Team Leader
Yuji Sugita
D.Sci.
Laboratory for Biomolecular Function Simulation
LocationKobe / Integrated Innovation Building
E-mailsugita[at]riken.jp
Please replace [at] with @.
In our laboratory, we carry out molecular dynamics simulations on Fugaku or other supercomputers to elucidate the relationships between structure, dynamics, and function in biomacromolecules, such as proteins, nucleic acids, glycans, and lipid molecules. We develop various free-energy calculation methods to evaluate free-energy differences between two thermodynamic states in biomacromolecules for understanding biomolecular functions more quantitatively. The developed methods are installed into GENESIS software, which is freeware and is available by everyone. We thus contribute not only to the basic life science but also to in-silico drug discovery.
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
Selected Publications
Kasahara K, Re S, Nawrocki G, et al.
Reduced efficacy of a Src kinase inhibitor in crowded protein solution.
Nature Communications
12(1), 4099 Fri Jul 02 00:00:00 JST 2021
doi: 10.1038/s41467-021-24349-5
Mori T, Jung J, Kobayashi C, et al.
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein.
Biophysical Journal
120(6), 1060-1071 Tue Mar 16 00:00:00 JST 2021
doi: 10.1016/j.bpj.2021.01.012
Oshima H, Re S, Sugita Y.
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method.
Journal of Chemical information and Modeling
60(11), 5382-5394 Mon Nov 23 00:00:00 JST 2020
doi: 10.1021/acs.jcim.0c00338
Kim S, Oshima H, Zhang H, et al.
CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
Journal of Chemical Theory and Computation
16(11), 7207-7218 Tue Nov 10 00:00:00 JST 2020
doi: 10.1021/acs.jctc.0c00884
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 Sun Dec 01 00:00:00 JST 2019
doi: 10.1073/pnas.1904707116
Oshima H, Re S, Sugita Y.
Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules.
Journal of Chemical Theory and Computation
15(10), 5199-5208 Tue Oct 08 00:00:00 JST 2019
doi: 10.1021/acs.jctc.9b00761
Niitsu A, Re S, Oshima H, et al.
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
Journal of Chemical information and Modeling
59(9), 3879-3888 Mon Sep 23 00:00:00 JST 2019
doi: 10.1021/acs.jcim.9b00416
Oshima H, Re S, Sakakura M, et al.
Population Shift Mechanism for Partial Agonism of AMPA Receptor.
Biophysical Journal
116(1), 57-68 Tue Jan 08 00:00:00 JST 2019
doi: 10.1016/j.bpj.2018.11.3122
Re S, Watabe S, Nishima W, et al.
Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase.
Scientific Reports
8(1), 1644 Fri Jan 26 00:00:00 JST 2018
doi: 10.1038/s41598-018-20012-0
Feig M, Yu I, Wang PH, et al.
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.
The Journal of Physical Chemistry. B
121(34), 8009-8025 Thu Aug 31 00:00:00 JST 2017
doi: 10.1021/acs.jpcb.7b03570
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 Tue Nov 01 00:00:00 JST 2016
doi: 10.7554/eLife.19274
Members
Yuji Sugita
Team Leader
Suyong Re
Senior Scientist
Takaharu Mori
Research Scientist
Isseki Yu
Research Scientist
Hiraku Oshima
Postdoctoral Researcher
News
Mar. 27, 2023 Research
How an early mutation in the COVID-19 virus helped it spread so fast
Apr. 28, 2022 BDR News
Four BDR scientists awarded MEXT prizes
Oct. 21, 2021 Research
Supercomputer simulations reveal how protein crowding in cells impacts interactions
Jul. 30, 2021 BDR News
RIKEN BDR signs MOU with Shinshu University for research and educational collaborations
Nov. 29, 2019 Research
Faster modeling of interactions between ligands and proteins