Molecular mechanism of protein folding by group II chaperonin

• Project/Area Number: 19370038
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tokyo University of Agriculture and Technology
• Principal Investigator: YOHDA Masafumi Tokyo University of Agriculture and Technology, 大学院・共生科学技術研究院, 教授 (50250105)
• Co-Investigator(Kenkyū-buntansha): 尾高 雅文 東京農工大学, 大学院・共生科学技術研究院, 准教授 (20224248)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000); Fiscal Year 2008: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2007: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
• Keywords: シャペロン / シャペロニン / 古細菌 / ストレス / フォールディング / フォールデイング

Research Abstract

超好熱性古細菌Thermococcus strain KS-1由来グループ2型シャペロニンは、ATPにより頂点ドメインに位置するhelical protrusionを中心とした構造変化が引き起こされ、open 構造からclosed 構造へと変化することで、補足した変性タンパク質をシャペロニン内部空洞に閉じ込め、foldingを促進する。このATP依存的な構造変化はサブユニット間の協同した作用により引き起こされるが、その詳細は解明されていない。我々は、シャペロニンリング内の特定の位置に、「ATP加水分解部位に変異を導入した変異体サブユニット」と「helical protrusion欠損変異体サブユニット」をそれぞれ様々に導入したシャペロニンを作成し、これらのシャペロニンのfolding活性やATP依存的な構造変化を生化学的実験およびX線小角散乱実験などを用いて解析し、サブユニット間の協同性を解析した。本解析の結果、2型シャペロニンのATP依存的なopen構造からclosed構造への変化では、最初にATP結合・加水分解により各サブユニットのhelical protrusionを中心とした局所的な構造変化が起こり、その後、隣接したhelical protrusion間の相互作用が起こることでclosed構造を形成するようになることを明らかにした。また、常温での機能解析を可能にするため、低温適応変異体を構築した。この変異体の変異アミノ酸は構造変化の情報伝達に重要な役割を持つことが示唆されている。

Research Products

• [Journal Article] Characterization of a sHsp ofSchizosaccharomyces pombe, SpHsp15.8, and the implication of its functionalmechanism by comparison with anothersHsp (2009)
  • Author(s): Sugino C, Hirose M, Tohda H,Yoshinari Y, Abe T, Giga-Hama Y, IizukaR, Shimizu M, Kidokoro S, Ishii N, Yohda M.
  • Journal Title: SpHsp16.0. Proteins 74 Pages: 6-17
  • Peer Reviewed
• [Journal Article] Construction and characterization ofthe hetero-oligomer of the group IIchaperonin from the hyperthermophilicarchaeon (2009)
  • Author(s): Sahlan M, Kanzaki T, Yohda M
  • Journal Title: Thermococcus sp. strain KS-1.Extremophiles 13 Pages: 437-445
  • Peer Reviewed
• [Journal Article] Characterization of a sHsp of Schizosaccharomyces pombe, SpHsp l5.8, and theimplication of its functional mechanism by comparison with another sHsp, SpHsp l6.0. (2009)
  • Author(s): Sugino C, Hirose M, Tohda H, Yoshinari Y, Abe T, Giga-Hama Y, Iizuka R, Shimizu M, Kidokoro s, Ishii N, & Yohda M.
