Breakthrough on the high pressure biomolecule reaction with computational chemistry of the volume change
| Project/Area Number |
25410025
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
Yu Isseki 国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 研究員 (90402544)
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| Research Collaborator |
Sugita Yuji 国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 主任研究員
Wang Po-hung 国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 特別研究員
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| Project Period (FY) |
2013-04-01 – 2017-03-31
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| Project Status |
Completed (Fiscal Year 2016)
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| Budget Amount *help |
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
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| Keywords | 高圧 / 細胞環境 / 分子混雑 / 分子動力学 / 蛋白質 / 水和 / 部分モル体積 / 深海 / 分子動力学シミュレーション |
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| Outline of Final Research Achievements |
This project investigates the influence of the high hydrostatic pressure on the structure and dynamics of proteins by calculating the protein volume in solution with all-atom molecular dynamics simulations. On the other hand, the cytoplasm, which is exposed to high pressure, is highly crowded with various kinds of proteins and nucleic acids. This project investigates also physicochemical characteristics of such a cellular environment and its response to high pressure. Throughout this project, the hydration volume of proteins and excluded volume effect of macromolecules in cell are understood at the molecular level. In addition, the computer programs to analyze the geometric properties of molecule are developed and parallelized in order to perform the project-related calculations on the super computer systems. These programs will be released near future.
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Report
(5 results)
Research Products
(17 results)
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[Presentation] 細胞内環境での蛋白質の分子運動と機能2015
Author(s)
Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
Organizer
生命医薬情報学連合大会2015大会スポンサーセッション生命科学におけるインフォマティクスと物理化学の融合
Place of Presentation
京都・京都大学・宇治キャンパス
Year and Date
2015-10-30
Related Report
Invited
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