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Analysis on the design principle of proteins with intrinsic sequence variations

Research Project

Project/Area Number 26440076
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionKobe University (2015-2016)
Mie University (2014)

Principal Investigator

Daizo Hamada  神戸大学, 工学研究科, 特命准教授 (60372132)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords抗体 / ALアミロイドーシス / フォールディング / 複合体形成 / 重水素交換 / 蛋白質間相互作用 / 蛋白質の安定性 / アミロイド / アミロイド線維 / φ値解析 / 水素・重水素交換 / X線結晶構造解析 / NMR / タンパク質のフォールディング / エネルギー地形 / 平衡論 / 速度論
Outline of Final Research Achievements

Here, we analysed the folding mechanism of immunoglobulin light chain variable domain (VL) which intrinsically have sequence variation, although folded into the same structure. We performed various thermodynamic, kinetic and structural analyses on the monomeric VL that we invented ourselves in another study and clarified the core region for folding of VL. We also found the unexpected heat-induce dimerization for original VL, which instinctively against general idea that dimeric proteins have to dissociate into monomers by heating. We clarified the mechanism of this heat-induce dimerization by a series of thermodynamic analysis. These pieces of information about the folding of VL will be applicable to improve the thermal stability of proteins used in various fields and also provided a significant insight into the development of strategy for prevention, diagnostics and treatment against AL amyloidosis which the amyloid formation by immunoglobulin light chain is associated with.

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

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results)

  • [Journal Article] Class II-like structural features and strong receptor binding of the non-classical HLA-G2 isoform homodimer.2017

    • Author(s)
      K.Kuroki, K.Mio, A.Takahashi, H.Matsubara, Y.Kasai, S.Manaka, M.Kikkawa, D.Hamada, C.Sato, K.Maenaka.
    • Journal Title

      J Immunology

      Volume: 198 Issue: 9 Pages: 3399-3403

    • DOI

      10.4049/jimmunol.1601296

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Residual structures in the unfolded state of starch-binding domain of glucoamylase revealed by near-UV circular dichroism and protein engineering techniques.2016

    • Author(s)
      Ota C, Ikeguchi M, Tanaka A, Hamada D
    • Journal Title

      Biochim Biophys Acta.

      Volume: 1864 Issue: 10 Pages: 1464-1472

    • DOI

      10.1016/j.bbapap.2016.05.002

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Crystal Structure of Human Herpesvirus 6B Tegument Protein U14.2016

    • Author(s)
      Wang B, Nishimura M, Tang H, Kawabata A, Mahmoud NF, Khanlari Z, Hamada D, Tsuruta H, Mori Y.
    • Journal Title

      PLoS Pathog.

      Volume: 12 Issue: 5 Pages: e1005594-e1005594

    • DOI

      10.1371/journal.ppat.1005594

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification and characterization of PKCγ, a kinase associated with SCA14, as an amyloidogenic protein.2015

    • Author(s)
      Takahashi H, Adachi N, Shirafuji T, Danno S, Ueyama T, Vendruscolo M, Shuvaev AN, Sugimoto T, Seki T, Hamada D, Irie K, Hirai H, Sakai N, *Saito N.
    • Journal Title

      Hum Mol Genet.

      Volume: 24 Issue: 2 Pages: 525-539

    • DOI

      10.1093/hmg/ddu472

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Decreasing amyloidogenicity of immunogloublin light chain variable domain by mutation of surface exposed residues and peptide inhibitor targeting partially unfolded state2016

    • Author(s)
      Daizo Hamada
    • Organizer
      30th Anniversary Symposium The Protein Society
    • Place of Presentation
      Baltimore, USA
    • Year and Date
      2016-07-16
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of dimerization by immunoglobulin light chain variable domain for inhibition of amyloid formation2016

    • Author(s)
      縄田万里奈、堤浩祟、小林祐大、雲財悟、峯昇平、中村勉、上垣浩一、上久保裕生、片岡幹夫、浜田大三
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Inhibition of amyloid formation by immunoglobulin light chain variable domain based on the analysis of structural fluctuations.2015

    • Author(s)
      Daizo Hamada. Hirotaka Tsutsumi1, Marina Nawata and Chiaki Ota
    • Organizer
      The international Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 低分解能解析により明らかとなった SBD の複数の変性状態2015

    • Author(s)
      太田 千晶、池口 雅道、浜田 大三、田中晶善
    • Organizer
      日本蛋白質科学会
    • Place of Presentation
      あわぎんホール(徳島県・徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Research-status Report
  • [Presentation] 免疫グロブリン関連アミロイドーシスの分子病態学ー揺らぎの伝播と制御ー2015

    • Author(s)
      浜田大三
    • Organizer
      第17回生命分子ダイナミクスセミナー
    • Place of Presentation
      東北大学
    • Year and Date
      2015-02-04
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 塩酸グアニジン変性における Aspergillus niger 由来グルコアミラーゼのデンプン結合ドメインの二つの異なる変性状態2014

    • Author(s)
      浜田大三、太田千晶、北澤桃子、三宅英雄、田中晶善
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] 平衡条件下において形成される二つの天然変性蛋白質融合蛋白質のフォールディング中間状態2014

    • Author(s)
      浜田大三
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] 免疫グロブリン軽鎖可変ドメインのアミロイド形成における構造揺らぎの役割2014

    • Author(s)
      浜田大三、小林祐大、堤浩祟、縄田万里奈
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜/横浜産貿ホール
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Research-status Report

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

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