  • Journal Title: Proteins 74 Pages: 6-17
  • Peer Reviewed
• [Journal Article] Formation of highly toxicsoluble amyloid beta oligomers by themolecular chaperone prefoldin (2008)
  • Author(s): Sakono M, Zako T, Ueda H, Yohda M, Maeda M
  • Journal Title: FEBS J 275 Pages: 5982-5993
  • Peer Reviewed
• [Journal Article] Role ofthe IXI/V motif in oligomer assemblyand function of StHsp14.0, a small heatshock protein from theacidothermophilic archaeon (2008)
  • Author(s): Saji H, Iizuka R, Yoshida T, Abe T, Kidokoro S, Ishii N, Yohda M
  • Journal Title: Sulfolobus tokodaii strain 7. Proteins 71 Pages: 771-782
  • Peer Reviewed
• [Journal Article] Overexpression ofprefoldin from the hyperthermophilicarchaeum Pyrococcus horikoshii OT3endowed Escherichia coli with organicsolvent tolerance (2008)
  • Author(s): Okochi M, Kanie K, Kurimoto M, YohdaM, Honda H
  • Journal Title: Appl Microbiol Biotechnol 79 Pages: 443-449
  • Peer Reviewed
• [Journal Article] Structure of aspartate racemasecomplexed with a dual substrateanalogue, citric acid (2008)
  • Author(s): Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, Yohda M
  • Journal Title: and implications for the reaction mechanism. Proteins 70 Pages: 1167-1174
  • Peer Reviewed
• [Journal Article] Structure and moleculardynamics simulation of archaealprefoldin : the molecular mechanism forbinding and recognition of nonnativesubstrate proteins (2008)
  • Author(s): Ohtaki A, Kida H, Miyata Y, Ide N,Yonezawa A, Arakawa T, Iizuka R,Noguchi K, Kita A, Odaka M, Miki K,Yohda M
  • Journal Title: J Mol Biol 376 Pages: 1130-1141
  • Peer Reviewed
• [Journal Article] Dynamics of group II chaperonin andprefoldin probed by 13C NMRspectroscopy (2008)
  • Author(s): Kurimoto E, Nishi Y, Yamaguchi Y,Zako T, Iizuka R, Ide N, Yohda M, KatoK
  • Journal Title: Proteins 70 Pages: 1257-1263
  • Peer Reviewed
• [Journal Article] Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1 (2008)
  • Author(s): Kida H, Sugano Y, Iizuka R, Fujihashi M, Yohda M, Miki, K
  • Journal Title: J Mol Biol 383 Pages: 465-474
  • Peer Reviewed
• [Journal Article] Sequentialaction of ATP-dependent subunitconformational change and interactionbetween helical protrusions in theclosure of the built-in lid of group Iichaperoninsaq (2008)
  • Author(s): Kanzaki T, Iizuka R, Takahashi K, Maki K, Masuda R, Sahlan M, Yebenes H, Valpuesta JM, Oka T, Furutani M, IshiiN, Kuwajima K, Yohda M
  • Journal Title: J Biol Chem 283 Pages: 34773-347843
  • Peer Reviewed
• [Journal Article] Functional characterization ofrecombinant prefoldin complexes from ahyperthermophilic archaeon (2008)
  • Author(s): Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, YohdaM
  • Journal Title: Thermococcus sp. strain KS-1. J Mol Biol 377 Pages: 972-983
  • Peer Reviewed
• [Journal Article] Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy. (2008)
  • Author(s): Kurimoto E, Nishi Y, YamaguchiY, Zako T, Iizuka R, Ide N, Yohda M, & Kato K.
  • Journal Title: Proteins 70 Pages: 1257-1263
  • Peer Reviewed
• [Journal Article] Role of the IXI/V motif in oligomer assembly and function of StHsp14.O, a small heat shock protein from the acidothermophilic archaeon, Sulfolobustokodaii strain 7 (2008)
  • Author(s): Saji H, Iizuka R, Yoshida T, Abe T, Kidokoro s, Ishii N, & Yohda M.
  • Journal Title: Proteins 71 Pages: 771-782
  • Peer Reviewed
• [Journal Article] Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins (2008)
  • Author(s): Ohtaki A, Kida H, Miyata Y, Ide N, Yonezawa A, Arakawa T, Iizuka R, Noguchi K, Kita A, Odaka M, Miki K, & Yohda M.
  • Journal Title: J. Mol. Biol. 376 Pages: 1130-1141
  • Peer Reviewed
• [Journal Article] Functional characterization of recombinant prefoldin complexes from a hyperthermophilic archaeon, Thermococcus sp. strain KS-1 (2008)
  • Author(s): Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara s, Imanaka T, & Yohda M.
  • Journal Title: J. Mol. Biol. 377 Pages: 972-983
  • 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 JM, Oka T, Furutani M, Ishii N, Kuwajima K, &Yohda M.
  • Journal Title: J. Biol. Chem. 283 Pages: 34773-34784
  • Peer Reviewed
• [Journal Article] Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1. J. Mol. Biol/., 383:465-474. (2008)
  • Author(s): Kida H, Sugano Y, Iizuka R, Fuiihashi M, Yohda M, & Miki K.
  • Journal Title: J. Mol. Biol. 383 Pages: 465-474
  • Peer Reviewed
• [Journal Article] Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile (2008)
  • Author(s): Hashimoto K, Suzuki H, Taniguchi K, Noguchi T, Yohda M. & Odaka M.
