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

M. Takano, H. K. Nakamura, J. Higo, M. Sasai

研究成果: Paper査読

抄録

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.

本文言語English
ページ2719-2726
ページ数8
DOI
出版ステータスPublished - 2003
外部発表はい
イベント2003 Congress on Evolutionary Computation, CEC 2003 - Canberra, ACT, Australia
継続期間: 2003 12 82003 12 12

Conference

Conference2003 Congress on Evolutionary Computation, CEC 2003
国/地域Australia
CityCanberra, ACT
Period03/12/803/12/12

ASJC Scopus subject areas

  • 計算数学

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