1999 年度実績報告書

プロテオーム時代の計算情報生物学

研究課題

研究課題/領域番号	11898023
研究機関	名古屋大学
研究代表者	郷通子名古屋大学, 大学院・理学研究科, 教授 (70037290)
研究分担者	中村春木大阪大学, 蛋白質研究所・附属生体分子解析研究センター, 教授 (80134485) 美宅成樹東京農工大学, 工学部, 教授 (10107542) 西川建国立遺伝学研究所, 生命情報研究センター, 教授 (10093288) 梅山秀明北里大学, 薬学部・生物分子設計学講座, 教授 (20050619) 木寺紹紀京都大学, 大学院・理学研究科, 助教授 (00186280)
キーワード	計算生物学 / 構造生物学 / ゲノム情報 / タンパク質立体構造 / 構造ゲノミックス / 機能ゲノミックス / プロテオーム / プロテオミックス
研究概要	ゲノム生物学の時代を迎え、ゲノム・プロテオームの計算生物学は生物科学全体に位置づけられる重要な分野となりつつある。第一線の研究者による重点的研究の組織化が待たれている現状を踏まえ、特定領域研究(A)の申請を目的として、研究方法、研究組織、研究経費などの企画調査を行った。国内のタンパク質の立体構造計算の分野は、大型コンピュータの最初の導入以来の研究の歴史をもち、世界に誇れるレベルの研究が行われているにも関わらず、これまでゲノム情報の特定領域研究にほとんど組み込まれてこなかった。米国と欧州のゲノム研究とは大きな違いを生じている。8月に第1回の班会議を開催して、構造ゲノミックスと機能ゲノミックスを中心とした公開国際シンポジウムを開催すること、特定領域研究(A)を申請することを決定した。予定通り、特定領域研究(A)「プロテオーム時代の情報構造生物学」(領域代表:郷通子)を申請した。2000年1月17、18日には海外から4名の若手の第1線の研究者を招いて、公開国際シンポジウム「プロテオーム時代の計算情報生物学」を東京で開催した。200名の参加者があり、活気に溢れた会場には、この分野に対する大学や企業の研究者からの期待感がよみとれた。一方、ミレニアム構想のもとに国家的プロジェクトとして特定領域研究(C)が、平成12年度から発足することが決定された。申請中の特定領域研究(A)「プロテオーム時代の情報構造生物学」は、「ゲノム情報科学の新展開」(領域代表:高木利久)の1項目「タンパク質高次構造に基づくゲノム情報科学」(班長:郷通子)として合流することになった。従って、本基盤研究(C)は、予定よりも少なくても1年早く、その目的を達成することができた。班員のほとんどが、この特定領域(C)のメンバーとして、5年間の「ゲノム情報科学」プロジェクトの重要な課題に取り組む。

研究成果

(44件)

すべてその他

すべて文献書誌 (44件)