  • Journal Title: J. Biol. Chem. 283 Pages: 36617-36623
  • NAID: 120007138471
  • Peer Reviewed
• [Journal Article] Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins. (2008)
  • Author(s): Ohtaki A, Kida H, Miyata Y, Ide N, Yonezawa A, Arakawa T, Iizuka R, Noguchi K, Kita A, Odaka M, Miki K, Yohda M.
  • Journal Title: J. Mol. Biol. 376 Pages: 1130-1141
  • Peer Reviewed
• [Journal Article] Functional characterization of recombinant prefoldin complexes from ahyperthermophilic archaeon,Thermococcus sp. strain KS-1. (2008)
  • Author(s): Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, Yohda M.
  • Journal Title: J. Mol. Biol. 377 Pages: 972-983
  • Peer Reviewed
• [Journal Article] Dynamics of the prefoldin and the group II chaperonin complex probed by 13C NMR spectroscopy (2008)
  • Author(s): Kurimoto E, Nishi Y, Yamaguchi Y, Zako T, Iizuka R, Ide N, Yohda M, Kato K
  • Journal Title: Proteins 70 Pages: 1257-1263
  • Peer Reviewed
• [Journal Article] Comparativeanalysis of the protein foldingactivities of two chaperonin subunitsof Thermococcus strain KS-1 : theeffects of beryllium fluoride (2007)
  • Author(s): Yoshida T, Iizuka R, Itami K, Yasunaga T, Sakuraba H, Ohshima T, Yohda M, Maruyama T
  • Journal Title: Extremophiles 11 Pages: 225-235
  • Peer Reviewed
• [Journal Article] Localization of prefoldininteraction sites in thehyperthermophilic group II chaperoninand correlations between binding rateand protein transfer rate (2007)
  • Author(s): Zako T, Murase Y, Iizuka R, YoshidaT, Kanzaki T, Ide N, Maeda M, FunatsuT, Yohda M
  • Journal Title: J Mol Biol 364 Pages: 110-120
  • Peer Reviewed
• [Presentation] 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): Yohda M, Kanzaki T, Masuda R, Sahlan M
  • Organizer: 第81回目本生化学会大会、第31会分子生物学会年会
  • Place of Presentation: 神戸国際会議場、神戸
  • Year and Date: 2008-12-12
• [Presentation] Structure, Function and Application of Hyperthermophilic Molecular Chaperones (2008)
  • Author(s): Yohda M, Sugano Y, Miyoshi E, Hanada M, Yonezawa A, Ohtaki A, Horiuchi H, Oda M, Tani T, Fujii I
  • Organizer: The 3rd International Workshop on Approaches t Single-Cell Analysis
  • Place of Presentation: Zurich, Switzerland
  • Year and Date: 2008-09-12
• [Presentation] ATP-DEPENDENT CONFORMATIONAL CHANGE MECHANISM OF GROUP II CHAPERONINS ELUCIDATED USINGCHAPERONIN COMPLEXES CONTAINING MUTANT SUBUNITS IN THE ORDERDED FASHION (2008)
  • Author(s): Yohda M, Kanzaki T, Iizuka R, Takahashi K, Masuda R, SahlanM, Maki K, Kuwajima K
  • Organizer: 22th Protein Society Symposium
  • Place of Presentation: San Diego, USA
  • Year and Date: 2008-07-22
• [Presentation] SUBSTRATE RECOGNITION MECHANISM OF PYROCOCCUS PREFOLDIN REVEALED BY X-RAY CRYSTAL STRUCTUIRE ANALYSIS AND MOLECULAR DYNAMICS SIMULATION (2008)
  • Author(s): Yohda M, Ohtaki A, Miyata Y, Kida H, Yonezawa A, Noguchi K, Miki K
  • Organizer: MOLECULAR CHAPERONES & STRESS RESPONSES
  • Place of Presentation: Cold Spring Harbor, USA
  • Year and Date: 2008-05-03
• [Presentation] ATP-DEPENDENT CONMORMATIONAL CHANGE MECHANISM OF GROUP II CHAPERONINS ELUCIDATED USING CHAPERONIN COMPLEXES (2008)
