| Project/Area Number |
12208006
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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 | Nagahama Institute of Bio-Science and Technology (2003-2004)
Nagoya University (2000-2002) |
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Principal Investigator |
GO Mitiko Nagahama Institute of Bio-Science and Technology, Faculty of Bio-Science, Professor, バイオサイエンス学部, 教授 (70037290)
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| Co-Investigator(Kenkyū-buntansha) |
TAKAHASHI Kenichi Nagahama Institute of Bio-Science and Technology, Faculty of Bio-Science, Associate Professor, バイオサイエンス学部, 助教授 (20322737)
SHIRAI Tsuyoshi Biomolecular Engineering Research Institute, Department of Computational Biology, Senior Research Scientist, 生命情報解析部門, 主任研究員 (00262890)
SODA Kunitsugu Nagaoka University of Technology, Department of Bioengineering, Professor, 生物系, 教授 (10011686)
YURA Kei Japan Atomic Energy Research Institute, Center for Fromotion of Computational Science and Engineering, Quantum Bioinformatics Group, Researcher, 計算科学技術推進センター, 副主任研究員 (50252226)
木寺 詔紀 京都大学, 大学院・理学研究科, 助教授 (00186280)
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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 |
¥112,800,000 (Direct Cost: ¥112,800,000)
Fiscal Year 2004: ¥24,000,000 (Direct Cost: ¥24,000,000)
Fiscal Year 2003: ¥24,000,000 (Direct Cost: ¥24,000,000)
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 | Prediction of genome function / Module / 3D-keynote / Cyanobacterium genome / Human genome annotation / Sugar-protein interaction / Hydrophobic cluster / Alternative splicing / タンパク質間ネットワーク / HetPDB-Navi / RNA・タンパク質相互作用 / FAMSBASE / タンパク質-RNA相互作用 / 水和 / タンパク質-リガンド相互作用 / Het PDB-Navi / ヒトゲノムアノテーション / すき間 / タンパク質-糖鎖相互作用 / 疎水核 / サブユニット相互作用 / タンパク質-糖鎖予測 / タンパク質立体構造予測 / タンパク質フォールディング / 形質転換 / タンパク質-リガンド相互作用予測法 / 確率的アラインメント法 / 疎水殻の自動同定 |
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| Research Abstract |
As a functional prediction method for ORFs inferred in genome sequences, we developed a method to convert structural and functional properties of protein modules into amino acid sequence patterns, called "3D-keynote". Using the method, we inferred a function of ORF, slr0197 from a cyanobacterium genome, which was subsequently verified by collaborative experiments. Furthermore, we made an automatic system to generate 3D-keynotes for each kind of functions and accomplished generations of 196 kinds of 3D-keynotes, whose prediction accuracies were evaluated to be about 85% on an average. Applying these to a cyanobacterium genome, we obtained clues for inferring the functions for about 12% of function-unknown ORFs. The 3D-keynotes were also used for human genome annotation in H-invitational (Yura ＆ Go).
A sugar-protein interaction prediction system was developed. Strict and loose evaluations of the prediction accuracy resulted in 25 and 66%, respectively, which were better than other existin
… More
g methods. To experimentally verify the prediction system, crystal structure analyses of sugar-binding proteins such as lectin, were done. We determined structures of six novel complex forms of congerin and obtained evidences supporting the existence of sugar-binding sites predicted by the prediction system (Shirai).
A chain topology of hydrophobic cluster residues was found to be a reduced representation of a whole chain of the protein molecule. From molecular dynamics simulations of a pseudo-peptide chain composed of hydrophobic cluster residues and cluster analyses of the generated structures, we defined roles of hydrophobic cluster residues as their non-specific hydrophobic aggregation forces made the protein chain compact to decrease the search space for conformations and accelerate the folding process (Soda).
Exhaustively analyzing human full-length cDNA data by the method we developed to identify alternative splicing (AS) regions, we found that most regions altered by AS were shorter than common sizes of protein domains, and indicated possibilities that AS of transcripts may lead to structural destabilization of and/or loss of interaction sites on their protein products and result in changing pathways of the protein network involved (Go ＆ Takahashi). Less
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