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Development of functional supramolecular crystalline nanomaterials based on rational design of super-quaternary structures of protein nanobuilding block complexes

Research Project

Project/Area Number 17KK0104
Research Category

Fund for the Promotion of Joint International Research (Fostering Joint International Research)

Allocation TypeMulti-year Fund
Research Field Bio-related chemistry
Research InstitutionShinshu University

Principal Investigator

Arai Ryoichi  信州大学, 学術研究院繊維学系, 准教授 (50344023)

Project Period (FY) 2018 – 2023
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥13,260,000 (Direct Cost: ¥10,200,000、Indirect Cost: ¥3,060,000)
Keywordsタンパク質ナノブロック / タンパク質複合体 / 人工タンパク質デザイン / タンパク質工学 / タンパク質結晶化 / ナノマテリアル / 機能性超分子複合体 / 計算科学 / 人工タンパク質複合体 / ナノバイオマテリアル / 機能性超分子 / 多孔質ナノマテリアル / タンパク質ナノブロック複合体
Outline of Final Research Achievements

Based on previous protein nanobuilding block research, I stayed in Baker lab at University of Washington for six months to conduct an international collaboration to rationally design and develop crystalline nanobiomaterials with symmetrically assembled artificial protein complexes by incorporating computational science to further develop our research. Using a protein design program, we designed artificial proteins with symmetrically linked complex with forming α-helix domains which constitute two-dimensional sheet-like crystalline nanobiomaterials. From the calculation results, the designed structures of the 2D lattice-like complexes were screened according to the shape complementarity and energy score of the interfaces, and the designed protein sequences to be experimentally tested were selected. These artificial genes were synthesized. The proteins were expressed by E. coli, purified, and their nanoscale structures were examined using electron microscopy.

Academic Significance and Societal Importance of the Research Achievements

以前は実験を基盤とした蛋白質工学及び蛋白質設計改変分野の研究が主体であったが、近年、発展が著しい計算科学を駆使した蛋白質デザイン研究分野を先導するワシントン大学Baker研究室に半年間滞在し、世界トップレベルの環境で国際共同研究を行うことにより、最先端の蛋白質デザイン研究に取り組んだことは、学術的にも意義がある。またその後、この成果や経験を利用して、様々な人工蛋白質の設計開発及び改良等にも継続的に取り組んで一定の成果を上げてきたことにより、将来的にバイオ医薬品等の開発につなげるための基盤となる試みは社会的意義があると考えられる。

Report

(7 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
  • 2018 Research-status Report
  • Research Products

    (44 results)

All 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (1 results) Journal Article (14 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 12 results,  Open Access: 5 results) Presentation (25 results) (of which Int'l Joint Research: 6 results,  Invited: 4 results) Book (1 results) Remarks (3 results)

  • [Int'l Joint Research] University of Washington(米国)2019

    • Year and Date
      2019-04-01
    • Related Report
      2023 Annual Research Report
  • [Journal Article] Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F42023

    • Author(s)
      Kurihara Kodai、Umezawa Koji、Donnelly Ann E.、Sperling Brendan、Liao Guanyu、Hecht Michael H.、Arai Ryoichi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 120 Issue: 38

    • DOI

      10.1073/pnas.2218281120

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Protein Cages and Nanostructures Constructed from Protein Nanobuilding Blocks2023

    • Author(s)
      Kobayashi Naoya、Arai Ryoichi
    • Journal Title

      Methods in Molecular Biology

      Volume: 2671 Pages: 79-94

    • DOI

      10.1007/978-1-0716-3222-2_4

    • ISBN
      9781071632215, 9781071632222
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] One-pot synthesis of fibrillar-shaped functional nanomaterial using microbial transglutaminase2023

    • Author(s)
      Sakono Masafumi、Nakamura Mitsuki、Ohshima Tatsuki、Miyakoshi Ayano、Arai Ryoichi、Minamihata Kosuke、Kamiya Noriho
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: - Issue: 6 Pages: 440-446

