| Project/Area Number |
15510163
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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 |
Applied genomics
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| Research Institution | Tokyo Institute of Technology |
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Principal Investigator |
OTA Motonori Tokyo Tech, GSIC, Associate Professor, 学術国際情報センター, 助教授 (40290895)
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| Co-Investigator(Kenkyū-buntansha) |
ISOGAI Yasuhiro Riken, Bio-metal Science, Senior Researcher, 城生体金属科学, 先任研究員 (00201921)
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| Project Period (FY) |
2003 – 2005
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| Project Status |
Completed (Fiscal Year 2005)
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| Budget Amount *help |
¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 2005: ¥500,000 (Direct Cost: ¥500,000)
Fiscal Year 2004: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 2003: ¥1,300,000 (Direct Cost: ¥1,300,000)
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| Keywords | tertiary structure / side-chain packing / 3D profile / modeller / local conformation / 測鎖パッキング / ラマチャンドランプロット / 二次構造 / エントロピー |
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| Research Abstract |
To design the artificial proteins that exhibit the structural specificity like naturally occurring proteins, we tried to develop the new structure-sequence compatibility functions and the new methodology to design functional proteins, and validate them with the experiments. Also we addressed to the stability analyses of point mutations and protein folding simulations and experiments. The insights obtained through these above activities are accumulated to enrich the design strategy. As for the new function, we developed one that evaluates the fitness of the small segment of amino acids on the local structure defined by the successive Ramachandran plot. We defined twelve types of Single Site Conformational Code (SSCC) and statistical potential was derived for them and amino acids. The accuracy of this function was estimated using the two types of decoy sets and we noticed its performance is better than the function that employs the output of DSSP as the definition of local conformation. Also we tried the transformation of the protein function between the homologous proteins. Based on the 3D structure of myoglobin, a phycocyanin sequence was minimally modified using the Modeller program and 3D-profile. The resulted sequence was synthesized and it has a part of α helices and binds HEM weekly. The sequence designed by the other method of digging a hole on phycocyanin for HEM, performs better : it has more α helical content and shows good HEM binding. Additionally, we could determined the NMR structure of artificial Cro repressor we designed before and published it in the Journal of Molecular Biology.
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