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Dynamics of Nucleosome Assembly in Solution Revealed by X-ray and Neutron Scattering

Research Project

Project/Area Number 25291037
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Biophysics
Research InstitutionYokohama City University

Principal Investigator

Sato Mamoru  横浜市立大学, 生命医科学研究科, 教授 (60170784)

Co-Investigator(Kenkyū-buntansha) ODA Takashi  横浜市立大学, 大学院生命医科学研究科, 特任助教 (00573164)
Co-Investigator(Renkei-kenkyūsha) KURUMIZAKA Hitoshi  早稲田大学, 大学院先進理工学研究科, 教授 (80300870)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2015: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2014: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2013: ¥9,230,000 (Direct Cost: ¥7,100,000、Indirect Cost: ¥2,130,000)
Keywords溶液散乱 / 小角散乱 / クロマチン / ヌクレオソーム / セントロメア / 分子動力学計算 / 粗視化モデル
Outline of Final Research Achievements

Solution X-ray and neutron scattering analyses have showed that both ends of double stranded DNA in H2A.B nucleosome are peeled off from the histone octamer and is exposed to the solvent. This facilitates the chromatin takes a looser conformation than H2A nucleosome. Also, solution X-ray scattering analysis indicates that conformation of higher-order nucleosome complex, H3-(CENP-A)-H3 tri-nucleosome is more opened than that of H3-H3-H3 tri-nucleosome. Furthermore, MD-SAXS analysis (solution X-ray scattering analysis combined with molecular dynamics calculation) using a coarse grained model as a tri-nucleosome has analyzed the dynamical structure of the chromatin in centromere and non-centromere regions at atomic resolution and elucidated the functional significance of the chromatin containing CENP-A nucleosome in the centromere.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (35 results)

All 2016 2015 2014 2013

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 8 results) Presentation (23 results) (of which Invited: 10 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Journal Article] Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail.2016

    • Author(s)
      Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama J, Sato M, Nishimura Y.
    • Journal Title

      Sci Rep.

      Volume: 6 Issue: 1 Pages: 22527-22527

    • DOI

      10.1038/srep22527

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular basis for SMC rod formation and its dissolution upon DNA binding2015

    • Author(s)
      Y. Soh, F. Bürmann, H. Shin, T. Oda, K. S. Jin, C. P. Toseland, C. Kim, H. Lee, S. J. Kim, M. Kong, M. Durand-Diebold, Y. Kim, H. M. Kim, N. K. Lee, M. Sato, B. Oh, S. Gruber
    • Journal Title

      Mol. Cell

      Volume: 57 Issue: 2 Pages: 290-303

    • DOI

      10.1016/j.molcel.2014.11.023

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A magnetic anti-cancer compound for magnet-guided delivery and magnetic resonance imaging.2015

    • Author(s)
      Eguchi H, Umemura M, Kurotani R, Fukumura H, Sato I, Kim J-H, Hoshino Y, Lee J, Amemiya N, Sato M, Hirata K, Sigh DJ, Masuda T, Yamamoto M, Urano T, Yoshida K, Tanigaki K, Yamamoto M, Sato M, Inoue S, Aoki I and Ishikawa Y.
    • Journal Title

      Sci. Rep.

      Volume: 5 Issue: 1 Pages: 9194-9194

    • DOI

      10.1038/srep09194

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure.2015

    • Author(s)
      Saikusa, K., Shimoyama, S., Asano, Y., Nagadoi, A., Sato, M., Kurumizaka, H., Nishimura, Y., and Akashi, S.
    • Journal Title

      Protein Science

      Volume: - Issue: 8 Pages: 20-27

    • DOI

      10.1002/pro.2673

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit.2015

    • Author(s)
      Yoshida H, Park S-Y, Oda T, Akiyoshi T, Sato M, Shirouzu M, Tsuda K, Kuwasako K, Unzai S, Muto Y, Urano T, Obayashi E.
    • Journal Title

      Genes Dev.

      Volume: 29 Issue: 15 Pages: 1649-1660

    • DOI

      10.1101/gad.267104.115

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of a novel DNA-binding domain of helicase-like transcription factor (HLTF) and its functional implication in DNA damage tolerance.2015

    • Author(s)
      Hishiki, A., Hara, K., Ikegaya, Y., Yokoyama, H., Shimizu, T., Sato, M., Hashimoto, H.
    • Journal Title

      J. Biol. Chem.

      Volume: 290 Issue: 21 Pages: 13215-13223

    • DOI

      10.1074/jbc.m115.643643

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Distinct features of the histone core structure in nucleosomes containing the histone H2A.B variant.2014

    • Author(s)
      Sugiyama M, Arimura Y, Shirayama K, Fujita R, Oba Y, Sato N, Inoue R, Oda T, Sato M, Heenan RK, Kurumizaka H.
    • Journal Title

      Biophys J.

      Volume: 106 Issue: 10 Pages: 2206-2213

    • DOI

      10.1016/j.bpj.2014.04.007

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A structure-based model of substrate discrimination by a non-canonical PDZ tandem in the intramembrane-cleaving protease RseP.2014

    • Author(s)
      檜作 洋平, 小田 隆, 田畑 早苗, 川上-田村 恵子, 大井 里香, 佐藤 衛, 高木 淳一, 秋山 芳展, 禾 晃和
    • Journal Title

      Structure

      Volume: 22 Issue: 2 Pages: 326-336

    • DOI

      10.1016/j.str.2013.12.003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm2013

    • Author(s)
      K. Nozawa, R. Ishitani, T. Yoshihisa, M. Sato, F. Arisaka, S. Kanamaru, N. Dohmae, D. Mangroo, B. Senger, H. D. Becker and O. Nureki
    • Journal Title

      Nucleic Acids Research

      Volume: 41 Issue: 6 Pages: 3901-3914

    • DOI

      10.1093/nar/gkt010

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Report of the wwPDB Small-Angle Scattering Task Force : Data Requirements for Biomolecular Modeling and the PDB2013

    • Author(s)
      J.Trewhella, W.A.Hendrickson, G.J.Kleywegt, A.Sali, M.Sato, T.Schwede, D.I.Svergun, J.A.Tainer, J.Westbrook, and H.M.Berman
    • Journal Title

      Structure

      Volume: 21 Issue: 6 Pages: 875-881

    • DOI

      10.1016/j.str.2013.04.020

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of a nucleosome containing histone H2A. B/H2A. Bbd that transiently associates with reorganized chromatin.2013

    • Author(s)
      Arimura Y., Kimura H., Oda T., Sato K., Osakabe A., Tachiwana H., Sato Y., Kinugasa Y., Ikura T., Sugiyama M., Sato M., Kurumizaka H.
    • Journal Title

      Sci Rep.

      Volume: 3 Issue: 1 Pages: 3510-3510

    • DOI

      10.1038/srep03510

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] MD-SAXSによるタンパク質のゆらぎ解析2015

    • Author(s)
      池口満徳, 小甲裕一, 佐藤 衛
    • Organizer
      日本結晶学会平成27年度年会
    • Place of Presentation
      大阪府立大学
    • Year and Date
      2015-10-18
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Coarse-Grained MD-SAXS method and application to nucleosomes2015

    • Author(s)
      Y. Kokabu, T. Oda, M. Sugiyama, H. Kurumizaka, M. Sato, M. Ikeguchi
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] タンパク質の天然変性領域を標的にした創薬2015

    • Author(s)
      佐藤 衛
    • Organizer
      翻訳後修飾プロテオミクス医療研究拠点の形成―平成26年度諮問委員会
    • Place of Presentation
      横浜市立大学附属病院
    • Year and Date
      2015-03-10
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] X線溶液散乱法を中心にした軟らかなタンパク質の相関構造解析2014

    • Author(s)
      佐藤 衛
    • Organizer
      大阪大学蛋白質研究所セミナー
    • Place of Presentation
      大阪大学蛋白質研究所
    • Year and Date
      2014-12-04 – 2014-12-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 赤痢菌IpaBによるMad2L2の機能阻害複合体の結晶学的研究2014

    • Author(s)
      片川裕理、原 幸大、花岡祐樹、菊池壮太郎、横山英志、金 文秀、笹川千尋、佐藤 衛、橋本 博
    • Organizer
      平成26年度日本結晶学会年会
    • Place of Presentation
      東京大学農学部
    • Year and Date
      2014-11-01 – 2014-11-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] X線溶液散乱を中心にした相関構造解析-揺らぎの大きい軟らかなタンパク質の構造解析を目指して2014

    • Author(s)
      佐藤 衛
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      国立京都国際会館
    • Year and Date
      2014-10-15 – 2014-10-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 細胞表層ストレス応答制御に関わる膜内切断プロテアーゼRsePのタンデムPDZドメインによる切断基質選別機構の解析2014

    • Author(s)
      檜作 洋平, 小田 隆, 田畑 早苗, 川上-田村 恵子, 大井里香, 佐藤 衛, 高木 淳一, 禾 晃和, 秋山 芳展
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      国立京都国際会館
    • Year and Date
      2014-10-15 – 2014-10-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural dynamics of tri-nucleosome studied by combination of coarse grained molecular simulation and SAXS2014

    • Author(s)
      Yusuke Takagi, Yuichi Kokabu, Takashi Oda, Hiroaki Tachiwana, Hiroo Kenzaki, Hitoshi Kurumizaka, Mamoru Sato, Mitsunori Ikeguchi, Shoji Takada
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural and mutational analysis of a PDZ tandem of intramembrane cleaving protease RseP2014

    • Author(s)
      Terukazu Nogi, Yohei Hizukuri, Sanae Tabata, Keiko Tamura-Kawakami, Takashi Oda, Mamoru Sato, Junichi Takagi, Yoshinori Akiyama
    • Organizer
      XXIII Congress of the International Union of Crystallography
    • Place of Presentation
      Palais des congress de Montreal, Quebec, Canada
    • Year and Date
      2014-08-05 – 2014-08-12
    • Related Report
      2014 Annual Research Report
  • [Presentation] DNA架橋損傷修復に関わる天然変性タンパク質Hefの構造研究2014

