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
Main Research Fields
- 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).
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
- Kiyoshi Yagi
- Senior Research Scientist
- Suyong Re
- Research Scientist
- Takaharu Mori
- Research Scientist
- Isseki Yu
- Research Scientist
- Jaewoon Jung
- Technical Scientist
- Bo Thomsen
- Special Postdoctoral Researcher
- Ai Niitsu
- Special Postdoctoral Researcher
- Po-hung Wang
- Postdoctoral Researcher
- Marta Kulik
- Postdoctoral Researcher
- Kenta Yamada
- Postdoctoral Researcher
- Daisuke Matsuoka
- Postdoctoral Researcher
- Donatas Surblys
- Postdoctoral Researcher
- Hiroki Otaki
- Visiting Scientist
- Wataru Mizukami
- Visiting Scientist
- Machiko Ishigaki
- Assistant
Careers
| Position | Deadline |
|---|---|
| Seeking a Postdoctoral Researcher (W23176) | Open until filled |
| Seeking a Postdoctoral Researcher (W23139) | Open until filled |
Contact Information
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: sugita [at] riken.jp