[文献書誌] Satoshi Kaneko et al.: "An Investigation of the Nature and Function of Module 10 in a Family F/10 Xylanase FXYN of Streptomyces olivaceoviridis E-86 by Module Shuffling with the Cex of Cellulomonas fimi and by Site-Directed Mutagenesis."FEBS Letters. 460・1. 61-66 (1999)
[文献書誌] Ken-ichi Takahashi et al.: "A Mini-Protein Designed by Removing a Module from Barnase: Molecular Modeling and NMR Measurements of the Conformation."Protein Engineering. 12・8. 673-673 (1999)
[文献書誌] Ota,M.et al.: "Feasibility in the inverse protein folding protocol."Protein Science. 8・5. 1001-1009 (1999)
[文献書誌] Fukami-Kobayashi,et al.: "Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history."Journal of Molecular Biology. 286・1. 279-290 (1999)
[文献書誌] Mitaku,S.et al.: "Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length."Protein Engineering. 12・11. 953-957 (1999)
[文献書誌] Mitaku,S.et al.: "Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system."Biophysical Chemistry. 82. 165-171 (1999)
[文献書誌] Shirai,H.et al.: "H3-rules: Identification of CDR-H3 structures in antibodies."FEBS Letters. 455. 188-197 (1999)
[文献書誌] Kim,S.T.et al.: "Enhanced conformational diversity search of CDR-H3 in antibodies: Roles of the first CDR-H3 residue."Proteins: Structures Function and Genetics. 37. 683-696 (1999)
[文献書誌] Kinoshita,K.et al.: "Structural motif of phosphate binding site common to various protein superfamilies: All-against-all structural comarison of protein-mononucleotide complexes."Protein Engineering. 12・1. 11-14 (1999)
[文献書誌] Kinoshita,K.et al.: "Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements."Protein Science. 8・6. 1210-1217 (1999)
[文献書誌] Ogata,K.et al.: "Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method."Journal of Molecular Graphics and Modelling. 16. 178-189 (1999)
[文献書誌] Yoneda,T.et al.: "A homology modeling method of an icosahedral viral capsid: Inclusion of surrounding protein structures."Journal of Molecular Graphics and Modelling. (in press).
[文献書誌] Takano,M.et al.: "Molecular dynamics of a 15-residue poly(L-alanine) in water: the helix formation and its energetics."Journal of American Chemical Society. 121・4. 605-612 (1999)
[文献書誌] Yamamoto,S.et al.: "Ab initio MO study on the potential energy surfaces for twisting around C11=C12 bond of protonated Schiff base of retinal."THEOCHEM. 461・462. 463-471 (1999)
[文献書誌] Kakitani,T.et al.: "Theory of excitation transfer in the intermediate coupling case."Journal of Physical Chemistry. 68. 3729-3737 (1999)
[文献書誌] Kakitani,T.et al.: "Color tuning mechanism of human red and green visual pigments."Photochemistry and Photobiology. 70. 686-693 (1999)
[文献書誌] Mitsutake,A.et al.: "Alpha-helix propensities of homo-oligomers in aqueous solution studied by multicanonical algorithm."Chemical Physics Letters. 309. 95-100 (1999)
[文献書誌] Sugita,Y.et al.: "Replica-exchange molecular dynamics method for protein folding."Chemical Physics Letters. 314. 141-151 (1999)
[文献書誌] J.An et al.: "Construction of an integrated enviroment for sequence,structure,property and function analysis of proteins."Genome Informatics. 10. 229-230 (1999)
[文献書誌] Saito, S et al.: "Kinetic Consistency in Protein Folding Prosess."Journal of Molecular Structure (Theochem). 462. 503-521 (1999)
[文献書誌] Yomo, T et al.: "Gradual Development of Protein-like Global Structures through Functional Selection."Nature Structural Biology. 6. 743-746 (1999)
[文献書誌] Kamatari, Y.O.et al.: "The compact and expanded denatured conformations of apomyoglobin in the methanol-water solvent."Protein Science. 8. 873-882 (1999)
[文献書誌] Salamov, Adaf,et al.: "Genome Analysis: Assigning protein coding regions to 3D structures"Protein Science. 8. 771-777 (1999)
[文献書誌] Suwa,M.et al.: "A Novel Measure Characterized by a Polar Energy Surface Approximation for Recognition and Classification of Transmembrane Protein Structures."Proteins: Structures,Function and Genetics. (in press).
[文献書誌] Suzuki,Y.et al.: "A method for detecting positive selection at single amino acid sites."Molecular Biology and Evolution. 16. 1315-1328 (1999)
[文献書誌] Bellgard,M.et al.: "Inferring the direction of evolutionary changes of genomic base composition"Trends in Genetics. 15・7. 254-256 (1999)
[文献書誌] Kanai,S.et al.: "Identification of new members of the GS ADP-forming family from de novo purine biosynthesis pathway."Journal of Moleclar Evolution. 48・4. 489-492 (1999)
[文献書誌] Beuckmann,C.T.et al.: "Binding of biliverdin,biliruvin,and thyroid hormones to lipocalin-type prostaglandin Dsynthase."Biochemistry. 38・25. 8006-8013 (1999)
[文献書誌] Miyazawa,S.et al.: "Self-consistent Estimation of Inter-residue Protein Contact Energies Based on an Equilibrium Mixture Approximation of Residues."PROTEINS: Structures,Function,and Genetics. 34. 49-68 (1999)
[文献書誌] Miyazawa,S.et al.: "An Empirical Energy Potential with a Reference State for Protein Fold and Sequence Recognition."PROTEINS: Structures,Function,and Genetics. 36. 357-369 (1999)
[文献書誌] Yura,K.et al.: "Putative mechanism of natural transformation as deduced from genome data."DNA Research. 6・2. 75-82 (1999)
[文献書誌] Sato,Y.et al.: "Module-intron correlation and intron sliding in family F/10 xylanase genes."Gene. 238・1. 93-101 (1999)
[文献書誌] Shirai,T.et al.: "Crystal structure of a protein with an artificial exon-shuffling,module M4-substituted chimra hemoglobin ba,at 2. 5 A resolution."Journal of Molecular Biology. 287・1. 369-382 (1999)
[文献書誌] Shiral,T.et al.: "High-resolution structure of conger eel galectin,congerin I,in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution."Structure. 7・10. 1223-1233 (1999)
[文献書誌] Kinoshita,K.et al.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)
[文献書誌] 梅山秀明(編集): "廣川有機薬科学実験講座1 創薬志向の分子設計"梅山秀明、福原健一(廣川書店). 260 (2000)
[文献書誌] Yamato,T.et al.(分担執筆): "Photosyntheses: Mechanisms and Effects"G.Garab (Kluwer Academic Publishers). 2416 (1999)
[文献書誌] 垣谷俊昭(分担執筆): "光がもたらす生命と地球の共進化"垣谷俊昭、三室守編(中部経済新聞社). 139 (1999)
[文献書誌] Hansmann,U.H.E.et al.(分担執筆): "Annual Reviews in Computational Physics VI"Stauffer,D.(World Scientific). 346 (1999)
[文献書誌] Nakamura,H.K.et al.(分担執筆): "Old and New Views of Protein Folding"K.Kuwajima and M.Arai (Elsevier,Amsterdam). 318 (1999)
[文献書誌] Soda,K.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)
[文献書誌] Gojobori,T.: "Molecular Strategies in Biological Evolution Part VI. Symmary"Annals of the New York Academy of Sciences. 434 (1999)
[文献書誌] Kikuno,R.et al.(分担執筆): "Comprehensive Natural Products Chemistry. Volume I"Barton et al.(Elsevier). 429 (1999)
[文献書誌] Go,M.et al.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)

