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Serial femtosecond X-ray crystallography (SFX) of metalloproteins containing light-sensitive chemical structures

Research Project

Project/Area Number 15K18487
Research Category

Grant-in-Aid for Young Scientists (B)

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

Principal Investigator

Mizohata Eiichi  大阪大学, 工学研究科, 講師 (90571183)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Keywords量子ビーム科学 / X線結晶構造解析 / 構造生物学 / 自由電子レーザー / 常温無損傷構造 / プロトン共役電子移動 / 窒素代謝 / 生物無機化学 / SACLA
Outline of Final Research Achievements

Copper-containing nitrite reductase (CuNiR) is involved in denitrification of the nitrogen cycle. Synchrotron X-rays rapidly reduce copper sites, induce its catalytic reactions, and decompose the substrate complex structure, which has made crystallographic studies of CuNiR difficult. Using X-ray free electron laser (XFEL) facility, SACLA, we determined intact structures of CuNiR with and without nitrite. Based on the obtained structures, we proposed a redox-coupled proton switch model, which provides a new explanation for proton-coupled electron transfer in CuNiR.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (30 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (6 results) Journal Article (13 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 11 results,  Open Access: 8 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Int'l Joint Research: 3 results,  Invited: 7 results) Remarks (3 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Int'l Joint Research] University of British Columbia(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Konstanz(ドイツ)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] University of British Columbia(カナダ)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] University of Konstanz(ドイツ)

    • Related Report
      2015 Research-status Report
  • [Int'l Joint Research] University of British Columbia(カナダ)

    • Related Report
      2015 Research-status Report
  • [Int'l Joint Research] Columbia University(米国)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Damage-free protein structure determination by X-ray free electron laser2017

    • Author(s)
      中根崇智, 岩田想, 溝端栄一
    • Journal Title

      生化学

      Volume: 89 Issue: 4 Pages: 571-576

    • DOI

      10.14952/SEIKAGAKU.2017.890571

    • NAID

      40021312521

    • ISSN
      0037-1017
    • Year and Date
      2017-08-25
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology2017

    • Author(s)
      Mizohata Eiichi、Nakane Takanori、Fukuda Yohta、Nango Eriko、Iwata So
    • Journal Title

      Biophysical Reviews

      Volume: 10 Issue: 2 Pages: 209-218

    • DOI

      10.1007/s12551-017-0344-9

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] X線自由電子レーザーによる膜タンパク質構造決定法2017

    • Author(s)
      溝端栄一
    • Journal Title

      バイオサイエンスとインダストリー

      Volume: 75 Pages: 415-417

    • NAID

      40021341234

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Trends in Methods for Accelerating Structure Determination of Membrane Proteins2017

    • Author(s)
      溝端栄一
    • Journal Title

      Nihon Kessho Gakkaishi

      Volume: 59 Issue: 4 Pages: 147-148

    • DOI

      10.5940/jcrsj.59.147

    • NAID

      130006032054

    • ISSN
      0369-4585, 1884-5576
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by SPring-8 and SACLA2017

    • Author(s)
      Eiichi Mizohata*, Yohta Fukuda, and Tsuyoshi Inoue
    • Journal Title

      SPring-8/SACLA Research Frontiers 2016

      Volume: 2016 Pages: 26-27

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate2017

    • Author(s)
      Tosha Takehiko、Kubo Minoru, et. al
    • Journal Title

      Nature Communications

      Volume: 8 Issue: 1 Pages: 1-9

    • DOI

      10.1038/s41467-017-01702-1

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography.2017

    • Author(s)
      Yamashita, K., et al.
    • Journal Title

      IUCrJ

      Volume: 4 Issue: 5 Pages: 639-647

    • DOI

      10.1107/s2052252517008557

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hydroxyethyl cellulose matrix applied to serial crystallography.2017

    • Author(s)
      Michihiro Sugahara, Takanori Nakane, Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Rie Tanaka, Toru Nakatsu, Eiichi Mizohata, Fumiaki Yumoto, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata, Eriko Nango, So Iwata
    • Journal Title

      Scientific reports

      Volume: 7 Issue: 1 Pages: 703-703

    • DOI

      10.1038/s41598-017-00761-0

    • NAID

      120006223637

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea2017

    • Author(s)
      T. Kono, S. Mehrotra, C. Endo, N. Kizu, M. Matsuda, H. Kimura, E. Mizohata, T. Inoue, T. Hasunuma, A. Yokota, H. Matsumura, H. Ashida
    • Journal Title

      Nature Commun.

