The second ATP-binding site of the chaperonin GroEL and its functional role

• Project/Area Number: 20370066
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities
• Principal Investigator: KUWAJIMA Kunihiro National Institutes of Natural Sciences Okazaki Research Facilities, 岡崎統合バイオサイエンスセンター, 教授 (70091444)
• 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: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2009: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2008: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
• Keywords: 分子シャペロン / シャペロニン / ATP結合 / アロステリック転移 / 生物物理 / 分子機械 / 分子認識 / 生体分子 / 蛋白質

Research Abstract

The Escherichia coli chaperonin GroEL, a molecular chaperone that mediates protein folding in the biological cell, expresses its chaperone function through ATP binding. In the present study, we investigated the ATP binding to GroEL by photo-affinity labeling, amino acid sequence analysis, stopped-flow fluorescence spectroscopy, and isothermal titration calorimetry. We found (1) that the second ATP-binding site is present and located near Tyr360, and (2) that in the absence of potassium ion, only the ATP binding to the primary site was observed, and its binding constant is an order of 10^4M^<-1>.

Research Products

• [Journal Article] Dissecting a bimolecular process of MgATP2. binding to the chaperonin GroEL. (2011)
  • Author(s): Chen, J., Makabe K., Nakamura T., Inobe, T. Kuwajima K.
  • Journal Title: J.Mol.Biol., in the press.
  • Peer Reviewed
• [Journal Article] Dissecting a bimolecular process of MgATP^<2-> binding to the chaperonin GroEL (2011)
  • Author(s): Jin Chen
  • Journal Title: J.Mol.Biol. Volume: 印刷中
  • Peer Reviewed
• [Journal Article] 何が蛋白質のフォールディング経路を決めるのか? (2010)
  • Author(s): 中村敬, 真壁幸樹, 桑島邦博
  • Journal Title: Medical Bio 9月号別冊「揺らぎと生体機能」オーム社東京 Pages: 52-57
• [Journal Article] Adaptation of a hyperthermophilic group II chaperonin to relatively moderate temperatures. (2010)
  • Author(s): Kanzaki, T., Ushioku, S., Nakagawa, A., Oka, T., Takahashi, K., Nakamura T., Kuwajima K. Yamagishi, A. Yohda, M.
  • Journal Title: Protein Eng.Des.Sel. 23 Pages: 393-402
  • Peer Reviewed
• [Journal Article] Different folding pathways taken by highly homologous proteins, goat α-lactalbumin and canine milk lysozyme. (2010)
  • Author(s): Nakamura T., Makabe K., Tomoyori, K., Maki, K., Mukaiyama, A. Kuwajima, K.
  • Journal Title: J.Mol.Biol. 396 Pages: 1361-1378
  • Peer Reviewed
• [Journal Article] Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. (2010)
  • Author(s): Ochi, A., Makabe K., Kuwajima K., Hori, H.
  • Journal Title: J.Biol.Chem. 285 Pages: 9018-9029
  • Peer Reviewed
• [Journal Article] 何がタンパク質のフォールディング経路を決めるのか? (2010)
  • Author(s): 中村敬
  • Journal Title: MedicalBio(オーム社) Volume: 10月号別冊 Pages: 49-54
• [Journal Article] Flexible recognition of the tRNA G18 methylation target site by Trm Hmethyltransferase through first binding and induced fit processes (2010)
  • Author(s): A.Ochi
  • Journal Title: J.Biol.Chem. 285 Pages: 9018-9029
  • Peer Reviewed
• [Journal Article] Adaptation of a hyperthermophilic group II chaperonin to relatively moderate temperatures (2010)
  • Author(s): T.Kanzaki
  • Journal Title: Protein.Eng.Des.Sel. 23 Pages: 393-402
  • Peer Reviewed
• [Journal Article] Different folding pathways taken by highly homologous proteins, goat α-lactalbumin and canine milk lysozyme (2010)
  • Author(s): T.Nakamura
  • Journal Title: J.Mol.Biol. 396 Pages: 1361-1378
  • Peer Reviewed
• [Journal Article] Non-native-helix formation is not necessary for folding of lipocalin : Comparison of burst-phase folding between tear lipocalin and β-lactoglobulin. (2009)
  • Author(s): Tsukamoto, S., Yamashita, T., Yamada, Y., Fujiwara, K., Maki, K., Kuwajima K., Matsumura, Y., Kihara, H., Tsuge, H. Ikeguchi, M.
