Centers & Labs

Chief Scientist Laboratories

Theoretical Molecular Science Laboratory

Chief Scientist: Yuji Sugita (D.Sci.)
Yuji  Sugita(D.Sci.)

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

Main Research Field

Chemistry

Related Research Fields

Physics / Materials Sciences / Biology & Biochemistry / Computer Science / Multidisciplinary

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

Selected Publications

  1. Re, S., Nishima, W., Tahara, T., and Sugita, Y.:
    "Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations"
    J.Phys.Chem.B 5, 4343-4348 (2014).
  2. Thomsen, B., Yagi, K., and Christiansen, O.:
    "A simple state-average procedure determining optimal coordinates for anharmonic vibrational calculations."
    Chem. Phys. Lett. 610, 288-297 (2014).
  3. Yasuaki Komuro, Suyong Re, Chigusa Kobayashi, Eiro Muneyuki and Yuji Sugita.:
    "CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase."
    J. Chem. Theory Comput., 10, 4133–4142 (2014).
  4. Kaoru Kumazaki, Shinobu Chiba, Mizuki Takemoto, Arata Furukawa, Ken-ichi Nishiyama, Yasunori Sugano, Takaharu Mori, Naoshi Dohmae, Kunio Hirata, Yoshiko Nakada-Nakura, Andrés D. Maturana, Yoshiki Tanaka, Hiroyuki Mori, Yuji Sugita, Fumio Arisaka, Koreaki Ito, Ryuichiro Ishitani, Tomoya Tsukazaki and Osamu Nureki.:
    "Structural basis of Sec-independent membrane protein insertion by YidC."
    Nature 509, 516-520 (2014).
  5. B. Thomsen, K. Yagi and O. Christiansen.:
    "Optimized coordinates in vibrational coupled cluster calculations."
    J. Chem. Phys. 140, 154102 (2014).
  6. K. Yagi and H. Otaki.:
    "Vibrational quasi-degenerate perturbation theory with optimized coordinates: Applications to ethylene and trans-1,3-butadiene."
    J. Chem. Phys. 140, 084113 (2014).
  7. Jaewoon Jung, Takaharu Mori and Yuji Sugita.:
    "Midpoint Cell Method for Hybrid (MPI+OpenMP) Parallelization of Molecular Dynamics Simulations."
    J. Comp. Chem. 35, 1064-1072 (2014).
  8. Kiyoshi Yagi and Hiroki Otaki.:
    "Vibrational quasi-degenerate perturbation theory with optimized coordinates: Applications to ethylene and trans-1,3-butadiene."
    J. Chem. Phys. 140, 084113 (2014).
  9. Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido and Yuji Sugita.:
    "Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimer."
    J. Comput. Chem. 35, 300-308 (2014).
  10. Takao Yoda, Yuji Sugita and Yuko Okamoto.:
    "Salt Effects on Hydrophobic-Core Formation in Folding of a Helical Mini Protein Studied by Molecular Dynamics Simulations."
    Proteins: Struct. Funct. Bioinf., 82, 933-943 (2014).

Lab Members

Principal Investigator

Yuji Sugita
Chief Scientist

Core Members

Kiyoshi Yagi
Senior Research Scientist
Takaharu Mori
Research Scientist
Isseki Yu
Research Scientist
Jaewoon Jung
Technical Scientist
Bo Thomsen
Special Postdoctoral Researcher
Raimondas Galvelis
Postdoctoral Researcher
Po-hung Wang
Postdoctoral Researcher
Kenta Yamada
Postdoctoral Researcher
Daisuke Matsuoka
Postdoctoral Researcher
Donatas Surblys
Postdoctoral Researcher
Wataru Nishima
Contract Researcher
Marta Kulik
Visiting Researcher
Mitsuhiro Sueyasu
Student Trainee
Hiroki Otaki
Visiting Scientist
Wataru Mizukami
Visiting Scientist
Masako Ishikawa
Assistant

Contact information

2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Email: sugita [at] riken.jp

Related links

Recent research results

Annual research report