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2023 Fiscal Year Annual Research Report

Development of the next-generation high-speed AFM and detailed dynamic behavior analysis of biomolecules

Research Project

Project/Area Number 20H00327
Research InstitutionKanazawa University

Principal Investigator

古寺 哲幸  金沢大学, ナノ生命科学研究所, 教授 (30584635)

Project Period (FY) 2020-04-01 – 2024-03-31
Keywords原子間力顕微鏡 / 生物物理学 / タンパク質 / 一分子イメージング / 生体分子
Outline of Annual Research Achievements

本年は、昨年度に引き続き、高速振幅計測器を実用化するために、企業とともに更なる広帯域化と操作性を向上させた電子回路の共同開発を継続した。自作したもの(Umeda et al., Applied Physics Letters 2021)の帯域の数倍の高速化が見込まれている。また、昨年度までに10 MHz程度の液中共振周波数を持つ超小型高速カンチレバーの開発を行っていたが、試料と反対側に反りかえってしまうことが問題となっていた。そこで、集積イオンビーム装置で加工するときの加工手順を見直すことで、反りを大幅に抑えることに成功した。また、昨年度までに非点の小さなレーザーダイオードを導入することで、カンチレバーの変位計測のためのレーザースポットの微小化に成功していたが、レーザーの戻り光ノイズが問題となっていた。そこで、高周波重畳法を導入し、戻り光ノイズを取り除くことに成功した。これにより、超微小高速カンチレバーの変位を高い精度で計測できるようになり、イメージング実験が大幅にやりやすくなった。
また、開発途中の次世代型高速AFMを用いて、バイオ応用研究を進めた。たとえば、ヒストンシャペロンであるNAP1とヒストンH2A-H2Bの複合体の構造を可視化することに成功した(Journal of Molecular Biology誌)。また、抗酸菌の天然変性ヒストン様タンパク質mycobacterial DNA-binding protein 1が、他の核酸結合タンパク質では報告のない、天然変性領域を介した新規のDNA凝集メカニズムを介して抗酸菌の休眠を誘導することを明らかにした(Nucleic Acids Research誌)。脳の神経細胞に豊富に存在し、記憶形成や忘却を担うタンパク質CaMKIIの動作中の姿をナノスケールで可視化することに成功した(Science Advances誌)。これらにより開発した顕微鏡装置の性能を示すとともに、生物学的に意義深い新知見を得ることができた。

Research Progress Status

令和5年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和5年度が最終年度であるため、記入しない。

  • Research Products

    (28 results)

All 2024 2023 2020 Other

All Int'l Joint Research (4 results) Journal Article (15 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 15 results,  Open Access: 13 results) Presentation (4 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results) Remarks (2 results) Patent(Industrial Property Rights) (3 results)

  • [Int'l Joint Research] Emory University/Colorado State University(米国)

    • Country Name
      U.S.A.
    • Counterpart Institution
      Emory University/Colorado State University
  • [Int'l Joint Research] Vilnius University(リトアニア)

    • Country Name
      LITHUANIA
    • Counterpart Institution
      Vilnius University
  • [Int'l Joint Research] ShanghaiTech University/Fudan University(中国)

    • Country Name
      CHINA
    • Counterpart Institution
      ShanghaiTech University/Fudan University
  • [Int'l Joint Research] CNRS UMR9198(フランス)

    • Country Name
      FRANCE
    • Counterpart Institution
      CNRS UMR9198
  • [Journal Article] S100A11 promotes focal adhesion disassembly via myosin II-driven contractility and Piezo1-mediated Ca2+ entry2024

    • Author(s)
      Mohammed Tareg Omer、Lin You-Rong、Akter Lucky、Weissenbruch Kai、Ngo Kien Xuan、Zhang Yanjun、Kodera Noriyuki、Bastmeyer Martin、Miyanari Yusuke、Taoka Azuma、Franz Clemens M.
    • Journal Title

      Journal of Cell Science

      Volume: 137 Pages: jcs261492

    • DOI

      10.1242/jcs.261492

    • Peer Reviewed / Open Access
  • [Journal Article] Atom Filtering Algorithm and GPU-Accelerated Calculation of Simulation Atomic Force Microscopy Images2024

    • Author(s)
      Amyot Romain、Kodera Noriyuki、Flechsig Holger
    • Journal Title

      Algorithms

      Volume: 17 Pages: 38

    • DOI

      10.3390/a17010038

    • Peer Reviewed / Open Access
  • [Journal Article] Removing the parachuting artifact using two-way scanning data in high-speed atomic force microscopy2023

