PROTEIN WORLD STUDIED BY PROTEIN DISTRIBUTION IN FAMILIES

• Project/Area Number: 20370058
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Nagoya University
• Principal Investigator: MITAKU Shigeki Nagoya University, 工学研究科, 教授 (10107542)
• Co-Investigator(Renkei-kenkyūsha): YOKOYAMA Yasunori 名古屋大学, 大学院・工学研究科, 助教 (80402486)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥20,670,000 (Direct Cost: ¥15,900,000、Indirect Cost: ¥4,770,000); Fiscal Year 2010: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2009: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2008: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
• Keywords: 理論生物学 / バイオインフォマティクス / 膜タンパク質 / 電荷分布 / タンパク質予測 / シミュレーション / ファミリー / ゲノム比較 / ファースカーブ / 自己相関関数 / フォースカーブ / 突然変異 / 進化 / ジンクフィンガー / DNA結合タンパク質

Research Abstract

The validity of the concept of protein world was investigated by analyzing all amino acid sequences from the total genomes of many organisms, using a high performance membrane protein predictor. The analyses of the distribution of exons containing membrane spanning regions lead to the conclusion that the exon shuffling extensively occurred in eukaryotic genomes. The number distribution of transmembrane regions in membrane proteins was analyzed for real genomes and simulated genomes of prokaryotic genomes. The result indicated that the single exponential distribution is due to the equilibrium of the change in the transmembrane numbers. The results for both eukaryotes and prokaryotes suggested that the families of membrane proteins have already reached to the equilibrium of random processes in genomes.

Research Products

• [Journal Article] How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes?. (2011)
  • Author(s): R.Sawada, S.Mitaku
  • Journal Title: Genes to Cells 16(1) Pages: 151-121
  • Peer Reviewed
• [Journal Article] How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes? (2011)
  • Author(s): R.Sawada, S.Mitaku
  • Journal Title: Genesto Cells Volume: 16(1) Pages: 115-121
  • Peer Reviewed
• [Journal Article] Effect of lipid phase transition on molecular assembly and structural stability of bacteriorhodopsin reconstituted into phosphatidylcholine liposomes with different acyl-chain lengths (2010)
  • Author(s): Y.Yokoyama, L.Negishi, T.Kitoh, M.Sonoyama, Y.Asami, S.Mitaku
  • Journal Title: J.Phys.Chem.B 114(47) Pages: 15706-15711
  • Peer Reviewed
• [Journal Article] SOSUImp1: high performance prediction system for single-spanning membrane proteins (2010)
  • Author(s): T.Tsuji, F.Akazawa, R.Sawada, S.Mitaku
  • Journal Title: Chem-Bio Informatics J. 10 Pages: 61-73
  • NAID: 130004138113
  • Peer Reviewed
• [Journal Article] Structural changes in bacteriorhodopsin in purple membranes induced by irreversible photobleaching with heterogeneous and homogeneous stability (2010)
  • Author(s): Y.Yokoyama, M.Sonoyama, S.Mitaku
  • Journal Title: Photochem.Photobiol 147 Pages: 127-133
  • Peer Reviewed
• [Journal Article] Characteristic amino acid distribution around segments unique to allergens (2010)
  • Author(s): N.Asakawa, N.Sakiyama, R.Teshima, S.Mitaku
  • Journal Title: J.Biochem. 147 Pages: 127-133
  • NAID: 10027873451
  • Peer Reviewed
• [Journal Article] Effect of lipid phase transition on molecular assembly and structural stability of bacteriorhodopsin reconstituted into phosphatidylcholine liposomes with different acyl-chain lengths (2010)
