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Analysis of structure and formation mechanism of polyubiquitin fibrils

Research Project

Project/Area Number 16K18503
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Structural biochemistry
Research InstitutionKyoto University

Principal Investigator

Morimoto Daichi  京都大学, 工学研究科, 助教 (40746616)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2019: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Keywordsポリユビキチン / アミロイド線維 / 重水素交換 / 反応中間体 / レオロジーNMR / 構造ゆらぎ / 流体力学的応力 / 線維反応中間体 / 線維重水素交換 / ユビキチン / アミロイド / NMR / 線維 / 蛋白質 / 生物物理
Outline of Final Research Achievements

Ubiquitin is a protein with high structural stability and solubility. However, upon thermal and hydrodynamic stress, its polymerized form, a polyubiquitin chain, forms fibrillar aggregates that are associated with neurodegenerative diseases such as Alzheimer’s disease. In this study, we investigated the structure and formation mechanism of polyubiquitin fibrils at atomic resolution by using nuclear magnetic resonance. In our analysis of fibril intermediates and hydrogen-deuterium exchange experiments of fibrils, we identified important structural changes and inter-molecular interactions in the formation of polyubiquitin fibrils. Furthermore, we established a new rheological nuclear magnetic resonance to monitor fibril formation in situ and detected conformational changes of side chains in polyubiquitin chains during their fibril formation.

Academic Significance and Societal Importance of the Research Achievements

長年多くの病理学者たちが抱いてきた不思議は、神経変性疾患で観察される異常タンパク質凝集体(封入体)のほとんどにユビキチンが含まれていることである。本研究は、どのようにしてポリユビキチン鎖が線維状凝集体を形成するかを原子分解能で解析したものであり、得られた研究成果は封入体の形成機構の理解、つまり神経変性疾患の発症機構の理解の一助となると考える。また、得られた構造学的情報は、熱や流体力学的応力によるマルチドメインタンパク質の構造変化や分子間相互作用を理解する上で重要な知見となり得ると考える。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (34 results)

All 2020 2019 2018 2017 2016

All Journal Article (21 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 18 results,  Open Access: 12 results,  Acknowledgement Compliant: 3 results) Presentation (13 results) (of which Int'l Joint Research: 1 results,  Invited: 8 results)

  • [Journal Article] Chain-length dependent physical properties and degradation of ubiquitin chains2020

    • Author(s)
      森本 大智、白川 昌宏
    • Journal Title

      生化学

      Volume: 92 Issue: 1 Pages: 7-13

    • DOI

      10.14952/SEIKAGAKU.2020.920007

    • ISSN
      0037-1017
    • Year and Date
      2020-02-25
    • Related Report
      2019 Annual Research Report
  • [Journal Article] Pinpoint analysis of a protein in slow exchange using F1F2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis2020

    • Author(s)
      Mayu Nishizawa、Erik Walinda、Daichi Morimoto、Kenji Sugase
    • Journal Title

      Journal of Biomolecular NMR

      Volume: -

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Visualizing protein motion in Couette flow by all-atom molecular dynamics2020

    • Author(s)
      Walinda Erik、Morimoto Daichi、Shirakawa Masahiro、Scheler Ulrich、Sugase Kenji
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129383-129383

    • DOI

      10.1016/j.bbagen.2019.06.006

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 生体分子レオロジーNMRの開発と応用2019

    • Author(s)
      森本 大智、菅瀬 謙治
    • Journal Title

      日本核磁気共鳴学会機関誌

      Volume: 10 Pages: 64-68

    • Related Report
      2019 Annual Research Report
  • [Journal Article] 高感度Rheo-NMRによるアミロイド線維化過程のその場観察2019

    • Author(s)
      森本 大智、菅瀬 謙治
    • Journal Title

      月刊「細胞」

      Volume: 51 Pages: 32-36

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR2018

    • Author(s)
      Walinda Erik、Morimoto Daichi、Sugase Kenji
    • Journal Title

      Methods

      Volume: 148 Pages: 28-38

    • DOI

      10.1016/j.ymeth.2018.04.026

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana2018

    • Author(s)
      Iwakawa Naoto、Mahana Yutaka、Ono Arina、Ohki Izuru、Walinda Erik、Morimoto Daichi、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 13 Issue: 1 Pages: 59-62

    • DOI

      10.1007/s12104-018-9851-2

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin2018

    • Author(s)
      Ishii Naoki、Walinda Erik、Iwakawa Naoto、Morimoto Daichi、Iwai Kazuhiro、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 13 Issue: 1 Pages: 149-153

