• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

3D Active Site Science in Biology

Planned Research

Project Area3D Active-Site Science
Project/Area Number 26105005
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionThe University of Tokyo

Principal Investigator

Sasaki Yuji  東京大学, 大学院新領域創成科学研究科, 教授 (30344401)

Co-Investigator(Kenkyū-buntansha) 関口 博史  公益財団法人高輝度光科学研究センター, 利用研究促進部門, 主幹研究員 (00401563)
柴山 修哉  自治医科大学, 医学部, 教授 (20196439)
宮澤 淳夫  兵庫県立大学, 生命理学研究科, 教授 (60247252)
久保 泰  国立研究開発法人産業技術総合研究所, 創薬プロファイリング研究センター, 副研究センター長 (10178030)
一柳 光平  大学共同利用機関法人高エネルギー加速器研究機構, 物質構造科学研究所, 特任准教授 (70435618)
Project Period (FY) 2014-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥111,280,000 (Direct Cost: ¥85,600,000、Indirect Cost: ¥25,680,000)
Fiscal Year 2018: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2017: ¥20,670,000 (Direct Cost: ¥15,900,000、Indirect Cost: ¥4,770,000)
Fiscal Year 2016: ¥20,670,000 (Direct Cost: ¥15,900,000、Indirect Cost: ¥4,770,000)
Fiscal Year 2015: ¥27,170,000 (Direct Cost: ¥20,900,000、Indirect Cost: ¥6,270,000)
Fiscal Year 2014: ¥36,790,000 (Direct Cost: ¥28,300,000、Indirect Cost: ¥8,490,000)
Keywords蛍光X線ホログラフィー / X線1分子追跡法 / 標識・無標識法 / タンパク質分子 / 結晶化 / 蛍光X線ホログラフィー / 価数変化 / X線1分子計測 / 3次元分子内部動態情報 / X線1分子追跡法 / バイオテクノロジー / X線 / 局部構造 / 1分子動態情報 / 新規計測手段 / 蛋白質構造動態 / X線1分子追跡法 / バイオ計測 / 中性子 / 1分子
Outline of Final Research Achievements

This study aimed to develop two methodologies for biomaterials, fluorescent x-ray holography and x-ray single molecule tracking. In X-ray single molecule tracking method, gold nanocrystal labeling is realized by molecular labeling method targeting disulfide bond (SS), three-dimensional molecular dynamics measurement is succeeded by microsecond time division, and new kinetic measurement of membrane protein molecules succeeded in. We also proposed a completely new dynamic measurements without labeling. In fluorescence X-ray holography, we applied and measured fluorescence X-ray holography for the first time in the world for determining the 3D site around heavy elements of protein molecules through hemoglobin and myoglobin. The basic data of the main target photosynthetic protein group PSII, which is the final goal, could also be measured.

Academic Significance and Societal Importance of the Research Achievements

生命科学の分野に日本発の2つの新しい計測手法を確立させることができた。それらの新計測方法で、今まで得られなかった注目元素の価数評価や3次元レベルの分子内部動態評価が可能になった。これらを軸に新しいタンパク質科学を発展させていく。

Report

(6 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (22 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (1 results) Journal Article (12 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 12 results,  Open Access: 9 results,  Acknowledgement Compliant: 3 results) Presentation (6 results) (of which Int'l Joint Research: 6 results) Book (2 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] SOLEIL(フランス)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Diffracted X-ray blinking tracks single protein motions2018

    • Author(s)
      Sekiguchi, H., Kuramochi, M., Ikesaki, K., Okamura, Y., Yoshimura, K., Matsubara, K., Chang, J. W., Ohta, N., Kubo, T., Mio, K., Suzuki, Y., Chavas, L. M., & Sasaki, Y.
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 1709-1709

    • DOI

      10.1038/s41598-018-35468-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] X-ray observations of single bio-supramolecular photochirogenesis2018

    • Author(s)
      Chang Jaewon、Nishijima Masaki、Sekiguchi Hiroshi、Ichiyanagi Kohei、Kuramochi Masahiro、Inoue Yoshihisa、Sasaki Yuji C.
    • Journal Title

      Biophysical Chemistry

      Volume: 242 Pages: 1-5

    • DOI

      10.1016/j.bpc.2018.07.003

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] DNA-binding induced conformational change of c-Myb R2R3 analyzed using diffracted X-ray tracking2018

    • Author(s)
      Hosoe Yuhi、Inaba Satomi、Sekiguchi Hiroshi、Sasaki Yuji C.、Oda Masayuki
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 503 Issue: 1 Pages: 338-343

    • DOI

      10.1016/j.bbrc.2018.06.025

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Progressing of 3D Protein Structure and Dynamics Measurements2018

    • Author(s)
      Ayana Sato-Tomita, Hiroshi Sekiguchi, Yuji C. Sasaki
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 87 Issue: 6 Pages: 061015-061015

    • DOI

      10.7566/jpsj.87.061015

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Time-Resolved Measurement of the ATP-Dependent Motion of the Group II Chaperonin by Diffracted Electron Tracking2018

    • Author(s)
      Naoki Ogawa, Yohei Y. Yamamoto, Keisuke Abe, Hiroshi Sekiguchi, Yuji Y. Sasaki, Akira Ishikawa, Judith Frydman, Masafumi Yohda
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 19 Issue: 4 Pages: 950-950

    • DOI

      10.3390/ijms19040950

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Nanoscale Dynamics of Protein Assembly Networks in Supersaturated Solutions2017

