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Direct observation of ligand and protein dynamics within hemoglobin at work

Research Project

Project/Area Number 16K07326
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionJichi Medical University

Principal Investigator

Shibayama Naoya  自治医科大学, 医学部, 教授 (20196439)

Project Period (FY) 2016-04-01 – 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: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywordsヘモグロビン / ダイナミクス / X線結晶構造解析 / 光解離 / アロステリー / 光解離法
Outline of Final Research Achievements

Hemoglobin is one of the best characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here, we capture the CO migration processes in human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatueres. We find that the photodissociated CO molecules migrate along different pathways in the α and β subunit by hopping between the internal cavities with correlated side-chain motions of large nonpolar residues. Our results provide a comprehensive picture of ligand movements in hemoglobin, and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.

Academic Significance and Societal Importance of the Research Achievements

ヒト・ヘモグロビンはアロステリック蛋白質の代表格として教科書にも載っており、そのガス配位子結合調節能はよく研究されている。しかし、酸素などのガス分子の通る道筋は結晶構造に見当たらず、ガス分子が蛋白質分子のどこをどのように移動していくのかは謎のままだ。今回の研究成果は、赤血球中のヘモグロビンが酸素を迅速に受け渡しする仕組みの理解につながると期待される。特に、ヘモグロビンが酸素濃度の低い末梢組織にやってきたとき、T状態特有のタンパク質分子内運動を使って酸素を迅速かつ巧妙に外部へ送り出すことを実験的に明らかにした。この発見は、生理学的にも、生物物理学的にも極めて重要な意味がある。

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

    (9 results)

All 2020 2018 2017 2016

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

  • [Journal Article] Direct observation of ligand migration within human hemoglobin at work2020

    • Author(s)
      Shibayama Naoya、Sato-Tomita Ayana、Ohki Mio、Ichiyanagi Kouhei、Park Sam-Yong
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 117 Issue: 9 Pages: 4741-4748

    • DOI

      10.1073/pnas.1913663117

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Allosteric transitions in hemoglobin revisited2020

    • Author(s)
      Shibayama Naoya
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129335-129335

    • DOI

      10.1016/j.bbagen.2019.03.021

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family2020

    • Author(s)
      Yun Ji-Hye、Ohki Mio、Park Jae-Hyun、Ishimoto Naito、Sato-Tomita Ayana、Lee Wonbin、Jin Zeyu、Tame Jeremy R. H.、Shibayama Naoya、Park Sam-Yong、Lee Weontae
    • Journal Title

      Science Advances

      Volume: 6 Issue: 6 Pages: 6-6

    • DOI

      10.1126/sciadv.aay2042

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Direct observation of conformational population shifts in crystalline human hemoglobin2017

    • Author(s)
      Shibayama Naoya、Ohki Mio、Tame Jeremy R. H.、Park Sam-Yong
    • Journal Title

      Journal of Biological Chemistry

      Volume: 292 Issue: 44 Pages: 18258-18269

    • DOI

      10.1074/jbc.m117.781146

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Size and Shape Controlled Crystallization of Hemoglobin for Advanced Crystallography2017

    • Author(s)
      Ayana Sato-Tomita、Naoya Shibayama
    • Journal Title

      Crystals

      Volume: 7 Issue: 9 Pages: 282-282

    • DOI

      10.3390/cryst7090282

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular mechanism of photoactivation of a light-regulated adenylate cyclase2017

    • Author(s)
      Ohki Mio、Sato-Tomita Ayana、Matsunaga Shigeru、Iseki Mineo、Tame Jeremy R. H.、Shibayama Naoya、Park Sam-Yong
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 114 Issue: 32 Pages: 8562-8567

    • DOI

      10.1073/pnas.1704391114

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Comprehensive structural and functional analysis of hemoglobin in single crystals2018

    • Author(s)
      柴山 修哉
    • Organizer
      日本生物物理学会第56回年会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Deciphering protein allosteric mechanisms from small structural changes in crystals2017

    • Author(s)
      Naoya Shibayama, Ayana Sato, Mio Ohki, Sam-Yong Park
    • Organizer
      日本生物物理学会第55回年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Direct observation of large-scale quaternary motions of hemoglobin in a crystalline state2016

    • Author(s)
      Naoya Shibayama, Mio Ohki, Sam-Yong Park
    • Organizer
      日本生物物理学会第54回年会
    • 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

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Published: 2016-04-21   Modified: 2021-02-19  

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