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Folding principle of proteins with different 3D structures in spite of high sequence identiry

Research Project

Project/Area Number 26330335
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionRitsumeikan University

Principal Investigator

Kikuchi Takeshi  立命館大学, 生命科学部, 教授 (90195206)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2014: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsアミノ酸配列相同性 / タンパク質立体構造 / フォールディング部位 / 残基間平均距離統計 / 進化的保存疎水残基 / Goモデル / 配列相同タンパク質 / フォールディング機構 / 配列解析 / 平均距離統計 / Goモデル / 分子動力学 / Go モデル
Outline of Final Research Achievements

The GA-related proteins which binds to human serum albumin and the GB-related domain, which binds to the constant (Fc) region of IgG were treated in this study. In particular, we treated proteins which share 88%, 95%, and even 98% sequence identity but exhibit different 3D structures, i.e., a 3α bundle structure or a 4β + α structure. An analysis based on inter-residue average distance statistics was used to address this problem in addition to an evolutionary analysis. First of all, our general methods were applied to lysozyme, b-trefoil proteins and so on and their effectiveness was confirmed. Then we applied our method to GA・GB-related proteins. As a result, the essential residues to determine the final structures were identified. Our results confirmed by our Go model simulations.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (12 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (2 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (9 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results)

  • [Int'l Joint Research] モレロス州立自治大学(メキシコ)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Properties of Amino Acid Sequences of Lysozyme-Like Superfamily Proteins Relating to Their Folding Mechanisms.2017

    • Author(s)
      Takuto Nakashima, Michirou Kabata, and Takeshi Kikuchi
    • Journal Title

      Journal of Proteomics & Bioinformatics

      Volume: 10 Issue: 4 Pages: 94-107

    • DOI

      10.4172/jpb.1000429

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures2014

    • Author(s)
      Masanari Matsuoka, Masatake Sugita, Takeshi Kikuchi
    • Journal Title

      BMC Research Notes

      Volume: 7 Issue: 1 Pages: 654-654

    • DOI

      10.1186/1756-0500-7-654

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Decoding Protein Sequencesto Extract Information of Folding Nuclei2017

    • Author(s)
      Takeshi Kikuchi
    • Organizer
      Protein & Peptide Conference (PepCon-2017)
    • Place of Presentation
      ヒルトン福岡シーホーク(福岡県博多市)
    • Year and Date
      2017-03-24
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] β-Trefoilタンパクのフォールディングに重要な残基に関する残基間平均距離統計に基づく解析2016

    • Author(s)
      桐岡拓也、菊地武司
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Lysozyme スーパーファミリーのアミノ酸配列解析によるフォールディング領域予測2016

    • Author(s)
      中島拓飛、加畑通朗、菊地武司
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Sequence analysis on the information of folding nuclei in proteins with interesting 3D properties2016

    • Author(s)
      Takeshi Kikuchi
    • Organizer
      Frontier of Structural Biology 2016
    • Place of Presentation
      New Orleans(USA)
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] β-Trefoilタンパクのフォールディングに重要な残基に関する残基間平均距離統計に基づく解析2016

    • Author(s)
      桐岡拓也、菊地武司
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県博多市)
    • Year and Date
      2016-06-08
    • Related Report
      2016 Annual Research Report
  • [Presentation] Lysozyme superfamilyにおけるフォールディング機構保存性の、残基間距離の統計情報を用いた予測2016

    • Author(s)
      中島拓飛、加畑通朗、菊地武司
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県博多市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 高い配列相同性を持ちながら異なる立体構造を持つタンパク質のアミノ酸配列と立体構造に基づく解析2015

    • Author(s)
      大西晃平、松岡雅成、杉田昌岳、菊地武司
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-14
    • Related Report
      2015 Research-status Report
  • [Presentation] TM1457 におけるアミノ酸配列と立体構造との関連2015

    • Author(s)
      大西晃平、菊地武司
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島県徳島市)
    • Year and Date
      2015-06-25
    • Related Report
      2015 Research-status Report
  • [Presentation] Analysis of the effect of amino acid mutations on the protein folding segments by means of sequence and evolutionary analyses2014

    • Author(s)
      松岡雅成 菊地武司
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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