  • Author(s): Y.Yokoyama, L.Negishi, T.Kitoh, M.Sonoyama, Y.Asami, S.Mitaku
  • Journal Title: Journal of Physical Chemistry B Volume: 114(47) Pages: 15706-15711
  • Peer Reviewed
• [Journal Article] SOSUImpl : high performance prediction system for single-spanning membrane proteins (2010)
  • Author(s): T.Tsuji, F.Akazawa, R.Sawada, S.Mitaku
  • Journal Title: Chem-Bio Informatics Journal Volume: 10 Pages: 61-73
  • Peer Reviewed
• [Journal Article] Structural changes in bacteriorhodopsin in purple membranes induced byirreversible photobleaching with heterogeneous and homogeneous stability (2010)
  • Author(s): Y.Yokoyama, M.Sonoyama, S.Mitaku
  • Journal Title: Photochemistry and Photobiology Volume: 86(2) Pages: 297-301
  • Peer Reviewed
• [Journal Article] Characteristic amino acid distribution around segments unique to allergens (2010)
  • Author(s): N.Asakawa, N.Sakiyama, R.Teshima, S.Mitaku
  • Journal Title: Journal of Biochemistry 147 Pages: 127-133
  • NAID: 10027873451
  • Peer Reviewed
• [Journal Article] Effect of molecular assembly on photocycle of reconstituted bacteriorhodopsin : significant blue shift of the late M intermediate in the liquid crystalline phase (2009)
  • Author(s): M.Sonoyama, T.Kikukawa, Y.Yokoyama, M.Demura, N.Kamo, S.Mitaku
  • Journal Title: Chem.Lett. 38 Pages: 1134-1135
  • Peer Reviewed
• [Journal Article] Prediction of fragile points of coiled coils (2009)
  • Author(s): H.Tanizawa, M.Taniguchi, G.D.Ghimire, S.Mitaku
  • Journal Title: Chem-Bio Informatics J. 38 Pages: 12-29
  • Peer Reviewed
• [Journal Article] Prediction of fragile points of coiled coils (2009)
  • Author(s): H.Tanizawa, M.Taniguchi, G.D.Ghimire, S.Mitaku
  • Journal Title: Chem-Bio Informatics Journal 9 Pages: 12-29
  • Peer Reviewed
• [Journal Article] Effect of molecular assembly on photocycle of reconstituted bacteriorhodopsin : significant blue shift of the late M intermediate in the liquid crystalline phase (2009)
  • Author(s): M.Sonoyama, T.Kikukawa, Y.Yokoyama, M.Demura, N.Kamo, S.Mitaku
  • Journal Title: Chemistry Letters 38 Pages: 1134-1135
  • Peer Reviewed
• [Journal Article] SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria (2008)
  • Author(s): K. Imai, N.Asakawa, T.Tsuji, F.Akazawa, A.Ino, M.Sonoyama, S.Mitaku
  • Journal Title: Bioinformation 2(9) Pages: 417-421
  • Peer Reviewed
• [Journal Article] A high performance prediction system of coiled coil domains containing heptad breaks (2008)
  • Author(s): H.Tanizawa, G.D.Ghimire, S.Mitaku
  • Journal Title: SOSUIcoil, Chem-Bio Informatics J. 8 Pages: 96-111
  • Peer Reviewed
• [Journal Article] Physicochemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling (2008)
  • Author(s): G.D.Ghimire, H.Tanizawa, M.Sonoyama, S.Mitaku
  • Journal Title: Chem- Bio Informatics J. 8 Pages: 49-57
  • NAID: 130004138183
  • Peer Reviewed
• [Journal Article] SOSUI-GramN : high performance prediction for sub-eellular localization of proteins in Gram-negative bacteria (2008)
  • Author(s): K. Imai, N. Asakawa, T. Tsuji, F. Akazawa, A. Ino, M. Sonoyama, S. Mitaku
  • Journal Title: Bioinformation 2(9) Pages: 417-421
  • Peer Reviewed
