| Project/Area Number |
12208005
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Nagoya University (2003-2004)
Tokyo University of Agriculture and Technology (2000-2002) |
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Principal Investigator |
MITAKU Shigeki Nagoya University, Graduate School of Engineering, Department of Applied Physics, Professor, 大学院工学研究科, 教授 (10107542)
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| Co-Investigator(Kenkyū-buntansha) |
SONOYAMA Masashi Nagoya University, Graduate School of Engineering, Department of Applied Physics, Associate Professor, 大学院理学研究科, 助教授 (40242242)
YAMATO Takahisa Nagoya University, Graduate School of Science, Departmet of Physics, Associate Professor, 大学院理学研究科, 助教授 (90251587)
YAMATO Ichiro Tokyo University of Science, Faculty of Industrial Science and Technology, Professor, 基礎工学部, 教授 (70111458)
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| Project Period (FY) |
2000 – 2004
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| Project Status |
Completed (Fiscal Year 2004)
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| Budget Amount *help |
¥104,800,000 (Direct Cost: ¥104,800,000)
Fiscal Year 2004: ¥20,000,000 (Direct Cost: ¥20,000,000)
Fiscal Year 2003: ¥20,000,000 (Direct Cost: ¥20,000,000)
Fiscal Year 2002: ¥30,800,000 (Direct Cost: ¥30,800,000)
Fiscal Year 2001: ¥34,000,000 (Direct Cost: ¥34,000,000)
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| Keywords | membrane protein / protein structure / protein function / prediction / simulation / molecular dynamics / genome / proteome / 膜タンパク質 / アミノ酸配列 / 膜組み込み装置 / 分子認識 / シグナルペプチド / 計算機シミュレーション / 光受容膜タンパク質 / ポリンチャネル / タンパク質分類 / 物理的予測 / 膜タンパク質予測 / ドッキング / バクテリオロドプシン / チャネル / バイオインフォマティクス / 構造予測 / 分子シミュレーション / 輸送体 / 受容体 / 構造・機能予測 / 構造・機能分類 / 立体構造予測 / バイオインフォマティックス |
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| Research Abstract |
The software systems were developed for predicting membrane proteins, signal peptides and mitochondria localization signals, analyzing amino acid sequences from total genomes. The parameters for the analysis and prediction are the electric charges, the hydrophobicity, amphiphilicity and the flexibility of polypeptides due to the density of glycine and proline. The developed systems are for (1) the improvement of membrane prediction, (2) the prediction of signal peptides and (3) the mitochondria localization of proteins. Using the methods for the membrane proteins prediction, all amino acid sequences from total genomes were analyzed and the ratio of membrane proteins was found to be almost constant. The distribution of transmembrane helices was discussed in view of the evolutionary generation of membrane proteins. The simulations of the dynamical structures and the function of light receptors and channel proteins were performed by the combination of the quantum chemistry and the molecular dynamics as well as the Brownian dynamics.
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