Biomolecular Dynamics Simulation Research Team
Research Areas
We examine hydration structure of proteins and ions by molecular dynamics simulations and integral equation theory. By combining these methods, we try to understand the relationship between hydration and conformational dynamics of proteins or other biomolecules.
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Research Subject
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List of Selected Publications
| (1) | 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. (2009) in press. |
| (2) | 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) |
| (3) | 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) |
| (4) | 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). |
| (5)* | 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). |
| (6)* | Sugita, Y., Kitao, A., and Okamoto, Y.: "Multidimensional replica-exchange method for free-energy calculations." J. Chem. Phys. 113, 6042-6051 (2000). |
| (7)* | Sugita, Y., and Okamoto, Y.: "Replica-exchange molecular dynamics method for protein folding." Chem. Phys. Lett. 329, 261-270 (1999). |