• [Journal Article] A high performance prediction system of coiled coil domains containing heptad breaks : SOSUIcoil (2008)
  • Author(s): H. Tanizawa, G. D. Ghimire, S. Mitaku
  • Journal Title: Chem-Bio Informatics Journal 8 Pages: 96-111
  • NAID: 130004054128
  • Peer Reviewed
• [Journal Article] Physicoohemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling (2008)
  • Author(s): G. D. Ghimire, H. Tanizawa, M. Sonoyama, S. Mitaku
  • Journal Title: Chem-Bio Informatics Journal 8 Pages: 49-57
  • Peer Reviewed
• [Presentation] BMB2010 ワークショップ「膜タンパク質の構造・機能から見るオルガネラの進化-膜貫通分布領域からみたオルガネラの進化- (2010)
  • Author(s): 美宅成樹
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会
  • Place of Presentation: 神戸ポートアイランド他国内学会24件
  • Year and Date: 2010-12-07
• [Presentation] BMB2010ワークショップ「膜タンパク質の構造・機能から見るオルガネラの進化-膜貫通分布領域からみたオルガネラの進化- (2010)
  • Author(s): 美宅成樹
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2010-12-07
• [Presentation] 生命史40億年に起こった3大事件の犯人探し (2010)
  • Author(s): 美宅成樹
  • Organizer: 日本学術会議シンポジウム「生命多様性をめぐる科学と社会の対話」in南北海道
  • Place of Presentation: 北海道黒松内町環境学習センター
  • Year and Date: 2010-09-23
• [Presentation] Analysis of amyloidogenic sequences using AUF and hydrophobic indexes (2010)
  • Author(s): S.Kushima, N.Sakiyama, N.Asakawa, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-22
• [Presentation] Analysis of bumps structure of purple membrane by atomic forcemicroscopy observation (2010)
  • Author(s): S.Ozaki, Y.Yokoyama, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-22
• [Presentation] AFM single-molecule force spectroscopy of bacteriorhodopsin in delipidatedpurple membrane (2010)
  • Author(s): K.Yamada, Y.Higashi, T.Yamada, S.Ozaki, Y.Yokoyama, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-22
• [Presentation] Effect of molecular assembly upon structure and structural stability of bacteriorhodopsin reconstituted into phospholipid liposomes (2010)
  • Author(s): T.Kitoh, Y.Yokoyama, L.Negishi, M.Sonoyama, Y.Asami, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-22
• [Presentation] Conformational changes of single oyster myosin molecules in air and in solution : Atomic force microscopy and prediction of fragile points (2010)
  • Author(s): M.Taniguchi, S.Tateishi, Y.Yasawa, H.Tanizawa, T.Yamane, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-22
• [Presentation] Simulation of force-distance curve by chemical potential model for bacteriorhodopsin (2010)
  • Author(s): T.Yamada, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-21
• [Presentation] Comparative genomics using coiled coil prediction ststem : SOSUIcoil (2010)
  • Author(s): T.Hattori, H.Tanizawa, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-21
• [Presentation] Genome scale analysis of subcellular locarization of proteins in Gramnegative bacteria (2010)
  • Author(s): M.Sakuma, K.Imai, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-21
• [Presentation] Genome-wide analysis of the proteins with positive charge autocorrelation (2010)
  • Author(s): R.Ke, S.Mitaku
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学・川内北キャンパス
  • Year and Date: 2010-09-21
• [Presentation] アシル鎖長の異なる3種類の脂質膜リボソームに再構成されたバクテリオロドプシンにおける分子集合状態ならびに構造安定性に対する脂質膜相転移の影響 (2010)
  • Author(s): 鬼頭琢、横山泰範、根岸瑠美、麻見安雄、園山正史、美宅成樹
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2010-06-17
• [Presentation] 生物史40億年に起こった3大事件の犯人探し (2010)