    • DOI

      10.1016/j.jbiosc.2023.03.015

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enzymatic fabrication of multifunctional amyloid-based protein assembly2023

    • Author(s)
      Mitsuki Nakamura, Ryoichi Arai, Noriho Kamiya, Masafumi Sakono
    • Journal Title

      Chemistry Letters

      Volume: - Issue: 7 Pages: 538-541

    • DOI

      10.1246/cl.230156

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multi-enzyme Machinery for Chitin Degradation in the Chitinolytic Bacterium Chitiniphilus shinanonensis SAY3T2023

    • Author(s)
      Sato Hiroaki、Sonoda Norie、Nakano Moe、Matsuyama Yuka、Shizume Arisa、Arai Ryoichi、Nogawa Masahiro、Taguchi Goro、Shimosaka Makoto
    • Journal Title

      Current Microbiology

      Volume: 80 Issue: 11 Pages: 360-360

    • DOI

      10.1007/s00284-023-03489-5

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions2023

    • Author(s)
      Ohara Naoya、Kawakami Norifumi、Arai Ryoichi、Adachi Naruhiko、Moriya Toshio、Kawasaki Masato、Miyamoto Kenji
    • Journal Title

      Journal of the American Chemical Society

      Volume: 145 Issue: 1 Pages: 216-223

    • DOI

      10.1021/jacs.2c09537

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans2022

    • Author(s)
      Irumagawa Shin、Hiemori Keiko、Saito Sayoko、Tateno Hiroaki、Arai Ryoichi
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 23 Issue: 2 Pages: 676-676

    • DOI

      10.3390/ijms23020676

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Production of pentaglycine-fused proteins using Escherichia coli expression system without in vitro peptidase treatment2022

    • Author(s)
      Sakono Masafumi、Oshima Tatsuki、Iwakawa Takako、Arai Ryoichi
    • Journal Title

      Protein Expression and Purification

      Volume: 194 Pages: 106068-106068

    • DOI

      10.1016/j.pep.2022.106068

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Rational thermostabilisation of four-helix bundle dimeric de novo proteins2021

    • Author(s)
      Irumagawa Shin、Kobayashi Kaito、Saito Yutaka、Miyata Takeshi、Umetsu Mitsuo、Kameda Tomoshi、Arai Ryoichi
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 7526-7526

    • DOI

      10.1038/s41598-021-86952-2

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Icosahedral 60-meric porous structure of designed supramolecular protein nanoparticle TIP602021

    • Author(s)
      Junya Obata, Norifumi Kawakami, Akihisa Tsutsumi, Erika Nasu, Kenji Miyamoto, Masahide Kikkawa, Ryoichi Arai
    • Journal Title

      Chemical Communications

      Volume: 79 Issue: 79 Pages: 10226-10229

    • DOI

      10.1039/d1cc03114g

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Design of helical linkers for fusion proteins and protein-based nanostructures2021

    • Author(s)
      Ryoichi Arai
    • Journal Title

      Methods in Enzymology

      Volume: 647 Pages: 209-230

    • DOI

      10.1016/bs.mie.2020.10.003

    • ISBN
      9780128208182
    • Related Report
      2020 Research-status Report
  • [Journal Article] Hyperstable De Novo Protein with a Dimeric Bisecting Topology2020

    • Author(s)
      Kimura Naoya、Mochizuki Kenji、Umezawa Koji、Hecht Michael H.、Arai Ryoichi
    • Journal Title

      ACS Synthetic Biology

      Volume: 9 Issue: 2 Pages: 254-259

    • DOI

      10.1021/acssynbio.9b00501

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Design of artificial protein complexes of protein nano-building blocks2019

    • Author(s)
      小林 直也、川上 了史、新井 亮一
    • Journal Title

      生化学

      Volume: 91 Issue: 2 Pages: 255-259

    • DOI

      10.14952/SEIKAGAKU.2019.910255

    • NAID

      40021942521

    • ISSN
      0037-1017
    • Year and Date
      2019-04-25
    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 蛋白質ナノブロックによるレクチン超分子複合体の創出戦略2019

