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Semi-comprehensive functional determination of crystal structures of hemoglobin

Research Project

Project/Area Number 19K06601
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionJichi Medical University

Principal Investigator

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

Project Period (FY) 2019-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2021: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2020: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2019: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywordsヘモグロビン / アロステリー / 酸素親和性 / MWCモデル / 結晶構造解析 / ゾル・ゲル法 / アロステリックモデル / 結晶構造 / 酸素平衡曲線 / 多孔性シリカゲル / 酸素平衡機能 / 構造機能相関
Outline of Research at the Start

Monod-Wyman-Changeuxの2状態アロステリックモデルは、生命科学における最も単純かつエレガントな理論モデルの一つである。しかし、原型のモデルでは、アロステリック蛋白質の典型であるヘモグロビンの挙動を定量的に記述できないこともまた知られている。本研究では、結晶中ヘモグロビンの酸素平衡曲線測定による結晶構造の直接機能決定、及び、水を含む多孔性シリカゲル中で状態間遷移を凍結したヘモグロビンの機能解析(全機能状態の洗い出し)を行う。これらの方法を駆使して、ヘモグロビン分子のとりうる全ての構造状態の機能を決定し、構造機能連関を説明する最終的なモデルを確立する。

Outline of Final Research Achievements

Structural changes associated with protein allsotery are often explained in terms of a two-state transition between the tense (T) state and the relaxed (R) state, using hemoglobin (Hb) as an example. However, the two-state model has not been successfully applied to the understanding of Hb allostery in a quantitative sense. Although Hb was one of the first proteins to be solved by X-ray crystallography, the correlation between its crystal structure and solution function has not yet been clarified and remains as an unresolved issue. In this study, we directly determined the functional properties of crystals of Hb, and analyzed the function of Hb whose transition between states was frozen in a porous silica gel containing water. We have elucidated the relationships between the structure and function of Hb.

Academic Significance and Societal Importance of the Research Achievements

ヘモグロビン(Hb)のアロステリック効果のメカニズムを理解するためには、溶液中に平衡状態で存在すると考えられる各構造とその機能を直接関連づけることが重要である。それにもかかわらず、この種の研究は国内外でほとんど行われていない。この現状を鑑み、かつ、研究代表者の柴山の経験と実績を踏まえ、本研究は立案・遂行された。本研究により、HbのR状態、T状態の持つ機能的柔軟性の構造的基盤が定義され、これらの成果は、Hbのアロステリック効果を説明する新しい構造機能連関モデルの創造へとつながることが期待される。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (12 results)

All 2023 2022 2021 2020

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

  • [Journal Article] いまさらヘモグロビン?ヘモグロビンのアロステリーを再考する2023

    • Author(s)
      柴山 修哉
    • Journal Title

      人工血液

      Volume: 31 Pages: 43-53

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation2022

    • Author(s)
      Nagatomo Shigenori、Shoji Mitsuo、Terada Takuto、Nakatani Kiyoharu、Shigeta Yasuteru、Hirota Shun、Yanagisawa Sachiko、Kubo Minoru、Kitagawa Teizo、Nagai Masako、Ohki Mio、Park Sam-Yong、Shibayama Naoya
    • Journal Title

      Biophysical Journal

      Volume: 121 Issue: 14 Pages: 2767-2780

    • DOI

      10.1016/j.bpj.2022.06.012

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] X-ray fluorescence holography of biological metal sites: Application to myoglobin2022

    • Author(s)
      Sato-Tomita Ayana、Ang Artoni Kevin R.、Kimura Koji、Marumi Riho、Happo Naohisa、Matsushita Tomohiro、Park Sam-Yong、Shibayama Naoya、Sasaki Yuji C.、Hayashi Kouichi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 635 Pages: 277-282

    • DOI

      10.1016/j.bbrc.2022.10.003

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Freezable and Unfreezable Hydration Water: Distinct Contributions to Protein Dynamics Revealed by Neutron Scattering2021

    • Author(s)
      Yamamoto Naoki、Kofu Maiko、Nakajima Kenji、Nakagawa Hiroshi、Shibayama Naoya
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 12 Issue: 8 Pages: 2172-2176

    • DOI

      10.1021/acs.jpclett.0c03786

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [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 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] いまさらヘモグロビン?2023

    • Author(s)
      柴山 修哉
    • Organizer
      低酸素研究会2023
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Fe-Tyr 配位結合をもつ 4 種類の天然変異ヘモグロビン M の結晶構造2023

    • Author(s)
      Shigenori Nagatomo, Ayana Sato-Tomita, Yumi Semba, Akihisa Miyagawa, Kiyoharu Nakatani, Mio Ohki, Kenji Mizutani, Sam-Yong Park, Naoya Shibayama
    • Organizer
      第61回日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ヘモグロビンM IwateとM BostonのFe-O伸縮振動の理論計算の改良およびヘモグロビンAとの構造の比較2023

    • Author(s)
      長友重紀、寺田拓人、庄司光男、重田育照、中谷清治、廣田俊、柳澤幸子、久保稔、北川禎三、長井雅子、 大木規央、朴三用、柴山修哉
    • Organizer
      第49回生体分子科学討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ヘモグロビンの構造・機能・動態研究の最前線2022

    • Author(s)
      柴山 修哉
    • Organizer
      第29回日本血液代替物学会年次大会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] ヘモグロビンM IwateとM Bostonにおけるヘム-チロシン結合の振動分光,結晶構造,理論計算による解析2021

    • Author(s)
      長友 重紀,寺田 拓人,庄司 光男,重田 育照,中谷 清治,廣田 俊,北川 禎三,長井 雅子,大木 規央,朴 三用,柴山 修哉
    • Organizer
      第47回生体分子科学討論会
    • Related Report
      2021 Research-status Report
  • [Presentation] ヘモグロビンの超精密制御機構の秘密2021

    • Author(s)
      柴山 修哉
    • Organizer
      第33 回生物無機化学夏季セミナー
    • Related Report
      2021 Research-status Report
    • Invited

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Published: 2019-04-18   Modified: 2025-01-30  

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