Elucidation of thermodynamic roles of hydration structure in protein functions
Project/Area Number |
17H04854
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Research Category |
Grant-in-Aid for Young Scientists (A)
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Allocation Type | Single-year Grants |
Research Field |
Biological physics/Chemical physics/Soft matter physics
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Research Institution | Keio University |
Principal Investigator |
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Project Period (FY) |
2017-04-01 – 2021-03-31
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Project Status |
Completed (Fiscal Year 2021)
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Budget Amount *help |
¥25,740,000 (Direct Cost: ¥19,800,000、Indirect Cost: ¥5,940,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥21,840,000 (Direct Cost: ¥16,800,000、Indirect Cost: ¥5,040,000)
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Keywords | 生体分子 / 機能的構造変化 / 水和構造 / 溶媒和自由エネルギー / 分子動力学シミュレーション / 溶液散乱実験 / ベイズ統計 / 蛋白質 / 構造アンサンブル / 自由エネルギー地形 / MDシミュレーション / 溶液X線散乱 / 生体分子の機能発揮機構 / X線回折散乱実験 / 蛋白質分子 / 蛋白質ダイナミックス / X線散乱回折実験 |
Outline of Final Research Achievements |
To reveal the role of water molecules in a protein functional motion in MD simulation, it is necessary to visualize a free-energy map (conformational ensemble) of protein motions and then investigate thermodynamic contribution of waters to the map. For these purposes, we have developed the two methods to analyse conformational ensembles of proteins; (i) the Bayesian optimization method of MD ensemble to obtain realistic ensemble that can reproduce experimental data, and (ii) the method to calculate solvation free energy changes along protein motions. By applying these methods to MD simulation and solution scattering experiments of proteins, we have begun to reveal that the mechanism of the protein conformational motions cannot be accounted without the thermodynamic contribution of waters surrounding the protein molecules.
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Academic Significance and Societal Importance of the Research Achievements |
生命の営みには『水』の存在が不可欠であるが、その大きな要因としては、生命活動の素過程を担うタンパク質や核酸といった生体分子が機能するためには、水環境が必須であることが挙げられる。では、なぜ生体分子は機能発現に水環境を必要とするのか?この疑問に答えるためには、生体分子近傍の水和構造を詳しく調べ、その構造を基に、生体分子の構造変化過程といった機能発揮過程において水が果たしている役割を熱力学的に明らかにする必要がある。本研究において開発された構造変化の解析方法は、このような熱力学的研究を可能にし、水和構造の役割を明らかにしつつある。
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Report
(5 results)
Research Products
(20 results)
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[Journal Article] Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation2018
Author(s)
Amane Kobayashi, Yuki Takayama, Koji Okajima, Mao Oide, Takahiro Yamamoto, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Yoshiki Kohmura, Masaki Yamamoto, Takahiko Hoshi, Yasufumi Torizuka
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Journal Title
Journal of Synchrotron Radiation
Volume: 25
Issue: 6
Pages: 1803-1818
DOI
Related Report
Peer Reviewed
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[Journal Article] Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging2017
Author(s)
H. Kameda, S. Usugi, M. Kobayashi, N. Fukui, S. Lee, K. Hongo, T. Mizobata, Y. Sekiguchi, Y. Masaki, A. Kobayashi, T. Oroguchi, M. Nakasako, Y. Takayama, M. Yamamoto, and Y. Kawata
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Journal Title
Journal of Biochemistry (Tokyo)
Volume: 161
Issue: 1
Pages: 55-65
DOI
NAID
Related Report
Peer Reviewed / Acknowledgement Compliant
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