    • Author(s)
      Matsushita Y.、Sekiguchi H.、Wong C. Jae、Nishijima M.、Ikezaki K.、Hamada D.、Goto Y.、Sasaki Y. C.
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 13883-13883

    • DOI

      10.1038/s41598-017-14022-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] First observation of metal ion-induced structural fluctuations of α-helical peptides by using diffracted X-ray tracking2017

    • Author(s)
      Usui Daiki、Inaba Satomi、Sekiguchi Hiroshi、Sasaki Yuji C.、Tanaka Toshiki、Oda Masayuki
    • Journal Title

      Biophysical Chemistry

      Volume: 228 Pages: 81-86

    • DOI

      10.1016/j.bpc.2017.07.005

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Asymmetry in the function and dynamics of the cytosolic group II chaperonin CCT/TRiC2017

    • Author(s)
      Yohei Y. YAMAMOTO, Yuko UNO, Eiryo SHA, Kentaro IKEGAMI, Noriyuki ISHII, Naoshi DOHMAE, Hiroshi SEKIGUCHI, Yuji C. SASAKI, Masafumi YOHDA
    • Journal Title

      PLOS ONE

      Volume: 12(5) Issue: 5 Pages: 0176054-0176054

    • DOI

      10.1371/journal.pone.0176054

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Development of an X-ray fluorescence holographic measurement system for protein crystals”2016

    • Author(s)
      A. Sato-Tomita, N. Shibayama, N. Happo, K. Kimura, T. Okabe, T. Matsushita, S.-Y. Park, Y. C. Sasaki, K. Hayashi, ,
    • Journal Title

      Rev. Sci. Inst.

      Volume: 87 Issue: 6 Pages: 063707-063707

    • DOI

      10.1063/1.4953453

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Time-resolved X-ray tracking of expansion and compression dynamics in supersaturating ion-networks2015

    • Author(s)
      Y. Matsushita, H. Sekiguchi, N. Ohta, K. Ichiyanagi, K. Ikezaki, Y. Goto, Y. C. Sasaki
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 17647-17647

    • DOI

      10.1038/srep17647

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Cooling dynamics of self-assembled monolayer coating for integrated gold nanocrystals on a glass substrate2015

    • Author(s)
      K. Ichiyanagi, H. Sekiguchi, T. Sato, S. Nozawa, A. Tomita, M. Hoshino, S. Adachi and Y. C. Sasaki
    • Journal Title

      J. Synchrotron Rad.

      Volume: 22 Issue: 1 Pages: 29

    • DOI

      10.1107/s1600577514019730

    • URL

      https://pure.teikyo.jp/en/publications/0dfc79a3-a246-4555-8cfe-21c102b5da47

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single Molecular Motions of MHC Class II Rely on Bound Peptides2015

    • Author(s)
      Haruo Kozono, Yufuku Matsushita, Naoki Ogawa, Yuko Kozono, Toshihiro Miyabe, Hiroshi Sekiguchi, Kouhei Ichiyanagi, Noriaki Okimoto Makoto Taiji, Osami Kanagawa, and Yuji C Sasaki
    • Journal Title

      Biophysical Journal

      Volume: 108 Issue: 2 Pages: 350-359

    • DOI

      10.1016/j.bpj.2014.12.004

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Rotational Brownian Motion of TRPV1 Channel Observed by Synchrotron Diffracted X-Ray Tracking and Laboratory X-Ray Blinking Analysis2018

    • Author(s)
      K. Mio et al.
    • Organizer
      Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel In Vivo Observations of Single Protein Motions Using Laboratory X-Ray Source2018

    • Author(s)
      Y. C. SASAKI et al.
    • Organizer
      Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of Advanced Diffracted X-Ray Tracking for Single Molecule Intra-Dynamics with Low Dose and Wide Angular Dynamic Range2018

    • Author(s)
      H. Sekiguchi et al.
    • Organizer
      Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Functional Analysis of Antifreeze Proteins for Cold Tolerance Behavior and X-Ray Single Molecule Observations in C-elegans2018

    • Author(s)
      M. Kuramochi et al.
    • Organizer
      Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In Vivo X-Ray Monitoring of Dynamics between Interleukin 2 and Interleukin 15 on NK Cells2018

    • Author(s)
      J. Chang et al.
    • Organizer
      Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] X-RAY FLUORESCENCE HOLOGRAPHY FOR PROTEINS: APPLICATION TO HEMOGLOBIN AND MYOGLOBIN2017

    • Author(s)
      Ayana Sato-Tomita, Naohisa Happo, Sam-Yong Park, Koichi Hayashi, Yuji C. Sasaki and Naoya Shibayama
    • Organizer
      Annual Meeting of Biophysical Society
    • Place of Presentation
      ニューオリンズ(米国)
    • Year and Date
      2017-02-11
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Book] 3D Local Structure and Functionality Design of Materials2018

    • Author(s)
      Daimon Hiroshi、Sasaki Yuji C
    • Total Pages
      220
    • Publisher
      World Scientific Publishing Co Ltd.
    • Related Report
      2018 Annual Research Report
  • [Book] 機能構造科学入門2016

    • Author(s)
      大門寛・佐々木裕次
    • Total Pages
      166
    • Publisher
      丸善
    • Related Report
      2016 Annual Research Report
  • [Patent(Industrial Property Rights)] 運動計測装置2016

    • Inventor(s)
      佐々木裕次
    • Industrial Property Rights Holder
      佐々木裕次
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2016-226495
    • Filing Date
      2016-11-22
    • Related Report
      2016 Annual Research Report

URL: 

Published: 2014-11-20   Modified: 2020-03-30  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi