only Cα atoms interacting with each other through simple potentials are considered. In addition to the observed agreement among the three models in terms of isotropic thermal fluctuation, principal component analysis showed that the coarse-grained models can also reproduce the anisotropy (or directionality) of the fluctuation, particularly of collective modes having relevance to molecular function. This indicates that the dependence of the essential dynamics of a protein molecule on the model granularity is weak, although it was also shown that incorporation of the Lennard–Jones-type potential into the harmonic-potential-based coarse-grained model improves the reproducibility to some degree, and that a plastic nature of structural dynamics observed in the full atomic model transforms into an elastic one in the coarse-grained models. The coarse-grained model can be applied to a molecular motor system, which may lead to a new view of biomolecular computing in the context of biological physics.
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Takano, M., Higo, J., Nakamura, H.K. et al. On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing. Nat Comput 3, 377–393 (2004). https://doi.org/10.1007/s11047-004-2639-6
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DOI: https://doi.org/10.1007/s11047-004-2639-6