    • Author(s)
      Kubo Shintaroh、Umeda Kenichi、Kodera Noriyuki、Takada Shoji
    • Journal Title

      Biophysics and Physicobiology

      Volume: 20 Pages: e200006

    • DOI

      10.2142/biophysico.bppb-v20.0006

    • Peer Reviewed / Open Access
  • [Journal Article] BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics2023

    • Author(s)
      Amyot Romain、Kodera Noriyuki、Flechsig Holger
    • Journal Title

      Journal of Structural Biology: X

      Volume: 7 Pages: 100086

    • DOI

      10.1016/j.yjsbx.2023.100086

    • Peer Reviewed / Open Access
  • [Journal Article] PQBP5/NOL10 maintains and anchors the nucleolus under physiological and osmotic stress conditions2023

    • Author(s)
      Jin Xiaocen、Tanaka Hikari、Jin Meihua、Fujita Kyota、Homma Hidenori、Inotsume Maiko、Yong Huang、Umeda Kenichi、Kodera Noriyuki、Ando Toshio、Okazawa Hitoshi
    • Journal Title

      Nature Communications

      Volume: 14 Pages: 9

    • DOI

      10.1038/s41467-022-35602-w

    • Peer Reviewed / Open Access
  • [Journal Article] Spatiotemporal resolution in high-speed atomic force microscopy for studying biological macromolecules in action2023

    • Author(s)
      Umeda Kenichi、McArthur Steven J、Kodera Noriyuki
    • Journal Title

      Microscopy

      Volume: 72 Pages: 151~161

    • DOI

      10.1093/jmicro/dfad011

    • Peer Reviewed / Open Access
  • [Journal Article] High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale2023

    • Author(s)
      Morioka Shin、Sato Shoko、Horikoshi Naoki、Kujirai Tomoya、Tomita Takuya、Baba Yudai、Kakuta Takahiro、Ogoshi Tomoki、Puppulin Leonardo、Sumino Ayumi、Umeda Kenichi、Kodera Noriyuki、Kurumizaka Hitoshi、Shibata Mikihiro
    • Journal Title

      Nano Letters

      Volume: 23 Pages: 1696~1704

    • DOI

      10.1021/acs.nanolett.2c04346

    • Peer Reviewed / Open Access
  • [Journal Article] Dynamics of Target DNA Binding and Cleavage by Staphylococcus aureus Cas9 as Revealed by High-Speed Atomic Force Microscopy2023

    • Author(s)
      Puppulin Leonardo、Ishikawa Junichiro、Sumino Ayumi、Marchesi Arin、Flechsig Holger、Umeda Kenichi、Kodera Noriyuki、Nishimasu Hiroshi、Shibata Mikihiro
    • Journal Title

      ACS Nano

      Volume: 17 Pages: 4629~4641

    • DOI

      10.1021/acsnano.2c10709

    • Peer Reviewed / Open Access
  • [Journal Article] Purification of Na+-Driven MotPS Stator Complexes and Single-Molecule Imaging by High-Speed Atomic Force Microscopy2023

    • Author(s)
      Terahara Naoya、Kodera Noriyuki
    • Journal Title

      Methods in Molecular Biology

      Volume: 2646 Pages: 109~124

    • DOI

      10.1007/978-1-0716-3060-0_10

    • Peer Reviewed
  • [Journal Article] Structural Dynamics of Amyloid-β Protofibrils and Actions of Anti-Amyloid-β Antibodies as Observed by High-Speed Atomic Force Microscopy2023

    • Author(s)
      Watanabe-Nakayama Takahiro、Tsuji Mayumi、Umeda Kenichi、Oguchi Tatsunori、Konno Hiroki、Noguchi-Shinohara Moeko、Kiuchi Yuji、Kodera Noriyuki、Teplow David B.、Ono Kenjiro
    • Journal Title

      Nano Letters

      Volume: 23 Pages: 6259~6268

    • DOI

      10.1021/acs.nanolett.3c00187

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods2023

    • Author(s)
      Ohtomo Hideaki、Yamane Tsutomu、Oda Takashi、Kodera Noriyuki、Kurita Jun-ichi、Tsunaka Yasuo、Amyot Romain、Ikeguchi Mitsunori、Nishimura Yoshifumi
    • Journal Title

      Journal of Molecular Biology

      Volume: 435 Pages: 168189

    • DOI

      10.1016/j.jmb.2023.168189

    • Peer Reviewed / Open Access
  • [Journal Article] Imaging single CaMKII holoenzymes at work by high-speed atomic force microscopy2023

