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RIKEN Quantitative Biology Center

Laboratory for Biomolecular Function Simulation

Team Leader: Yuji Sugita (D. Sci.)
Yuji  Sugita(D. Sci.)

We utilize molecular dynamics and Brownian dynamics simulations to understand protein dynamics and functions in cellular environments as well as to model the structures of protein/nucleic acids complexes or membrane protein structures. To achieve this goal, we collaborate with experimentalists in QBiC and other universities/institutes. We also carry out “very” large-scale molecular simulations of biological systems using K computer or other supercomputers. Our team also develops coarse-grained molecular simulation methods for understanding the essential mechanisms underlying biological phenomena in cells.

Main Research Field

Chemistry

Related Research Fields

Complex systems / Mathematical and physical sciences / Biological Sciences

Keywords

  • Molecular Dynamics
  • Protein Dynamics
  • Free Energy Calculation
  • Generalized-Ensemble Algorithm
  • Protein-Ligand Interaction

Selected Publications

  1. Ando, T., Yu, I., Feig, M., and Sugita, Y.:
    "Thermodynamics of Macromolecular Association in heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model"
    J. Phys. Chem. B 120, 11856-11865 (2016).
  2. Yu, I., Mori, T., Ando, T., Harada, R., Jung, J., Sugita, Y., and Feig, M.:
    "Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm"
    eLife, 5, e19274 (2016).
  3. Feig, M., Harada, R., Mori, T., Yu, I., Takahashi, K. & Sugita, Y.:
    "Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology"
    J. Mol. Graph. Model. 58, 1-9 (2015)
  4. Miyashita, N., Re, S. & Sugita, Y.:
    "REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function"
    Int. J. Quantum Chem. 115, 325-332 (2015)
  5. Li, P., Miyashita, N., Im, W., Ishido, S. & Sugita, Y.:
    "Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers"
    J. Comput. Chem. 35, 300-308 (2014)
  6. Mori, T., Jung, J. & Sugita, Y.:
    "Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems"
    J. Chem. Theory Comput. 9, 5629-5640 (2013)
  7. Feig, M. & Sugita, Y.:
    "Reaching new levels of realism in modeling biological macromolecules in cellular environments"
    J. Mol. Graph. Model. 45, 144-156 (2013)
  8. Harada, R., Tochio, N., Kigawa, T., Sugita, Y. & Feig, M.:
    "Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions"
    J. Am. Chem. Soc. 135, 3696-3701 (2013)
  9. Kajikawa, M., Li, P., Goto, E., Miyashita, N., Aoki-Kawasumi, M., et al.:
    "The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation"
    J. Virol. 86, 5288-5296 (2012)
  10. Harada, R., Sugita, Y. & Feig, M.:
    "Protein Crowding Affects Hydration Structure and Dynamics"
    J. Am. Chem. Soc. 134, 4842-4849 (2012)

Lab Members

Principal Investigator

Yuji Sugita
Team Leader

Core Members

Suyong Re
Senior Scientist
Takaharu Mori
Research Scientist
Isseki Yu
Research Scientist
Hiraku Oshima
Postdoctoral Researcher
Ai Niitsu
Postdoctoral Researcher

Contact information

Integrated Innovation Building 7F
6-7-1 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan

Email: sugita [at] riken.jp

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