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Characterization of conformational dynamics of the active end of amyloid fibril to elucidate mechanisms underlying the fibril elongation

Research Project

Project/Area Number 23870043
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Biophysics
Research Institution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) (2012)
National Institutes of Natural Sciences Okazaki Research Facilities (2011)

Principal Investigator

YAGI Maho  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, 特任助教 (40608999)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2011: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywordsアミロイド / アルツハイマー病 / 抗体 / NMR / X線結晶構造解析
Research Abstract

To characterize the conformational dynamics of the active end of amyloid fibril, we attempted to design small-sized amyloid fibril models. We successfully prepared tandem repeats of amyloid β (Aβ) molecules as minimal models of the amyloid fibrils by genetic manipulation. It was revealed that the tandem-repeat Aβ was recognized by the specific antibody directed against the end point of Aβ amyloid fibrils and served as nucleus which promoted the amyloid fibrillization. Furthermore, we found that bacterial molecular chaperones and ganglioside-embedding bicelles could suppress formation of Aβ fibrils.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • Research Products

    (40 results)

All 2013 2012 2011 Other

All Journal Article (17 results) (of which Peer Reviewed: 16 results) Presentation (21 results) (of which Invited: 2 results) Remarks (2 results)

  • [Journal Article] NMR characterization of interaction of GroEL with amyloid β as a model ligand.2013

    • Author(s)
      M.Yagi-Utsumi, T.Kunihara, T.Nakamura, Y.Uekusa, K.Makabe, K.Kuwajima, and K.Kato
    • Journal Title

      FEBS Lett.

      Volume: 587 Issue: 11 Pages: 605-609

    • DOI

      10.1016/j.febslet.2013.04.007

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Nuclear magnetic resonance approaches for characterizing interactions between the bacterial chaperonin GroEL and unstructured proteins.2013

    • Author(s)
      Nishida N, Yagi-Utsumi M, Motojima F, Yoshida M, Shimada I, Kato K.
    • Journal Title

      J Biosci Bioeng

      Volume: 116 Issue: 2 Pages: 160-164

    • DOI

      10.1016/j.jbiosc.2013.02.012

    • NAID

      110009657195

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural and functional mosaic nature of MHC class I molecules in their peptide-free form.2013

    • Author(s)
      E.Kurimoto, K.Kuroki, Y.Yamaguchi, M.Yagi-Utsumi, T.Igaki, T.Iguchi, K.Maenaka, and K.Kato
    • Journal Title

      Mol. Immunol.

      Volume: 55 Issue: 3-4 Pages: 393-399

    • DOI

      10.1016/j.molimm.2013.03.014

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments2013

    • Author(s)
      Mahesh S. Chandak, Takashi Nakamura, Toshio Takenaka, Tapan K. Chaudhuri, Maho Yagi-Utsumi, Jin Chen, Koichi Kato, Kunihiro Kuwajima
    • Journal Title

      Protein Science

      Volume: 22 Issue: 4 Pages: 486-491

    • DOI

      10.1002/pro.2221

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin2013

    • Author(s)
      Soichiro Kitazawa, Tomoshi Kameda, Maho Yagi-Utsumi, Kenji Sugase, Nicola J. Baxter, Koichi Kato, Michael P. Williamson, Ryo Kitahara.
    • Journal Title

      Biochemistry

      Volume: 52 Issue: 11 Pages: 1874-1885

    • DOI

      10.1021/bi301420m

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide. Biochem. Biophys2013

    • Author(s)
      Maho Yagi-Utsumi, Yoshiki Yamaguchi, Pornthip Boonsri, Takeshi Iguchi, Kazuo Okemoto, Shunji Natori, Koichi Kato
    • Journal Title

      Res. Commun

      Volume: 431 Issue: 2 Pages: 136-140

    • DOI

      10.1016/j.bbrc.2013.01.009

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins.2013

    • Author(s)
      T.Yamaguchi, T.Uno, Y.Uekusa, M.Yagi-Utsumi, and K.Kato
    • Journal Title

      Chem. Commun.

