Laboratory for Biomolecular Function Simulation | RIKEN BDR

Laboratory for Biomolecular Function Simulation

Team Leader

Yuji SugitaD.Sci.

Photo of principal investigator

  • Location:Kobe / Integrated Innovation Building
  • E-mail:sugita[at]riken.jpPlease replace [at] with @.
  • Lab Website

Research Summary

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 Theme

  • 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

Main Publications List

  • Kasahara K, Re S, Nawrocki G, et al.
    Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.
    Nature Communications 12. 4099 (2021) doi: 10.1038/s41467-021-24349-5
  • Re S, Oshima H, Kasahara K, et al.
    Encounter Complexes and Hidden Poses of Kinase-Inhibitor Binding on the Free-Energy Landscape.
    Proceedings of the National Academy of Sciences of the United States of America 116, 18404–18409 (2019). doi: 10.1073/pnas.1904707116
  • Ando T, Yu I, Feig M, Sugita Y.
    Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.
    Journal of Physical Chemistry B 120(46). 11856-11865 (2016) doi : 10.1021/acs.jpcb.6b06243
  • Yu I, Mori T, Ando T, 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, et al.
    Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
    Journal of Molecular Graphics and Modelling 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.
    International Journal of Quantum Chemistry 115(5). 325-332 (2015) doi : 10.1002/qua.24785
  • Li PC, Miyashita N, Im W, et al.
    Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers.
    Journal of Computational Chemistry 35(4). 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.
    Journal of Chemical Theory and Computation 9(12). 5629-5640 (2013) doi : 10.1021/ct400445k
  • Feig M, Sugita Y.
    Reaching new levels of realism in modeling biological macromolecules in cellular environments.
    Journal of Molecular Graphics and Modelling 45. 144-156 (2013) doi : 10.1016/j.jmgm.2013.08.017
  • Harada R, Tochio N, Kigawa T, et al.
    Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions.
    Journal of the American Chemical Society 135(9). 3696-3701 (2013) doi : 10.1021/ja3126992
  • Kajikawa M, Li PC, Goto E, et al.
    The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation.
    Journal of Virology 86(9). 5288-5296 (2012) doi : 10.1128/jvi.00219-12
  • Harada R, Sugita Y, Feig M.
    Protein Crowding Affects Hydration Structure and Dynamics.
    Journal of the American Chemical Society 134(10). 4842-4849 (2012) doi : 10.1021/ja211115q