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Development of Protein Design Methods and Their Experimental Verification

Research Project

Project/Area Number 18H02395
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Zhang Kam  国立研究開発法人理化学研究所, 生命機能科学研究センター, チームリーダー (60558906)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2020: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2019: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2018: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Keywords計算タンパク質設計 / Protein design / Computation / Evolutionary algorithm / Protein folding / Repeat proteins / Fragment assembly / Protein Design / EDA method
Outline of Final Research Achievements

We have developed a computational protein design method with backbone flexibility, which exploits local structural environments in known protein structures together with energy to guide sequence design. It is based on customized libraries of non-contiguous in-contact amino acid residue motifs. We have applied this new method in the design of a four-fold symmetric eight-bladed beta-propeller and a two-fold symmetric double-psi beta-barrel core of RNA polymerase. These designs have been validated by X-ray crystallography that the experimentally determined structures closely matches the computationally design models.

Academic Significance and Societal Importance of the Research Achievements

私たちが開発した柔軟なバックボーン タンパク質設計法は、現在の最先端のタンパク質設計の可能性を拡張しました。 それは、新しいバイオ センサー、治療法、および診断法の開発に大きな可能性を示しています。 RNA ポリメラーゼの 2 重対称ダブル psi ベータ バレル コアの成功した設計は、現代の複雑なタンパク質は、祖先のより単純なタンパク質からの遺伝子重複、融合、および多様化イベントから進化した可能性があるという考えを支持しています。

Report

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

Research Products

(5 results)

All 2021 2020 2019 2018

All Journal Article (5 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 5 results,  Open Access: 2 results)

  • [Journal Article] Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking2021

    • Author(s)
      Berenger Francois、Kumar Ashutosh、Zhang Kam Y. J.、Yamanishi Yoshihiro
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 61 Pages: 1-12

    • DOI

      10.1021/acs.jcim.0c01452

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A protein sequence fitness function for identifying natural and nonnatural proteins2020

    • Author(s)
      Kaushik Rahul、Zhang Kam Y. J.
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: 88 Pages: 1271-1284

    • DOI

      10.1002/prot.25900

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A structural homology approach for computational protein design with flexible backbone2019

    • Author(s)
      Simoncini David、Zhang Kam Y J、Schiex Thomas、Barbe Sophie
    • Journal Title

      Bioinformatics

      Volume: 35 Pages: 2418-2426

    • DOI

      10.1093/bioinformatics/bty975

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Computational design of symmetrical eight-bladed β-propeller proteins2019

    • Author(s)
      Noguchi Hiroki、Addy Christine、Simoncini David、Wouters Staf、Mylemans Bram、Van Meervelt Luc、Schiex Thomas、Zhang Kam Y. J.、Tame Jeremy R. H.、Voet Arnout R. D.
    • Journal Title

      IUCrJ

      Volume: 6 Pages: 46-55

    • DOI

      10.1107/s205225251801480x

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Fragger: a protein fragment picker for structural queries2018

    • Author(s)
      Berenger Francois、Simoncini David、Voet Arnout、Shrestha Rojan、Zhang Kam Y.J.
    • Journal Title

      F1000Research

      Volume: 6 Pages: 1722-1722

    • DOI

      10.12688/f1000research.12486.1

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research

URL: 

Published: 2018-04-23   Modified: 2022-01-27  

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