Role of water molecules in biomolecular functions and interactions
| Project/Area Number |
26800227
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Biological physics/Chemical physics/Soft matter physics
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| Research Institution | Keio University |
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Principal Investigator |
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| Project Period (FY) |
2014-04-01 – 2016-03-31
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| Project Status |
Completed (Fiscal Year 2015)
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| Budget Amount *help |
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
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| Keywords | 生体分子 / 機能的構造揺らぎ / 水和構造 / 水素結合ネットワーク / 分子動力学シミュレーション / 分子力場 / 低温X線結晶構造解析 / ダイナミックス / グルタミン酸脱水素酵素 |
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| Outline of Final Research Achievements |
In this study, we investigated how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, glutamate dehydrogenase (GDH), through molecular dynamics simulation supported by structural analyses and biochemical experiments. The results show that ‘wetting’/’drying’ and ‘adsorption’/’dissociation’ of a few water molecules at an active-site cleft worked as a switch for the functional motions of GDH. Thus, this study demonstrates the importance of water molecules in understanding protein functions.
In addition, we are now developing a new MD potential parameter set, which can account experimental hydration structures around protein surfaces. Our analyses using MD and quantum-chemistry calculation show that the potential parameter set, which explicitly consider loan pairs of polar atoms, is necessary to reproduce the hydration structures obtained by X-ray crystal structural analyses.
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Report
(3 results)
Research Products
(14 results)
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[Journal Article] Cryogenic coherent x-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA2015
Author(s)
Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi,Yu Masaki, Asahi Fukuda, Saki Hashimoto, Masayoshi Nakasako, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu et al.,
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Journal Title
Journal of Physics B: Atomic, Molecular and Optical Physics
Volume: 48
Issue: 18
Pages: 184003-184003
DOI
Related Report
Peer Reviewed
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[Journal Article] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser.2015
Author(s)
Takayama, Y., Inui, Y., Sekiguchi, Y., Kobayashi, A., Oroguchi, T., Yamamoto, M., Matsunaga, S., and Nakasako, M.
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Journal Title
PLANT AND CELL PHYSIOLOGY
Volume: 未定
Issue: 7
Pages: 1-15
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Single shot three-dimensional imaging of high-index-faceted nanocrystals with femtosecond X-ray free electron laser pulses2014
Author(s)
R. Xu, H. Jiang, C. Song, Z. Huang, J. A. Rodriguez, C-C. Chen, D. Nam, J. Park, M. Gallagher-Jones, S. Kim, S. Kim, A. Suzuki, Y. Takayama, T. Oroguchi, Y. Takahashi, J. Fan, Y. Zou, T. Hatsui, Y. Inubushi, T. Kameshima, K. Yonekura et al.
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Journal Title
Nat. Commun.
Volume: 5
Issue: 1
Pages: 4061-4061
DOI
Related Report
Peer Reviewed / Open Access
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