Conversion of Interaction Energies of Protein Induced by Solvent Water
| Project/Area Number |
23651202
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| Research Category |
Grant-in-Aid for Challenging Exploratory Research
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| Allocation Type | Multi-year Fund |
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| Research Field |
System genome science
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| Research Institution | Osaka University (2014)
Kyoto University (2011-2013) |
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Principal Investigator |
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| Project Period (FY) |
2011-04-28 – 2015-03-31
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| Project Status |
Completed (Fiscal Year 2014)
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| Budget Amount *help |
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
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| Keywords | 溶媒和 / エネルギー / ゆらぎ / 溶液理論 / MDシミュレーション / 自由エネルギー / 分子シミュレーション / 相関解析 / 分布関数 / 構造エネルギー / 生体分子 / 液体論 / パスウェイ / 相関 / 生物物理 / 応用数学 / 計算物理 / 自己組織化 |
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| Outline of Final Research Achievements |
The intramolecular energy and the solvation free energy of a protein fluctuate in response to its structure. In the present work, we conduct correlation analyses for a variety of interaction components of protein in explicit solvent; the solvent employed is not only pure water but also a mixed solvent of urea and water and all-atom computation of solvation free energy is carried out using molecular dynamics simulation and the method of energy representation. It is seen in pure-water solvent that the variations of the structural energy and the hydration free energy compensate each other during the course of equilibrium fluctuation and that the hydration free energy varies in strong correlation to the electrostatic component of the solute-solvent interaction energy. In the transfer energetics from pure-water solvent to the urea-water mixed solvent, on the other hand, it is found that the van der Waals component in the solute-solvent energy plays a dominant role.
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Report
(5 results)
Research Products
(119 results)
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[Journal Article] High-Energy X-ray Diffraction Study on the Intramolecular Structure of 2-Aminoethanol in the Liquid State2013
Author(s)
Y. Kameda, H. Deguchi, Y. Kubota, H. Furukawa, Y. Yagi, Y. Imai, M. Tatsumi, N. Yamazaki, N. Watari, T. Hirata, N. Matubayasi
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Journal Title
Bull. Chem. Soc. Japan
Volume: 86
Issue: 1
Pages: 99-103
DOI
NAID
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Peer Reviewed
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[Journal Article] Hydration structure around CO_2 captured in aqueous amine solutions observed by high energy X-ray scattering2011
Author(s)
H.Deguchi, Y.Kubota, H.Furukawa, Y.Yagi, Y.Imai, M.Tatsumi, N.Yamazaki, N.Watari, T.Hirata, N.Matubayasi, Y.Kameda
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Journal Title
Int.J.Greenhouse Gas Control
Volume: 5
Issue: 6
Pages: 1533-1539
DOI
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Peer Reviewed
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[Presentation] 分子動力学計算によるCO2化学吸収液の解析
Author(s)
古川 博敏、窪田 善之、狩野 康人、櫻庭 俊、松林 伸幸
Organizer
文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI）の構築」プロジェクト 次世代ナノ統合シミュレーションソフトウェアの研究開発 公開シンポジウム
Place of Presentation
ニチイ学館 神戸ポートアイランドセンター（神戸市中央区）
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