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Elucidation of the molecular mechanism of multi-specific substrate recognition by the methyltransferase

Research Project

Project/Area Number 16H06693
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Biomolecular chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

Nakakido Makoto  東京大学, 大学院工学系研究科(工学部), 助教 (80784511)

Project Period (FY) 2016-08-26 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords分子認識 / 多重特異性 / メチル基転移酵素 / 相互作用 / 物理化学 / 蛋白質 / 酵素 / 翻訳後修飾
Outline of Final Research Achievements

In this study, we aimed to reveal the molecular mechanism how a multi-specific enzyme recognizes its substrate. We selected SMYD2, a methyltransferase which has methylation activity to a variety of substrates including histone and non-histone proteins, as a model protein. We prepared SMYD2, its substrate p53, and several SMYD2 mutants with mutations on amino acid residues that are supposed to be involved in substrate recognition as recombinant protein and conducted the analysis of the interaction between SMYD2 wild-type/mutants and p53. Though the analyses, we quantitatively described the contribution of each amino acid residue on substrate recognition.

Report

(3 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • Research Products

    (20 results)

All 2018 2017 2016 Other

All Journal Article (7 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 7 results,  Open Access: 2 results) Presentation (12 results) (of which Int'l Joint Research: 2 results) Remarks (1 results)

  • [Journal Article] Regulation of poly(ADP-Ribose) polymerase 1 functions by post-translational modifications2018

    • Author(s)
      Piao L, Fujioka K, Nakakido M, Hamamoto R.
    • Journal Title

      Front Biosci (Landmark Ed)

      Volume: in press

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Production and characterization of a novel site-specific-modifiable anti-OX40-receptor single-chain variable fragment for targeted drug delivery.2018

    • Author(s)
      Tanabe A, Nakano K, Nakakido M, Nagatoishi S, Tanaka Y, Tsumoto K, Uchimaru K, Watanabe T.
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 496 Issue: 2 Pages: 614-620

    • DOI

      10.1016/j.bbrc.2018.01.051

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.2018

    • Author(s)
      Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro J, and Tsumoto K
    • Journal Title

      J Biochem.

      Volume: in press

    • NAID

      40021625331

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular basis for governing the morphology of type I collagen fibrils by Osteomodulin2018

    • Author(s)
      Tashima T, Nagatoishi S, Caaveiro J, Nakakido M, Sagara H, Kusano-Arai O, Iwanari H, Mimuro H, Hamakubo T, Ohnuma S, Tsumoto K
    • Journal Title

      Commun. Biol.

      Volume: in press

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Biophysical characterization of the interaction between heme and proteins responsible for heme transfer in Streptococcus pyogenes.2017

    • Author(s)
      Hoshino M, Nakakido M, Nagatoishi S, Aikawa C, Nakagawa I, Tsumoto K.
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 493 Issue: 2 Pages: 1109-1114

    • DOI

      10.1016/j.bbrc.2017.09.055

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Thermodynamic analyses of amino acid residues at the interface of an antibody B2212A and its antigen roundabout homolog 1.2017

    • Author(s)
      Yui A, Akiba H, Kudo S, Nakakido M, Nagatoishi S and Tsumoto K
    • Journal Title

      J. Biochem.

      Volume: 162 Pages: 255-258

    • DOI

      10.1093/jb/mvx050

    • NAID

      40021380511

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regulation of Poly(ADP-Ribose) Polymerase 1 Functions by Post-Translational Modifications2017

    • Author(s)
      Piao L, Fujioka K, Nakakido M, Hamamoto R.
    • Journal Title

      Frontiers in bioscience

      Volume: 印刷中

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Analysis of the denaturation midpoint to design the VHH with high thermal stability2018

    • Author(s)
      Emina Ikeuchi,Daisuke Kuroda, Makoto Nakakido, Maiko Yoshida, Narutoshi Tsukahara, Akikazu Murakami, Kouhei Tsumoto
    • Organizer
      62nd Annual Meeting of the Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 分子シミュレーションと物理化学解析による抗体の熱安定性に関する研究2018

    • Author(s)
      河上 恵理、黒田 大祐、中木戸 誠、津本 浩平
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Structural, physicochemical and computational analysis to reveal the mechanism of recognition of phosphorylated antigen by an antibody2018

    • Author(s)
      Kawade R, Akiba H, Nakakido M, Kuroda D, Maruyama T, Okumura S, Kevin E, Caaveiro J, Tsumoto K
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Physicochemical analysis of antigen-antibody interaction associated with charge exchange of amino acids2017

    • Author(s)
      Kouhei Yoshida, Masato Kiyoshi, Daisuke Kuroda, Makoto Nakakido, Satoru Nagatoishi, Shinji Soga, Hiroki Shirai, Kouhei Tsumoto
    • Organizer
      The Second International Symposium on Biofunctional Chemistry (ISBC 2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] "Weak electrostatic interaction of an extracellular matrix protein plays a key role in a shapecontrol2017

    • Author(s)
      田島卓実、長門石 暁、カアベイロ ホセ、中木戸 誠、相良 洋、三室 仁美、大沼 信一、津本 浩平
    • Organizer
      第17回 日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 抗ペプチド抗体による硫酸化CCR5ペプチド認識機構の熱力学的解析2017

    • Author(s)
      宮鍋 一紘、秋葉 宏樹、中木戸 誠、カアベイロ ホセ、高松 佑一郎、山下 雄史、津本 浩平
    • Organizer
      第17回 日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] アミノ酸電荷交換に関する抗原-抗体相互作用の物理化学解析2017

    • Author(s)
      吉田 浩平、木吉 真人、中木戸 誠、長門石 暁、曽我 真司、白井 宏樹、津本 浩平
    • Organizer
      第11回 バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] B2212A一本鎖抗体と抗原ROBO1の界面に存在するアミノ酸残基の役割の解明に向けた熱力学的解析2017

    • Author(s)
      由井 杏奈、工藤 翔太、秋葉 宏樹、中木戸 誠、長門石 曉、井上 豪、浜窪 隆雄、津本 浩平
    • Organizer
      第11回 バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] インターロイキン11シグナルを制御するシングルドメイン抗体の探索2017

    • Author(s)
      森 千夏、中木戸 誠、長門石 曉 、津本 浩平
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 基質選択的な阻害を目指したメチル基転移酵素SMYD2の多重特異的基質認識機構の解明2017

    • Author(s)
      青木将洋、中木戸 誠、津本 浩平
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ファージディスプレイによるメチル化リジン特異的抗体の取得2017

    • Author(s)
      石井 美咲、中木戸 誠、津本 浩平
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] PRMT6 increases cytoplasmic localization of p21CDKN1A in cancer cells through arginine methylation and makes more resistant to cytotoxic agents2016

    • Author(s)
      Makoto Nakakido, Yusuke Nakamura, Ryuji Hamamoto
    • Organizer
      第75回日本癌学会学術総会
    • Place of Presentation
      パシフィコ横浜(神奈川県、横浜市)
    • Year and Date
      2016-10-06
    • Related Report
      2016 Annual Research Report
  • [Remarks] 研究室HP

    • URL

      http://park.itc.u-tokyo.ac.jp/phys-biochem/

    • Related Report
      2017 Annual Research Report

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Published: 2016-09-02   Modified: 2019-03-29  

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