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2022 Fiscal Year Annual Research Report

Neutron Structural Biology for New Generation

Research Project

Project/Area Number 18H05229
Research InstitutionKyoto University

Principal Investigator

杉山 正明  京都大学, 複合原子力科学研究所, 教授 (10253395)

Co-Investigator(Kenkyū-buntansha) 中川 洋  国立研究開発法人日本原子力研究開発機構, 原子力科学研究部門 原子力科学研究所 物質科学研究センター, 研究主幹 (20379598)
矢木 真穂  名古屋市立大学, 大学院薬学研究科, 研究員 (40608999)
富永 大輝  一般財団法人総合科学研究機構(総合科学研究センター(総合科学研究室)及び中性子科学センター(研究開発, 中性子科学センター, 副主任研究員 (50513694)
佐藤 衛  横浜市立大学, 生命医科学研究科, 客員教授 (60170784)
井上 倫太郎  京都大学, 複合原子力科学研究所, 准教授 (80563840)
齋尾 智英  徳島大学, 先端酵素学研究所, 教授 (80740802)
苙口 友隆  慶應義塾大学, 理工学部(矢上), 講師 (90589821)
小田 隆  立教大学, 理学部, 助教 (00573164)
Project Period (FY) 2018-06-11 – 2023-03-31
Keywords階層間連携ダイナミクス / 中性子溶液散乱 / タンパク質重水素化 / ドメインライゲーション / 計算機連携解析
Outline of Annual Research Achievements

生体高分子の運動は構造と同様に階層性を持つが、その中でも実験手法が存在しなった時空間ゾーン(時間:ピコ秒 ー マイクロ秒, 空間:サブナノメートル ー サブミクロンメートル)の測定・解析手法をJ-PRAC/MLFの最新の中性子散乱・分光装置を主として用いることで、「中性子測定法」を基軸として確立した。研究では、種々の生物学的に意義深い試料を用いて、新たな試料重水素化調製法・生体試料対応測定法・計算機解析法の開発を有機的に連動させて行った。更に並行して開発手法による対象の生体高分子の運動解明を行い、その運動に相関する機能を明らかした

Research Progress Status

令和4年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和4年度が最終年度であるため、記入しない。

  • Research Products

    (25 results)

All 2023 2022 Other

All Journal Article (13 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 13 results,  Open Access: 4 results) Presentation (10 results) (of which Int'l Joint Research: 10 results,  Invited: 5 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water2023

    • Author(s)
      Nakagawa Hiroshi、Yamamoto Naoki
    • Journal Title

      Life

      Volume: 13 Pages: 318~318

    • DOI

      10.3390/life13020318

    • Peer Reviewed / Open Access
  • [Journal Article] Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance2022

    • Author(s)
      Okuda Aya、Shimizu Masahiro、Inoue Rintaro、Urade Reiko、Sugiyama Masaaki
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 62 Pages: n/a-n/a

    • DOI

      10.1002/anie.202214412

    • Peer Reviewed
  • [Journal Article] Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer2022

    • Author(s)
      Tominaga Taiki、Nakagawa Hiroshi、Sahara Masae、Oda Takashi、Inoue Rintaro、Sugiyama Masaaki
    • Journal Title

      Life

      Volume: 12 Pages: 675~675

    • DOI

      10.3390/life12050675

    • Peer Reviewed / Open Access
  • [Journal Article] Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach2022

    • Author(s)
      Yunoki Yasuhiro、Matsumoto Atsushi、Morishima Ken、Martel Anne、Porcar Lionel、Sato Nobuhiro、Yogo Rina、Tominaga Taiki、Inoue Rintaro、Yagi-Utsumi Maho、Okuda Aya、Shimizu Masahiro、Urade Reiko、Terauchi Kazuki、Kono Hidetoshi、Yagi Hirokazu、Kato Koichi、Sugiyama Masaaki
    • Journal Title

      Communications Biology

      Volume: 5 Pages: n/a-n/a

    • DOI

      10.1038/s42003-022-03143-z

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations2022

    • Author(s)
      Shimizu Masahiro、Okuda Aya、Morishima Ken、Inoue Rintaro、Sato Nobuhiro、Yunoki Yasuhiro、Urade Reiko、Sugiyama Masaaki
    • Journal Title

      Scientific Reports

      Volume: 12 Pages: n/a-n/a

    • DOI

      10.1038/s41598-022-13982-9

    • Peer Reviewed
  • [Journal Article] Tracking the Structural Development of Amyloid Precursors in the Insulin B Chain and the Inhibition Effect by Fibrinogen2022

    • Author(s)
      Yamamoto Naoki、Inoue Rintaro、Makino Yoshiteru、Sekiguchi Hiroshi、Shibayama Naoya、Naito Akira、Sugiyama Masaaki、Chatani Eri
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 126 Pages: 10797~10812

    • DOI

      10.1021/acs.jpcb.2c05136

    • Peer Reviewed
  • [Journal Article] Heat-Induced Conformational Transition Mechanism of Heat Shock Factor 1 Investigated by Tryptophan Probe2022

    • Author(s)
      Kawagoe Soichiro、Kumashiro Munehiro、Mabuchi Takuya、Kumeta Hiroyuki、Ishimori Koichiro、Saio Tomohide
    • Journal Title

      Biochemistry

      Volume: 61 Pages: 2897~2908

    • DOI

      10.1021/acs.biochem.2c00492

    • Peer Reviewed
  • [Journal Article] Identification of an endoplasmic reticulum proteostasis modulator that enhances insulin production in pancreatic β cells2022