    • Author(s)
      Tsujioka Shotaro、Sumino Ayumi、Nagasawa Yutaro、Sumikama Takashi、Flechsig Holger、Puppulin Leonardo、Tomita Takuya、Baba Yudai、Kakuta Takahiro、Ogoshi Tomoki、Umeda Kenichi、Kodera Noriyuki、Murakoshi Hideji、Shibata Mikihiro
    • Journal Title

      Science Advances

      Volume: 9 Pages: eadh1069

    • DOI

      10.1126/sciadv.adh1069

    • Peer Reviewed / Open Access
  • [Journal Article] Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions2023

    • Author(s)
      Amyot Romain、Nakamoto Kaho、Kodera Noriyuki、Flechsig Holger
    • Journal Title

      Frontiers in Molecular Biosciences

      Volume: 10 Pages: 1264161

    • DOI

      10.3389/fmolb.2023.1264161

    • Peer Reviewed / Open Access
  • [Journal Article] Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy2023

    • Author(s)
      Nishiyama Akihito、Shimizu Masahiro、Narita Tomoyuki、Kodera Noriyuki、Ozeki Yuriko、Yokoyama Akira、Mayanagi Kouta、Yamaguchi Takehiro、Hakamata Mariko、Shaban Amina Kaboso、Tateishi Yoshitaka、Ito Kosuke、Matsumoto Sohkichi
    • Journal Title

      Nucleic Acids Research

      Volume: 52 Pages: 816~830

    • DOI

      10.1093/nar/gkad1149

    • Peer Reviewed
  • [Journal Article] Structural Dynamics of E6AP E3 Ligase HECT Domain and Involvement of a Flexible Hinge Loop in the Ubiquitin Chain Synthesis Mechanism2023

    • Author(s)
      Takeda Kazusa、Flechsig Holger、Muro Ikumi、Amyot Romain、Kobayashi Fuminori、Kodera Noriyuki、Ando Toshio、Konno Hiroki
    • Journal Title

      Nano Letters

      Volume: 23 Pages: 11940~11948

    • DOI

      10.1021/acs.nanolett.3c04150

    • Peer Reviewed / Open Access
  • [Presentation] Video imaging of biological molecules in action by high-speed atomic force microscopy2023

    • Author(s)
      Noriyuki Kodera
    • Organizer
      The 40th International Conference of the Microscopy Society of Thailand
    • Int'l Joint Research / Invited
  • [Presentation] Recent progress in high-speed atomic force microscopy2023

    • Author(s)
      Noriyuki Kodera, Kenichi Umeda, Kazuma Tatsumi, Karen Kamoshita
    • Organizer
      9th Multifrequency AFM Conference
    • Int'l Joint Research / Invited
  • [Presentation] High-speed atomic force microscopy for studying dynamic behaviors of biomolecules2023

    • Author(s)
      Noriyuki Kodera
    • Organizer
      NanoBiocom2023
    • Int'l Joint Research / Invited
  • [Presentation] Video imaging of biological molecules in action by high-speed AFM2023

    • Author(s)
      Noriyuki Kodera
    • Organizer
      NanospecFY2023
    • Int'l Joint Research / Invited
  • [Remarks] 抗酸菌における決定的な休眠誘導機構を発見 -天然変性タンパク質による新規のDNA凝集メカニズム-

    • URL

      https://nanolsi.kanazawa-u.ac.jp/highlights/29790/

  • [Remarks] ヒストンシャペロンとヒストンの複合体構造を 統合的な相関構造解析法により初めて解明

    • URL

      https://nanolsi.kanazawa-u.ac.jp/highlights/27756/

  • [Patent(Industrial Property Rights)] 走査型プローブ顕微鏡およびZ駆動装置2020

    • Inventor(s)
      古寺哲幸, 清水将裕, 安藤敏夫
    • Industrial Property Rights Holder
      古寺哲幸, 清水将裕, 安藤敏夫
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      特許第7273408号
  • [Patent(Industrial Property Rights)] マニピュレータ機能付き原子間力顕微鏡2020

    • Inventor(s)
      古寺哲幸, 高野純ら他4名
    • Industrial Property Rights Holder
      古寺哲幸, 高野純ら他4名
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      特許第7282370号
  • [Patent(Industrial Property Rights)] 電気生理学的解析を可能にした原子間力顕微鏡2020

    • Inventor(s)
      古寺哲幸, 米川拓臣, 執行航希, 渡邉信嗣, 安藤敏夫
    • Industrial Property Rights Holder
      古寺哲幸, 米川拓臣, 執行航希, 渡邉信嗣, 安藤敏夫
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      特許第7282371号

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Published: 2024-12-25  

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