      Volume: 49 Issue: 12 Pages: 1235-1237

    • DOI

      10.1039/c2cc38016a

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] 超高磁場NMRを用いた糖脂質クラスター上におけるAβの構造研究2013

    • Author(s)
      矢木 真穂
    • Journal Title

      生物物理

      Volume: 53 Pages: 32-33

    • NAID

      10031139024

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Protein encapsulation within synthetic molecular hosts2012

    • Author(s)
      D. Fujita, K. Suzuki, S. Sato, M. Yagi-Utsumi, Y. Yamaguchi, N. Mizuno, T. Kumasaka, M. Takata, M. Noda, S. Uchiyama, K. Kato, and M. Fujita
    • Journal Title

      Nature Communications

      Volume: 3 Issue: 1 Pages: 1093-1093

    • DOI

      10.1038/ncomms2093

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] NMR and mutational identification of the collagen-binding site of the chaperone Hsp47.2012

    • Author(s)
      Maho Yagi-Utsumi, Sumi Yoshikawa, Yoshiki Yamaguchi, Yohei Nishi, Eiji Kurimoto, Yoshihito Ishida, Takayuki Homma, Jun Hoseki, Yoshimi Nishikawa, Takaki Koide, Kazuhiro Nagata, Koichi Kato.
    • Journal Title

      PLoS One

      Volume: 7 Issue: 9 Pages: e45930-e45930

    • DOI

      10.1371/journal.pone.0045930

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex.2012

    • Author(s)
      H.Yagi, K.Ishimoto, T.Hiromoto, H.Fujita, T.Mizushima, Y.Uekusa, M.Yagi-Utsumi, E.Kurimoto, M.Noda, S.Uchiyama, F.Tokunaga, K. Iwai, and K.Kato
    • Journal Title

      EMBO Rep.

      Volume: 13 Issue: 5 Pages: 462-468

    • DOI

      10.1038/embor.2012.24

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Expression and purification of isotopicaly labeled amyloid β as ubiquitin-fused protein in E. coli2012

    • Author(s)
      Maho Yagi-Utsumi
    • Journal Title

      Protein Science Society of Japan Archives,

      Volume: 5

    • URL

      http://www.pssj.jp/archives/Protocol/Expression/amy_02/amy_02_01.html

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Expression and purification of isotopicaly labeled amyloid β as ubiquitin-fused protein in E. coli.2012

    • Author(s)
      Maho Yagi-Utsumi
    • Journal Title

      Protein Science Society of Japan Archives

      Volume: 5

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 大腸菌発現系による安定同位体標識アミロイドssの調製法2012

    • Author(s)
      矢木-内海真穂
    • Journal Title

      蛋白質科学会アーカイブ

      Volume: 5

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural and molecular basis of carbohydrate?protein interaction systems as potential therapeutic targets.2011

    • Author(s)
      Y.Kamiya, M.Yagi-Utsumi, H.Yagi, and K.Kato
    • Journal Title

      Curr. Pharm. Des.

      Volume: 17 Issue: 17 Pages: 1672-1684

    • DOI

      10.2174/138161211796355074

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets2011

    • Author(s)
      Yukiko Kamiya, Maho Yagi-Utsumi, Hirokazu Yagi, Koichi Kato
    • Journal Title

      Current Pharmaceutical Design

      Volume: 17 Pages: 1672-1684

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution.2011

    • Author(s)
      T.Hirano, O.Serve, M.Yagi-Utsumi, E.Takemoto, T.Hiromoto, T.Satoh, T.Mizushima, and K.Kato
    • Journal Title

      J. Biol. Chem.

      Volume: 286 Issue: 43 Pages: 37496-37502

    • DOI

      10.1074/jbc.m111.256354

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] NMR approaches for characterizing molecular recognition process of intrinsically disordered proteins, Fifth Korea-Japan Seminars on Biomolecular Sciences2013

