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In vivo formation and new design of protein oligomers based on 3D domain swapping

Research Project

Project/Area Number 18H02088
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 37010:Bio-related chemistry
Research InstitutionNara Institute of Science and Technology

Principal Investigator

Hirota Shun  奈良先端科学技術大学院大学, 先端科学技術研究科, 教授 (90283457)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2019: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2018: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Keywordsタンパク質 / 3Dドメインスワッピング / 金属タンパク質 / 多量化 / タンパク質デザイン / 超分子 / 多量体 / ヘムタンパク質 / 銅タンパク質
Outline of Final Research Achievements

3D domain swapping is a phenomenon in which the same protein molecule exchanges the same structural region between molecules. Domain swapping was first reported in 1994. In recent years, there has been an increase in knowledge about the structure of domain-swapped proteins, but the mechanism and conditions under which domain swapping occurs in vivo have not been elucidated. In addition, oligomerization of proteins is useful for enhancing their structures and functions. However, it is difficult to artificially construct a protein nanostructure, and a general method has not been established yet. In this study, the mechanism and conditions of in vivo domain swapping are investigated. Protein oligomers with unique structures are constructed based on domain swapping.

Academic Significance and Societal Importance of the Research Achievements

本研究は、生体内でタンパク質多量化機構を分子レベルで解明し、機能性タンパク質多量体の創製を行う、新しい試みである。アンフィンセンのドグマではタンパク質はアミノ酸配列が決まれば、その立体構造が一意的に決まるとされているが、生体内でタンパク質は3Dドメインスワッピングし、必ずしも立体構造が一意的に決まらない。そのため、生体内でタンパク質がドメインスワッピングする機構や条件を解明することは重要である。また、タンパク質高次構造体形成の制御方法を開発することは、生体適合性に優れた物質輸送技術の創出に繋がる。

Report

(3 results)
  • 2021 Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (48 results)

All 2020 2019 2018 Other

All Int'l Joint Research (5 results) Journal Article (6 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 6 results,  Open Access: 3 results) Presentation (37 results) (of which Int'l Joint Research: 9 results,  Invited: 9 results)

  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Jadavpur University(インド)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Gadjah Mada University(インドネシア)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Sun Yat-Sen University(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] National Chiao Tung University(台湾)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] 3D Domain Swapping of Azurin from Alcaligenes xylosoxidans2020

    • Author(s)
      Robby Noor Cahyono, Masaru Yamanaka, Satoshi Nagao, Naoki Shibata, Yoshiki Higuchi, Shun Hirota
    • Journal Title

      Metallomics

      Volume: 12 Issue: 3 Pages: 337-345

    • DOI

      10.1039/c9mt00255c

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Domain-Swapping Design by Polyproline Rod Insertion2019

    • Author(s)
      Shota Shiga Masaru Yamanaka, Wataru Fujiwara, Shun Hirota, Shuichiro Goda, Koki Makabe
    • Journal Title

      ChemBioChem

      Volume: 20 Issue: 19 Pages: 2454-2457

    • DOI

      10.1002/cbic.201900179

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Determination of proton concentration at cardiolipin-containing membrane interfaces and its relation with the peroxidase activity of cytochrome c2019

    • Author(s)
      Parui Partha Pratim、Sarakar Yeasmin、Majumder Rini、Das Sanju、Yang Hongxu、Yasuhara Kazuma、Hirota Shun
    • Journal Title

      Chemical Science

      Volume: 10 Issue: 39 Pages: 9140-9151

    • DOI

      10.1039/c9sc02993a

    • NAID

      120006726658

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Protein surface charge effect on 3D domain swapping in cells for c-type cytochromes2019

    • Author(s)
      Yang Hongxu、Yamanaka Masaru、Nagao Satoshi、Yasuhara Kazuma、Shibata Naoki、Higuchi Yoshiki、Hirota Shun
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

      Volume: 1867 Issue: 11 Pages: 140265-140265

    • DOI

      10.1016/j.bbapap.2019.140265

    • NAID

      120006726659

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conferment of CO-Controlled Dimer-Monomer Transition Property to Thermostable Cytochrome c′ by Mutation in the Subunit-Subunit Interface2019

    • Author(s)
      Yamanaka Masaru、Nakayama Ryoko、Fujii Sotaro、Wakai Satoshi、Sambongi Yoshihiro、Hirota Shun
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 92 Issue: 3 Pages: 702-709

    • DOI

      10.1246/bcsj.20180311

    • NAID

      130007614161

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Oligomerization of Cytochrome c, Myoglobin, and Related Heme Proteins by 3D Domain Swapping2019

    • Author(s)
      Shun Hirota
    • Journal Title

      Journal of Inorganic Biochemistry

      Volume: 194 Pages: 170-179

    • DOI

      10.1016/j.jinorgbio.2019.03.002

    • NAID

      120006763862

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] Reaction Mechanism Elucidation and Supramolecular Creation of Metalloproteins2020