  • Author(s): 美宅成樹
  • Organizer: 日本学術会議公開シンポジウム「生物多様性をめぐる科学と社会の対話」
  • Place of Presentation: 豊岡市民プラザ
  • Year and Date: 2010-05-22
• [Presentation] 生体膜関連シンポジウム「膜タンパク質-その物理と進化」 (2010)
  • Author(s): 美宅成樹、澤田隆介、辻敏行、横山泰範
  • Organizer: 日本膜学会第32回年会
  • Place of Presentation: 産業技術総合研究所臨海副都心センター東京都江車区
  • Year and Date: 2010-05-14
• [Presentation] Computational analysis of genome sequences by coarse graining of physical properties (2010)
  • Author(s): 美宅成樹
  • Organizer: International Symposium on Fifty Years of Biophysics Research at Nagoya University
  • Place of Presentation: Nagoya University
  • Year and Date: 2010-03-13
• [Presentation] 遺伝子の側面から生物の世界全体を見る (2009)
  • Author(s): 美宅成樹
  • Organizer: サイエンスアゴラ2009 シンポジウム「統合生物学」―生物をまとめて調べると見えてくる世界―
  • Place of Presentation: 国際研究交流大学村メディアホール (東京国際交流館)
  • Year and Date: 2009-11-02
• [Presentation] Effect of protein-lipid interaction of irreversible photobleaching of bacteriorhodopsin in purple membrane (2009)
  • Author(s): 成重太助, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-11-01
• [Presentation] Photobleaching of bacteriorhodopsin reconstituted in DMPC and DPPC bilayer (2009)
  • Author(s): 鬼頭琢, 根岸瑠美, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-11-01
• [Presentation] Identification of cytoplasmic and extracellular side of bacteriorhodopsin for force spectroscopy (2009)
  • Author(s): 東陽介, 尾崎聡, 渡邉直哉, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-11-01
• [Presentation] Development of the prediction method of membrane protein topology (2009)
  • Author(s): T.Tsuji, S.Mitaku
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-11-01
• [Presentation] Circular dichroism measurement of bacteriorhodopsin reconstituted in DMPC and DPPC bilayer in visible region (2009)
  • Author(s): 根岸瑠美, 鬼頭琢, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-10-31
• [Presentation] Analysis of DNA binding proteins with charge periodicity from human genome (2009)
  • Author(s): R.Ke, N.Sakiyama, S.Mitaku
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-10-31
• [Presentation] Simulation of force-distance curve of bacteriorhodopsin (2009)
  • Author(s): T.Yamada, S.Mitaku
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島
  • Year and Date: 2009-10-30
• [Presentation] バクテリオロドプシンのアルカリ化に伴う二次元結晶構造の崩壊過程 (2009)
  • Author(s): 東陽介, 尾崎聡, 渡邉直哉, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-22
• [Presentation] アミノ酸配列における正の電荷相関を持つタンパク質の機能解析 (2009)
  • Author(s): 柯閏聡, 美宅成樹
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-22
• [Presentation] N末端シグナル配列に基づくタンパク質の高精度細胞内局在予測システムの開発 (2009)
  • Author(s): 崎山則征, 美宅成樹
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-22
• [Presentation] 紫膜バクテリオロドプシンの光退色現象におけるタンパク質―脂質間相互作用の影響 (2009)
  • Author(s): 成重太助, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-21
• [Presentation] 脂質二層膜に再構成されたバクテリオロドプシンの脂質相転移への影響 (2009)
  • Author(s): 鬼頭琢, 根岸瑠美, 横山泰範, 園山正史, 美宅成樹
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-21
• [Presentation] Accurate Classification of Amino Acid Sequences by Physical Parameters Reveals the Conservation of Protein Groups in Evolution (2009)
  • Author(s): S. Mitaku
  • Organizer: ATI International Forum 2009 "Protein Structure Determination and Utilization"
  • Place of Presentation: Japan Proton Accelerator Research Complex (J-PARC), Tokai-mura
