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

The elaborately designed domain motion of the multidomain protein CCS and its physical origin

Research Project

Project/Area Number 20K22629
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeMulti-year Fund
Review Section 0701:Biology at molecular to cellular levels, and related fields
Research InstitutionKyoto University

Principal Investigator

Shimizu Masahiro  京都大学, 複合原子力科学研究所, 研究員 (00879869)

Project Period (FY) 2020-09-11 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords分子動力学シミュレーション / 金属タンパク質 / 銅タンパク質 / 小角散乱法 / 小角散乱 / アンサンブルモデリング
Outline of Research at the Start

タンパク質のナノスケール分子運動はその機能に深く関わっている。本研究では銅輸送タンパク質Copper Chaperone for Superoxide dismutase (CCS) をモデルに、タンパク質の機能的ナノスケール運動の実態とその物理的起源を解明する。CCSは細胞膜のトランスポーターから銅(I)イオンを受け取り、それを酵素の銅結合部位に渡すが、その基盤となる分子運動は未解明である。そこで小角散乱法と分子動力学法を組み合わせた新規解析法を創出し、銅輸送を担うCCSの分子運動を同定する。

Outline of Final Research Achievements

Copper chaperone for superoxide dismutase (CCS) is a protein consisting of multiple structural domains, and responsible for intracellular copper ion transport to an enzyme. The relationship between function and molecular motion of CCS was studied by small-angle X-ray scattering and computational simulations. Our results suggested the significance of cooperation of all structural domain including a domain which does not bind copper ion for copper binding or holding of CCS. To obtain the result above, we also established a modeling method for visualizing possible behavior of a biomolecule which combines molecular dynamics simulation and small-angle scattering data. Our idea is that when a long-time molecular dynamics simulation of a biomolecules matches a small-angle scattering profile of the molecule, the simulation trajectory is regarded as a possible structural pool of that. Feasibility of the idea was confirmed for some proteins.

Academic Significance and Societal Importance of the Research Achievements

本研究で提案した溶液散乱測定と理論計算による分子運動解析のアイデアは、今まで困難であった「X線結晶構造等の原子解像度データと、低解像度ながらも分子運動情報を含む小角散乱データを統合した生体分子ダイナミクス理解」への新規な道筋を与えている。加えて、この解析は他の実験データにも応用可能であり、様々な生体高分子実験データを統合し生体分子への理解を深めるための普遍的技術たりうることから、広く関連学術分野への波及効果が期待される。

Report

(3 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • Research Products

    (6 results)

All 2022 2021

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

  • [Journal Article] Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach2022

    • Author(s)
      Yunoki Yasuhiro、Matsumoto Atsushi、Morishima Ken、Martel Anne、Porcar Lionel、Sato Nobuhiro、Yogo Rina、Tominaga Taiki、Inoue Rintaro、Yagi-Utsumi Maho、Okuda Aya、Shimizu Masahiro、Urade Reiko、Terauchi Kazuki、Kono Hidetoshi、Yagi Hirokazu、Kato Koichi、Sugiyama Masaaki
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 184-184

    • DOI

      10.1038/s42003-022-03143-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation2021

    • Author(s)
      Okuda Aya、Shimizu Masahiro、Morishima Ken、Inoue Rintaro、Sato Nobuhiro、Urade Reiko、Sugiyama Masaaki
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 1-13

    • DOI

      10.1038/s41598-021-85219-0

    • NAID

      120006997066

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deuteration Aiming for Neutron Scattering2021

    • Author(s)
      Okuda Aya、Inoue Rintaro、Morishima Ken、Saio Tomohide、Yunoki Yasuhiro、Yagi-Utsumi Maho、Yagi Hirokazu、Shimizu Masahiro、Sato Nobuhiro、Urade Reiko、Kato Koichi、Sugiyama Masaaki
    • Journal Title

      Biophysics and Physicobiology

      Volume: 18 Issue: 0 Pages: 16-27

    • DOI

      10.2142/biophysico.bppb-v18.003

    • NAID

      130008000165

    • ISSN
      2189-4779
    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Dynamics of multi-domain protein ER-60 revealed by small angle X-ray scattering data and molecular dynamics simulations2021

    • Author(s)
      Masahiro Shimizu、Aya Okuda、Ken Morishima、Nobuhiro Sato、Rintaro Inoue、Reiko Urade、Masaaki Sugiyama
    • Organizer
      25th Congress and General Assembly of the International Union of Crystallography (the XXV IUCr Congress)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] X線小角散乱データと粗視化分子動力学計算に基づく生体分子の構造ダイナミクスの解明2021

    • Author(s)
      清水 将裕、奥田 綾、守島 健、柚木 康弘、佐藤 信浩、井上 倫太郎、裏出 令子、杉山 正明
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] X線小角散乱データと分子動力学計算に基づくマルチドメインタンパク質ER-60の動態解析2021

    • Author(s)
      清水 将裕、奥田 綾、守島 健、佐藤 信浩、井上 倫太郎、裏出 令子、杉山 正明
    • Organizer
      2020年度量子ビームサイエンスフェスタ
    • Related Report
      2020 Research-status Report

URL: 

Published: 2020-09-29   Modified: 2024-01-30  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi