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Analysis of conformational changes in ribosome during protein synthesis reaction cycle

Research Project

Project/Area Number 22570165
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionJapan Atomic Energy Agency

Principal Investigator

ISHIDA Hisashi  独立行政法人日本原子力研究開発機構, 量子ビーム応用研究部門, 研究副主幹 (60360418)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2010: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsリボソーム / 電子顕微鏡 / 分子動力学 / 伸長因子EF-G / tRNA 転位 / 分子動力学シミュレーション / 伸長因子EFG / tRNA転位 / 電子顕微鏡像 / チェット様運動 / ラチェット様運動 / 当てはめ / 立体構造構築
Research Abstract

To understand the mechanism of reverse tRNA translocation in ribosome, all-atom molecular dynamics simulations of ribosome-mRNA-tRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers : one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which triggered P-tRNA to move over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which located the two tRNAs in the hybrid state. Conformational change of EF-G was interpreted as the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with the A/P-tRNA.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (12 results)

All 2013 2012 2011 2010

All Journal Article (1 results) (of which Peer Reviewed: 1 results) Presentation (11 results)

  • [Journal Article] Molecular Dynamics Simulation System for structural analysis of biomolecules by high performance computing2011

    • Author(s)
      Ishida, H
    • Journal Title

      Progress in Nuclear Science and Technology

      Volume: 2 Pages: 470-476

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Free-energy landscape of tRNA translocation through ribosome revealed by electron microscopy density map and molecular dynamics simulations2013

    • Author(s)
      Ishida, H and Matsumoto, A
    • Organizer
      Biophysical society 57th annual meeting
    • Place of Presentation
      Philadelphia, USA
    • Year and Date
      2013-02-04
    • Related Report
      2012 Final Research Report
  • [Presentation] Energy landscape of translocation of tRNA molecules through ribosome revealed by electron microscopy density map and molecular dynamics simulations2013

    • Author(s)
      Hisashi Ishida
    • Organizer
      Biophysical society 57th annual meeting
    • Place of Presentation
      Philadelphia, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] Dynamics of tRNA translocation revealed by electron microscopy density map and molecular dynamics simulations2012

    • Author(s)
      Ishida, H and Matsumoto, A
    • Organizer
      Mini-Symposium on Modeling, Simulation and Function of Biomolecular Assemblies
    • Place of Presentation
      Tokyo
    • Year and Date
      2012-11-09
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Free-energy landscape of translocation through ribosome analysed using MD simulations and cryo-EM density maps2012

    • Author(s)
      Ishida, H. and Matsumoto, A
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      2012-09-24
    • Related Report
      2012 Final Research Report
  • [Presentation] Free-energy landscape of translocation through ribosome analysed using MD simulations and cryo-EM density maps2012

    • Author(s)
      石田恒
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] 分子動力学シミュレーションプログラムSCUBAの開発とタンパク質-核酸複合体の大規模シミュレーション2012

    • Author(s)
      石田恒
    • Organizer
      第4回HPCI戦略プログラム合同研究交流会
    • Place of Presentation
      神戸
    • Related Report
      2012 Annual Research Report
  • [Presentation] Energy landscape of translocation of tRNA molecules through ribosome revealed by electron microscopy density map and molecular dynamics simulations2011

    • Author(s)
      Ishida, H. and Matsumoto, A
    • Organizer
      CECAM workshop on "Dynamics of protein-nucleic acid interactions : Integrating simulations with experiment"
    • Place of Presentation
      Switzerland, Zurich
    • Year and Date
      2011-09-16
    • Related Report
      2012 Final Research Report
  • [Presentation] Energy landscape of translocation of tRNA molecules through ribosome revealed by electron microscopy density map and molecular dynamics simulations2011

    • Author(s)
      Hisashi Ishida, Atsushi Matsumoto
    • Organizer
      CECAM workshop on "Dynamics of protein-nucleic acid interactions : Integrating simulations with experiment"
    • Place of Presentation
      ETHZ(Switzerland, Zurich)(招待講演)
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] Ribosome dynamics and tRNA movement using electron microscopy density map and molecular dynamics simulations2011

    • Author(s)
      石田恒
    • Organizer
      7^<th> Asian Biophysics Association Symposium & Annual Meeting of the Indian Biophysical Society
    • Place of Presentation
      New Delhi, India
    • Year and Date
      2011-01-30
    • Related Report
      2010 Annual Research Report
  • [Presentation] Molecular Dynamics Simulation System for structural analysis of biomolecules by high performance computing2010

    • Author(s)
      石田恒
    • Organizer
      Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo 2010 (SNA+MC2010)
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      2010-10-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Analysis of translocation of tRNA molecules through ribosome using electron microscopy density map and molecular dynamics simulations2010

    • Author(s)
      石田恒
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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