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Laboratory for Biomolecular Function Simulation

Yuji Sugita


Team Leader

Yuji Sugita (D.Sci.)

Sugita of RIKEN

Original HP

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.

Research Topics

  • Effects of intracellular crowding on the dynamics of protein and water interactions
  • Simulations and data analysis of large-scale protein structural changes
  • Slow dynamics using Brownian dynamics simulations

Selected Publications

  • Ando, T., Yu, I., Feig, M. & 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) doi:10.1021/acs.jpcb.6b06243
  • Yu, I., Mori, T., Ando, T., Harada, R., Jung, J., Sugita, Y., et al.
    "Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm"
    Elife 5, e19274 (2016) doi:10.7554/eLife.19274
  • 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) doi:10.1016/j.jmgm.2015.02.004
  • Miyashita, N., Re, S. & Sugita, Y.
    "REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function"
    Int. J. Quantum Chem. 115, 325-332 (2015) doi:10.1002/qua.24785
  • 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) doi:10.1002/jcc.23494
  • 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) doi:10.1021/ct400445k
  • Feig, M. & Sugita, Y.
    "Reaching new levels of realism in modeling biological macromolecules in cellular environments"
    J. Mol. Graph. Model. 45, 144-156 (2013) doi:10.1016/j.jmgm.2013.08.017
  • 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) doi:10.1021/ja3126992
  • Kajikawa, M., Li, P., Goto, E., Miyashita, N., Aoki-Kawasumi, M., Mito-Yoshida, 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) doi:10.1128/jvi.00219-12
  • Harada, R., Sugita, Y. & Feig, M.
    "Protein Crowding Affects Hydration Structure and Dynamics"
    J. Am. Chem. Soc. 134, 4842-4849 (2012) doi:10.1021/ja211115q