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Structural analysis of modified NCP using mass spectrometry

Research Project

Project/Area Number 17K07313
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionYokohama City University

Principal Investigator

AKASHI Satoko  横浜市立大学, 生命医科学研究科, 教授 (10280728)

Project Period (FY) 2017-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords質量分析 / ヌクレオソームコア粒子 / 構造解析 / 蛋白質 / 生体分子 / 分析科学
Outline of Final Research Achievements

To clarify structural changes in nucleosomes caused by modifications, such as DNA methylation and histone acetylation, we performed biophysical analysis of modified nucleosome core particles (NCPs) that were reconstituted in vitro. In the analysis of modified NCPs, mono- and di-NCP were prepared with 147 and 366 base-pair (bp) DNA oligomers. Further, we prepared NCPs with DNA oligomers having AT or CG rich sequences, and characterized their biophysical properties by mass spectrometry and small angle X-ray scattering. No structural information is available for these NCPs due to difficulty in crystallization. We established a mass spectrometric method to reliably determine the methylation levels of DNA fragments with ~400 bp.

Academic Significance and Societal Importance of the Research Achievements

極めて多くのサイトがメチル化されたDNAを用いて再構成されたDNAの構造解析のための要素技術を質量分析を駆使して開発できたことは、エピゲノム科学研究の基盤構築に貢献できると考えられる。特に、今後クライオ電顕による構造解析を組み合わせることで、このような研究が大幅に進展すると考えられるが、そのための準備段階として、有用な知見が得られた。

Report

(5 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (48 results)

All 2021 2020 2019 2018 2017 Other

All Journal Article (12 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 12 results,  Open Access: 7 results,  Acknowledgement Compliant: 1 results) Presentation (34 results) (of which Int'l Joint Research: 4 results,  Invited: 7 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Structural plasticity of a designer protein sheds light on β‐propeller protein evolution2021

    • Author(s)
      Mylemans Bram、Laier Ina、Kamata Kenichi、Akashi Satoko、Noguchi Hiroki、Tame Jeremy R. H.、Voet Arnout R. D.
    • Journal Title

      The FEBS Journal

      Volume: 288 Issue: 2 Pages: 530-545

    • DOI

      10.1111/febs.15347

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mass Spectrometric Characterization of Histone H3 Isolated from <i>in-Vitro</i> Reconstituted and Acetylated Nucleosome Core Particle2020

    • Author(s)
      Kazumi Saikusa, Haruna Hidaka, Shunsuke Izumi, Satoko Akashi
    • Journal Title

      Mass Spectrometry

      Volume: 9 Issue: 1 Pages: A0090-A0090

    • DOI

      10.5702/massspectrometry.A0090

    • NAID

      130007933311

    • ISSN
      2186-5116, 2187-137X
    • Year and Date
      2020-10-31
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Screening of protein-ligand interactions under crude conditions by native mass spectrometry2020

    • Author(s)
      Takano Kotaro、Arai Shunsuke、Sakamoto Seiji、Ushijima Hiroshi、Ikegami Takahisa、Saikusa Kazumi、Konuma Tsuyoshi、Hamachi Itaru、Akashi Satoko
    • Journal Title

      Analytical and Bioanalytical Chemistry

      Volume: 412 Issue: 17 Pages: 4037-4043

    • DOI

      10.1007/s00216-020-02649-x

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Native Mass Spectrometry of Protein and DNA Complexes Prepared in Nonvolatile Buffers2020

    • Author(s)
      Saikusa Kazumi、Kato Daiki、Nagadoi Aritaka、Kurumizaka Hitoshi、Akashi Satoko
    • Journal Title

      Journal of the American Society for Mass Spectrometry

      Volume: 31 Issue: 3 Pages: 711-718

    • DOI

      10.1021/jasms.9b00145

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins2019

    • Author(s)
      Tamura Risako、Oi Rika、Akashi Satoko、Kaneko Mika K.、Kato Yukinari、Nogi Terukazu
    • Journal Title

