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New approaches for biostructure modeling from low-resolution experimental data

Research Project

Project/Area Number 16K07286
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Miyashita Osamu  国立研究開発法人理化学研究所, 計算科学研究センター, 上級研究員 (10620528)

Project Period (FY) 2016-10-21 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2018: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2017: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2016: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Keywordsモデリング / シミュレーション / クライオ電子顕微鏡 / X線結晶構造解析 / 計算構造生物学 / タンパク質 / 構造モデリング / フィッティング / ハイブリッドアプローチ / 分子動力学シミュレーション / ハイブリッドモデリング / 電子顕微鏡 / ベイズ統計 / 生体高分子
Outline of Final Research Achievements

In this research, we have developed new approaches to address some limitations of the flexible fitting method for constructing detailed atomic structure models from low-resolution cryo-electron microscope data by utilizing molecular dynamics simulations. First, we established a method to evaluate the accuracy of resulting models by performing multiple fitting trials with different parameters. In addition, we have developed an algorithm that refines the estimation of the three-dimensional lattice size of electron microscopy data, which is important for accurate modeling.

Academic Significance and Societal Importance of the Research Achievements

生体分子の構造に関する情報は創薬など応用のために重要であり、クライオ電子顕微鏡はそういった構造情報を得るために盛んに使われている新しい方法である。本研究では分子動力学シミュレーションを活用することにより、低解像度のクライオ電子顕微鏡データから原子レベルの詳細なモデルを構築するための手法、フレキシブルフィッティング、について、よりモデルの精度を高めるための新しいアルゴリズムの開発を行った。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (34 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (4 results) Journal Article (11 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 11 results,  Open Access: 6 results,  Acknowledgement Compliant: 3 results) Presentation (18 results) (of which Int'l Joint Research: 4 results,  Invited: 16 results) Book (1 results)

  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] CNRS(France)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] CNRS(France)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps2020

    • Author(s)
      Tiwari Sandhya P.、Chhabra Sahil、Tama Florence、Miyashita Osamu
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: - Issue: 5 Pages: 2570-2580

    • DOI

      10.1021/acs.jcim.9b01107

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Integrative/Hybrid Modeling Approaches for Studying Biomolecules2020

    • Author(s)
      Srivastava Ashutosh、Tiwari Sandhya Premnath、Miyashita Osamu、Tama Florence
    • Journal Title

      Journal of Molecular Biology

      Volume: 432 Issue: 9 Pages: 2846-2860

    • DOI

      10.1016/j.jmb.2020.01.039

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images2020

    • Author(s)
      Dasgupta Bhaskar、Miyashita Osamu、Tama Florence
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129420-129420

    • DOI

      10.1016/j.bbagen.2019.129420

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning2019

    • Author(s)
      Mori Takaharu、Kulik Marta、Miyashita Osamu、Jung Jaewoon、Tama Florence、Sugita Yuji
    • Journal Title

      Structure

      Volume: 27 Issue: 1 Pages: 161-174.e3

    • DOI

      10.1016/j.str.2018.09.004

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Searching for 3D structural models from a library of biological shapes using a few 2D experimental images2018

    • Author(s)
      Tiwari Sandhya P.、Tama Florence、Miyashita Osamu
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: 1 Pages: 320-320

    • DOI

      10.1186/s12859-018-2358-0

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics2018

    • Author(s)
      Srivastava Ashutosh、Nagai Tetsuro、Srivastava Arpita、Miyashita Osamu、Tama Florence
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 19 Issue: 11 Pages: 3401-3401

    • DOI

      10.3390/ijms19113401

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Gaussian mixture model for coarse-grained modeling from XFEL2018

    • Author(s)
      Nagai Tetsuro、Mochizuki Yuki、Joti Yasumasa、Tama Florence、Miyashita Osamu
    • Journal Title

      Optics Express

      Volume: 26 Issue: 20 Pages: 26734-26734

    • DOI

      10.1364/oe.26.026734

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 1.Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution2018

    • Author(s)
      Nakano, M., Miyashita, O., Jonic, S., Tokuhisa, A. & Tama, F.
    • Journal Title

      J. Synchrotron Rad.

      Volume: 25 Issue: 4 Pages: 1010-1021

    • DOI

      10.1107/s1600577518005568

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations2017

    • Author(s)
      Miyashita O, Kobayashi C, Mori T, Sugita Y, Tama F
    • Journal Title

      J. Comp. Chem

      Volume: 38 Issue: 16 Pages: 1447-1461

    • DOI

      10.1002/jcc.24785

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Hybrid Approach for Biological Structure Modeling: Cryo-electron Microscopy and X-ray Free Electron Laser Data2017

