Laboratory for Biomolecular Function Simulation

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

• 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

• 2019/11/29 Research Faster modeling of interactions between ligands and proteins