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

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

Research output: Contribution to conferencePaper

Abstract

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.

Original languageEnglish
Pages2719-2726
Number of pages8
DOIs
Publication statusPublished - 2003 Jan 1
Event2003 Congress on Evolutionary Computation, CEC 2003 - Canberra, ACT, Australia
Duration: 2003 Dec 82003 Dec 12

Conference

Conference2003 Congress on Evolutionary Computation, CEC 2003
CountryAustralia
CityCanberra, ACT
Period03/12/803/12/12

ASJC Scopus subject areas

  • Computational Mathematics

Cite this

Takano, M., Nakamura, H. K., Higo, J., & Sasai, M. (2003). Molecular dynamics simulation using coarse-grained model to study protein function and beyond. 2719-2726. Paper presented at 2003 Congress on Evolutionary Computation, CEC 2003, Canberra, ACT, Australia. https://doi.org/10.1109/CEC.2003.1299432