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In-cell protein crystallization for structure analysis

Research Project

Project/Area Number 20K21244
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 37:Biomolecular chemistry and related fields
Research InstitutionTokyo Institute of Technology

Principal Investigator

Takafumi Ueno  東京工業大学, 生命理工学院, 教授 (70332179)

Project Period (FY) 2020-07-30 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2021: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2020: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Keywordsタンパク質結晶 / タンパク質集合体 / 結晶構造解析 / 細胞内結晶化 / タンパク質工学 / タンパク質結晶構造解析 / 細胞内タンパク質結晶 / 多孔性材料
Outline of Research at the Start

本研究では、単独では構造決定が困難な標的タンパク質を遺伝子的に融合した多孔性タンパク質複合結晶を細胞内結晶化により合成し、標的タンパク質の高分解能構造決定の実現に挑む。
そこで、研究期間内に、
(1) 多孔性タンパク質結晶の細胞内結晶化と最適化
(2) 標的タンパク質を融合した多孔性タンパク質結晶の細胞内合成と構造決定
(3) 迅速構造解析に向けた大腸菌を用いる標的タンパク質融合多孔性タンパク質結晶合成を達成する。

Outline of Final Research Achievements

The determination of high-resolution protein structures has attracted attention in various fields, from life science to pharmaceutical applications. However, the purification of proteins remains a major common problem that has not yet been solved. In this study, we attempted to realize high-resolution structure determination of target proteins by intracellular crystallization of porous protein crystals fused with target proteins with pores of several nm in diameter. Target protein-fused porous protein crystals were synthesized in living cells. By fusing the target protein to a specific site of the template crystalline protein, the structure was determined by using the microcrystal beamline of a large synchrotron facility.

Academic Significance and Societal Importance of the Research Achievements

近年の結晶構造解析装置の急速な進歩に伴い、国内外でも数μmサイズの細胞内で結晶化するタンパク質の構造解析も報告されつつある。しかしながら、エンジニアリングしたタンパク質の結晶を細胞内合成し構造決定に成功した例は、数例のみである。本研究は、細胞内タンパク質結晶化、標的タンパク質融合多孔性タンパク結晶化と超微小結晶構造解析を一貫して行うことによりはじめて達成できる。得られる成果は生命現象の理解から医薬応用まで様々な分野で渇望されている高分解能タンパク質構造の迅速決定を可能とし、その高い社会的インパクトとニーズにより、新しい生体分子化学の領域を切り開くと考えられる。

Report

(3 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • Research Products

    (56 results)

All 2022 2021 2020 Other

All Int'l Joint Research (3 results) Journal Article (11 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 11 results,  Open Access: 2 results) Presentation (37 results) (of which Int'l Joint Research: 1 results,  Invited: 3 results) Book (1 results) Remarks (2 results) Patent(Industrial Property Rights) (2 results) (of which Overseas: 2 results)

  • [Int'l Joint Research] TATA基礎科学研究(インド)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] 南洋理工大学(シンガポール)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] 清華大学(中国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Controlled Uptake of an Iridium Complex inside Engineered apo‐Ferritin Nanocages: Study of Structure and Catalysis**2022

    • Author(s)
      Taher Mohd、Maity Basudev、Nakane Taiki、Abe Satoshi、Ueno Takafumi、Mazumdar Shyamalava
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 61 Issue: 13

    • DOI

      10.1002/anie.202116623

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Importance of the Subunit?Subunit Interface in Ferritin Disassembly: A Molecular Dynamics Study2022

    • Author(s)
      Li Zhipeng、Maity Basudev、Hishikawa Yuki、Ueno Takafumi、Lu Diannan
    • Journal Title

      Langmuir

      Volume: 38 Issue: 3 Pages: 1106-1113

    • DOI

      10.1021/acs.langmuir.1c02753

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Engineering of protein crystals for use as solid biomaterials2022

    • Author(s)
      Kojima Mariko、Abe Satoshi、Ueno Takafumi
    • Journal Title

      Biomaterials Science

      Volume: 10 Issue: 2 Pages: 354-367

    • DOI

      10.1039/d1bm01752g

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein Needles Designed to Self‐Assemble through Needle Tip Engineering2022

    • Author(s)
      Kikuchi Kosuke、Fukuyama Tatsuya、Uchihashi Takayuki、Furuta Tadaomi、Maeda Yusuke T.、Ueno Takafumi
    • Journal Title