  • Journal Title: Proteins 76 Pages: 226-236
  • Peer Reviewed
• [Journal Article] Non-native α-helix formation is not necessary for folding of lipocalin : comparison of burst-phase folding between tear lipocalin and B-lactoglobulin (2009)
  • Author(s): S.Tsukamoto
  • Journal Title: Proteins 76 Pages: 226-236
  • Peer Reviewed
• [Journal Article] Non-native α-helix formation is not necessary for folding of lipocalin : Comparison of burst-phase folding between tear lipocalin and β-lactoglobulin (2009)
  • Author(s): S. TSUKAMOTO
  • Journal Title: Proteins (掲載確定印刷中)
  • Peer Reviewed
• [Journal Article] Asymmetry of the GroEL-GroES complex under physiological conditions as revealed by small-angle X-ray scattering. (2008)
  • Author(s): Inobe, T., Takahashi, K., Maki, K., Enoki, S., Kamagata, K., Kadooka, A., Arai, M. Kuwajima K.
  • Journal Title: Biophys.J. 94 Pages: 1392-1402
  • Peer Reviewed
• [Journal Article] Probing force- induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding. (2008)
  • Author(s): Ishii, T., Murayama, Y., Katano, A., Maki, K., Kuwajima K. Sano, M.
  • Journal Title: Biochem. Biophys. Res.Commun. 375 Pages: 586-591
  • Peer Reviewed
• [Journal Article] Sequential action of ATP-dependent subunit conformational change and interaction between helical protrusions in the closure of the built-in lid of group II chaperonins. (2008)
  • Author(s): Kanzaki, T., Iizuka, R., Takahashi, K., Maki, K., Masuda, R., Sahlan, M., Yebenes, H., Valpuesta, J.M., Oka, T., Furutani, M., Ishii, N., Kuwajima K., Yohda, M.
  • Journal Title: J.Biol.Chem. 283 Pages: 34773-34784
  • Peer Reviewed
• [Journal Article] 真性体および組換え体αラクトアルブミンの構造の安定性とダイナミクス (2008)
  • Author(s): 桑島邦博
  • Journal Title: Milk Science 56 Pages: 119-122
• [Journal Article] Sequential Action of ATP-dependent Subunit Conformational Change and Interaction between Helical Protrusions in the Closure of the Built-in Lid of Group II Chaperonins (2008)
  • Author(s): T. KANZAKI
  • Journal Title: J. Biol. Chem. 283 Pages: 34773-34784
  • Peer Reviewed
• [Journal Article] Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding (2008)
  • Author(s): T. ISHII
  • Journal Title: Biochem. Biophys. Res. Commun. 375 Pages: 586-591
  • Peer Reviewed
• [Presentation] Molecular mechanisms of the Escherichia coli chanperonin function (2011)
  • Author(s): 邦博桑島
  • Organizer: 3rd APPA Conference
  • Place of Presentation: Shanghai University, Shanghai, China
  • Year and Date: 2011-05-07
• [Presentation] Solution-phase H/D exchange coupled with FT-ICR MS to probe conformational dynamics of the ATP-dependent chaperone, GroEL (2011)
  • Author(s): Q.Zhang, H.-M.Zhang, J.Chen, M.R.Emmett, C.L.Hendricksonl, K.Kuwajima A.G.Marshall
  • Organizer: 8th North America FT MS Conference
  • Place of Presentation: Key West, Florida, USA
• [Presentation] Folding mechanism of β_2-microglobulin and its relationship to dialysis-related amyloidosis (2011)
  • Author(s): A.Mukaiyama, T.Nakamura, K.Makabe, K.Maki, Y.Goto, K.Kuwajima
  • Organizer: 3rd Japan-Korea Seminar on Biomolecular Sciences-Experiments and simulations
  • Place of Presentation: Lotte Hotel, Jeju, Korea
• [Presentation] "Identification of fatty-acid binding site in the anti-tumor complex of of-lactalbuin by 920-MHz NMR spectroscopy," IPR Seminar "Cooperation in Protein Science between Asian and Pacific Countries" (2010)
  • Author(s): 邦博桑島
  • Organizer: the Institute for Protein Research
  • Place of Presentation: Osaka University
  • Year and Date: 2010-06-14
• [Presentation] Identification of fatty-acid binding site in the anti-tumor complex of of α-lactalbuin by 920-MHz NMR spectroscopy (2010)