    • Author(s)
      入間川 伸,新井 亮一
    • Journal Title

      医学のあゆみ

      Volume: 269 Pages: 690-696

    • Related Report
      2019 Research-status Report
  • [Presentation] Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F42023

    • Author(s)
      栗原航大, 梅澤公二, Ann E. Donnelly, Michael H. Hecht, 新井亮一
    • Organizer
      第23回日本蛋白質科学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Structures of de novo proteins from a binary-patterned library and the applications to constructing protein nanobuilding blocks2023

    • Author(s)
      Ryoichi Arai
    • Organizer
      Library Design for Protein Engineering 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 人工タンパク質ナノ粒子IP60とレクチンを融合した機能性タンパク質複合体の開発2023

    • Author(s)
      内田翔汰, 川上了史, 舘野 浩章, 新井亮一
    • Organizer
      第46回日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 新規人工酵素Syn-F4エンテロバクチンエステラーゼのX線結晶構造解析2022

    • Author(s)
      栗原航大, 梅澤公二, Ann E. Donnelly, Michael H. Hecht, 新井亮一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Research-status Report
  • [Presentation] イソペプチド結合タグを用いた多価抗体タンパク質ナノブロック複合体の開発2022

    • Author(s)
      髙橋五月, 浅野竜太郎, 山本雷蔵, 迫野昌文, 新井亮一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Research-status Report
  • [Presentation] 多価レクチンナノブロックWA20-ACG複合体の開発2021

    • Author(s)
      入間川 伸,舘野 浩章,新井 亮一
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] 三量体レクチンを用いた蛋白質ナノブロックの自己組織化超分子複合体の創製2021

    • Author(s)
      貝川 はるか,舘野 浩章,新井 亮一
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] Barium ion responsive reversible assembly of protein supramolecule TIP602021

    • Author(s)
      大原 直也,川上 了史,新井 亮一,宮本 憲二
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] 蛋白質ナノブロックによる機能性人工蛋白質複合体の創製に向けて2021

    • Author(s)
      新井 亮一
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Icosahedral 60-meric porous structure of designed protein nanoparticle TIP602021

    • Author(s)
      Ryoichi Arai, Norifumi Kawakami, Junya Obata, Akihisa Tsutsumi, Kenji Miyamoto, Masahide Kikkawa
    • Organizer
      The Protein Society, the 36th Annual Symposium
    • Related Report
      2021 Research-status Report
  • [Presentation] Self-assembling lectin nano-building blocks enhance avidity to glycans through polyvalent effect2021

    • Author(s)
      Shin Irumagawa, Hiroaki Tateno, Ryoichi Arai
    • Organizer
      The Protein Society, the 36th Annual Symposium
    • Related Report
      2021 Research-status Report
  • [Presentation] Self-assembling functional complexes of protein nanobuilding blocks with a trimeric lectin2021

    • Author(s)
      Haruka Kaigawa, Hiroaki Tateno, Ryoichi Arai
    • Organizer
      The Protein Society, the 36th Annual Symposium
    • Related Report
      2021 Research-status Report
  • [Presentation] Structural Basis for Quenchbody (Q-body): Crystal Structures of the Fab Fragment of Anti-Osteocalcin Antibody KTM2192020

    • Author(s)
      Shuma Yazaki, Misaki Komatsu, Jinhua Dong, Hiroshi Ueda, Ryoichi Arai
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Rational Stabilization of Dimeric Four-Helix Bundle De Novo Proteins Using Molecular Dynamics Simulation2020

    • Author(s)
      Shin Irumagawa, Kaito Kobayashi, Yutaka Saito, Takeshi Miyata, Mitsuo Umetsu, Tomoshi Kameda, Ryoichi Arai
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] 分子標的蛍光インジケーターとグルタチオンS-トランスフェラーゼ複合体のX結晶構造解析2020