      Small

      Volume: 18 Issue: 10 Pages: 2106401-2106401

    • DOI

      10.1002/smll.202106401

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic Behavior of Cargo Proteins Regulated by Linker Peptides on a Protein Needle Scaffold2022

    • Author(s)
      Nguyen Que D.、Kikuchi Kosuke、Kojima Mariko、Ueno Takafumi
    • Journal Title

      Chemistry Letters

      Volume: 51 Issue: 1 Pages: 73-76

    • DOI

      10.1246/cl.210599

    • NAID

      130008137585

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Design of a gold clustering site in an engineered apo-ferritin cage2022

    • Author(s)
      Lu Chenlin、Maity Basudev、Peng Xue、Ito Nozomi、Abe Satoshi、Sheng Xiang、Ueno Takafumi、Lu Diannan
    • Journal Title

      Communications Chemistry

      Volume: 5 Issue: 1 Pages: 1-11

    • DOI

      10.1038/s42004-022-00651-1

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Solubility enhancement of poorly water soluble domperidone by complexation with the large ring cyclodextrin2021

    • Author(s)
      Ismail Abbas、Kerdpol Khanittha、Rungrotmongkol Thanyada、Tananuwong Kanitha、Ueno Takafumi、Ekasit Sanong、Muangsin Nongnuj、Krusong Kuakarun
    • Journal Title

      International Journal of Pharmaceutics

      Volume: 606 Pages: 120909-120909

    • DOI

      10.1016/j.ijpharm.2021.120909

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Design of in‐cell protein crystal for environmentally responsive construction of a supramolecular filament2021

    • Author(s)
      Abe Satoshi、Pham Thuc Toan、Negishi Hashiru、Yamashita Keitaro、Hirata Kunio、Ueno Takafumi
    • Journal Title

      Angewandte Chemie International Edition

      Volume: - Issue: 22 Pages: 12341-12345

    • DOI

      10.1002/anie.202102039

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] The Versatile Manipulations of Self-Assembled Proteins in Vaccine Design2021

    • Author(s)
      Nguyen Que Dan、Kikuchi Kosuke、Maity Basudev、Ueno Takafumi
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Issue: 4 Pages: 1934-1934

    • DOI

      10.3390/ijms22041934

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] In-Cell Engineering of Protein Crystals with Nanoporous Structures for Promoting Cascade Reactions2021

    • Author(s)
      Nguyen Tien K.、Abe Satoshi、Kasamatsu Makoto、Maity Basudev、Yamashita Keitaro、Hirata Kunio、Kojima Mariko、Ueno Takafumi
    • Journal Title

      ACS Applied Nano Materials

      Volume: 4 Issue: 2 Pages: 1672-1681

    • DOI

      10.1021/acsanm.0c03129

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Single-molecule level dynamic observation of disassembly of the apo-ferritin cage in solution2020

    • Author(s)
      Maity Basudev、Li Zhipeng、Niwase Kento、Ganser Christian、Furuta Tadaomi、Uchihashi Takayuki、Lu Diannan、Ueno Takafumi
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 22 Issue: 33 Pages: 18562-18572

    • DOI

      10.1039/d0cp02069a

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Functionalization of amyloid beta peptide into ferritin cage and observation of the cage disassembly.2022

    • Author(s)
      Basudev Maity, Shiori Kameyama, Satoshi Abe, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] Analysis of Dynamic Behavior of Aromatic Interactions using Protein Cages2022

    • Author(s)
      Yuki Hishikawa, Asuka Asanuma, Basudev Maity, Satoru Nagatoishi, Kouhei Tsumoto, Satoshi Abe, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] Dynamics structural analysis of miniprotein by in-cell crystal engineering2022

    • Author(s)
      Mariko Kojima, Yuki Hishikawa, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Akio Kitao, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] 無細胞タンパク質結晶エンジニアリングによる構造解析2022

    • Author(s)
      田中 潤子, 安部 聡, 金丸 周司, 上野 隆史
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] In-cell crystal engineering for the development of solid biomaterials2022

    • Author(s)
      Satoshi Abe, Mariko Kojima, Junko Tanaka, Yuto Nakasuji, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] Structural investigation of a semi-clathrate hydrate formation using porous ferritin crystals2022

    • Author(s)
      Jiaxin Tian, Basudev Maity, Satoshi Abe, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] Design of the heteroepitaxial vertical assembly of asymmetric protein needles2022