    • Author(s)
      Shun Hirota
    • Organizer
      The 100th Chemical Society of Japan Annual Meeting (中止)
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Amino Acid Sequence Design of The Hinge Region in Domain Swapping for Construction of Protein Supramolecules2020

    • Author(s)
      Satoshi Nagao, Ayaka Idomoto, Ayaka Suda, Hisashi Kobayashi, Naoki Shibata, Yoshiki Higuchi, Shun Hirota
    • Organizer
      The 100th Chemical Society of Japan Annual Meeting (中止)
    • Related Report
      2019 Annual Research Report
  • [Presentation] ポプラプラストシアニンの多量化と2量体の性質2020

    • Author(s)
      猪俣惇平、Le MOUEL Korantin、山中優、廣田俊
    • Organizer
      日本化学会第100春季大会(中止)
    • Related Report
      2019 Annual Research Report
  • [Presentation] ドメインスワップ構造を基に設計した融合タンパク質による可動型超分子の構築2020

    • Author(s)
      山中優、廣田俊
    • Organizer
      日本化学会第100春季大会(中止)
    • Related Report
      2019 Annual Research Report
  • [Presentation] The Design of Artificial Domain-Swapped Proteins by Polyproline-Rod Insertion2020

    • Author(s)
      Shota Shiga, Masaru Yamanaka, Wataru Hujiwara Shun Hirota, Shuichiro Goda, Koki Makabe
    • Organizer
      The 100th Chemical Society of Japan Annual Meeting (中止)
    • Related Report
      2019 Annual Research Report
  • [Presentation] NMR Characterization of Dynamic Properties of Cytochrome c bound to Membranes using Lipid Bicelles2019

    • Author(s)
      Satoshi Nagao, Hisashi Kobayashi, Shun Hirota
    • Organizer
      15th International Symposium on Applied Bioinorganic Chemistry (ISABC15)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Conferment of CO-Controlled Dimer-Monomer Transition Property to Thermostable Cytochrome c′ by Mutation in the Subunit Interface2019

    • Author(s)
      Masaru Yamanaka, Ryoko Nakayama, Sotaro Fujii, Satoshi Wakai, Yoshihiro Sambongi, Shun Hirota
    • Organizer
      15th International Symposium on Applied Bioinorganic Chemistry (ISABC15)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Oxygen Activation by Cu-Amyloid-β Peptide: Models Relevant for Alzheimer’s Disease2019

    • Author(s)
      Leonie Berthonnaud, Charlene Esmieu, Shun Hirota, Christelle Hureau
    • Organizer
      15th International Symposium on Applied Bioinorganic Chemistry (ISABC15)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NMR Characterization of Dynamic Properties of Cytochrome c Bound to Membranes Using Phospholipid Bicelles2019

    • Author(s)
      Satoshi Nagao, Hisashi Kobayashi, Shun Hirota
    • Organizer
      第19回蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 金属結合部位を有するドメインスワップしたミオグロビン 2 量体のデザインと性質2019

    • Author(s)
      井戸本彩花、長尾聡、柴田直樹、樋口芳樹、廣田俊
    • Organizer
      第19回蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Construction of Protein Supramolecules Based on Domain Swapping2019

    • Author(s)
      Masaru Yamanaka, Satoshi Nagao, Chunguang Ren, Mohan Zhang, Akiya Oda, Yoshiki Higuchi, Shun Hirota
    • Organizer
      第19回蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Construction of Protein Supramolecules Based on Domain-Swapping Mechanism2019

    • Author(s)
      Masaru Yamanaka, Satoshi Nagao, Chunguang Ren, Mohan Zhang, Akiya Oda, Yoshiki Higuchi, Shun Hirota
    • Organizer
      33rd Annual Symposium of the Protein Society
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Oligomerization of Cytochrome c, Myoglobin, and Related Heme Proteins by 3D Domain Swapping2019

    • Author(s)
      Shun Hirota
    • Organizer
      19th International Conference on Biological Inorganic Chemistry (ICBIC19)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Domain Swapping of Azurin from Alcaligenes xylosoxidans and Characterization of Its Dimer2019

    • Author(s)
      Rooby Noor Cahyono、山中優、長尾聡、柴田直樹、樋口芳樹、廣田俊
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] フェリチンゲルの作製と金属吸着2019

    • Author(s)
      山中優、荻原理生、廣田俊
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] ドメインスワッピングを利用したミオグロビンへの金属結合部位の導入2019

    • Author(s)
      井戸本彩花、長尾聡、柴田直樹、樋口芳樹、廣田俊
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Constructing Heme Protein Supramolecules by 3D Domain Swapping2019

    • Author(s)
      Shun Hirota
    • Organizer
      2nd International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering (BioMIC 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 新規フェリチンゲルの作製と遷移金属捕捉等の活用2019

    • Author(s)
      廣田俊
    • Organizer
      けいはんなビジネスメッセ2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] 金属結合部位を導入したドメインスワップミオグロビン2量体の構造と性質2019

    • Author(s)
      井戸本彩花、長尾聡、柴田直樹、樋口芳樹、廣田俊
    • Organizer
      第9回CSJ化学フェスタ2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Oligomerization of Heme Proteins by 3D Domain Swapping2019