  • Author(s): K.Kuwajima
  • Organizer: IPR Seminar"Cooperation in Protein Science between Asian and Pacific Countries, "
  • Place of Presentation: the Institute for Protein Research, Osaka University(大阪)
  • Year and Date: 2010-06-14
• [Presentation] 蛋白質フォールディング問題とバイオサイエンス (2010)
  • Author(s): 桑島邦博
  • Organizer: 蛋白研-統合バイオ共同セミナー
  • Place of Presentation: 大阪大学蛋白質研究所
  • Year and Date: 2010-04-22
• [Presentation] Molecular Mechanisms of Protein Folding (2010)
  • Author(s): 邦博桑島
  • Organizer: The Overseas Sokendai Lecture in Bangkok FY2010&The Inaugural CU-IMS Joint Symposium
  • Place of Presentation: Chulalongkorn University, Bangkok, Thailand
• [Presentation] Identification of fatty-acid binding site in the anti-tumor complex of of α-lactalbuin by 920-MHz NMR spectroscopy (2010)
  • Author(s): 邦博桑島
  • Organizer: The 10th KIAS Conference on Protein Structure and Function, Korea Institute for Advanced Study (KIAS), Seoul, Korea
  • Place of Presentation: Seoul, Korea
• [Presentation] 蛋白質フォールディング経路の速度論的理解 (2010)
  • Author(s): 桑島邦博
  • Organizer: 2010年日本物理学会秋季大会シンポジウム「揺らぎが決める生体分子の構造形成と機能発現」
  • Place of Presentation: 大阪府立大学・中百舌鳥キャンパス
• [Presentation] "Is the Folding Pathway Conserved in Homologous Proteins?," Bit Life Science's 3rd Annual Protein and Peptide Conference "After a Solution of the Machines of Life," (2010)
  • Author(s): 邦博桑島
  • Organizer: Beijing International Convention Center
  • Place of Presentation: Beijing, China
• [Presentation] Molecular mechanisms of protein folding," 2010 Annual Meeting of Asian CORE Program "Frontiers of Materials, Photo-, and Theoretical Molecular Sciences (2010)
  • Author(s): 邦博桑島
  • Organizer: Insitute of Atomic and Molecular Sciences, Academia Sinica
  • Place of Presentation: Taipei, Taiwan
• [Presentation] Dissecting a bimolecular mechanism of ATP binding to the chaperonin GroEL," 4^th International Symposium of "Molecular Science of Fluctuations toward Biological Functions (2010)
  • Author(s): J.Chen, K.Makabe, K.Kuwajima
  • Organizer: Piaza Omi, Ohtsu
  • Place of Presentation: Piaza Omi, Ohtsu
• [Presentation] The molten globule state and its biological function in α-lactalbumin", 4^th International Symposium of "Molecular Science of Fluctuations toward Biological Functions" (2010)
  • Author(s): T.Nakamura, K.Makabe, T.Aizawa, K.Kawano, M.Demura K.Kuwajima
  • Organizer: Piaza Omi, Ohtsu
• [Presentation] Folding study of outer surface protein A The 4^th International Symposium of Molecular science of fluctuations toward biological functions (2010)
  • Author(s): K.Makabe, T.Nakamura, K.Kuwajima
  • Organizer: Piaza Omi, Ohtsu
• [Presentation] Dissect a bimolecular mechanism of ATP binding to the chaperonin GroEL (2010)
  • Author(s): J.Chen, K.Makabe, K.Kuwajima
  • Organizer: YSF forum, OzBio2010 conference, 12^th IUBMB conference, 21^st FAOBMB conference
  • Place of Presentation: Melbourne, Australia
• [Presentation] Folding study of outer surface protein A (2010)
  • Author(s): K.Makabe, T.Nakamura, K.Kuwajima
  • Organizer: 24^th annual symposium of the protein society
  • Place of Presentation: San Diego, USA
• [Presentation] Dissect a bimolecular mechanism of ATP binding to the chaperonin GroEL (2010)
  • Author(s): J.Chen, K.Makabe, K.Kuwajima
  • Organizer: 35^th FEBS Congress
  • Place of Presentation: Gothenburg, Sweden
• [Presentation] Identification of fatty-acid binding site in the anti-tumor complex of of α-lactalbuin by 920-MHz NMR spectroscopy (2010)
  • Author(s): K.Kuwajima
  • Organizer: The 10th KIAS Conference on Protein Structure and Function