1999 年度 実績報告書

プロテオーム時代の計算情報生物学

研究代表者

郷 通子 名古屋大学, 大学院・理学研究科, 教授 (70037290)

研究成果

[文献書誌] Satoshi Kaneko et al.: "An Investigation of the Nature and Function of Module 10 in a Family F/10 Xylanase FXYN of Streptomyces olivaceoviridis E-86 by Module Shuffling with the Cex of Cellulomonas fimi and by Site-Directed Mutagenesis."FEBS Letters. 460・1. 61-66 (1999)

[文献書誌] Ken-ichi Takahashi et al.: "A Mini-Protein Designed by Removing a Module from Barnase: Molecular Modeling and NMR Measurements of the Conformation."Protein Engineering. 12・8. 673-673 (1999)

[文献書誌] Ota,M.et al.: "Feasibility in the inverse protein folding protocol."Protein Science. 8・5. 1001-1009 (1999)

[文献書誌] Fukami-Kobayashi,et al.: "Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history."Journal of Molecular Biology. 286・1. 279-290 (1999)

[文献書誌] Mitaku,S.et al.: "Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length."Protein Engineering. 12・11. 953-957 (1999)

[文献書誌] Mitaku,S.et al.: "Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system."Biophysical Chemistry. 82. 165-171 (1999)

[文献書誌] Shirai,H.et al.: "H3-rules: Identification of CDR-H3 structures in antibodies."FEBS Letters. 455. 188-197 (1999)

[文献書誌] Kim,S.T.et al.: "Enhanced conformational diversity search of CDR-H3 in antibodies: Roles of the first CDR-H3 residue."Proteins: Structures Function and Genetics. 37. 683-696 (1999)

[文献書誌] Kinoshita,K.et al.: "Structural motif of phosphate binding site common to various protein superfamilies: All-against-all structural comarison of protein-mononucleotide complexes."Protein Engineering. 12・1. 11-14 (1999)

[文献書誌] Kinoshita,K.et al.: "Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements."Protein Science. 8・6. 1210-1217 (1999)

[文献書誌] Ogata,K.et al.: "Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method."Journal of Molecular Graphics and Modelling. 16. 178-189 (1999)

[文献書誌] Yoneda,T.et al.: "A homology modeling method of an icosahedral viral capsid: Inclusion of surrounding protein structures."Journal of Molecular Graphics and Modelling. (in press).

[文献書誌] Takano,M.et al.: "Molecular dynamics of a 15-residue poly(L-alanine) in water: the helix formation and its energetics."Journal of American Chemical Society. 121・4. 605-612 (1999)

[文献書誌] Yamamoto,S.et al.: "Ab initio MO study on the potential energy surfaces for twisting around C11=C12 bond of protonated Schiff base of retinal."THEOCHEM. 461・462. 463-471 (1999)

[文献書誌] Kakitani,T.et al.: "Theory of excitation transfer in the intermediate coupling case."Journal of Physical Chemistry. 68. 3729-3737 (1999)

[文献書誌] Kakitani,T.et al.: "Color tuning mechanism of human red and green visual pigments."Photochemistry and Photobiology. 70. 686-693 (1999)

[文献書誌] Mitsutake,A.et al.: "Alpha-helix propensities of homo-oligomers in aqueous solution studied by multicanonical algorithm."Chemical Physics Letters. 309. 95-100 (1999)

[文献書誌] Sugita,Y.et al.: "Replica-exchange molecular dynamics method for protein folding."Chemical Physics Letters. 314. 141-151 (1999)

[文献書誌] J.An et al.: "Construction of an integrated enviroment for sequence,structure,property and function analysis of proteins."Genome Informatics. 10. 229-230 (1999)