    • Author(s)
      Maho Yagi-Utsumi, Takumi Yamaguchi,Yoshinori Uekusa Koichi Kato.
    • Organizer
      Experiments and Simulations
    • Place of Presentation
      High1 Resort (Korea)
    • Year and Date
      2013-02-25
    • Related Report
      2012 Final Research Report
  • [Presentation] NMR spectroscopic characterization of the pathogenic interaction of amyloid β peptide with GM1 clusters2013

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      Pure and Applied Chemistry International Conference 2013 (PACCON 2013)
    • Place of Presentation
      Bangsaen Beach(Thailand)
    • Year and Date
      2013-01-24
    • Related Report
      2012 Final Research Report
  • [Presentation] NMR法による神経変性疾患関連タンパク質とガングリオシドクラスターとの相互作用解析2012

    • Author(s)
      矢木真穂、山口拓実、植草義徳、加藤晃一
    • Organizer
      第34回生体膜と薬物の相互作用シンポジウム
    • Place of Presentation
      京都大学薬学部(京都)
    • Year and Date
      2012-11-16
    • Related Report
      2012 Final Research Report
  • [Presentation] Spectroscopic characterization of conformational transitions of membrane-binding peptides upon their specific interactions with glycolipids2012

    • Author(s)
      Maho Yagi-Utsumi, Pornthip Boonsri, Yoshiki Yamaguchi, Koichi Kato
    • Organizer
      4th Japan-Korea Seminar on Biomolecular Sciences Experiments and Simulations
    • Place of Presentation
      東大寺総合文化センター(奈良)
    • Year and Date
      2012-01-10
    • Related Report
      2011 Annual Research Report
  • [Presentation] Conformational transition and intermolecular interaction of amyloid β molecules promoted on ganglioside clusters2011

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      The International Symposium on Nuclear Magnetic Resonance 2011
    • Place of Presentation
      大さん橋ホール(神奈川)
    • Year and Date
      2011-11-16
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] NMR characterization of interaction modes of amyloid β with ganglioside clusters2011

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      3rd Asian Communications of Glycobiology and Glycotechnology
    • Place of Presentation
      Shanghai Institute of Organic Chemistry(China)
    • Year and Date
      2011-10-27
    • Related Report
      2012 Final Research Report
  • [Presentation] NMR characterization of interaction modes of amyloid β with ganglioside clusters2011

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      3^<rd> Asian Communications of Glycobiology and Glycotechnology
    • Place of Presentation
      Shanghai Institute of Organic Chemistry(中華人民共和国)
    • Year and Date
      2011-10-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] Conformational transition and intermoleciilar interaction of amyloid β molecules promoted on GM1 clusters2011

    • Author(s)
      Maho Yagi-Utsumi
    • Organizer
      瀋陽薬科大学大学院特別講義
    • Place of Presentation
      瀋陽薬科大学(中華人民共和国)(招待講演)
    • Year and Date
      2011-10-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] NMR spectroscopic characterization of the pathogenic interaction of amyloid β peptide with ganglioside clusters2011

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      第71回岡崎コンファレンス「糖鎖分子科学の新たな展望」
    • Place of Presentation
      岡崎コンファレンスセンター(愛知)
    • Year and Date
      2011-10-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] ガングリオシドクラスターを舞台とするアミロイドβの重合開始機構2011

    • Author(s)
      矢木真穂
    • Organizer
      第1回「認知症研究を知る若手研究者の集まり」
    • Place of Presentation
      あいち健康プラザ(愛知)
    • Year and Date
      2011-07-31
    • Related Report
      2011 Annual Research Report
  • [Presentation] ガングリオシドクラスターが誘起するアミロイドβ重合の開始機構の解明2011

