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Development of new protein cages using domain swapping

Research Project

Project/Area Number 15K13744
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field 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, 物質創成科学研究科, 教授 (90283457)

Co-Investigator(Renkei-kenkyūsha) HIGUCHI Yoshiki  兵庫県立大学, 大学院生命理学研究科, 教授 (90183574)
NAGAO Satoshi  奈良先端科学技術大学院大学, 物質創成科学研究科, 助教 (30452535)
Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsタンパク質 / 生体分子 / ナノバイオ / 超分子化学 / タンパク質構造体 / タンパク質ケージ / ドメインスワッピング / 蛋白質 / 蛋白質構造体 / 蛋白質ケージ / 超分子
Outline of Final Research Achievements

Cytochrome (cyt) cb562 oligomers were constructed, and it was found that the dimer of cyt cb562 forms a domain-swapped structure. Three domain-swapped cyt cb562 dimers formed a unique cage structure with a Zn-SO4 cluster inside the cavity. The Zn-SO4 cluster consisted of fifteen Zn2+ and seven SO42- ions, whereas six additional Zn2+ ions were detected inside the cavity. Fusion proteins comprising the subunits of different homo oligomeric proteins were designed. The two subunits were connected with a 3-helix bundle protein in the fusion proteins. A tetramer and a hexamer were constructed with the fusion proteins, and the structures of the tetramer and hexamer were analyzed by small-angle X-ray scattering and high-speed atomic force microscopy methods.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (20 results)

All 2017 2016 2015

All Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Acknowledgement Compliant: 3 results,  Open Access: 1 results) Presentation (17 results) (of which Int'l Joint Research: 11 results,  Invited: 9 results)

  • [Journal Article] Formation and Carbon Monoxide-Dependent Dissociation of Allochromatium vinosum Cytochrome c' Oligomers Using Domain-Swapped Dimers2017

    • Author(s)
      M. Yamanaka, M. Hoshizumi, S. Nagao, R. Nakayama, N. Shibata, Y. Higuchi, and S. Hirota
    • Journal Title

      Protein Science

      Volume: 26 Issue: 3 Pages: 464-474

    • DOI

      10.1002/pro.3090

    • NAID

      120006334944

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effect of Methionine80 Heme Coordination on Domain Swapping of Cytochrome c2017

    • Author(s)
      S. Hirota, N. Yamashiro, Z. Wang, and S. Nagao
    • Journal Title

      Journal of Biological Inorganic Chemistry

      Volume: 22 Issue: 5 Pages: 705-712

    • DOI

      10.1007/s00775-017-1446-3

    • NAID

      120006334946

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Domain-swapped Cytochrome cb562 Dimer and Its Nanocage Encapsulating a Zn-SO4 Cluster in the Internal Cavity2015

    • Author(s)
      Takaaki Miyamoto, Mai Kuribayashi, Satoshi Nagao, Yasuhito Shomura, Yoshiki Higuchi, Shun Hirota
    • Journal Title

      Chemical Science

      Volume: 6 Issue: 12 Pages: 7336-7342

    • DOI

      10.1039/c5sc02428e

    • NAID

      120006334940

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Protein Nanostructures Constructed by Fusing Two Oligomerization Domains with a 3-Helix Bundle Linker2017

    • Author(s)
      Takaaki Miyamoto and Shun Hirota
    • Organizer
      97th Chemical Society of Japan Annual Meeting
    • Place of Presentation
      慶応義塾大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] Construction of a Triangle-shaped Structure with a Unit Protein Based on Cytochrome c5552017

    • Author(s)
      Akiya Oda, Ikki Ueda, Masaru Yamanaka, Satoshi Nagao, Naoki Shibata, Yoshiki Higuchi, and Shun Hirota
    • Organizer
      97th Chemical Society of Japan Annual Meeting
    • Place of Presentation
      慶応義塾大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] Cytochrome c: Domain Swapping, Self-Modification, and Molecular Recognition2017

    • Author(s)
      Shun Hirota, Satoshi Nagao, Masaru Yamanaka, and Yoshiki Higuchi
    • Organizer
      5th Symposium on Advanced Biological Inorganic Chemistry
    • Place of Presentation
      Kolkata, India
    • Year and Date
      2017-01-07
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Construction of Heme Protein Supramolecules by Domain Swapping2016

    • Author(s)
      Shun Hirota, Satoshi Nagao, Masaru Yamanaka, and Yoshiki Higuchi
    • Organizer
      8th Asian Biological Inorganic Chemistry Conference
    • Place of Presentation
      Auckland, New Zealand
    • Year and Date
      2016-12-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structure and Function of Heme Protein Oligomers Constructed by Domain Swapping2016