      Protein Science

      Volume: 23 Issue: 4 Pages: 823-836

    • DOI

      10.1002/pro.3580

    • Related Report
      2019 Research-status Report 2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural visualization of key steps in nucleosome reorganization by human FACT2019

    • Author(s)
      Mayanagi Kouta、Saikusa Kazumi、Miyazaki Naoyuki、Akashi Satoko、Iwasaki Kenji、Nishimura Yoshifumi、Morikawa Kosuke、Tsunaka Yasuo
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 10183-10183

    • DOI

      10.1038/s41598-019-46617-7

    • NAID

      120007133123

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Rapid and Definitive Analysis of In Vitro DNA Methylation by Nano-electrospray Ionization Mass Spectrometry2019

    • Author(s)
      Ushijima Hiroshi, Maekawa Rena, Igarashi Eri, Akashi Satoko
    • Journal Title

      Journal of the American Society for Mass Spectrometry

      Volume: 30 Issue: 11 Pages: 2335-2346

    • DOI

      10.1007/s13361-019-02304-5

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Photoinduced in Vivo Magnetic Resonance Imaging (MRI) with Rapid CO Release from an MnCO-Protein Needle Composite2018

    • Author(s)
      Hyodo Fuminori、Sho Takeya、Maity Basudev、Fujita Kenta、Tachibana Yoko、Akashi Satoko、Mano Megumi、Hishikawa Yuki、Matsuo Masayuki、Ueno Takafumi
    • Journal Title

      Chemistry - A European Journal

      Volume: 24 Issue: 45 Pages: 11578-11583

    • DOI

      10.1002/chem.201802445

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry2018

    • Author(s)
      Saikusa Kazumi、Osakabe Akihisa、Kato Daiki、Fuchigami Sotaro、Nagadoi Aritaka、Nishimura Yoshifumi、Kurumizaka Hitoshi、Akashi Satoko
    • Journal Title

      Analytical Chemistry

      Volume: 90 Issue: 13 Pages: 8217-8226

    • DOI

      10.1021/acs.analchem.8b01649

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system2018

    • Author(s)
      Suzuki Rika、Sakakura Masayoshi、Mori Masaki、Fujii Moe、Akashi Satoko、Takahashi Hideo
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 71 Issue: 4 Pages: 213-223

    • DOI

      10.1007/s10858-018-0192-3

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] The crystal structure and oligomeric form of Escherichia coli l , d -carboxypeptidase A2018

    • Author(s)
      Meyer Karen、Addy Christine、Akashi Satoko、Roper David I.、Tame Jeremy R.H.
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 499 Issue: 3 Pages: 594-599

    • DOI

      10.1016/j.bbrc.2018.03.195

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Crystal structure of the overlapping dinucleosome composed of hexasome and octasome2017

    • Author(s)
      Daiki Kato, Akihisa Osakabe, Yasuhiro Arimura, Yuka Mizukami, Naoki Horikoshi, Kazumi Saikusa, Satoko Akashi, Yoshifumi Nishimura, Sam-Yong Park, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Atsushi Matsumoto, Hidetoshi Kono, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka
    • Journal Title

      Science

      Volume: 356 Issue: 6334 Pages: 205-208

    • DOI

      10.1126/science.aak9867

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 生体内の現象の観測を目指したネイティブ質量分析2021

    • Author(s)
      明石知子
    • Organizer
      第74回イオン反応研究会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 生細胞からサンプリングした試料のネイティブ質量分析2020

    • Author(s)
      荒井駿佑,坂本和香,高野航太朗,小沼剛,明石知子
    • Organizer
      第68回質量分析総合討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] イオンモビリティ質量分析と分子シミュレーションのデータ同化によるH2A-H2B二量体の構造解析2020

    • Author(s)
      七種和美,明石知子,渕上壮太郎
    • Organizer
      第68回質量分析総合討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ネイティブ質量分析によるSOD1の金属結合の定量解析2020

