RIKEN Center for Biosystems Dynamics Research Laboratory for Biomolecular Function Simulation
Team Leader: Yuji Sugita (D.Sc.)
Research Summary
![Yuji Sugita(D.Sc.)](/medialibrary/riken/research/labs/qbic/computational_biology_research_core/biomolecular_function_simulation/yuji_sugita_170829.jpg?h=160&w=120)
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 Fields
- Chemistry
Related Research Fields
- Complex Systems
- Mathematical & 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)
Recent Research Results
Related Links
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
Contact Information
Integrated Innovation Building 7F
6-7-1 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan
Email: sugita [at] riken.jp