Structural fluctuations and functional expression of the chaperonin complexes

2012 Fiscal Year Final Research Report

• Project Area: Molecular Science of Fluctuations toward Biological Functions
• Project/Area Number: 20107009
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities
• Principal Investigator: KUWAJIMA Kunihiro 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 教授 (70091444)
• Co-Investigator(Renkei-kenkyūsha): MAKABE Koki 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 助教 (20508072)
• Project Period (FY): 2008 – 2012
• Keywords: 蛋白質 / フォールディング / 分子シャペロン / シャペロニン / 構造揺らぎ / 水素交換法 / 二次元NMR

Research Abstract

The molecular chaperone is an important concept that connects a molecular-level biological process, protein folding, to cellular-level biological processes. In this project, we studied physicochemical relationships between structural fluctuations and functional expression of the chaperonin complexes. To elucidate how the biological functions utilize the structural fluctuations of the complexes, we investigated hydrogen/deuterium (H/D)-exchange reactions of the GroES portion of various chaperonin complexes by dimethylsulfoxide-quenched H/D-exchange two-dimensional NMR spectroscopy.

Research Products

• [Journal Article] NMR characterization of the interaction of GroEL with amyloid β as a model ligand. (2013)
  • Author(s): Yagi-Utsumi, M., Kunihara, T., Nakamura, T., Uekusa, Y., Makabe, K., Kuwajima, K. & Kato, K.
  • Journal Title: FEBS Lett. Volume: (In press)
  • Peer Reviewed
• [Journal Article] Molecular mechanisms of the cytotoxicity of human α-lactalbumin made lethal to tumor cells (HAMLET) and other protein-oleic acid complexes. (2013)
  • Author(s): Nakamura, T., Aizawa, T., Kariya, R., Okada, S., Demura, M., Kawano, K., Makabe, K. & Kuwajima, K.
  • Journal Title: J. Biol. Chem. Volume: 288 Pages: 14408-14416
  • Peer Reviewed
• [Journal Article] The H/D-Exchange Kinetics of the Escherichia coli Co-Chaperonin GroES Studied by 2D NMR and DMSO-Quenched Exchange Methods. (2013)
  • Author(s): Chandak, M.S., Nakamura, T., Makabe, K., Takenaka, T., Mukaiyama, A., Chaudhuri, T.K., Kato, K. & Kuwajima, K.
  • Journal Title: J. Mol. Biol. Volume: (In press)
  • Peer Reviewed
• [Journal Article] The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments. (2013)
  • Author(s): Chandak, M.S., Nakamura, T., Takenaka, T., Chaudhuri, T.K., Yagi-Utsumi, M., Chen, J., Kato, K. & Kuwajima, K.
  • Journal Title: Protein Sci. Volume: 22 Pages: 486-491
  • Peer Reviewed
• [Journal Article] Structural insights into the stability perturbations induced by N-terminal variation in human and goat α-lactalbumin. (2013)
  • Author(s): Makabe, K., Nakamura, T. & Kuwajima, K.
  • Journal Title: Protein Eng. Des. Sel. Volume: 26 Pages: 165-170
  • Peer Reviewed
• [Journal Article] Native-state heterogeneity of β_2-microglobulin as revealed by kinetic folding and real-time NMR experiments. (2013)
  • Author(s): Mukaiyama, A., Nakamura, T., Makabe, K., Maki, K., Goto, Y. & Kuwajima, K.
  • Journal Title: J. Mol. Biol. Volume: 425 Pages: 257-272
  • Peer Reviewed
• [Journal Article] The molten globule of β_2-microglobulin accumulated at pH 4 and its role in protein folding. (2013)
  • Author(s): Mukaiyama, A., Nakamura, T., Makabe, K., Maki, K., Goto, Y. & Kuwajima, K.
  • Journal Title: J. Mol. Biol. Volume: 425 Pages: 273-291
  • Peer Reviewed
• [Journal Article] Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry. (2013)
  • Author(s): Zhang, Q., Chen, J., Kuwajima, K., Zhang, H.M., Xian, F., Young, N.L. & Marshall, A.G.
  • Journal Title: Sci Rep Volume: 3 Pages: 1247
  • Peer Reviewed
• [Journal Article] Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone. (2012)
  • Author(s): Chen, J., Yagi, H., Sormanni, P., Vendruscolo, M., Makabe, K., Nakamura, T., Goto, Y. & Kuwajima, K.
  • Journal Title: FEBS Lett. Volume: 586 Pages: 1120-1127
  • Peer Reviewed