    • Author(s)
      Kosuke Kikuchi, Takafumi Ueno
    • Organizer
      102nd CSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] タンパク質ケージ内芳香族クラスターによる蛍光分子特性制御2021

    • Author(s)
      菱川湧輝, MAITYBASUDEV, 吉沢道人, 森本 正和, 安部聡, 上野隆史
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] 迅速タンパク質結晶化とサブミクロン結晶構造解析2021

    • Author(s)
      安部 聡, 田中潤子, 上野隆史
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] 無細胞タンパク質合成を利用した結晶化とサブミクロン結晶構造解析2021

    • Author(s)
      安部聡, 上野隆史
    • Organizer
      70th Symposium on Macromolecules
    • Related Report
      2021 Annual Research Report
  • [Presentation] Effect of Alanine substitution at the 2-fold symmetric interface of the ferritin cage2021

    • Author(s)
      Jiaxin Tian, Basudev Maity, Satoshi Abe, Kenji Yasuda, Takeshi Murata, Takafumi Ueno
    • Organizer
      70th Symposium on Macromolecules
    • Related Report
      2021 Annual Research Report
  • [Presentation] βヘリックスタンパク質分子針の末端設計による二次元集合制御2021

    • Author(s)
      菊池 幸祐, 福山達也, 古田 忠臣, 内橋 貴之, 前多裕介, 上野 隆史
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] タンパク質分子針の末端構造設計による二次元集合パターン制御2021

    • Author(s)
      菊池 幸祐, 福山達也, 古田 忠臣, 前多裕介, 内橋 貴之, 上野 隆史
    • Organizer
      第1回発動分子科学研究会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 細胞内タンパク質結晶を利用した天然変性タンパク質の構造解析2021

    • Author(s)
      小島摩利子, 安部聡, 上野隆史
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] DESIGN OF IN-CELL PROTEIN CRYSTALS FOR DEVELOPMENT OF BIO-SOLID MATERIALS2021

    • Author(s)
      Satoshi Abe, Takafumi Ueno
    • Organizer
      22nd American Conference on Crystal Growth and Epitaxy (ACCGE-22)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] タンパク質ケージ結晶を用いた芳香族クラスターの動的挙動解析2021

    • Author(s)
      菱川湧輝, 野谷大樹, MAITYBASUDEV, 長門石 曉, 津本浩平, 安部聡, 上野隆史
    • Organizer
      The 70th SPSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] タンパク質分子針の末端設計による二次元集合パターン制御2021

    • Author(s)
      菊池幸祐, 福山達也, 古田忠臣, 前多裕介, 内橋貴之, 上野隆史
    • Organizer
      The 70th SPSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] The role of helix modification in building hybrid ferritin cages2021

    • Author(s)
      Jiaxin Tian, Kenji Yasuda, Basudev Maity, Satoshi Abe, Takeshi Murata, Takafumi Ueno
    • Organizer
      The 70th SPSJ Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] β-ヘリックス人工分子針の動的集合設計2021

    • Author(s)
      菊池幸祐, 福山達也, Maity Basudev, 古田忠臣, 前多裕介, 内橋貴之, 上野隆史
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質ケージ内における芳香族分子集積と反応制御2021

    • Author(s)
      菱川湧輝, 野谷大樹, Basudev Maity, 安部聡, 上野隆史
    • Organizer
      日本化学会第101回春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Energy Analysis of Miniprotein by in Vivo Protein Crystallization2021

    • Author(s)
      小島 摩利子, 菱川 湧輝, 安部 聡, 古田 忠臣, Tran Phuoc Duy, 北尾 彰朗, 上野 隆史
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Design of the two-dimensional protein assembly patterns by β-helical protein needle2020

    • Author(s)
      菊池 幸祐, 上野 隆史
    • Organizer
      第69回高分子討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] 無細胞タンパク質合成による微小結晶構造解析2020

    • Author(s)
      小島摩利子, 安部聡, 上野隆史
    • Organizer
      第14回バイオ関連化学シンポジウム2020
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質ケージを利用した芳香族クラスターの構築と外来分子内包2020

    • Author(s)
      菱川湧輝, 野谷大樹, Basudev Maity, 安部聡, 上野隆史
    • Organizer
      発動分子科学第5回領域会議
    • Related Report
      2020 Research-status Report
  • [Presentation] Construction of Fibril Protein Assemblies From Engineered Protein Crystals2020

