| Project/Area Number |
10680644
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Soka University |
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Principal Investigator |
KOBAYASHI Yukio Soka University Faculty of Engineering Associate professor, 工学部, 助教授 (10247281)
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| Project Period (FY) |
1998 – 1999
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| Project Status |
Completed (Fiscal Year 1999)
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| Budget Amount *help |
¥1,500,000 (Direct Cost: ¥1,500,000)
Fiscal Year 1999: ¥300,000 (Direct Cost: ¥300,000)
Fiscal Year 1998: ¥1,200,000 (Direct Cost: ¥1,200,000)
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| Keywords | island model / protein structure prediction / secondary structure / tertiary structure / prion |
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| Research Abstract |
I simulated the folding process of prion protein by the island model to elucidate the transition from PrPィイD1cィエD1 to PrPィイD1ScィエD1. The NMR structure of PrP contains two β-strands and three α-helices. The presence of β-strands is in contrast with model predictions of an all-helical structure of PrPィイD1cィエD1. The present problems are as follows : (1) the packing simulation of two β-strands and three α-helices, (2) the improvement of our statistical mechamical method for protein secondary structure prediction to predict the initial secondary structures of PrP.
Our previous works showed that the tertiary structures of several proteins can be predicted provided that the positions of secondary structures are known. The packing simulation of PrP, however, did not yield the tertiary structure similar to the NMR structure. This indicates that the presence of β-strands may be important for the initiation of the transition from PrPィイD1cィエD1 to PrPィイD1ScィエD1.
To predict protein secondary structures by our statistical mechanical method, the statistical weights of residue pairs in α-helix and β-strand are necessary. These parameters, however, have not been optimized properly and thus the prediction results of proteins for estimation have reached the accuracy of only 68%, which may not be sufficient for packing secondary structures into the correct tertiary structure. The improvement is in progress.
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