  • Author(s): T. Kanzaki, R. Iizuka, K. Takahashi, H. Yebenes, R. Masuda, K. Maki, N. Ishii, M. Sahlan, J. M. Valpuesta, K. Kuwajima, M. Yohda
  • Organizer: MOLECULAR CHAPERONES & STRESS RESPONSES
  • Place of Presentation: Cold Spring Harbor, USA
  • Year and Date: 2008-05-02
• [Presentation] STRUCTURE,FUNCTION AND APPLICATION OFHYPERTHERMOPHILIC MOLECULARCHAPERONES (2008)
  • Author(s): Yohda M, Sugano Y, Miyoshi E, HanadaM, Yonezawa A, Ohtaki A, Horiuchi H,Oda M, Tani T, Fujii I
  • Organizer: The 3rd International Workshop on Approaches to Single-Cell Analysis
  • Place of Presentation: ETH, Zurich, Switzerland
• [Presentation] Rebuilt and characterization ofhetero-oligomeric group II chaperonincomplexes of Thermococcus sp. strainKS-1 (2008)
  • Author(s): Sahlan M, Kanzaki T, Yohda M
  • Organizer: 33rd FEBS Congress and 11th IUBMB Conference
  • Place of Presentation: Athens, Greece
• [Presentation] Studies on the contribution ofhelical protrusion to ATP-dependentconformational change of group IIchaperonin using chaperonin complexeswith helical protrusion deletions (2008)
  • Author(s): Kanzaki T, Masuda R, Iizuka R,Takahashi K, Maki K, Kuwajima K, YohdaM
  • Organizer: 33rd FEBS Congress and 11th IUBMB Conference
  • Place of Presentation: Athens, Greece
• [Presentation] Recent progress of theresearches on molecular chaperones andprotein folding diseasesa (2008)
  • Author(s): Yohda M
  • Organizer: The 2nd Gruber-Soedigdo Lecture2008
  • Place of Presentation: Instutute of Bandung, Bandung, Indonesia (Invited)
• [Presentation] RECOGNITION MECHANISM OF PYROCOCCUSPREFOLDIN REVEALED BY X-RAY CRYSTALSTRUCTUIRE ANALYSIS AND MOLECULARDYNAMICS SIMULATION (2008)
  • Author(s): Yohda M, Ohtaki A, Miyata Y, Kida H,Yonezawa A, Noguchi K, Miki, K
  • Organizer: MOLECULAR CHAPERONES, STRESS RESPONSES
  • Place of Presentation: Cold Spring Harbor, USA
• [Presentation] ATP-DEPENDENTCONMORMATIONAL CHANGE MECHANISM OFGROUP II CHAPERONINS ELUCIDATED USINGCHAPERONIN COMPLEXES (2008)
  • Author(s): Kanzaki T, Iizuka R, Takahashi K, Hugo Yebenes H, Masuda R, Maki K, IshiiN, Sahlan M, Valpuesta JM, Kuwajima K, Yohda M
  • Organizer: MOLECULAR CHAPERONES, STRESS RESPONSES
  • Place of Presentation: Cold Spring Harbor, USA
• [Presentation] FORMATION OF HIGHLY SOLUBLEAMYLOID BETA OLIGOMERS BY THEMOLECULAR CHAPERONE PREFOLDINa (2008)
  • Author(s): Sakono M. Zako T, Ueda H, Yohda M, Maeda M
  • Organizer: MOLECULAR CHAPERONES, STRESS RESPONSES
  • Place of Presentation: Cold Spring Harbor, USA
• [Presentation] Sequential action of ATP dependentsubunit conformational change andinteraction between helicalprotrusions in the closure of thebuilt-in lid of group II chaperonins (2008)
  • Author(s): Yohda M, Kanzaki T, Masuda R, Sahlan M
  • Organizer: 第31回日本分子生物学会年会/第81回日本生化学会大会
  • Place of Presentation: 神戸国際会議場、神戸(Invited)
• [Presentation] Dynamic analysis of helical protrusion of group II chaperonins using fluorescent probes (2007)
  • Author(s): 増田 莉恵、神前 太郎、飯塚 怜、高橋 一暢、槙 亙介、石井 則行、桑島 邦博、養王田 正文
  • Organizer: 日本生物物理学会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2007-12-21
• [Presentation] グループII型シャペロニンのサブユニット間協同性におけるATPaseの役割 (2007)
  • Author(s): 神前 太郎、飯塚 怜、高橋 一暢、槙 亙介、石井 則行、Muhamad Sahlan、古谷 昌弘、桑島 邦博、養王田 正文
