| Project/Area Number |
26840056
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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 |
Biophysics
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| Research Institution | University of Tsukuba |
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Principal Investigator |
Harada Ryuhei 筑波大学, 数理物質系, 特別研究員(PD) (60612174)
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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 |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
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| Keywords | 分子動力学シミュレーション / タンパク質の天然構造予測 / タンパク質の構造変化予測 / タンパク質 / 立体構造変化 / フォールディング / 構造サンプリング / 機能発現 / 超並列シミュレーション / 自由エネルギー地形 |
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| Outline of Final Research Achievements |
Methods for predicting conformational transitions have been developed based on structural fluctuations of proteins. As computational schemes, the following two processes are repeated: (I) Selections of structures of proteins that have high potential to transit to other meta-stable states, where the candidates are selected based on a set of appropriate reaction coordinates. (II) Short-time molecular dynamics simulations restarting from the structures as conformational search. The above processes are powerful for predicting conformational transitions of proteins efficiently.
According to the strategy, we have developed several sampling methods for predicting conformational transitions, and applied them to biological systems. For instance, our methods have successfully predicted the native state of a mini-protein, chignolin. Furthermore, large-amplitude domain motions of T4 lysozyme in explicit water have been reproduced with our methods.
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