  • Year and Date: 2009-05-09
• [Presentation] Numbers of membrane proteins coded in 248 prokaryote genomes (2009)
  • Author(s): R.Sawada, R.Ke, T.Tsuji, M.Sonoyama, S.Mitaku
  • Organizer: 53th Annual meeting of Biophysical Society,Boston Convention and Exhibition Center, USA
  • Place of Presentation: 他国際会議11件
  • Year and Date: 2009-02-28
• [Presentation] Numbers of membrane proteins coded in 248 prokaryote genomes (2009)
  • Author(s): R. Sawada, R. Ke, T. Tsuji, M. Sonoyama, S. Mi taku
  • Organizer: 53^<th> Annual meeting of Biophysical Society
  • Place of Presentation: Boston Convention and Exhibition Center, USA
• [Presentation] シンポジウム「理論解析と実験から見出される生物物理学」、「各生物体を特徴付けるゲノムからの全アミノ酸配列の物理的情報解析」 (2008)
  • Author(s): 美宅成樹
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡国際会議場、福岡県
  • Year and Date: 2008-12-03
• [Presentation] Effect of molecular assembly oh photointermediates of bRreconstituted into dimyristoylphosphatidylcholine vesicles (2008)
  • Author(s): M. Sonoyama, T. Kikukawa, Y. Yokoyama, M. Demura, N. Kamo, S. Mitaku
  • Organizer: 13^<th> International Conference on Retinal Proteins
  • Place of Presentation: Casa Convalescencia, Barcelona, Spain
• [Presentation] Structural changes of bacteriorhodopsin in purple membrane induced by irreversible photobleaching (2008)
  • Author(s): Y. Yokoyama, M. Sonoyama, S. Mitaku
  • Organizer: 13^<th> International Conference on Retinal Proteins
  • Place of Presentation: Casa Convalescencia, Barcelona, Spain
• [Presentation] Multiple states in photobleaching of reconstituted bacteriorhodopsin (2008)
  • Author(s): L. Negishi, S. Mitaku
  • Organizer: 13^<th> International Conference on Retinal Proteins
  • Place of Presentation: Casa Convalescencia, Barcelona, Spain
• [Presentation] Analysis of human proteins with a charge periodicity of 28 residues in amino acid sequences (2008)
  • Author(s): R. Ke, N. Sakiyama, M. Sonoyama, S. Mitaku
  • Organizer: The joint 2^<nd> Pacific Rim International Conference on Protein Science and 4^<th> Asian-Oceania Human Proteome Organization
  • Place of Presentation: Cairns Convention Centre, Australia
• [Presentation] Prediction of nuclear proteins with a charge periodicity of 28 residues in eukaryote genomes (2008)
  • Author(s): N. Sakiyama, R. Ke, M. Sonoyama, S. Mitaku
  • Organizer: The joint 2^<nd> Pacific Rim International Conference on Protein Science and 4^<th> Asian-Oceania Human Proteome Organization
  • Place of Presentation: Cairns Convention Centre, Australia
• [Presentation] Development of a high performance prediction method for single spanning membrane proteins (2008)
  • Author(s): T. Tsuj I, S, Mitaku
  • Organizer: The joint 2^<nd> Pacific Rim International Conference on Protein Science and 4^<th> Asian-Oceania Human Proteome Organization
  • Place of Presentation: Cairns Convention Centre, Australia
• [Book] 世界に通じる科学英語論文の書き方 執筆・投稿・査読・発表 (2010)
  • Author(s): R.A.ガイル・B.ガステル著美宅成樹訳
  • Total Pages: 322
  • Publisher: 丸善株式会社
• [Book] 世界に通じる科学英語論文の書き方 執筆・投稿・査読・発表 (2010)
  • Author(s): R.A.ガイル・B.ガステル 著, 美宅成樹 訳
  • Total Pages: 322
  • Publisher: 丸善株式会社
• [Remarks] ホームページ等
  • URL: http://bp.nuap.nagoya-u.ac.jp/sosui/sosuigramn/sosuigramn_submit.html
• [Remarks]
  • URL: http://bp.nuap.nagoya-u.ac.jp/sosui/sosuigramn/sosuigramn_submit.html