    • Author(s)
      矢木真穂、加藤晃一
    • Organizer
      第30回 日本糖質学会年会
    • Place of Presentation
      ハイブ長岡(新潟)
    • Year and Date
      2011-07-12
    • Related Report
      2012 Final Research Report
  • [Presentation] ガングリオシドクラスターが誘起するアミロイドβ重合の開始機構の解明2011

    • Author(s)
      矢木真穂、加藤晃一
    • Organizer
      第30回日本糖質学会年会
    • Place of Presentation
      ハイブ長岡(新潟)
    • Year and Date
      2011-07-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] GM1クラスターを舞台とするアミロイドβの重合開始機構2011

    • Author(s)
      矢木真穂
    • Organizer
      第12回若手NMR研究会
    • Place of Presentation
      琵琶湖リゾートクラブ(滋賀)(招待講演)
    • Year and Date
      2011-06-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] ガングリオシドクラスターを舞台とするアミロイドβの構造転移と分子間相互作用2011

    • Author(s)
      矢木真穂、加藤晃一
    • Organizer
      第11回日本蛋白質科学会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪)
    • Year and Date
      2011-06-08
    • Related Report
      2012 Final Research Report
  • [Presentation] ガングリオシドクラスターを舞台とするアミロイドβの構造転移と分子間相互作用2011

    • Author(s)
      矢木真穂、加藤晃一
    • Organizer
      第11回日本蛋白質科学会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪)(招待講演)
    • Year and Date
      2011-06-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] NMR approaches for characterizing molecular recognition process of intrinsically disordered proteins

    • Author(s)
      M. Yagi-Utsumi, T. Yamaguchi, Y. Uekusa, and K. Kato
    • Organizer
      Fifth Korea-Japan Seminars on Biomolecular Sciences: Experiments and Simulations
    • Place of Presentation
      High1 Resort (Korea)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] NMR spectroscopic characterization of the pathogenic interaction of amyloid β peptide with GM1 clusters

    • Author(s)
      Maho Yagi-Utsumi, Koichi Kato
    • Organizer
      Pure and Applied Chemistry International Conference 2013 (PACCON 2013)
    • Place of Presentation
      Bangsaen Beach(Thailand)
    • Related Report
      2012 Annual Research Report
  • [Presentation] NMR法による神経変性疾患関連タンパク質とガングリオシドクラスターとの相互作用解析

    • Author(s)
      矢木真穂、山口拓実、植草義徳、加藤晃一
    • Organizer
      第34回生体膜と薬物の相互作用シンポジウム
    • Place of Presentation
      京都大学薬学部(京都)
    • Related Report
      2012 Annual Research Report
  • [Presentation] NMR Analyses of the Conformational Transition of the Antibacterial Peptide Sarcotoxin IA Interacting with Lipid A

    • Author(s)
      Maho Yagi-Utsumi, Pornthip Boonsri, Yoshiki Yamaguchi, and Koichi Kato
    • Organizer
      4th Asian Communications of Glycobiology and Glycotechnology (ACGG 4th Conference)
    • Place of Presentation
      ICC JEJU (Korea)
    • Related Report
      2012 Annual Research Report
  • [Presentation] アミロイドβの構造転移と分子間相互作用

    • Author(s)
      矢木真穂
    • Organizer
      大阪大学蛋白質研究所セミナー・包括脳ネットワーク研究会「第3回神経科学と構造生物学の融合研究会」
    • Place of Presentation
      大阪大学蛋白質研究所(大阪)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] NMR法を用いたザルコトキシンIAとリピドAとの相互作用解析

    • Author(s)
      矢木真穂、Pornthip Boonsri、山口芳樹、加藤晃一
    • Organizer
      第31回日本糖質学会年会
    • Place of Presentation
      鹿児島市民文化ホール(鹿児島)
    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.ims.ac.jp/topics/2010/110217.html

    • Related Report
      2012 Final Research Report
  • [Remarks]

    • URL

      http://www.ims.ac.jp/topics/2010/110217.html

    • Related Report
      2011 Annual Research Report

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Published: 2011-09-05   Modified: 2019-07-29  

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