• [Journal Article] Sequential four-state folding/unfolding of goat α-lactalbumin and its N-terminal variants. (2012)
  • Author(s): Tomoyori, K., Nakamura, T., Makabe, K., Maki, K., Saeki, K. & Kuwajima, K.
  • Journal Title: Proteins Volume: 80 Pages: 2191-2206
  • Peer Reviewed
• [Journal Article] Dissecting a bimolecular process of MgATP^<2-> binding to the chaperonin GroEL. (2011)
  • Author(s): Chen, J., Makabe, K., Nakamura, T., Inobe, T. & Kuwajima, K.
  • Journal Title: J. Mol. Biol. Volume: 410 Pages: 343-356
  • Peer Reviewed
• [Journal Article] Solubilization and folding of a fully active recombinant Gaussia luciferase with native disulfide bonds by using a SEP-Tag. (2011)
  • Author(s): Rathnayaka, T., Tawa, M., Nakamura, T., Sohya, S., Kuwajima, K., Yohda, M. & Kuroda, Y.
  • Journal Title: Biochim. Biophys. Acta Volume: 1814 Pages: 1775-1778
  • Peer Reviewed
• [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. Volume: 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. Volume: 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. Volume: 285 Pages: 9018-9029
  • Peer Reviewed
• [Journal Article] Non-native alpha-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 Volume: 76 Pages: 226-236
  • 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. Volume: 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. Volume: 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. Volume: 283 Pages: 34773-34784
  • Peer Reviewed
• [Presentation] Sequential four-state folding/unfolding of goat α-lactalbumin and its N-terminal variants. (2013)
  • Author(s): Kuwajima, K.
  • Organizer: 17th Hiroshima International Symposium on Synchrotron Radiation - Progress in materials science and synchrotron radiation -
  • Place of Presentation: Hiroshima Univ.
  • Year and Date: 20130228-0301
• [Presentation] Structural fluctuation of free GroES and the GroES-SR1 complex studied by the use of hydrogen/deuterium (H/D) exchange. (2013)
  • Author(s): Chandak, M.S., Nakamura, T., Makabe, K., Takenaka, T., Mukaiyama, A., Chaudhuri, T.K., Chen, J., Kato, K. & Kuwajima, K.
  • Organizer: 57th Annual Meeting of the Biophysical Society (USA)
  • Place of Presentation: Philadelphia, USA
  • Year and Date: 20130202-06
• [Presentation] The structure and function of HAMLET and its related protein complexes. (2012)
  • Author(s): Kuwajima, K.
  • Organizer: 3rd HAMLET Conference
  • Place of Presentation: Lund, Sweden
  • Year and Date: 20121207-08
• [Presentation] Structural fluctuations and functional expression of the chaperonin complexes. (2012)
  • Author(s): Kuwajima, K.
  • Organizer: 6th International Symposium "Molecular Science of Fluctuations toward Biological Functions,"
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 20121205-06
• [Presentation] シャペロニン超分子複合体の水素交換反応 (2012)
  • Author(s): 桑島邦博
  • Organizer: 大阪大学蛋白質研究所セミナー「分子シャペロンの機能発現の新展開と細胞制御」
  • Place of Presentation: 大阪
  • Year and Date: 20121115-16
• [Presentation] Molecular Mechanisms of the Escherichia coli Chaperonin Function. (2011)
  • Author(s): Kuwajima, K.
  • Organizer: 3rd Asia Pacific Protein Association (APPA) Conference
  • Place of Presentation: Shanghai, China
  • Year and Date: 20110506-09
• [Book] Water and Biomolecules-Physical Chemistry of Life Phenomena (分担執筆) (2009)
  • Author(s): Kuwajima, K.
  • Total Pages: 307
  • Publisher: Springer-Verlag, Berlin & Heidelberg
• [Remarks]
  • URL: http://researchmap.jp/read0007744/
• [Patent(Industrial Property Rights)] 蛋白質-化学療法剤複合体及びその製造方法,並びに医薬 (2012)
  • Inventor(s): 桑島邦博、中村敬、真壁幸樹、岡田誠治
  • Industrial Property Rights Holder: 自然科学研究機構、熊本大学
  • Industrial Property Number: 特願2012-147492
  • Filing Date: 2012-06-29
• [Patent(Industrial Property Rights)] 球状蛋白質の準安定状態を用いた抗癌細胞作用のある分子の作成 (2011)
  • Inventor(s): 桑島邦博、中村敬、真壁幸樹
  • Industrial Property Rights Holder: 自然科学研究機構
  • Industrial Property Number: 特願2011-238611
  • Filing Date: 2011-10-31