  • Place of Presentation: Korea Institute for Advanced Study, Seoul(Korea)
• [Presentation] Molecular Mechanisms of Protein Folding (2010)
  • Author(s): K.Kuwajima
  • Organizer: The Overseas Sokendai Lecture in Bangkok FY2010 & The Inaugural CU-IMS Joint Symposium
  • Place of Presentation: Chulalongkorn University, Bangkok(Thailand)
• [Presentation] Molecular Mechanisms of Protein Folding (2010)
  • Author(s): K.Kuwajima
  • Organizer: 2010 Annual Meeting of Asian CORE Program "Frontiers of Materials, Photo-, and Theoretical Molecular Sciences"
  • Place of Presentation: Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan
• [Presentation] Is the folding pathway conserved in homologous proteins? (2010)
  • Author(s): K.Kuwajima
  • Organizer: PepCon-2010
  • Place of Presentation: Beijing International Convention Center, China
• [Presentation] A Potassium Switch of ATP-Induced GroEL Conformational Changes (2009)
  • Author(s): J.Chen, K.Makabe, K.Kuwajima
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Sciences .Experiments and Simulations (Asian Core Program by JSPS), Symposion Hall
  • Place of Presentation: Nagoya University
• [Presentation] The molten globule state and its biological function in-lactalbumin (2009)
  • Author(s): T.Nakamura, K.Makabe, T.Aizawa, K.Kawano, M.Demura, K.Kuwajima
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Sciences-Experiments and Simulations (Asian Core Program by JSPS), Symposion Hall
  • Place of Presentation: Nagoya University
• [Presentation] Role of the Main-Chain Hydrogen Bonding in-Sheet Register (2009)
  • Author(s): K.Makabe, S.Koide, K.Kuwajima
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Sciences.Experiments and Simulations (Asian Core Program by JSPS)
  • Place of Presentation: Symposion Hall Nagoya University
• [Presentation] Hydrogen-exchange kinetics of the Escherichia coli chaperonin complex (2009)
  • Author(s): A.Mukaiyama, T.Takahashi, K.Makabe, K.Kuwajima
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Science-Experiments and Simulations (Asian Core Program by JSPS)
  • Place of Presentation: Symposion Hall, Nagoya University
• [Presentation] A minor component of native β2-microglobulin and its relationship to dialysis-related amyloidosis (2009)
  • Author(s): 邦博桑島
  • Organizer: The 9th KIAS.SNU Conference on Protein Structure and Function
  • Place of Presentation: Seoul National University, Seoul, Korea
• [Presentation] 大腸菌シャペロニンの構造ダイナミクスと機能発現 (2009)
  • Author(s): 桑島邦博
  • Organizer: 第58高分子討論会シンポジウム「生体に学ぶセンシング,物質輸送,分離」
  • Place of Presentation: 熊本大学工学部
• [Presentation] Hydrogen-exchange kinetics of the Escherichia coli chaperonin complex," Japan-Korea Symposium on Molecular Science 2009 "Chemical Dynamics in Materials and Biological Molecular Sciences (2009)
  • Author(s): 邦博桑島
  • Organizer: Asian Core Program by JSPS
  • Place of Presentation: Awaji Yumebutai International Conference Center
• [Presentation] 大腸菌シャペロニンの構造ダイナミクスと機能発現 (2009)
  • Author(s): 桑島邦博
  • Organizer: 第9回日本蛋白質科学会年会ワークショップ「生体分子の揺らぎと機能
  • Place of Presentation: 熊本全日空ホテル
• [Presentation] 相同蛋白質のフォールディング機構:αラクトアルブミンとリゾチームの比較研究 (2009)
  • Author(s): 桑島邦博
  • Organizer: 次世代スパコンプロジェクト・ナノ分野グランドチャレンジ研究開発・ナノ統合拠点分子科学WG連続研究会「タンパク質制御(フォールディング)
  • Place of Presentation: 東京医科歯科大学
• [Presentation] Folding mechanism of homologous proteins : A comparative study betweenα-lactalbumin and lysozyme (2009)
  • Author(s): 邦博桑島
  • Organizer: 科研費特定領域研究「水と生体分子」成果取りまとめ公開シンポジウム
  • Place of Presentation: 岡崎コンファレンスセンター
• [Presentation] Pathway vs.funnel perspectives of protein folding (2009)
  • Author(s): 邦博桑島
