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Image processing of the diffraction patterns and 3D reconstruction of biomolecules by XFEL single particle experiment

Research Project

Project/Area Number 18K14642
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Nakano Miki  国立研究開発法人理化学研究所, 計算科学研究センター, 研究員 (40625894)

Project Period (FY) 2018-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2021: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2020: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
KeywordsX線自由電子レーザー / 単粒子解析 / 画像解析 / コヒーレントX線イメージング / 位相回復 / 構造生物学 / 生物物理 / コンピューターシミュレーション / X線自由電子レーザー
Outline of Final Research Achievements

I have developed a computational algorithm, slice matching method, to reconstruct a 3D intensity distribution by iteratively estimating the sample orientation and beam intensity captured on the diffraction patterns obtained by XFEL single-particle experiment.
Using this method, we estimated the experimental conditions for high-resolution reconstruction of molecular structures, optimized computational parameters, and evaluated the resolution dependence of molecular size through simulations.
Furthermore, we performed the analysis of the diffraction patterns of gold nanoparticles with a size of about 50 nm retained in a normal temperature and pressure solution, which were actually obtained by the XFEL experiment performed at SACLA. We succeeded in reconstructing the 3D structure of gold nanoparticles by performing a series of data processing, such as diffraction pattern selection, angle and beam intensity estimation, and noise removal.

Academic Significance and Societal Importance of the Research Achievements

生理的条件下での生体高分子の3次元構造の取得は、生命現象の理解や創薬において重要な課題である。X線自由電子レーザー(XFEL)による単粒子立体構造解析は、結晶化が難しい生体分子や生体組織を自然に近い状態で観察できる新しい構造生物学的手法として期待されている。しかし、XFELの強いビームを用いても、単粒子の生体分子から得られる回折強度は極めて弱くSN比が小さいため、回折像の分別やノイズの除去が課題であった。本研究で開発した手法を用いて、常温常圧溶液中の金微粒子の3次元構造の復元を実現できた。本研究の成果は、次のステップである常温常圧状態での生体高分子の3次元構造取得に向けての重要な一歩となる。

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (20 results)

All 2023 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (1 results) Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 3 results) Presentation (13 results) (of which Int'l Joint Research: 2 results) Remarks (3 results)

  • [Int'l Joint Research] IMPMC, Sorbonne University(フランス)

    • Related Report
      2018 Research-status Report
  • [Journal Article] Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction2023

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Journal Title

      Structural Dynamics

      Volume: 10 Issue: 2 Pages: 024101-024101

    • DOI

      10.1063/4.0000175

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis2022

    • Author(s)
      Nakano Miki、Miyashita Osamu、Joti Yasumasa、Suzuki Akihiro、Mitomo Hideyuki、Niida Yoshiya、Yang Ying、Yumoto Hirokatsu、Koyama Takahisa、Tono Kensuke、Ohashi Haruhiko、Yabashi Makina、Ishikawa Tetsuya、BESSHO YOSHITAKA、Ijiro Kuniharu、Nishino Yoshinori、Tama Florence
    • Journal Title

      Optica

      Volume: 9 Issue: 7 Pages: 776-784

    • DOI

      10.1364/optica.457352

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching2019

    • Author(s)
      Miki Nakano, Osamu Miyashita and Florence Tama
    • Journal Title

      Biophysics and Physicobiology

      Volume: 16 Issue: 0 Pages: 367-376

    • DOI

      10.2142/biophysico.16.0_367

    • NAID

      130007752746

    • ISSN
      2189-4779
    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] XFELを用いた単粒子解析で復元された 分子構造の解像度における分サイズの影響2023

    • Author(s)
      中野美紀、宮下治、タマ フロハンス
    • Organizer
      第36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
      2022 Annual Research Report
  • [Presentation] Molecular size effect on the single-particle analysis using X-ray free electron laser2022

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2022 Annual Research Report
  • [Presentation] X線自由電子レーザー単粒子解析を使用した 溶液中の金ナノ粒子の三次元構造決定2022

    • Author(s)
      中野美紀, 宮下治, 城地保昌, 鈴木明大, 西野吉則, Florence Tama
    • Organizer
      第35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
      2021 Research-status Report
  • [Presentation] Molecular size effect on the single-particle 3D structure reconstruction analysis using X-ray free electron laser2022

    • Author(s)
      Miki Nakanoa, Osamu Miyashita and Florence Tama
    • Organizer
      The 4th R-CCS International Symposium
    • Related Report
      2021 Research-status Report
  • [Presentation] Simulation study of tree dimensional reconstruction of ribosome from Xray free electron laser diffraction patterns2021

    • Author(s)
      Miki Nakano, Tama Florence, Miyashita Osamu
    • Organizer
      20th Annual Meeting of the Protein Society Meeting of Japan
    • Related Report
      2020 Research-status Report
  • [Presentation] Requirement for 3D-reconstruction of biomolecule structure from single particle analysis using X-ray free electron laser diffraction images2021

    • Author(s)
      Miki Nakano, Tama Florence, Miyashita Osamu
    • Organizer
      The 3rd R-CCS International Symposium
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] シミュレーションデータによるX線自由電子レーザー回折像からの生体分子三次元構造の復元手法の検討2020

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Organizer
      第33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
      2019 Research-status Report
  • [Presentation] Simulation study of 3D-reconstruction of biomolecule structure from X-ray free electron laser diffraction images2020

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Organizer
      64th Annual Meeting of the Biophsical Society
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] XFEL単粒子解析による分子復元構造への回折パターンサイズの影響2020

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Organizer
      日本物理学会第75回年次大会
    • Related Report
      2019 Research-status Report
  • [Presentation] Effect of binning size of XFEL diffraction patterns on the resolution of reconstructed 3D-molecular structure2019

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Organizer
      Chem-Bio Informatics Society(CBI) Annual Meeting 2019
    • Related Report
      2019 Research-status Report
  • [Presentation] シミュレーションによるX線自由電子レーザー実験回折像からの巨大生体分子三次元構造再構築の定量的解析2019

    • Author(s)
      Miki Nakano, Osamu Miyashita, Slavica Jonic, and Florence Tama
    • Organizer
      第74回日本物理学会春季年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Quantitative evaluation of the diffraction images for single particle analysis by X-ray free electron laser experiment2018

    • Author(s)
      Miki Nakano, Osamu Miyashita, Slavica Jonic, and Florence Tama
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Simulation study of 3D-reconstruction of large biomolecule from the diffraction images obtained by X-ray free electron laser experiment2018

    • Author(s)
      Miki Nakano, Osamu Miyashita, Slavica Jonic, and Florence Tama
    • Organizer
      Chem-Bio Informatics Society(CBI) Annual Meeting 2018
    • Related Report
      2018 Research-status Report
  • [Remarks] 理化学研究所計算科学研究センター 計算構造生物学研究チーム

    • URL

      https://www.r-ccs.riken.jp/jp/overview/lab/csbru.html

    • Related Report
      2019 Research-status Report
  • [Remarks] 計算構造生物学研究チーム|理化学研究所 計算科学研究センター(R-CCS)

    • URL

      https://www.r-ccs.riken.jp/jp/overview/lab/csbru.html

    • Related Report
      2018 Research-status Report
  • [Remarks] Computational Structural Biology Research Team

    • URL

      https://www.r-ccs.riken.jp/en/overview/researchdiv/computational-structural-biology-research-team

    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2024-01-30  

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