      Volume: 8 Issue: 1 Pages: 14007-14007

    • DOI

      10.1038/ncomms14007

    • NAID

      120005947453

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] 連続フェムト秒解析で観る亜硝酸還元酵素の反応機構2017

    • Author(s)
      溝端栄一
    • Journal Title

      医学のあゆみ:生命現象を観る(医歯薬出版株式会社)

      Volume: 262 Pages: 407-412

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent2016

    • Author(s)
      Takanori Nakane, Shinya Hanashima, Mamoru Suzuki, Haruka Saiki, Taichi Hayashi, Keisuke Kakinouchi, Shigeru Sugiyama, Satoshi Kawatake, Shigeru Matsuoka, Nobuaki Matsumori, et al
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 113 Issue: 46 Pages: 13039-13044

    • DOI

      10.1073/pnas.1602531113

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      PNAS

      Volume: 113 Issue: 11 Pages: 2828-2933

    • DOI

      10.1073/pnas.1517770113

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      J. Biochem

      Volume: 未定 Issue: 5 Pages: 527-538

    • DOI

      10.1093/jb/mvv133

    • NAID

      40020833586

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 膜蛋白質の構造決定を加速化する技術の動向 ~XFELを用いた実験的位相決定法~2018

    • Author(s)
      溝端栄一
    • Organizer
      第31回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Damage-free protein structure determination using X-ray free electron laser at SACLA2017

    • Author(s)
      Eiichi Mizohata
    • Organizer
      Janelia Conference -Challenges in Structural Biology-
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Redox-dependent structural change in nitrite reductase visualized by SPring-8 and SACLA2017

    • Author(s)
      Eiichi Mizohata
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Proteins in Serial Femtosecond Crystallography2016

    • Author(s)
      Eiichi Mizohata
    • Organizer
      14th Conference of the Asian Crystallographic Association
    • Place of Presentation
      ハノイ、ベトナム
    • Year and Date
      2016-12-04
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] SACLAが解明した銅含有亜硝酸還元酵素の常温無損傷構造2016

    • Author(s)
      溝端栄一
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県・福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] SACLAが拓く構造生物学の新時代2016

    • Author(s)
      溝端栄一
    • Organizer
      LSBM Symposium 2016, "超分子構造の計算科学"
    • Place of Presentation
      東京大学先端科学技術研究センター(東京都・目黒区)
    • Year and Date
      2016-05-12
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Damage-free structure determination by SFX at SACLA2015

    • Author(s)
      Mizohata E
    • Organizer
      Workshop on serial femtosecond crystallography, SAXS, & Cryo-EM
    • Place of Presentation
      Genentech Hall, UCSF, USA
    • Year and Date
      2015-06-16
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] タンパク質の形を迅速に決定する手法で拓く、タンパク質構造ダイナミクス研究の新時代

    • URL

      https://academist-cf.com/journal/?p=2958

    • Related Report
      2016 Research-status Report
  • [Remarks] 膜タンパク質の構造を迅速に解明する手法を開発! -新薬の設計を SACLA の新技術で加速

    • URL

      http://www.eng.osaka-u.ac.jp/ja/dat/news/1477546358_1.pdf

    • Related Report
      2016 Research-status Report
  • [Remarks] 生命現象を支える化学反応の真の姿を解明!

    • URL

      http://resou.osaka-u.ac.jp/ja/research/2016/20160301_1

    • Related Report
      2015 Research-status Report
  • [Patent(Industrial Property Rights)] 重原子化化合物、膜タンパク質の結晶化を促進するための組成物、および該組成物を用いた膜タンパク質の構造解析方法2017

    • Inventor(s)
      杉山, 花島, 溝端栄一, 村田, 井上, 斎木, 島田, 松森
    • Industrial Property Rights Holder
      杉山, 花島, 溝端栄一, 村田, 井上, 斎木, 島田, 松森
    • Industrial Property Rights Type
      特許
    • Filing Date
      2017-02-27
    • Related Report
      2016 Research-status Report
    • Overseas

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Published: 2015-04-16   Modified: 2022-01-27  

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