    • Author(s)
      PHAM Toan Thuc, 安部 聡, 根岸 走, 上野 隆史
    • Organizer
      69th Symposium on Macromolecules
    • Related Report
      2020 Research-status Report
  • [Presentation] Construction of Filament Protein Assembly From Autonomous Cross-Linked Crystals2020

    • Author(s)
      PHAM Toan Thuc, 安部 聡, 根岸 走, 上野 隆史
    • Organizer
      14th Bio-related Chemistry Symposium
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質結晶工学による新機能材料2020

    • Author(s)
      上野隆史
    • Organizer
      第28回ポリマー材料フォーラム
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] GPCR 内包を目指したタンパク質ハイブリッド結晶の構築2020

    • Author(s)
      田中潤子, 安部聡, 長田俊哉, 上野隆史
    • Organizer
      第 10 回 CSJ 化学フェスタ
    • Related Report
      2020 Research-status Report
  • [Presentation] Molecular design of protein needle for norovirus vaccine2020

    • Author(s)
      Nguyen Dan Que, 上野 隆史
    • Organizer
      第 10 回 CSJ 化学フェスタ
    • Related Report
      2020 Research-status Report
  • [Presentation] Protein Crystals for Designing Multiple Nanofunctions2020

    • Author(s)
      上野 隆史
    • Organizer
      The 58th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 細胞内タンパク質結晶化の最適化と迅速構造解析2020

    • Author(s)
      安部 聡, 小島摩利子, 小暮遼河, 上野隆史
    • Organizer
      第14回バイオ関連シンポジウム
    • Related Report
      2020 Research-status Report
  • [Presentation] フェリチンケージのサブユニット界面を利用した多核金結合サイトの構築2020

    • Author(s)
      菱川湧輝, Basudev Maity, 安部聡, Diannan Lu, 上野隆史
    • Organizer
      第70回錯体化学会討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質ケージの内部空間設計による芳香族クラスターの構築2020

    • Author(s)
      菱川湧輝, 野谷大樹, Basudev Maity, 安部聡, 上野隆史
    • Organizer
      第14回バイオ関連化学シンポジウム
    • Related Report
      2020 Research-status Report
  • [Presentation] In vivo Protein Crystal Engineering for Structure Analysis of Meta-stable State Mini-protein2020

    • Author(s)
      小島 摩利子, 安部 聡, 上野 隆史
    • Organizer
      第69回高分子討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質の迅速結晶化とサブミクロン結晶の構造解析2020

    • Author(s)
      安部 聡, 小島摩利子, 上野隆史
    • Organizer
      第69回高分子討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] かご状タンパク質フェリチンのサブユニット界面における金集積機構の解明2020

    • Author(s)
      菱川湧輝, Basudev Maity, 安部聡, Diannan Lu, 上野隆史
    • Organizer
      第69回高分子学会年次大会
    • Related Report
      2020 Research-status Report
  • [Presentation] タンパク質の細胞内迅速・微量結晶化と構造解析2020

    • Author(s)
      安部 聡, 小島摩利子, 小暮遼河, 上野隆史
    • Organizer
      第69回高分子学会年次大会
    • Related Report
      2020 Research-status Report
  • [Book] Cell-Inspired Materials and Engineering2021

    • Author(s)
      H. Tabe and T. Ueno
    • Total Pages
      257
    • Publisher
      Springer
    • Related Report
      2021 Annual Research Report
  • [Remarks] 上野研究室

    • URL

      http://www.ueno.bio.titech.ac.jp/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] Ueno Lab

    • URL

      http://www.ueno.bio.titech.ac.jp/index.html

    • Related Report
      2020 Research-status Report
  • [Patent(Industrial Property Rights)] タンパク質結晶の製造方法及び結晶構造解析方法2021

    • Inventor(s)
      上野 隆史/安部 聡/小島
    • Industrial Property Rights Holder
      上野 隆史/安部 聡/小島
    • Industrial Property Rights Type
      特許
    • Filing Date
      2021
    • Related Report
      2020 Research-status Report
    • Overseas
  • [Patent(Industrial Property Rights)] タンパク質固体材料の製造2020

    • Inventor(s)
      上野 隆史/安部 聡/小島 摩利子
    • Industrial Property Rights Holder
      上野 隆史/安部 聡/小島 摩利子
    • Industrial Property Rights Type
      特許
    • Filing Date
      2020
    • Related Report
      2020 Research-status Report
    • Overseas

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Published: 2020-08-03   Modified: 2023-01-30  

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