Theoretical Molecular Science Laboratory

This laboratory focuses on theoretical and computational studies on molecular structures and dynamics to understand and predict molecular functions. Currently, our major interests are (i) large-scale conformational changes of biomolecules, (ii) proton and electron transfers in solution or in biomolecules, (iii) electronic and vibrational states of molecular systems, and (iv) environmental effects on molecular functions. For this purpose, we perform large-scale computer simulations using K computer or other supercomputers.

Research Subjects

• Molecular dynamics and functions of membrane proteins
• Generalized-ensemble simulations of N-glycans in solution
• Hydration of ions and biomolecules

Publications

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.