    • Author(s)
      矢崎 崇真, 岡島 崇文, 瀧 真清, 新井 亮一
    • Organizer
      第14回バイオ関連化学シンポジウム
    • Related Report
      2020 Research-status Report
  • [Presentation] 新規人工酵素Syn-F4エンテロバクチンエステラーゼのX線結晶構造解析2020

    • Author(s)
      栗原 航大, 梅澤 公二, Sha Tao, Ann E Donnelly, Michael H Hecht, 新井 亮一
    • Organizer
      第14回バイオ関連化学シンポジウム
    • Related Report
      2020 Research-status Report
  • [Presentation] 自己組織化レクチンナノブロックWA20-ACG複合体の開発2020

    • Author(s)
      入間川 伸、 舘野 浩章、新井 亮一
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] 人工蛋白質ナノ粒子TIP60の正20面体型60量体多孔質構造2020

    • Author(s)
      小幡 隼也、川上 了史、包 明久、宮本 憲二、吉川 雅英、新井 亮一
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] 三量体レクチンを用いたレクチンナノブロックの自己組織化タンパク質超分子複合体の創製2020

    • Author(s)
      貝川 はるか、舘野 浩章、新井 亮一
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Thermal Reconstruction of Protein Nanobuilding Block Complexes Using an Ultra-Stable de Novo Protein Domain2019

    • Author(s)
      Naoya Kimura, Naoya Kobayashi, Michael H. Hecht, Ryoichi Arai
    • Organizer
      Gordon Research Conference, Proteins
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Thermal Reconstruction of Protein Nano-building Block Complexes Using an Ultra-Stable de Novo Protein Domain2019

    • Author(s)
      Naoya Kimura, Naoya Kobayashi, Ryoichi Arai
    • Organizer
      The Protein Society, 33rd Annual Symposium
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Thermal Reconstruction of Protein Nanobuilding Block Complexes Using an Ultra-Stable de Novo Protein Domain2019

    • Author(s)
      Naoya Kimura, Naoya Kobayashi, Michael H. Hecht, Ryoichi Arai
    • Organizer
      RosettaCON 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Thermal Reconstruction of Protein Nanobuilding Block Complexes Using an Ultra-Stable de Novo Protein Domain2019

    • Author(s)
      Naoya Kimura, Naoya Kobayashi, Michael H. Hecht, Ryoichi Arai
    • Organizer
      Innovations in Imaging for the Life Sciences
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] タンパク質ナノブロックによる自己組織化ナノ構造複合体の創製2019

    • Author(s)
      新井 亮一
    • Organizer
      第26回ペプチドフォーラム
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Self-Assembling Supramolecular Nanostructures Constructed from Protein Nano-Building Blocks2019

    • Author(s)
      Ryoichi Arai
    • Organizer
      IPNF 2019 (International Powder and Nanotechnology Forum)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Book] クライオ電子顕微鏡ハンドブック(第4章第6節人工設計タンパク質ナノ粒子TIP60の立体構造解析)2023

    • Author(s)
      新井亮一,川上了史,小幡隼也,包明久,那須英里圭,宮本憲二,吉川雅英
    • Total Pages
      10
    • Publisher
      エヌ・ティー・エス
    • ISBN
      9784860438043
    • Related Report
      2022 Research-status Report
  • [Remarks] 信州大学 新井亮一研究室

    • URL

      http://fiber.shinshu-u.ac.jp/arai/index.html

    • Related Report
      2023 Annual Research Report 2022 Research-status Report 2021 Research-status Report 2020 Research-status Report
  • [Remarks] 信州大学 研究者総覧 新井亮一

    • URL

      http://soar-rd.shinshu-u.ac.jp/profile/ja.OVkUjFkV.html

    • Related Report
      2022 Research-status Report
  • [Remarks] 信州大学新井亮一研究室ホームページ

    • URL

      http://fiber.shinshu-u.ac.jp/arai/index.html

    • Related Report
      2019 Research-status Report

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Published: 2018-01-25   Modified: 2025-01-30  

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