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Directed evolution of peptides that recognize dye structures and its application for research tools

Research Project

Project/Area Number 18H02103
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 37030:Chemical biology-related
Research InstitutionThe University of Tokyo (2020-2021)
Saitama University (2018-2019)

Principal Investigator

Terai Takuya  東京大学, 大学院理学系研究科(理学部), 特任准教授 (00508145)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2020: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
Fiscal Year 2019: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2018: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Keywords有機色素 / ペプチド / 細胞イメージング / タンパク質精製 / 進化分子工学
Outline of Final Research Achievements

In this study we aimed to develop novel molecular tools based on small molecule-peptide complexes by integrating two approaches: "rational design of small organic molecules" and " modification of biological macromolecules using directed evolution”. Specifically, we aimed to obtain peptides and proteins that recognize the structure of organic dye molecules by evolutionary molecular engineering, which would be useful for various chemical biology applications. As a result of the research, we succeeded in identification of "polypeptides that reversibly recognize conformational changes of dye molecules" by cDNA display method, and also developed a sensor molecule where the fluorescence intensity of labelled organic dyes is changed as a result of the conformation change of the protein in response to calcium concentration.

Academic Significance and Societal Importance of the Research Achievements

現代の生物学研究では蛍光イメージングや光遺伝学的摂動、タンパク質精製などで様々な分子ツールが使われているが、そのほとんどは有機合成低分子あるいは生体高分子のいずれかであり、両方を活用した分子ツールは極めて稀である。そもそも化学において有機低分子と生体高分子は歴史的、学問分野的に独立して研究されており、これらを融合させようとする試み(chemi-genetics)は最近になってようやく注目されつつある。本研究では、特に有機合成色素とタンパク質(ポリペプチド)との複合化に着目し、両者の相互作用があって初めて機能を発揮する新たな分子ツールの開発を行った。

Report

(4 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (44 results)

All 2022 2021 2020 2019 2018 Other

All Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 3 results) Presentation (29 results) (of which Int'l Joint Research: 6 results) Remarks (2 results) Patent(Industrial Property Rights) (3 results) (of which Overseas: 1 results)

  • [Journal Article] Barcodes, co-cultures, and deep learning take genetically encoded biosensor multiplexing to the nth degree2022

    • Author(s)
      Terai Takuya、Campbell Robert E.
    • Journal Title

      Molecular Cell

      Volume: 82 Issue: 2 Pages: 239-240

    • DOI

      10.1016/j.molcel.2021.12.017

    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Journal Article] Interleukin-17A Peptide Aptamers with an Unexpected Binding Moiety Selected by cDNA Display under Heterogenous Conditions2021

    • Author(s)
      Anzai Hiroki、Terai Takuya、Wakabayashi-Nakao Kanako、Noguchi Taro、Kumachi Shigefumi、Tsuchiya Masayuki、Nemoto Naoto
    • Journal Title

      ACS Medicinal Chemistry Letters

      Volume: 12 Issue: 9 Pages: 1427-1434

    • DOI

      10.1021/acsmedchemlett.1c00217

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V2020

    • Author(s)
      Yamamoto Yasuhide、Terai Takuya、Kumachi Shigefumi、Nemoto Naoto
    • Journal Title

      ACS Combinatorial Science

      Volume: 22 Issue: 4 Pages: 165-171

    • DOI

      10.1021/acscombsci.9b00167

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photocrosslinking of cDNA Display Molecules with Their Target Proteins as a New Strategy for Peptide Selection2020

    • Author(s)
      Terai Takuya、Koike Tomoyuki、Nemoto Naoto
    • Journal Title

      Molecules

      Volume: 25 Issue: 6 Pages: 1472-1472

    • DOI

      10.3390/molecules25061472

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] In vitro selection of anti-gliadin single-domain antibodies from a na?ve library for cDNA-display mediated immuno-PCR2020

    • Author(s)
      Jayathilake Chathuni、Kumachi Shigefumi、Arai Hidenao、Motohashi Maiko、Terai Takuya、Murakami Akikazu、Nemoto Naoto
    • Journal Title

      Analytical Biochemistry

      Volume: 589 Pages: 113490-113490

    • DOI

      10.1016/j.ab.2019.113490

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] cDNA Display Mediated Immuno-PCR (cD-IPCR): A Novel PCR-based Antigen Detection Method2019

    • Author(s)
      Jayathilake Chathuni、Terai Takuya、Nemoto Naoto
    • Journal Title

      BIO-PROTOCOL

      Volume: 9 Issue: 24

    • DOI

      10.21769/bioprotoc.3457

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A novel immuno-PCR method using cDNA display2019

    • Author(s)
      Anzai Hiroki、Terai Takuya、Jayathilake Chathuni、Suzuki Takeru、Nemoto Naoto
    • Journal Title

      Analytical Biochemistry

      Volume: - Pages: 1-6

    • DOI

      10.1016/j.ab.2019.04.017

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Selection of peptides that associate with dye-conjugated solid surfaces in a pH-dependent manner using cDNA display2019