    • Author(s)
      田尻道子、畔上奈々子、古川良明、明石知子
    • Organizer
      第68回質量分析総合討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Reconstitution and structural characterization of di-nucleosome with fully methylated DNA2020

    • Author(s)
      Hiroshi Ushijima,Takashi Oda,Takashi Umehara, Tsuyoshi Konuma, Satoko Akashi
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Structural Stability and Dynamics of NCPs Reconstituted with Diverse DNA Sequences2020

    • Author(s)
      Tsuyoshi Konuma, Kohei Hashimoto, Kanako Sato, Satoko Akashi
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 高メチル化DNAを用いたdi-nucleosomeの再構成と構造解析2020

    • Author(s)
      牛島弘嗣、小田隆、梅原崇史、小沼剛、明石知子
    • Organizer
      第93回日本生化学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ネイティブ質量分析による生命金属科学への挑戦2020

    • Author(s)
      明石知子、田尻道子、古川良明
    • Organizer
      第93回日本生化学会年会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Native mass spectrometry for Bio-Metal Science2020

    • Author(s)
      明石知子
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 夾雑環境下で蛋白質複合体を検出するネイティブ質量分析システムの開発2020

    • Author(s)
      小沼剛、坂本和香、高野航太郎、荒井駿佑、畔上奈々子、坂田優佑、明石知子
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Native mass spectrometry of protein-ligand complexes under crude conditions2020

    • Author(s)
      Kotaro Takano, Shunsuke Arai, Hiroshi Ushijima, Tsuyoshi Konuma, Kazumi Saikusa, Satoko Akashi
    • Organizer
      The 10th Asian Oceanic Mass Spectrometry Conference (10th AOMSC)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 生理的環境に近い状態で調製されたタンパク質およびDNAのネイティブ質量分析2019

    • Author(s)
      高野航太朗,七種和美,小沼剛,明石知子
    • Organizer
      第67回質量分析総合討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] ESI-TOF-MSを用いた簡便で正確なDNAメチル化追跡法2019

    • Author(s)
      牛島弘嗣,前川怜奈,五十嵐愛莉,明石知子
    • Organizer
      第67回質量分析総合討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] 質量分析を用いたアセチル化に伴うヌクレオソームの構造変化の解析2019

    • Author(s)
      七種和美,日高はる菜,新屋大貴,畔上奈々子,加藤大貴,胡桃坂仁志,泉俊輔,明石知子
    • Organizer
      第67回質量分析総合討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] Accurate Mass Determination of Long DNA Fragments Prepared for Structural Biology Study of Epigenetic DNA methylation2019

    • Author(s)
      Hiroshi Ushijima, Rena Maekawa, Eri Igarashi, Satoko Akashi
    • Organizer
      The 67th ASMS Conference
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 夾雑環境下でのネイティブ質量分析法の構築2019

    • Author(s)
      明石知子
    • Organizer
      第19回日本蛋白質科学会年会・第71回細胞生物学会大会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] 電子顕微鏡構造からFACTを介したクロマチンリモデリングの分子機構にせまる2019

    • Author(s)
      津中康夫、真柳浩太、七種和美、宮崎直幸、明石知子、岩崎憲治、西村善文、森川耿右
    • Organizer
      第19回日本蛋白質科学会年会・第71回細胞生物学会大会
    • Related Report
      2019 Research-status Report
  • [Presentation] メチル化DNAを用いたdiNCPの再構成と構造特性解析2019

    • Author(s)
      牛島弘嗣,前川怜奈,五十嵐愛莉,橋本洸平,小沼剛,大橋和音,明石知子
    • Organizer
      第92回日本生化学会
    • Related Report
      2019 Research-status Report
  • [Presentation] Native mass spectrometry of biomolecular complexes2019

    • Author(s)
      明石知子
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] FACTによって引き起こされるヘキサゾーム構造の電子顕微鏡解析2019

    • Author(s)
      津中 康央, 真柳 浩太, 七種 和美, 宮崎 直幸, 明石 知子, 岩崎 憲治, 西村 善文, 森川 耿右
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 生細胞抽出物に対するネイティブ質量分析法の開発2019