    • Author(s)
      Shun Hirota
    • Organizer
      Japan-Korea-Taiwan Bioinorganic Chemistry Symposium
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Application of Supramolecular Science for Drug Design2016

    • Author(s)
      Shun Hirota
    • Organizer
      The Symposium of Annual Scientific Meeting 2016 of Indonesian Pharmacist Association
    • Place of Presentation
      Jogjakarta, Indonesia
    • Year and Date
      2016-09-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Domain Swapping in c-Type Cytochromes and Myoglobin2016

    • Author(s)
      Shun Hirota, Satoshi Nagao, Partha Pratim Parui, Megha Subhash Deshpande, Chunguang Ren, Yugo Hayashi, Takaaki Miyamoto, Yin-Wu Lin, and Yoshiki Higuchi
    • Organizer
      30th Anniversary Symposium of the Protein Society
    • Place of Presentation
      Baltimore, USA
    • Year and Date
      2016-07-16
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Construction of Zn-SO4 Cluster-encapsulating Protein Nanocage by Domain Swapping2016

    • Author(s)
      Takaaki Miyamoto, Mai Kuribayashi, Satoshi Nagao, Yasuhito Shomura, Yoshiki Higuchi, and Shun Hirota
    • Organizer
      30th Anniversary Symposium of the Protein Society
    • Place of Presentation
      Baltimore, USA
    • Year and Date
      2016-07-16
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Domain Swapping of c-Type Cytochromes and Myoglobin2016

    • Author(s)
      Shun Hirota, Satoshi Nagao, Yugo Hayashi, Takaaki Miyamoto, Chunguang Ren, Masaru Yamanaka, Ying-Wu Lin, Hirofumi Komori, Yasuhito Shomura, and Yoshiki Higuchi
    • Organizer
      Ninth International Conference on Porphyrins and Phthalocyanines
    • Place of Presentation
      Nanjing, China
    • Year and Date
      2016-07-03
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ドメインスワップしたシトクロムcb562二量体が形成するZn-SO4クラスター内包タンパク質ナノケージの結晶構造2016

    • Author(s)
      宮本昂明、長尾聡、庄村康人、樋口芳樹、廣田俊
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Domain-swapped Cytochrome cb562 Dimer and Its Nanocage Encapsulating a Zn-SO4 Cluster in the Internal Cavity2016

    • Author(s)
      Takaaki Miyamoto, Mai Kuribayashi, Satoshi Nagao, Yasuhito Shomura, Yoshiki Higuchi, Shun Hirota
    • Organizer
      96th Spring Conference of the Chemical Society of Japan
    • Place of Presentation
      Doshisha University (Kyotanabe, Kyoto)
    • Year and Date
      2016-03-24
    • Related Report
      2015 Research-status Report
  • [Presentation] Construction of Heme Protein Oligomers by Domain Swapping2015

    • Author(s)
      Shun Hirota
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015 (Pacifichem 2015)
    • Place of Presentation
      Hilton Hawaiian Village (Honolulu, USA)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ドメインスワッピングとは?:タンパク質の超分子化2015

    • Author(s)
      廣田俊
    • Organizer
      第28回生物無機化学夏季セミナー
    • Place of Presentation
      山喜旅館(静岡県伊東市)
    • Year and Date
      2015-08-28
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Formation of Cytochrome cb562 Oligomers by Domain Swapping2015

    • Author(s)
      Takaaki Miyamoto, Mai Kuribayashi, Satoshi Nagao, Yasuhito Shomura, Yoshiki Higuchi, Shun Hirota
    • Organizer
      29th Annual Symposium of The Protein Society
    • Place of Presentation
      Palau de Congressos de Barcelona (Barcelona, Spain)
    • Year and Date
      2015-07-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Construction of Dimeric Heme Proteins by Domain Swapping2015

    • Author(s)
      Shun Hirota
    • Organizer
      17th International Conference on Biological Inorganic Chemistry (ICBIC17)
    • Place of Presentation
      China National Convention Center (Beijing, China)
    • Year and Date
      2015-07-20
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Cytochrome c and Myoglobin Oligomers Formed by Domain Swapping2015

    • Author(s)
      Shun Hirota
    • Organizer
      International Symposium on Metal Complexes (ISMEC2015)
    • Place of Presentation
      Hotel Plaza (Wroclaw, Poland)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ドメインスワップしたシトクロムcb562の構造と性質2015

    • Author(s)
      宮本昂明、栗林麻衣、長尾聡、庄村康人、樋口芳樹、廣田俊
    • Organizer
      第25回金属の関与する生体関連反応シンポジウム
    • Place of Presentation
      長崎大学(長崎県長崎市)
    • Year and Date
      2015-05-30
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2018-12-17  

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