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Computational design and thermal stability analysis of oligomeric proteins

Research Project

Project/Area Number 18K14668
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 43040:Biophysics-related
Research InstitutionCenter for Novel Science Initatives, National Institutes of Natural Sciences

Principal Investigator

Kobayashi Naoya  大学共同利用機関法人自然科学研究機構(新分野創成センター、アストロバイオロジーセンター、生命創成探究, 生命創成探究センター, 特任研究員 (60781945)

Project Period (FY) 2018-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2019: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsタンパク質デザイン / オリゴマー構造 / 改変酵素 / 熱安定性解析 / 物性スクリーニング / ペプチドバーコーディング / 超並列デザイン / 酵素 / オリゴマーデザイン / タンパク質安定化 / 相互作用面デザイン / 計算機デザイン
Outline of Final Research Achievements

The aim of this study is to develop a fundamental technique to clarify how oligomer formation contributes to structural stabilization using a synthetic biological approach. For this purpose, we attempted to develop a method for predicting thermally stabilized mutants by computer design, to analyze the thermal stability of rationally designed proteins, and to develop a technique for creating oligomers from monomeric structures by computer design.
The methods developed in this work, such as thermal stabilization mutant prediction methods, diverse symmetry oligomer structure generation programs, and physicochemical property screening systems using peptide barcodes, provide fundamental technologies for high-throughput analysis of higher-order structure formation and structural stability of proteins.

Academic Significance and Societal Importance of the Research Achievements

本研究では、タンパク質の熱安定性や会合状態を合理的に改変するための計算機技術や改変したタンパク質の物性をハイスループット解析する技術を開発した。これらの技術を組合せ、応用することにより、創ることを通してタンパク質の高次構造形成への理解を深めることができるようになる。また、これまで天然になかった立体構造とアミノ酸配列からなるタンパク質を創り出せることにより、新たなタンパク質機能の発現が期待できる。

Report

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

    (10 results)

All 2020 2019 2018

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

  • [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 Annual Research Report 2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks2018

    • Author(s)
      Kobayashi Naoya、Inano Kouichi、Sasahara Kenji、Sato Takaaki、Miyazawa Keisuke、Fukuma Takeshi、Hecht Michael H、Song Chihong、Murata Kazuyoshi、Arai Ryoichi
    • Journal Title

      ACS Synthetic Biology

      Volume: 7 Issue: 5 Pages: 1381-1394

    • DOI

      10.1021/acssynbio.8b00007

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Self-assembling Supramolecular Complex Nanostructures Constructed from <i>de Novo</i> Protein Nanobuilding Blocks2018

    • Author(s)
      小林直也、新井亮一
    • Journal Title

      Seibutsu Butsuri

      Volume: 58 Issue: 6 Pages: 313-315

    • DOI

      10.2142/biophys.58.313

    • NAID

      130007521690

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Toward creation of artificial proteins self-assembling into diverse symmetric structures: computational design and experimental screening2020

    • Author(s)
      Naoya Kobayashi, Nobuyasu Koga
    • Organizer
      The 1st International Symposium on Molecular Engine
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 多様なタンパク質複合体構造の合理デザインに向けて2018

    • Author(s)
      小林直也, 古賀信康
    • Organizer
      第18回日本蛋白質科学会年会(新潟)
    • Related Report
      2018 Research-status Report
  • [Presentation] Toward design of thermostable beta-glucosidase with structure-based sequence profile2018

    • Author(s)
      Kobayashi, N., Minami, S., Uchiyama, T., Sunagawa, N., Igarashi, K., and Koga, N.
    • Organizer
      International Symposium on "Artificial Cell Reactor Science and Technology" (Tokyo)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Cumulative thermostabilization of beta-glucosidase with structure-based sequence profile information2018

    • Author(s)
      Kobayashi, N.
    • Organizer
      分子研研究会「New Frontier in Protein Design & Engineering」(愛知)
    • Related Report
      2018 Research-status Report
  • [Presentation] Toward design of thermostable beta-glucosidase with structure-based sequence profile2018

    • Author(s)
      Kobayashi, N., Minami, S., Uchiyama, T., Sunagawa, N., Igarashi, K., Noji, H., and Koga, N.
    • Organizer
      第56回日本生物物理学会年会 (岡山)
    • Related Report
      2018 Research-status Report
  • [Presentation] 立体構造に基づく配列プロファイルを利用したβ-グルコシダーゼの熱安定化2018

    • Author(s)
      小林直也, 南慎太朗, 小杉貴洋, 内山拓, 砂川直輝, 五十嵐圭日子, 野地博行, 古賀信康
    • Organizer
      最終成果報告会―人工細胞リアクタが拓くイノベーション―(東京)
    • Related Report
      2018 Research-status Report
  • [Patent(Industrial Property Rights)] 耐熱性βグルコシダーゼ2018

    • Inventor(s)
      古賀信康, 小林直也, 南慎太朗
    • Industrial Property Rights Holder
      自然科学研究機構
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2018-172810
    • Filing Date
      2018
    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2021-02-19  

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