    • Author(s)
      小田 隆、小林裕也、舘岡太郎、宮城泰城、石黒あかり、有田恭平、禾 晃和、石野良純、杉山正明、佐藤 衛
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜(横浜)
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] SAXS & MD Simulation to Investigate Protein Flexibility in Solution2013

    • Author(s)
      Mamoru Sato
    • Organizer
      International Symposium on Diffraction Structural Biology (ISDSB2013)
    • Place of Presentation
      Nagoya Trade & Industry Center
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 天然変性領域をターゲットにした抗体医薬の創成を目指して2013

    • Author(s)
      佐藤 衛
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] REV7-REV3複合体構造から示唆されるREV7/Mad2L2と赤痢菌タンパク質IpaBとの相互作用2013

    • Author(s)
      菊池 壮太郎、原 幸大、清水 敏之、佐藤 衛、橋本 博
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Protein Dynamics Investigated by SAXS and MD Simulation2013

    • Author(s)
      Mamoru Sato
    • Organizer
      International Conference on Structural Genomics-Structural Life Science-(ICSG2013-SLS)
    • Place of Presentation
      Keio Plaza Hotel Sapporo in Sapporo
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Structural study on REV7, the adaptor protein coordinating REV1 and REV3 polymerase in ttanslesion DNA synthesis2013

    • Author(s)
      Sotaro Kikuchi, Kodai Hara, Toshiyuki Shimizu, Mamoru Sato, Hiroshi Hashimoto
    • Organizer
      International Conference on Structural Genomics-Structural Life Science-(ICSG2013-SLS)
    • Place of Presentation
      Keio Plaza Hotel Sapporo in Sapporo
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural analysis of the PDZ tandem fragment of the bacterial intramembrane-cleaving protease RseP2013

    • Author(s)
      Terukazu Nogi, Yohei Hizukuri, Takashi Oda, Sanae Tabata, Keiko Tamura-Kawakami, Mamoru Sato, Junichi Takagi, Yoshinori Akiyama
    • Organizer
      International Conference on Structural Genomics-Structural Life Science-(ICSG2013-SLS)
    • Place of Presentation
      Keio Plaza Hotel Sapporo in Sapporo
    • Related Report
      2013 Annual Research Report
  • [Presentation] 将来光源を用いた新しいタンパク質の構造・機能研究2013

    • Author(s)
      佐藤 衛
    • Organizer
      第31回関西界面科学セミナー
    • Place of Presentation
      SPring-8 普及棟
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 大腸菌膜内切断プロテアーゼRsePの基質認識におけるPDZドメインの役割2013

    • Author(s)
      檜作 洋平, 禾 晃和, 小田 隆, 田畑 早苗, 川上-田村 恵子, 佐藤 衛, 高木 淳一, 秋山 芳展
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2013 Annual Research Report
  • [Presentation] ヒトヒストンバリアントH2A.Bの解析2013

    • Author(s)
      有村泰宏、小田 隆、佐藤浩一、藤田理紗、松本亮平、田口裕之、堀越直樹、越阪部晃永、立和名博昭、杉山正明、佐藤 衛、木村 宏、胡桃坂仁志
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2013 Annual Research Report
  • [Presentation] 天然変性タンパク質(領域)をターゲットにした創薬2013

    • Author(s)
      佐藤 衛
    • Organizer
      静岡県立大学薬学部第238回月例薬学セミナー
    • Place of Presentation
      静岡県立大学小講堂
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 表層ストレス応答を制御する腸内切断プロテアーゼRsePのタンデムPDZドメインによる基質選別機構2013

    • Author(s)
      Yohei Hizukuri, Takashi Oda, Sanae Tabata, Tamura-Kawakami Keiko, Mamoru Sato, Junichi Takagi, Terukazu Nogi, Yoshimori Akiyama
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      国立京都国際会館
    • Related Report
      2013 Annual Research Report
  • [Presentation] N-terminal phosphorylated tail of HP1α behaves like an extended hard acidic string to promote the binding to methylated histone H3K9 tail2013

    • Author(s)
      Mayumi Kawaguchi, Hideaki Shimojo, Kyoko Hamada, Jun-ichi Nakayama, Takashi Oda, Mamoru Sato, Yoshifumi Nishimura
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Annual Research Report
  • [Presentation] 低エミッタンス高輝度光源を用いたタンパク質の新しい構造解析法の提案2013

    • Author(s)
      佐藤 衛
    • Organizer
      第3世代中型高輝度放射光源(SLiT-J)の実現に向けて―先端学術研究と産業技術支援―
    • Place of Presentation
      東北大学金属材料研究所
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Patent(Industrial Property Rights)] 新規抗PAD4抗体2016

    • Inventor(s)
      佐藤 衛、山田道之、金澤 智、豊浦雅義、庄屋雄二、斉藤憲二
    • Industrial Property Rights Holder
      佐藤 衛、山田道之、金澤 智、豊浦雅義、庄屋雄二、斉藤憲二
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016-03-07
    • Related Report
      2015 Annual Research Report
    • Overseas

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Published: 2013-05-21   Modified: 2019-07-29  

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