    • Author(s)
      宮下 治, タマ フロハンス
    • Journal Title

      Seibutsu Butsuri

      Volume: 57 Issue: 2 Pages: 090-094

    • DOI

      10.2142/biophys.57.090

    • NAID

      130005509479

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Effect of the crystal environment on side-chain conformational dynamics in Cyanovirin-N investigated through crystal and solution molecular dynamics simulations2016

    • Author(s)
      Ahlstrom LS, Vorontsov II, Shi J, Miyashita O
    • Journal Title

      PLoS One

      Volume: 12 Issue: 1 Pages: e0170337-e0170337

    • DOI

      10.1371/journal.pone.0170337

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Reconstruction of Low-resolution (Bio) Molecular Structures from Simulated Atomic Force Microscopy Images2020

    • Author(s)
      宮下治
    • Organizer
      The 1st International Conference on Big Data and Machine Learning in Microscopy
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Hybrid Approach for Biomolecular Structure Modeling2020

    • Author(s)
      宮下治
    • Organizer
      2nd R-CCS international symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] クライオEMデータを活用した生体分子ハイブリッド構造モデリング2019

    • Author(s)
      宮下治
    • Organizer
      近畿化学協会コンピュータ化学部会 公開講演会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Hybrid Approach for Structural Biology: Simulation and Experimental Data2019

    • Author(s)
      宮下治
    • Organizer
      CBI 学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Hybrid Structure Modeling of Biomolecules from Cryo-EM Data2019

    • Author(s)
      宮下治
    • Organizer
      日本顕微鏡学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] XFEL単粒子実験データ解析アルゴリズムの開発2019

    • Author(s)
      宮下治
    • Organizer
      PCXSS Workshop
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Cryo-cooling effect on DHFR crystal studied by replica-exchange molecular dynamics simulations2019

    • Author(s)
      Osamu Miyashita
    • Organizer
      BioXFEL International Conference
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 構造解析へのハイブリッドアプローチ:電子顕微鏡とX線結晶解析実験データの活用2018

    • Author(s)
      宮下治
    • Organizer
      日本結晶学会 2018年度年会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 構造解析へのハイブリッドアプローチ:電子顕微鏡とX線自由電子レーザーからの実験データの活用2018

    • Author(s)
      宮下治
    • Organizer
      第 1 回水和ナノ構造研究会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] XFEL単粒子観測実験データ解析アルゴリズムの開発2018

    • Author(s)
      宮下治
    • Organizer
      放射光学会若手研究会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Dynamics hidden within X-ray crystallographic data2018

    • Author(s)
      Osamu Miyashita
    • Organizer
      Telluride Workshop: Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 計算構造生物学による生体超分子構造解析2018

    • Author(s)
      宮下治
    • Organizer
      クライオ電顕解析における情報解析技術ワークショップ
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Computational Structure Modeling from Cryo-EM Data2017

    • Author(s)
      宮下治
    • Organizer
      Dynamic Structural Biology Symposium
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 構造解析へのハイブリッドアプローチ : 電子顕微鏡とX線自由電子レーザーからの実験データの活用2017

    • Author(s)
      宮下治
    • Organizer
      第4回 大型実験施設とスーパーコンピュータとの連携利用シンポジウム-生体物質のダイナミクス-
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] XFEL単粒子実験データ解析アルゴリズムの開発2017

    • Author(s)
      宮下治
    • Organizer
      PCXSS Workshop
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 計算機シミュレーションと実験データの融合利用2017

    • Author(s)
      宮下治
    • Organizer
      XFEL構造生物ミーティング
    • Place of Presentation
      SACLA,兵庫県佐用郡
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Structure Modeling from Cryo-EM Data using Flexible Fitting Approach2016

    • Author(s)
      宮下治
    • Organizer
      日本生物物理学会
    • Place of Presentation
      つくば国際会議場,茨城県つくば市
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 電子顕微鏡データを活用した構造解析へのハイブリッドアプローチ2016

    • Author(s)
      宮下治
    • Organizer
      理研シンポジウム「クライオ電顕に期待すること」
    • Place of Presentation
      理研横浜,神奈川県横浜市
    • Related Report
      2016 Research-status Report
    • Invited
  • [Book] Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data2018

    • Author(s)
      Osamu Miyashita, Florence Tama
    • Total Pages
      19
    • Publisher
      Springer
    • Related Report
      2018 Research-status Report

URL: 

Published: 2016-10-24   Modified: 2021-02-19  

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