Chief Scientist Laboratories Theoretical Molecular Science Laboratory
Chief Scientist: Yuji Sugita (D.Sc.)
Research Summary
To understand biological functions of proteins or biological membranes, we study their structures and dynamics using multi-scale simulations, which include all-atom molecular dynamics (MD) simulations, coarse-grained MD simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, integral equation theories, and so on. By performing all-atom MD simulations with enhanced conformational sampling techniques, we investigate hydration effect on protein folding and denaturation. We also study conformational dynamics of membrane proteins and functional roles of phospholipid molecules surrounding membrane proteins by all-atom or coarse-grained MD simulations. Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine chemical reactions occurred in enzymes. Furthermore, we develop novel simulation algorithms and new models for biomolecules to overcome difficulties in the current computer simulations of biomolecules
Research Subjects:
- Clarify the dynamics of membrane and membrane proteins
- Clarify the protein-glycan interactions
- Develop new theory and computational method that integrates both theoretical chemistry and biophysics
- Understand macromolecular crowding environments in cells
Main Research Fields
- Chemistry
Related Research Fields
- Physics
- Materials Sciences
- Biology & Biochemistry
- Computer Science
- Multidisciplinary
Selected Publications
- 1.
Yaokun Lei, Kiyoshi Yagi, Yuji Sugita.:
"Learning QM/MM Potential using Equivariant Multiscale Model"
J. Chem. Phys. 160, 214109 (2024) - 2.
Jaewoon Jung, Cheng Tan, Yuji Sugita.:
"GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems"
Nature Comm. 15, 3370 (2024) - 3.
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska.:
"Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch"
Proc. Natl. Acad. Sci. USA 121(15), e2317197121 - 4.
Kazuki Watanabe, Qingci Zhao, Ryosuke Iwatsuki, Ryota Fukui, Weitong Ren, Yuji Sugita, Noritaka Nishida.:
"Deciphering the multi-state conformational equilibrium of HDM2 in the regulation of p53 binding: Perspectives from molecular dynamics simulation and NMR analysis"
J. Am. Chem. Soc. 146, 9790-9800 (2024) - 5.
Ryo Nishihara, Hisham M. Dokainish, Yoshiki Kihara, Hiroki Ashiba, Yuji Sugita, Ryoji Kurita.:
"Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin"
ACS Central Science 10(2), 283-290 (2024) - 6.
Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada.:
"Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study"
PLoS Comp. Biol. 19, e1011321 (2023) - 7.
Cheng Tan, Ai Niitsu, Yuji Sugita.:
"Highly charged proteins and their repulsive interactions antagonize biomolecular condensation"
JACS Au 3, 834-848 (2023) - 8.
George A. Pantelopulos, Daisuke Matsuoka, James M. Hutchison, Charles R. Sanders, Yuji Sugita, John E. Straub, Dave. Thirumalai.:
"Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99"
Proc. Natl. Acad. Sci. USA 119, e2212207119 (2022) - 9.
Mao Oide, Yuji Sugita.:
"Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood"
J. Chem. Phys. 157, 075101 (2022) - 10.
Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita.:
"The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein"
eLife 11, e75720 (2022)
Recent Research Results
Nov. 1, 2016
Strange behavior in the crowded cellular environment
Annual research report
Related Links
Lab Members
Principal investigator
- Yuji Sugita
- Chief Scientist
Core members
- Jaewoon Jung
- Senior Technical Scientist
- Tomoaki Yagi
- Research Scientist
- Elisa Rioual
- Special Postdoctoral Researcher
- Haeri Im
- Postdoctoral Researcher
- Azuki Mizutani
- Postdoctoral Researcher
- Tarun Maity
- Postdoctoral Researcher
- Yuko Okamoto
- Senior Visiting Scientist
- Wataru Mizukami
- Visiting Scientist
- Mao Oide
- Visiting Scientist
- Shoji Takada
- Visiting Scientist
- Joanna Trylska
- Visiting Scientist
- Eiro Muneyuki
- Visiting Scientist
- Kiyoshi Yagi
- Visiting Scientist
- Isseki Yu
- Visiting Scientist
- Taiki Wakabayashi
- Junior Research Associate
- Masahiro Motohashi
- Junior Research Associate
- Machiko Ishigaki
- Assistant
Contact Information
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: sugita@riken.jp