  • Organizer: 日本生物物理学会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2007-12-21
• [Presentation] 低温適合化シャペロニンの機能解析 (2007)
  • Author(s): 牛奥 修三、神前 太郎、山岸 明彦、養王田 正文
  • Organizer: 日本分子生物学会・日本生化学会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2007-12-11
• [Presentation] 蛍光ロープを用いたGroup II型シャペロニンのhelical protrusionの動的解析 (2007)
  • Author(s): 増田 莉恵、神前 太郎、飯塚 怜、高橋 一暢、積 瓦介、石井 則行、桑島 邦博、養王田 正文
  • Organizer: 日本分子生物学会・日本生化学会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2007-12-11
• [Presentation] グループII型シャペロニンのサブユニット間協同性におけるATPaseの役割 (2007)
  • Author(s): 神前 太郎、飯塚 怜、高橋 一暢、積 瓦介、石井 則行、Sahlan Muhamad、古谷 昌弘、桑島 邦博、養王田 正文
  • Organizer: 日本分子生物学会・日本生化学会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2007-12-11
• [Presentation] THE INTERACTION OF HELICAL PROTRUTIONS IS IMPORTANT IN THE PROTEIN FOLDING CYCLE OF GROUP II CHAPERONINS (2007)
  • Author(s): Kanzaki T, Iizuka R, Takahashi K, Maki K, Ishii N, Sahlan M, Furutani M, Kuwajima K, Yohda M
  • Organizer: The 2007 World Conference of Stress
  • Place of Presentation: Budapest, Hungary
  • Year and Date: 2007-08-26
• [Presentation] ゲループII型シャペロニンのサブユニット間協調性におけるhelical protrusionの機能 (2007)
  • Author(s): 神前 太郎、飯塚 怜、高橋 一暢、槙 瓦介、石井 則行、Muhamad Sahalan、古谷 昌弘、桑島 邦博、養王田 正文
  • Organizer: 日本蛋白質科学会
  • Place of Presentation: 宮城県仙台市
  • Year and Date: 2007-05-24
• [Presentation] Construction and characterization of the α8β8 hetero-oligomer of group II chaperonin from Thermococcus sp.strain KS-1 (2007)
  • Author(s): Muhamad Sahalan、神前 太郎、飯塚 怜、養王田 正文、
  • Organizer: 日本蛋白質科学会
  • Place of Presentation: 宮城県仙台市
  • Year and Date: 2007-05-24
• [Presentation] 超好熱性古細菌Thermococcus sp.strain KS-1(T.KS-1)由来シャペロニンの低温適応化 (2007)
  • Author(s): 牛奥 修三、神前 太郎、山岸 明彦、養王田 正文
  • Organizer: 日本蛋白質科学会
  • Place of Presentation: 宮城県仙台市
  • Year and Date: 2007-05-24
• [Presentation] TWOSMALL HEAT SHOCK PROTEINS OF A FISSIONYEAST FUNCTION IN DIFFERENT MANNER TOCOPE WITH WIDE RANGE OF TEMPERATURESAND VARIOUS DENATURED PROTEINS (2007)
  • Author(s): Yohda M, Sugino C, Hirose M, IizukaR, Shimizu M, Kidokoro S, Ishii N
  • Organizer: 3rdCell Stress Society InternationalCongress on Stress Responses inBiology and Medicine and 2nd WorldConference of Stress
  • Place of Presentation: Budapest, Hungary
• [Presentation] INTERACTION OF PREFOLDIN WITHGROUP II CHAPERONIN IN THE PRESENCE OFVARIOUS NUCLEOTIDES (2007)
  • Author(s): Zako T, Murase Y, Zhukov A, KarlssonR, Shimizu M, Iizuka R, Maeda M, YohdaM
  • Organizer: 3rd Cell StressSociety International Congress onStress Responses in Biology andMedicine and 2nd World Conference ofStress
  • Place of Presentation: Budapest, Hungary
• [Presentation] THE INTERACTIONOF HELICAL PROTRUTIONS IS IMPORTANT INTHE PROTEIN FOLDING CYCLE OF GROUP IICHAPERONINS (2007)
  • Author(s): Kanzaki T, Iizuka R, Takahashi K, Maki K, Ishii N, Sahlan M, Furutani M, Kuwajima K, Yohda M(他 4 件)
  • Organizer: 3rd Cell Stress SocietyInternational Congress on StressResponses in Biology and Medicine and2nd World Conference of Stress
  • Place of Presentation: Budapest, Hungary
• [Book] Protein Folding Systems(ASM Press) (2007)
  • Author(s): Robb FT, Iizuka R, Yohda M
  • Publisher: Archaea-MOLECULAR AND CELLULAR BIOLOGY-ed. Cavicchioli R