    • DOI

      10.1007/s12104-018-09868-5

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Isolation and characterization of a minimal building block of polyubiquitin fibrils2018

    • Author(s)
      Morimoto Daichi、Walinda Erik、Shinke Mayo、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 2711-2711

    • DOI

      10.1038/s41598-018-21144-z

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils2018

    • Author(s)
      Morimoto Daichi、Nishizawa Ryo、Walinda Erik、Takashima Shingo、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      Polymers

      Volume: 10 Issue: 3 Pages: 240-240

    • DOI

      10.3390/polym10030240

    • NAID

      120006501309

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Overview of Relaxation Dispersion NMR Spectroscopy to Study Protein Dynamics and Protein-Ligand Interactions2018

    • Author(s)
      Walinda Erik、Morimoto Daichi、Sugase Kenji
    • Journal Title

      Current Protocols in Protein Science

      Volume: 92 Issue: 1

    • DOI

      10.1002/cpps.57

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] F1F2-selective NMR spectroscopy2017

    • Author(s)
      Walinda Erik、Morimoto Daichi、Shirakawa Masahiro、Sugase Kenji
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 68 Issue: 1 Pages: 41-52

    • DOI

      10.1007/s10858-017-0113-x

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Biological and Physicochemical Functions of Ubiquitylation Revealed by Synthetic Chemistry Approaches2017

    • Author(s)
      Morimoto Daichi、Walinda Erik、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 18 Issue: 6 Pages: 1145-1145

    • DOI

      10.3390/ijms18061145

    • NAID

      120006318888

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] High-sensitivity Rheo-NMR spectroscopy for protein studies.2017

    • Author(s)
      Morimoto D., Walinda E., Iwakawa N., Nishizawa M., Kawata Y., Yamamoto A., Shirakawa M., Scheler U., Sugase K.
    • Journal Title

      Anal. Chem.

      Volume: 89 Issue: 14 Pages: 7286-7290

    • DOI

      10.1021/acs.analchem.7b01816

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance.2017

    • Author(s)
      Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, Suetake I, Arita K, Nakanishi M
    • Journal Title

      Mol Cell

      Volume: 68 Issue: 2 Pages: 350-360

    • DOI

      10.1016/j.molcel.2017.09.037

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Real-time observation of the interaction between thioflavin T and an amyloid protein by using high-sensitivity Rheo-NMR.2017

    • Author(s)
      Iwakawa N., Morimoto D., Walinda E., Kawata Y., Shirakawa M., Sugase K.
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 18 Issue: 11 Pages: 2271-2271

    • DOI

      10.3390/ijms18112271

    • NAID

      120006501319

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Practical considerations for investigation of protein conformational dynamics by 15N R 1ρ relaxation dispersion.2017

    • Author(s)
      Walinda E, Morimoto D, Shirakawa M, Sugase K.
    • Journal Title

      Biomol NMR.

      Volume: 印刷中 Issue: 3 Pages: 201-209

    • DOI

      10.1007/s10858-017-0097-6

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Efficient identification and analysis of chemical exchange in biomolecules by R1rho relaxation dispersion with Amaterasu2016

    • Author(s)
      Walinda, E. Morimoto, D. Nishizawa, M. Shirakawa, M. Sugase, K.
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 16 Pages: 2539-2541

    • DOI

      10.1093/bioinformatics/btw188

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The evolving world of ubiquitin: transformed polyubiquitin chains.2016

    • Author(s)
      Morimoto, D. and Shirakawa, M.
    • Journal Title

      Biomolecular Concepts

      Volume: 7 Issue: 3 Pages: 157-67

    • DOI

      10.1515/bmc-2016-0009

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dual Function of Phosphoubiquitin in E3 Activation of Parkin2016

    • Author(s)
      Walinda, E. Morimoto, D. Sugase, K. Shirakawa, M.
    • Journal Title

      J Biol Chem

      Volume: 291 Issue: 32 Pages: 16879-16891

    • DOI

      10.1074/jbc.m116.728600

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Ubiquitylation Directly Induces Fold Destabilization of Proteins.2016

    • Author(s)
      Morimoto D , Walinda E, Fukada H, Sugase K, Shirakawa M
    • Journal Title

      Sci Rep.

