杉田理論分子科学研究室

当研究室では、理論科学的手法を用いて、生体分子を含む様々な分子系の構造とダイナミクスを解析し、分子機能を理解し、予測・デザインすることを目指します。特に、タンパク質や核酸、糖鎖や生体膜などの大規模構造変化、溶液中または生体分子中でのプロトン・電子移動、分子系の電子状態と振動状態、溶媒や分子混雑などの環境が分子機能に与える影響などに興味を持っています。そのため、「京」などのスーパーコンピュータを用いた大規模シミュレーションも積極的に行います。

研究テーマ

• 膜蛋白質のダイナミクスと機能解明
• 溶液中の糖鎖構造の拡張アンサンブルシミュレーション
• 水とイオン、生体分子

主要論文

1. M. Kajikawa, P. Li, E. Goto, N. Miyashita, M. Aoki-Kawasumi, M. Mito-Yoshida, Y. Sugita, and S. Ishido.:
   "B7-2 is recognized by inter-transmembrane loop of KSHV MIR2,"
   J. Virol. 86 (2012) 5288-5296.
2. F. Ogushi, R. Ishitsuka, T. Kobayashi, and Y. Sugita.:
   "Rapid flip-flop motions of cholesterol, diacylgrycerol, and ceramide in phospholipid bilayers."
   Chem. Phys. Lett. 522 (2012) 96-102.
3. S. Re, N. Miyashita, Y. Yamaguchi, and Y. Sugita.:
   "Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation."
   Biophysical Journal (Letter) 101 (2011) L44-L46.
4. Y. Matsumoto, T. Tosha, A. V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, and Y. Shiro.:
   "Crystal structure of Quinol-Dependent Nitric Oxide Reductase from Beobacillus Strearothermophilus."
   Nature Struct. Mol. Biol. 19 (2012) 238-246.
5. T. Mori, F. Ogushi, and Y. Sugita.:
   "Voronoi analysis of lipid surface area in protein-membrane systems."
   J. Comp. Chem. 33 (2012) 286-293.
6. Y. Sugita, M. Ikeguchi and C. Toyoshima.:
   "Insight into the relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations."
   Proc. Natl. Acad. Sci. USA 107 (2010) 21465-21469.
7. T. Mori, R. Ishitani, T. Tsukazaki, O. Nureki and Y. Sugita.:
   "Molecular Mechanisms Underlying the Early Stage of Protein Translocation through Sec Translocon."
   Biochemistry 49 (2010) 945-950.
8. S. Re, J. Jung, S. Ten-no and Y. Sugita.:
   "Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation."
   J. Comp. Chem. 32 (2011) 260-270.
9. N. Miyashita, J.E. Straub, D. Thirumalai and Y. Sugita.:
   "Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations."
   J. Am. Chem. Soc. (Communication) 131 (2009) 3438-3439.
10. T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, D.G. Vassylyev, K. Ito and O. Nureki.:
    "Conformational transition of Sec machinery inferred from bacterial SecYE structures."
    Nature 455 (2008) 988-992.