    • Author(s)
      Takuya Terai, Hiroki Anzai, and Naoto Nemoto
    • Journal Title

      ACS Omega

      Volume: 4 Issue: 4 Pages: 7378-7384

    • DOI

      10.1021/acsomega.9b00631

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Synthesis of unsymmetrical Si-rhodamine fluorophores and application to a far-red to near-infrared fluorescence probe for hypoxia2018

    • Author(s)
      Hanaoka Kenjiro、Kagami Yu、Piao Wen、Myochin Takuya、Numasawa Koji、Kuriki Yugo、Ikeno Takayuki、Ueno Tasuku、Komatsu Toru、Terai Takuya、Nagano Tetsuo、Urano Yasuteru
    • Journal Title

      Chemical Communications

      Volume: 54 Issue: 50 Pages: 6939-6942

    • DOI

      10.1039/c8cc02451k

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of a Series of Practical Fluorescent Chemical Tools To Measure pH Values in Living Samples2018

    • Author(s)
      Takahashi Shodai、Kagami Yu、Hanaoka Kenjiro、Terai Takuya、Komatsu Toru、Ueno Tasuku、Uchiyama Masanobu、Koyama-Honda Ikuko、Mizushima Noboru、Taguchi Tomohiko、Arai Hiroyuki、Nagano Tetsuo、Urano Yasuteru
    • Journal Title

      Journal of the American Chemical Society

      Volume: 印刷中 Issue: 18 Pages: 5925-5933

    • DOI

      10.1021/jacs.8b00277

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] cDNA display法によるユビキチン化酵素(E3)基質配列のスクリーニング手法の開発研究2022

    • Author(s)
      劉建和、寺井琢也、CAMPBELL Robert
    • Organizer
      日本化学会 第102春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ピペラジン誘導体と HaloTag-緑色蛍光タンパク質(GFP)融合タン パク質を用いた二酸化炭素検出蛍光バイオセンサーの開発2022

    • Author(s)
      柳町拓海、Kelvin Tsao、Wenchao Zhu、寺井琢也、Robert E. Campbell
    • Organizer
      日本化学会 第102春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Rapid construction of L-lactate biosensor color variants by transposon-mediated insertion2022

    • Author(s)
      Fu Chai, Karl Matthew Lin, Yusuke Nasu, Takuya Terai, Robert E. Campbell
    • Organizer
      日本化学会 第102春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 細胞内ナトリウムイオンのイメージングを目指した蛍光タンパク質有機分子融合型センサーの開発2022

    • Author(s)
      竹内 志織、Wenchao Zhu、寺井 琢也、Robert Campbell
    • Organizer
      日本化学会 第102春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 小分子キレーターと蛍光タンパク質を用いた化学遺伝学的Ca2+センサーの開発2022

    • Author(s)
      朱 文超、寺井 琢也、那須 雄介、Robert Campbell
    • Organizer
      日本化学会 第102春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 指向性進化を活用した新規 chemi-geneticカルシウム蛍光センサーの開発2021

    • Author(s)
      寺井 琢也、朱 文超、程 大洲、那須 雄介、CAMPBELL Robert
    • Organizer
      第15回 バイオ関連化学シンポジウム
    • Related Report
      2020 Annual Research Report
  • [Presentation] Photoactive Yellow Protein タグを用いたchemi-genetic蛍光カルシウムイオンセンサーの開発2021

    • Author(s)
      門屋 颯人、那須 雄介, 寺井 琢也, Campbell Robert
    • Organizer
      第15回 バイオ関連化学シンポジウム
    • Related Report
      2020 Annual Research Report
  • [Presentation] Prototype Screening of HaloTag-based Chemigenetic Indicators2021

    • Author(s)
      Dazhou Cheng, Wenchao Zhu, Takuya Terai, Yusuke Nasu, Robert E. Campbell
    • Organizer
      第15回 バイオ関連化学シンポジウム
    • Related Report
      2020 Annual Research Report
  • [Presentation] Development of a new type of chemi-genetic calcium ion indicator2021

    • Author(s)
      Wenchao Zhu, Takuya Terai, Yusuke Nasu, Robert E. Campbell
    • Organizer
      Pacifichem 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In vitro selection of polypeptides using cDNA display technology2021

    • Author(s)
      Takua Terai, Naoto Nemoto
    • Organizer
      Pacifichem 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chemi-genetic fluorescent probes for visualizing local dynamics of metal ions2021

    • Author(s)
      Takuya Terai, Tomoya Hirata, Ryo Taguchi, Wenchao Zhu, Yasuteru Urano, Robert Earl Campbell
    • Organizer
      Pacifichem 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Self-complementing split fluorescent protein-based biosensors for calcium ion2021

    • Author(s)
      Issei Yamaguchi, Yusuke Nasu, Takuya Terai, Robert E Campbell
    • Organizer
      Pacifichem 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] cDNA display 技術を活用したプロテアーゼ蛍光プローブの開発2021