[文献書誌] Saito, S et al.: "Kinetic Consistency in Protein Folding Prosess."Journal of Molecular Structure (Theochem). 462. 503-521 (1999)

[文献書誌] Yomo, T et al.: "Gradual Development of Protein-like Global Structures through Functional Selection."Nature Structural Biology. 6. 743-746 (1999)

[文献書誌] Kamatari, Y.O.et al.: "The compact and expanded denatured conformations of apomyoglobin in the methanol-water solvent."Protein Science. 8. 873-882 (1999)

[文献書誌] Salamov, Adaf,et al.: "Genome Analysis: Assigning protein coding regions to 3D structures"Protein Science. 8. 771-777 (1999)

[文献書誌] Suwa,M.et al.: "A Novel Measure Characterized by a Polar Energy Surface Approximation for Recognition and Classification of Transmembrane Protein Structures."Proteins: Structures,Function and Genetics. (in press).

[文献書誌] Suzuki,Y.et al.: "A method for detecting positive selection at single amino acid sites."Molecular Biology and Evolution. 16. 1315-1328 (1999)

[文献書誌] Bellgard,M.et al.: "Inferring the direction of evolutionary changes of genomic base composition"Trends in Genetics. 15・7. 254-256 (1999)

[文献書誌] Kanai,S.et al.: "Identification of new members of the GS ADP-forming family from de novo purine biosynthesis pathway."Journal of Moleclar Evolution. 48・4. 489-492 (1999)

[文献書誌] Beuckmann,C.T.et al.: "Binding of biliverdin,biliruvin,and thyroid hormones to lipocalin-type prostaglandin Dsynthase."Biochemistry. 38・25. 8006-8013 (1999)

[文献書誌] Miyazawa,S.et al.: "Self-consistent Estimation of Inter-residue Protein Contact Energies Based on an Equilibrium Mixture Approximation of Residues."PROTEINS: Structures,Function,and Genetics. 34. 49-68 (1999)

[文献書誌] Miyazawa,S.et al.: "An Empirical Energy Potential with a Reference State for Protein Fold and Sequence Recognition."PROTEINS: Structures,Function,and Genetics. 36. 357-369 (1999)

[文献書誌] Yura,K.et al.: "Putative mechanism of natural transformation as deduced from genome data."DNA Research. 6・2. 75-82 (1999)

[文献書誌] Sato,Y.et al.: "Module-intron correlation and intron sliding in family F/10 xylanase genes."Gene. 238・1. 93-101 (1999)

[文献書誌] Shirai,T.et al.: "Crystal structure of a protein with an artificial exon-shuffling,module M4-substituted chimra hemoglobin ba,at 2. 5 A resolution."Journal of Molecular Biology. 287・1. 369-382 (1999)

[文献書誌] Shiral,T.et al.: "High-resolution structure of conger eel galectin,congerin I,in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution."Structure. 7・10. 1223-1233 (1999)

[文献書誌] Kinoshita,K.et al.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)

[文献書誌] 梅山 秀明(編集): "廣川有機薬科学実験講座1 創薬志向の分子設計"梅山秀明、福原健一(廣川書店). 260 (2000)

[文献書誌] Yamato,T.et al.(分担執筆): "Photosyntheses: Mechanisms and Effects"G.Garab (Kluwer Academic Publishers). 2416 (1999)

[文献書誌] 垣谷俊昭(分担執筆): "光がもたらす生命と地球の共進化"垣谷俊昭、三室守編(中部経済新聞社). 139 (1999)

[文献書誌] Hansmann,U.H.E.et al.(分担執筆): "Annual Reviews in Computational Physics VI"Stauffer,D.(World Scientific). 346 (1999)

[文献書誌] Nakamura,H.K.et al.(分担執筆): "Old and New Views of Protein Folding"K.Kuwajima and M.Arai (Elsevier,Amsterdam). 318 (1999)

[文献書誌] Soda,K.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)

[文献書誌] Gojobori,T.: "Molecular Strategies in Biological Evolution Part VI. Symmary"Annals of the New York Academy of Sciences. 434 (1999)

[文献書誌] Kikuno,R.et al.(分担執筆): "Comprehensive Natural Products Chemistry. Volume I"Barton et al.(Elsevier). 429 (1999)

[文献書誌] Go,M.et al.(分担執筆): "Old and New Views of Protein Folding"Kuwajima,K.and Arai,M.(Elsevier Science). 318 (1999)

1999 年度実績報告書

郷通子名古屋大学, 大学院・理学研究科, 教授 (70037290)

[文献書誌] 梅山秀明(編集): "廣川有機薬科学実験講座1 創薬志向の分子設計"梅山秀明、福原健一(廣川書店). 260 (2000)