      Volume: 6 Issue: 1 Pages: 39453-39453

    • DOI

      10.1038/srep39453

    • NAID

      120005947214

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Fibrillar protein aggregate formation of poly-ubiquitin revealed by physical property analysis2019

    • Author(s)
      Morimoto Daichi、Walinda Erik、Sugase Kenji、Shirakawa Masahiro
    • Organizer
      The 92nd annual meeting of the japanese biochemical society
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Amyloid formation of poly-ubiquitin chains investigated by biological rheo-NMR spectroscopy2019

    • Author(s)
      Morimoto Daichi、Walinda Erik、Iwakawa Naoto、Yamamoto Akihiko、Shirakawa Masahiro、Scheler Ulrich、Sugase Kenji
    • Organizer
      EUROISMAR 2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] バイオレオロジーNMR法の開発と応用2019

    • Author(s)
      Morimoto Daichi
    • Organizer
      The 20th Young NMR Scientist Meeting
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Amyloid fibril formation of poly-ubiquitin revealed by physical property analysis2019

    • Author(s)
      Morimoto Daichi、Walinda Erik、Sugase Kenji、Shirakawa Masahiro
    • Organizer
      Joint Annual Meeting of 71st JSCB and 19th PSSJ
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Atomic-level structural characterization of amyloid formation by using Rheo-NMR spectroscopy2018

    • Author(s)
      Morimoto Daichi、Walinda Erik、Iwakawa Naoto、Sugase Kenji、Shirakawa Masahiro
    • Organizer
      The 18th Annual Meeting of the Protein Science Society of Japan
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Elucidation of amyloid fibril formation mechanism by using novel Rheo-NMR spectroscopy2018

    • Author(s)
      Morimoto Daichi、Walinda Erik、Iwakawa Naoto、Scheler Ulrich、Yamamoto, Akihiko、Sugase Kenji、Shirakawa Masahiro
    • Organizer
      EUROMAR 2018
    • Related Report
      2018 Research-status Report
  • [Presentation] Development of high-sensitivity Rheo-NMR spectroscopy2018

    • Author(s)
      Morimoto Daichi、Walinda Erik、Scheler Ulrich、Yamamoto, Akihiko、Sugase Kenji、Shirakawa Masahiro
    • Organizer
      The 19th Young NMR Scientist Meeting
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Elucidation of amyloid fibril formation mechanism by using Rheo-NMR spectroscopy2017

    • Author(s)
      Daichi Morimoto, Erik Walinda, Naoto Iwakawa, Ulrich Scheler, Akihiko Yamamoto, Masahiro Shirakawa, and Kenji Sugase
    • Organizer
      The 56th Annual Meeting of the Nuclear Magnetic Resonance Society of Japan.
    • Related Report
      2017 Research-status Report
  • [Presentation] Ubiquitylation-induced protein aggregation.2016

    • Author(s)
      Morimoto, D., Walinda, E., Fukada, H, Sugase, K., Hoshino, M., Fujii, T., Namba, K., Komatsu, M., Tanaka, K., and Shirakawa, M.
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan.
    • Place of Presentation
      Tsukuba
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Highly Sensitive Rheo-NMR Spectroscopy For Proteins.2016

    • Author(s)
      Morimoto, D., Walinda, E., Nishizawa, M., Scheler, U., Yamamoto, A., Shirakawa, M., and Sugase, K.
    • Organizer
      The 55th Annual Meeting of the Nuclear Magnetic Resonance Society of Japan.
    • Place of Presentation
      Hiroshima
    • Year and Date
      2016-11-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Elucidation of formation mechanism of ubiquitin-positive aggregates in cells.2016

    • Author(s)
      Morimoto, D., Walinda, E., Fukada, H, Sugase, K., Kageyama, S., Hoshino, M., H., Namba, K., Komatsu, M., Tanaka, K., and Shirakawa, M.
    • Organizer
      The 89th Annual Meeting of the Japanese Biochemical Society.
    • Place of Presentation
      Sendai
    • Year and Date
      2016-09-25
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Detection of Metastable States of Polyubiquitin Fibrils.2016

    • Author(s)
      Morimoto, D., Walinda, E., Shinke, M., Sugase, K., and Shirakawa, M.
    • Organizer
      The XXVIIth International Conference on Magnetic Resonance in Biological Systems.
    • Place of Presentation
      Kyoto
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Functional regulation of protein by SUMOylation and ubiquitylation.2016

    • Author(s)
      Morimoto, D.
    • Organizer
      The 371st CBI meeting.
    • Place of Presentation
      Osaka
    • Related Report
      2016 Research-status Report
    • Invited

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Published: 2016-04-21   Modified: 2021-02-19  

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