    • Author(s)
      寺井 琢也、藤谷 聡、根本 直人
    • Organizer
      日本化学会 第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Towards a chemigenetic calcium ion sensor based on an engineered calmodulin and an environmentally sensitive synthetic dye fluorophore2021

    • Author(s)
      Peter Wojnicki, Kelvin Tsao, Yusuke Nasu, Takuya Terai, Robert Earl Campbell
    • Organizer
      日本化学会 第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] cDNA display技術を活用した酵素基質ペプチドの網羅探索2020

    • Author(s)
      寺井琢也、藤谷聡、根本直人
    • Organizer
      日本化学会 第100春季年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 核酸光架橋を利用した新規ペプチドアプタマー探索法の開発2020

    • Author(s)
      寺井琢也、小池知幸、根本直人
    • Organizer
      日本薬学会第140年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 光架橋塩基を活用した新規ペプチドアプタマー探索法の基盤開発2019

    • Author(s)
      小池知幸、寺井琢也、根本直人
    • Organizer
      日本ケミカルバイオロジー学会第14回年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 分子夾雑系内淘汰によるIL-17A結合ペプチドの取得2019

    • Author(s)
      寺井琢也、安齋宏紀、根本直人
    • Organizer
      日本ケミカルバイオロジー学会第14回年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] cDNA display法を用いたpH感受性色素結合ペプチドの探索とタンパク質精製への応用2019

    • Author(s)
      寺井琢也、安齋宏紀、山田陸、根本直人
    • Organizer
      第13回バイオ関連化学シンポジウム2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] cDNA display法によるプロテアーゼ基質ペプチドの網羅的スクリーニング2019

    • Author(s)
      藤谷聡、寺井琢也、根本直人
    • Organizer
      第13回バイオ関連化学シンポジウム2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Functionalization of liposomes using artificially evolved peptides against lipid membranes2019

    • Author(s)
      Takuya Terai, Shota Kobayashi, Yuki Yoshikawa, Yasuhito Utsugi, Naoto Nemoto
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] cDNA displayの光架橋によるペプチドアプタマー探索の基盤研究2019

    • Author(s)
      寺井琢也、小池知幸、根本直人
    • Organizer
      新学術領域「分子夾雑の生命化学」第2回関東地区シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] A cDNA display mediated novel immuno-PCR method2019

    • Author(s)
      Chathuni Jayathilate, Hiroki Anzai, Takuya Terai, Naoto Nemoto
    • Organizer
      Next Generation Protein Analysis and Detection (3rd ed.)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] cDNA display法を用いた夾雑環境下での試験管内淘汰2019

    • Author(s)
      安齋 宏紀、根本 直人、寺井 琢也
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] In vitro selection of peptide aptamers that recognize a specific conformation of an organic dye2019

    • Author(s)
      寺井 琢也、安齋 宏紀、山田 陸、根本 直人
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 進化分子工学による低分子認識ポリペプチドの開発2019

    • Author(s)
      寺井 琢也、安齋 宏紀、山田 陸、根本 直人
    • Organizer
      Future Trend in Polymer Science 2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] pH応答型タンパク質精製システムを目指した低分子結合ペプチドの探索研究2018

    • Author(s)
      山田 陸、安齋 宏紀、寺井 琢也、根本 直人
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] cDNA display法を用いたプロテアーゼの基質探査法の開発2018

    • Author(s)
      藤谷 聡、寺井 琢也、根本 直人
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Development of Phenolphthalein Binding Peptide Aptamers Using cDNA Display2018

    • Author(s)
      Hiroki Anzai, Riku Yamada, Takuya Terai, Naoto Nemoto
    • Organizer
      10th International Peptide Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Remarks] 東京大学大学院理学系研究科化学専攻生体分子化学研究室ホームページ

    • URL

      https://www.chem.s.u-tokyo.ac.jp/campbell/

    • Related Report
      2020 Annual Research Report
  • [Remarks] 埼玉大学工学部応用化学科根本研究室ホームページ

    • URL

      http://park.saitama-u.ac.jp/~nemoto/

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
  • [Patent(Industrial Property Rights)] A novel immune-PCR method using cDNA display2020

    • Inventor(s)
      根本直人、安斎宏紀、鈴木武尊、熊地重文、寺井琢也
    • Industrial Property Rights Holder
      埼玉大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2020
    • Related Report
      2019 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] 光架橋塩基を活用した、新規ペプチドアプタマー探索用標的モジュール、新規ペプチドアプタマー探索用リンカー及びそれらを用いる新規ペプチドアプタマーの探索方法2020

    • Inventor(s)
      根本直人、寺井琢也
    • Industrial Property Rights Holder
      埼玉大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2020-043550
    • Filing Date
      2020
    • Related Report
      2019 Annual Research Report
  • [Patent(Industrial Property Rights)] 分子精製用リガンド、分子精製用タグペプチド及びこれらを用いた分子精製方法2018

    • Inventor(s)
      根本直人、寺井琢 也、安齋宏紀、山田 陸
    • Industrial Property Rights Holder
      埼玉大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2018-162831
    • Filing Date
      2018
    • Related Report
      2018 Annual Research Report

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

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