    • Author(s)
      Shun Hirota
    • Organizer
      The 6th National Conference on Biophysical Chemistry (NCBPC-6)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] シトクロムc:多量化と膜相互作用2019

    • Author(s)
      廣田俊
    • Organizer
      日本薬学会東海支部特別講演会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Construction of a Two-Dimensional Protein Array Utilizing a Cytochrome c555-Based Protein2019

    • Author(s)
      Cheng Xie, Masaru Yamanaka, Satoshi Nagao, Naoki Shibata, Yoshiki Higuchi, Shun Hirota
    • Organizer
      99th Chemical Society of Japan Annual Meeting
    • Related Report
      2018 Annual Research Report
  • [Presentation] Oligomerization of Azurin from Alcaligenes xylosoxidans and Characterization of Its Dimer2019

    • Author(s)
      Robby Noor Cahyono, Masaru Yamanaka, Satoshi Nagao, Shun Hirota
    • Organizer
      99th Chemical Society of Japan Annual Meeting
    • Related Report
      2018 Annual Research Report
  • [Presentation] Design of Stable Domain-Swapped Myoglobin Oligomers2019

    • Author(s)
      Satoshi Nagao, Ayaka Suda, Hisashi Kobayashi, Naoki Shibata, Yoshiki Higuchi, Shun Hirota
    • Organizer
      99th Chemical Society of Japan Annual Meeting
    • Related Report
      2018 Annual Research Report
  • [Presentation] 耐熱性シトクロムcのサブユニット界面変異によるCO応答性2量体-単量体変換特性の付与2019

    • Author(s)
      山中優、中山諒子、若井暁、藤井創太郎、三本木至宏、廣田俊
    • Organizer
      日本化学会第99春季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 金属結合性を有するドメインスワップしたミオグロビン2量体のデザインと性質2019

    • Author(s)
      井戸本彩花、長尾聡、柴田直樹、樋口芳樹、廣田俊
    • Organizer
      日本化学会第99春季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Supramolecular Assemblies of c-Type Cytochromes Based on 3D Domain Swapping2018

    • Author(s)
      Shun Hirota
    • Organizer
      233rd ECS Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Construction of Protein Supramolecules by 3D Domain Swapping2018

    • Author(s)
      Shun Hirota
    • Organizer
      The 18th Annual Meeting of the Protein Science Society of Japan (Workshop: 35th Anniversary of Protein Engineering since 1983)
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 球状蛋白質のドメインスワッピングを実現するループのリデザイン2018

    • Author(s)
      志賀翔多、山中優、廣田俊、真壁幸樹
    • Organizer
      第18回蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] NMR Study on Dynamic Properties of Cytochrome c Bound to Lipid Bicelles2018

    • Author(s)
      Satoshi Nagao, Hisashi Kobayashi, Shun Hirota
    • Organizer
      The 18th Annual Meeting of the Protein Science Society of Japan
    • Related Report
      2018 Annual Research Report
  • [Presentation] Domain Swapping-Based Assemblies of c-Type Cytochromes2018

    • Author(s)
      Shun Hirota, Satoshi Nagao, Masaru Yamanaka, Yoshiki Higuchi
    • Organizer
      Tenth International Conference on Porphyrins and Phthalocyanines (ICPP-10)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] バイセルと溶液NMRを組合せた手法で可能になるシトクロムcと脂質膜の相互作用の高分解能解析2018

    • Author(s)
      長尾聡、小林紀、廣田俊
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] サブユニット界面変異による耐熱性シトクロムc′へのCo依存的2量体-単量体遷移特性の付与2018

    • Author(s)
      山中優、中山諒子、藤井創太郎、岩井暁、三本木至宏、廣田俊
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] シトクロムcの多量体形成におけるアニオンの影響に関する理論的研究2018

    • Author(s)
      根木秀佳、吉田紀生、廣田俊、東雅大
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Picobiology of Metalloproteins: Vibrational Spectroscopic Studies of Cytochrome c and Hydrogenase2018

    • Author(s)
      廣田俊、太虎林、樋口芳樹、柳澤幸子、小倉尚志
    • Organizer
      第56回日本生物物理学会年会(シンポジウム:ピコバイオロジーが目指すもの)
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 脂質バイセルに結合したシトクロムcの動的性質のNMR研究2018

    • Author(s)
      長尾聡、小林紀、廣田俊
    • Organizer
      第57回NMR討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Activation/Inactivation Mechanism between the Ni-SIr and Ni-SIa States of [NiFe] Hydrogenase Studied by Utilizing Ni-SIr-to-Ni-SIa Photoactivation2018

    • Author(s)
      Hulin Tai, Shun Hirota, Koji Nishikawa, Yoshiki Higuchi, Liang-nian Ji, Zong-wan Mao
    • Organizer
      中国化学会第十四回全国生物無機化学学術会議
    • Related Report
      2018 Annual Research Report

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Published: 2018-04-23   Modified: 2023-01-30  

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