Theoretical Molecular Science Laboratory
Associate Chief Scientist
Yuji SUGITA (D.Sci.)
To understand structural and functional relationships in biomolecules is one of the molst important issues in molecular biology. In this laboratory, we study the relationships by computer simulations based on statistical mechanics and quantum chemistry. Current research targets are protein folding and stability, ion-transport by membrane proteins, chemical reactions in enzymes, and so on. We also try to develop novel computational models and methods to overcome the limitations in computational chemistry for biomolecules.
- Development of conformational sampling methods for biomolecules
- Molecular dynamics simulations of membrane proteins and phospholipids
- Development of QM/MM calculation methods for enzymatic reactions
- Mori, T., Ishitani, R., Tsukazaki, T., Nureki, O., and Sugita, Y.:
"Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon."
Biochemistry, 49, 945-950 (2010). - Imai, T., and Sugita, Y.:
"Dynamic Correlation between Pressure-Induced Protein Structural Transition and Water Penetration."
J. Phys. Chem. B, 114, 2281-2286 (2010). - Miyashita, N., Straub, J.E., Thirumalai, D., and Sugita, Y.:
"Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations."
J. Am. Chem. Soc. 131, 3438-3439 (2009). - Re, S., Jung, J., Ten-no, S., and Sugita, Y.:
"A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase."
Chem. Phys. Lett. 480, 284-288 (2009). - Tsukazaki, T., Mori, H., Fukai, S., Ishitani, R., Mori, T., Dohmae, N., Perederina, A., Sugita, Y., Vassylyev, D.G., Ito, K., and Nureki, O.:
"Conformational transition of Sec machinery inferred from bacterial SecYE structures."
Nature. 455, 988-992 (2008). - Ishitani, R., Sugita, Y., Dohmae, D., Furuya, N., Hattori, M., and Nureki, O.:
"Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study."
Proc. Natl. Acad. Sci. USA, 105, 15393-15398 (2008) - Jung, J., Choi, C.H., Sugita, Y., and Ten-no, S.:
"New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals."
J. Chem. Phys. 127, 204102 (2007). - Sugita, Y., Miyashita, N., Ikeguchi, M., Kidera, A., and Toyoshima, C.:
"Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca2+-pump."
J. Am. Chem. Soc. 127, 6150-6151 (2005). - Sugita, Y., Kitao, A., and Okamoto, Y.:
"Multidimensional replica-exchange method for free-energy calculations."
J. Chem. Phys. 113, 6042-6051 (2000). - Sugita, Y., and Okamoto, Y.:
"Replica-exchange molecular dynamics method for protein folding."
Chem. Phys. Lett. 329, 261-270 (1999).
Principal Investigator
- Yuji SUGITA
- Associate Chief Scientist
Staff Scientist
- Suyong RE
- ASI Research Scientist
Postdoctoral Fellow
- Andrei PISLIAKOV
- Foreign Postdoctoral Researcher
- Fumiko OGUSHI
- Contract Researcher
- Chigusa IWAHASHI-KOBAYASHI
- Contract Researcher
- Pai-Chi LI
- Wataru NISHIMA
- Postdoctoral Researcher
Student Trainee
- Yasuaki KOMURO
- Junior Research Associate