Laboratory for Biomolecular Function Simulation
Team Leader
Yuji SugitaD.Sci.
- 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
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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