Computational Analysis for Amyloid Formation
| Project/Area Number |
23770175
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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 | Chiba Institute of Technology (2012-2013)
Nagoya University (2011) |
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Principal Investigator |
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| Project Period (FY) |
2011 – 2013
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| Project Status |
Completed (Fiscal Year 2013)
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| Budget Amount *help |
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
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| Keywords | アミロイド / シミュレーション / タンパク質 / プリオン / 分子動力学 / プリオン病 / カーネル法 / 主成分分析 / アミロイド病 / アルツハイマー病 / 分子動力学法 / レプリカ交換法 / 多変量解析法 |
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| Research Abstract |
The developing mechanism of prion diseases has remained unclear. In this study, based on molecular dynamics simulations, we investigated the structural instability in prion protein (PrP), which promotes a partial helix-to-sheet conformational conversion. This instability of PrP facilitates the formation of active intermediate precursors (PrP*) that can lead to the conformational conversion of the normal prion protein (PrPC) to the pathogenic isoform (PrPSc). We propose a novel method to systematically construct a free-energy landscape by mapping massive protein structural data into a reduced space according to their secondary structures, named secondary structure principal component analysis (SSPCA). The definite existence of PrP* was confirmed in the free-energy landscape. The existence ratio in number of PrP* to its normal form was estimated to be 0.07. The SSPCA method has great potential to solve various challenges in studying highly flexible molecular systems, other than PrPs.
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Report
(4 results)
Research Products
(8 results)