    • Author(s)
      Miyake Masato、Sobajima Mitsuaki、Kurahashi Kiyoe、Shigenaga Akira、Denda Masaya、Otaka Akira、Saio Tomohide、Sakane Naoki、Kosako Hidetaka、Oyadomari Seiichi
    • Journal Title

      Cell Chemical Biology

      Volume: 29 Pages: 996~1009.e9

    • DOI

      10.1016/j.chembiol.2022.01.002

    • Peer Reviewed
  • [Journal Article] Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding2022

    • Author(s)
      Kawagoe Soichiro、Ishimori Koichiro、Saio Tomohide
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 23 Pages: 2485~2485

    • DOI

      10.3390/ijms23052485

    • Peer Reviewed / Open Access
  • [Journal Article] Biophysical elucidation of neural network and chemical regeneration of neural tissue2022

    • Author(s)
      Muraoka Takahiro、Saio Tomohide、Okumura Masaki
    • Journal Title

      Biophysics and Physicobiology

      Volume: 19 Pages: n/a-n/a

    • DOI

      10.2142/biophysico.bppb-v19.0024

    • Peer Reviewed
  • [Journal Article] Biological Significance of Intrinsically Disordered Protein Structure2022

    • Author(s)
      Sato Mamoru
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 22 Pages: 26~37

    • DOI

      10.1273/cbij.22.26

    • Peer Reviewed
  • [Journal Article] Biochemical analysis of the replication initiator protein of staphylococcal plasmid pC1942022

    • Author(s)
      Maekawa Michinari、Oda Takashi、Hanai Ryo
    • Journal Title

      Biochimie

      Volume: 202 Pages: 85~93

    • DOI

      10.1016/j.biochi.2022.08.011

    • Peer Reviewed
  • [Journal Article] Effect of water activity on the mechanical glass transition and dynamical transition of bacteria2022

    • Author(s)
      Sogabe Tomochika、Nakagawa Hiroshi、Yamada Takeshi、Koseki Shigenobu、Kawai Kiyoshi
    • Journal Title

      Biophysical Journal

      Volume: 121 Pages: 3874~3882

    • DOI

      10.1016/j.bpj.2022.09.001

    • Peer Reviewed
  • [Presentation] “Conformational distribution of a multi-domain protein enzyme investigated by paramagnetic NMR and ESR2023

    • Author(s)
      T. Saio
    • Organizer
      3rd India-Japan NMR WORK SHOP
    • Int'l Joint Research / Invited
  • [Presentation] Structural insight into regulation and dysregulation of protein assembly and folding2023

    • Author(s)
      T. Saio
    • Organizer
      The 1st IMEG Meeting of The Research Center for High Depth Omics, Kumamoto
    • Int'l Joint Research / Invited
  • [Presentation] Structural and kinetic views of regulators for protein folding and assembly2022

    • Author(s)
      T. Saio
    • Organizer
      International Symposium on Unfolded Proteins, Protein folding, and Disease-causing Aggregation, Korea
    • Int'l Joint Research / Invited
  • [Presentation] Integrated Method with Analytical Ultracentrifugation and Small-Angle Scattering (AUC-SAS) for the Structural Analysis of a Biomacromolecule in a Polydisperse Solution2022

    • Author(s)
      K. Morishima, A. Okuda, N. Sato, M. Shimizu, Y. Yunoki, R. Inoue, R. Urade, M. Sugiyama
    • Organizer
      XVIII International Small Angle Scattering Conference-SAS2022
    • Int'l Joint Research
  • [Presentation] Solution Structure Analysis of the Multi-domain Protein, ER-60 by Small Angle Scattering2022

    • Author(s)
      A. Okuda, M. Shimizu, K. Morishima, R. Inoue, N. Sato, Y. Yunoki, R. Urade, M. Sugiyama
    • Organizer
      XVIII International Small Angle Scattering Conference-SAS2022
    • Int'l Joint Research
  • [Presentation] Domain Conformation of Multi-domain Protein ER-60 Studied with Hybrid Approach of Coarse-grained Simulations and Small-angle X-ray Scattering2022

    • Author(s)
      M. Shimizu, A. Okuda, K. Morishima, N. Sato, R. Inoue, Y. Yunoki, R. Urade, M. Sugiyama
    • Organizer
      XVIII International Small Angle Scattering Conference-SAS2022
    • Int'l Joint Research
  • [Presentation] Dynamics and Structure of Intrinsically Disordered Region of Hef as Studied by Solution Scattering2022

    • Author(s)
      R. Inoue, T. Oda, H. Nakagwa, T. Tominaga, Y. Kawakita, M. Sato, M. Sugiyama
    • Organizer
      XVIII International Small Angle Scattering Conference - SAS2022
    • Int'l Joint Research
  • [Presentation] Future Perspective of Biological Small-Angle Scattering2022

    • Author(s)
      M.Sugiyama
    • Organizer
      US-Japan workshop, Oak Ridge
    • Int'l Joint Research / Invited
  • [Presentation] SANS for soft matter”, Neutron Scattering on continuous sources - future developments2022

    • Author(s)
      R. Inoue, M. Sugiyama
    • Organizer
      US-Japan workshop, Oak Ridge
    • Int'l Joint Research / Invited
  • [Presentation] KumatorI Deuteration Station (KIDS)2022

    • Author(s)
      M. Sugiyama
    • Organizer
      Dunet meeting
    • Int'l Joint Research
  • [Book] 実験医学別冊 相分離解析プロトコール “中性子散乱”2022

    • Author(s)
      1.中川洋、松尾龍人
    • Total Pages
      6
    • Publisher
      羊土社
  • [Remarks] 新世代中性子構造生物学の開拓

    • URL

      http://www.rri.kyoto-u.ac.jp/PSlab/s-project.html#project2

URL: 

Published: 2023-12-25  

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