RIKEN Center for Biosystems Dynamics Research Laboratory for Biomolecular Function Simulation

Team Leader: Yuji Sugita (D.Sc.)

Japanese Page

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.

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)