    • Author(s)
      小沼 剛、高野 航太朗、荒井 駿佑、坂田 優佑、明石 知子
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Insertion of the PA tag into a target protein and promotion of the crystallization by utilizing the NZ-1 Fab as a crystallization chaperone2019

    • Author(s)
      Risako Tamura, Rika Oi, Satoko Akashi, Mika K. Kaneko, Yukinari Kato, Terukazu Nogi
    • Organizer
      16th Conference of the Asian Crystallographic Association
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] (CCG)n配列を含む二重鎖DNAからなるヌクレオソームコア粒子の再構成の試み2018

    • Author(s)
      橋本洸平、長土居有隆、小沼剛、明石知子
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 不揮発性緩衝液で調製した巨大タンパク質複合体の観測の試み2018

    • Author(s)
      明石知子
    • Organizer
      第10回LC/MSワークショップ
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 質量分析によるヌクレオソームにおけるヒストンアセチル化の解析2018

    • Author(s)
      日高はる菜、泉俊輔、明石知子、七種和美
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Structural Diversity of nucleosomes characterized by nanoESI-MS and structural calculation2018

    • Author(s)
      Kazumi Saikusa, Akihisa Osakabe, Daiki Kato, Sotaro Fuchigami, Aritaka Nagadoi, Yoshifumi Nishimura, Hitoshi Kurumizaka, Satoko Akashi
    • Organizer
      22nd International Mass Spectrometry Conference
    • Related Report
      2018 Research-status Report
  • [Presentation] イオンモビリティ質量分析で得られたヌクレオソームの構造多様性2018

    • Author(s)
      七種和美、渕上壮太郎、明石知子
    • Organizer
      第66回質量分析総合討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] 巨大タンパク質-DNA複合体NCPのイオンモビリティ質量分析と構造計算2018

    • Author(s)
      七種和美、渕上壮太郎、明石知子
    • Organizer
      第7回イオン移動度研究会
    • Related Report
      2018 Research-status Report
  • [Presentation] ネイティブ質量分析 -ヌクレオソームから生命現象をつかさどる金属の解析まで-2018

    • Author(s)
      明石知子
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 不揮発性緩衝液で調製したタンパク質複合体のNative質量分析2017

    • Author(s)
      七種和美、加藤大貴、長土居有隆、胡桃坂仁志、明石知子
    • Organizer
      第65回質量分析総合討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] ヌクレオソームコア粒子のESI-MSにおける電荷分布の解析2017

    • Author(s)
      前川怜奈、大橋和音、長土居有隆、明石知子
    • Organizer
      第65回質量分析総合討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] 再構成したヌクレオソームのネイティブ質量分析2017

    • Author(s)
      明石知子
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Structural and biochemical analysis of overlapping dinucleosome containing histone variants and histone modifications2017

    • Author(s)
      Wataru Kobayashi, Maya Aihara, Daiki Kato, Masako Koyama, Kazumi Saikusa, Satoko Akashi, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka
    • Organizer
      EMBO Conference “The Nucleosome: From Atoms to Genomes”
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] ネイティブな状態を捕える質量分析の構造生物学での展開2017

    • Author(s)
      明石知子
    • Organizer
      2017年度生命科学系合同年次大会
    • Related Report
      2017 Research-status Report
  • [Book] 生命金属ダイナミクス: 生体内における金属の挙動と制御2021

    • Author(s)
      明石知子、田尻道子
    • Total Pages
      10
    • Publisher
      (株)エヌ・ティー・エス
    • ISBN
      9784860437060
    • Related Report
      2020 Annual Research Report
  • [Remarks] 横浜市立大学生命医科学研究科構造エピゲノム科学研究室

    • URL

      http://www-mls.tsurumi.yokohama-cu.ac.jp/lab/stbiol.html

    • Related Report
      2018 Research-status Report

URL: 

Published: 2017-04-28   Modified: 2022-01-27  

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