  • Organizer: Korea-Japan Seminars on Biomolecular Sciences.Experiments and Simulations (Asian Core Program by JSPS)Korea Institute for Advanced Study (KIAS)
  • Place of Presentation: Korea
• [Presentation] シャペロニンの構造揺らぎとフォールディング介助機能 (2009)
  • Author(s): 桑島邦博
  • Organizer: 科研費新学術領域研究「揺らぎと生体機能」第1回公開シンポジウム
  • Place of Presentation: 京都テレサ
• [Presentation] Hydrogen-exchange kinetics of the Escherichia coli chaperonin complex (2009)
  • Author(s): K.Kuwajima
  • Organizer: Japan-Korea Symposium on Molecular Science 2009 "Chemical Dynamics in Materials and Biological Molecular Sciences"
  • Place of Presentation: Awaji Yumebutai International Conference Center, Awajishima, Japan
• [Presentation] A minor component of native β2-microglobulin and its relationship to dialysis-related amyloidosis (2009)
  • Author(s): K.Kuwajima
  • Organizer: The 9th KIAS-SNU Conference on Protein Structure and Function, Seoul National University
  • Place of Presentation: Seoul National University, Seoul, Korea
• [Presentation] Hydrogen-exchange kinetics of the Escherichia coli chaperonin complex (2009)
  • Author(s): K.Kuwajima
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Sciences -Experiments and Simulations
  • Place of Presentation: Nagoya University, Nagoya, Japan
• [Presentation] Molecular Mechanisms of the Chaperone Function of GroEL (2008)
  • Author(s): 桑島邦博
  • Organizer: 8th KIAS-Yonsei Conference on Protein Structure and Function
  • Place of Presentation: Seoul, Korea.
  • Year and Date: 2008-10-11
• [Presentation] Folding Mechanisms of Homologous Proteins : A Comparative Study between Lysozyme and α-Lactalbumin (2008)
  • Author(s): 桑島邦博
  • Organizer: ACS 236^<th> National Meeting Symposium
  • Place of Presentation: Philadelphia, U. S. A.
  • Year and Date: 2008-08-21
• [Presentation] αラクトアルブミンとリゾチームのフォールディング経路はなぜ違うのか? (2008)
  • Author(s): 桑島邦博
  • Organizer: 札幌生体高分子シンポジウム
  • Place of Presentation: 北海道大学・学術交流会館
• [Presentation] Molecular Mechanisms of the Chaperone Function of GroEL (2008)
  • Author(s): 邦博桑島
  • Organizer: the 8th KIAS-Yonsei Conference on Protein Structure and Function
  • Place of Presentation: Seoul (Korea)
• [Presentation] Folding Mechanisms of Homologous Proteins : A Comparative Study between Lysozyme and alph-Lactalbumin (2008)
  • Author(s): 邦博桑島
  • Organizer: ACS 236^th National Meeting Symposium Protein Folding Dynamics: Experiment and Theory
  • Place of Presentation: Philadelphia (U.S.A.)
• [Presentation] Folding Mechanism of Homologous Proteins : A Comparative Study ofα-Lactalbumin and Lysozyme (2008)
  • Author(s): 邦博桑島
  • Organizer: 膜蛋白質研究国際フロンティア国際シンポジウム
  • Place of Presentation: 千里ライフサイエンスセンター(吹田市)
• [Presentation] 相同蛋白質のフォールディング機構イヌ乳リゾチームとヤギαラクトアルブミンの比較研究 (2008)
  • Author(s): 桑島邦博
  • Organizer: 次世代スーパーコンピュータプロジェクト「ナノ分野グランドチャレンジ研究開発」第2回公開シンポジウム
  • Place of Presentation: 岡崎コンファレンスセンター
• [Presentation] Folding Mechanisms of Homologous Proteins : A Comparative Study between Lysozyme and α-Lactalbumin (2008)
  • Author(s): 邦博桑島
  • Organizer: 2nd Pacific Rim International Conference of Protein Science
  • Place of Presentation: Cairns (Australia)
• [Book] A.Experimental and Simulation Studies of the Folding/Unfolding of Goat α-Lactalbumin In : Water and Biomolecules-Physical Chemistry of Life Phenomena. (Kuwajima.K, Goto.Y, Hirata.F, Kataoka.M.& Terazima. M, Eds.) (2009)
  • Author(s): Kuwajima, K., Oroguchi, T., Nakamura, T., Ikeguchi, M. Kidera
  • Publisher: Springer-Verlag.
• [Book] Water and Biomolecules-Physical Chemistry of Life Phenomena (2009)
  • Author(s): K. Kuwajima
  • Total Pages: 307
  • Publisher: Springer-Verlag, Berlin & Heidelberg
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