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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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
Title of host publication2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings
PublisherIEEE Computer Society
Pages2719-2726
Number of pages8
Volume4
DOIs
Publication statusPublished - 2003
Externally publishedYes
Event2003 Congress on Evolutionary Computation, CEC 2003 - Canberra, ACT
Duration: 2003 Dec 82003 Dec 12

Other

Other2003 Congress on Evolutionary Computation, CEC 2003
CityCanberra, ACT
Period03/12/803/12/12

Fingerprint

Molecular Dynamics Simulation
Molecular dynamics
Proteins
Protein
Computer simulation
Molecules
Molecular Motor
Information Structure
Structural Dynamics
Computing
Complex Dynamics
Model
Principal Component Analysis
Structural dynamics
Simulation Model
Principal component analysis
Motion
Atoms

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. In 2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings (Vol. 4, pp. 2719-2726). [1299432] IEEE Computer Society. https://doi.org/10.1109/CEC.2003.1299432

Molecular dynamics simulation using coarse-grained model to study protein function and beyond. / Takano, Mitsunori; Nakamura, H. K.; Higo, J.; Sasai, M.

2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings. Vol. 4 IEEE Computer Society, 2003. p. 2719-2726 1299432.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Takano, M, Nakamura, HK, Higo, J & Sasai, M 2003, Molecular dynamics simulation using coarse-grained model to study protein function and beyond. in 2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings. vol. 4, 1299432, IEEE Computer Society, pp. 2719-2726, 2003 Congress on Evolutionary Computation, CEC 2003, Canberra, ACT, 03/12/8. https://doi.org/10.1109/CEC.2003.1299432
Takano M, Nakamura HK, Higo J, Sasai M. Molecular dynamics simulation using coarse-grained model to study protein function and beyond. In 2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings. Vol. 4. IEEE Computer Society. 2003. p. 2719-2726. 1299432 https://doi.org/10.1109/CEC.2003.1299432
Takano, Mitsunori ; Nakamura, H. K. ; Higo, J. ; Sasai, M. / Molecular dynamics simulation using coarse-grained model to study protein function and beyond. 2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings. Vol. 4 IEEE Computer Society, 2003. pp. 2719-2726
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