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2013 Fiscal Year Final Research Report

Physicochemical studies of YB-1 functions and structures

Research Project

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Project/Area Number 24750166
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Chemistry related to living body
Research InstitutionThe University of Tokyo

Principal Investigator

NAGATOISHI Satoru  東京大学, 工学(系)研究科(研究院), 助教 (30550248)

Project Period (FY) 2012-04-01 – 2014-03-31
Keywords天然変性型蛋白質 / 熱力学 / 相互作用 / 核酸
Research Abstract

Y-box binding protein 1(YB-1) is a nucleic acid-binding protein that regulates transcription and translation, and is overexpressed in cancer cells. It has been reported that the bindings of YB-1 to specific genomic DNAs or mRNAs are involved in tumorigenesis. Therefore, it is plausible to suppose that YB-1 is a new target to regulate the cellular systems due to treatment of human diseases and elucidation of new cellular functions. However, the binding mechanism of YB-1 to nucleic acids is still unclear. Here, we carried out physicochemical analyses of the structural and binding properties of YB-1 using spectrometry and calorimetry. The recombinant YB-1 had thermodynamically unique bindings to the single-strand DNA with Y-box sequence and to the single-strand DNA with Y-box mRNA sequence. The DNA and RNA binding sites of YB-1 were identified by using a full length and deletion mutants of YB-1. We further studied the effects of salt and temperature on the binding to DNA or RNA.

  • Research Products

    (16 results)

All 2014 2013 2012 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (8 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Affinity Improvement of a Therapeutic Antibody by Structure-Based Computational Design : Generation of Electrostatic Interactions in the Transition State Stabilizes the Antibody-Antigen Complex2014

    • Author(s)
      M. Kiyoshi, J. M. M. Caaveiro, E. Miura, S. Nagatoishi, M. Nakakido, S. Soga, H. Shirai, S. Kawabata and K. Tsumoto
    • Journal Title

      PLoS One

      Volume: 9 Pages: e87099

    • DOI

      10.1371/journal.pone.0087099

    • Peer Reviewed
  • [Journal Article] Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer2013

    • Author(s)
      A. Pica, I. Russo Krauss, A. Merlino, S. Nagatoishi, N. Sugimoto and F. Sica
    • Journal Title

      FEBS J.

      Volume: 280 Pages: 6581–6588

    • DOI

      10.1111/febs.12561

    • Peer Reviewed
  • [Journal Article] Hyperthin nanochains composed of self-polymerizing protein shackles2013

    • Author(s)
      R. Matsunaga, S. Yanaka, S. Nagatoishi and K. Tsumoto
    • Journal Title

      Nat. Commun.

      Volume: 4 Pages: 2211

    • DOI

      10.1038/ncomms3211

    • Peer Reviewed
  • [Journal Article] Identification and characterization of the X-dimer of human P-cadherin : Implications for homophilic cell adhesion2012

    • Author(s)
      S. Kudo, J. M. M. Caaveiro, S. Goda, S. Nagatoishi, K. Ishii, T. Matsuura, Y. Sudou, T. Kodama, T. Hamakubo and K. Tsumoto
    • Journal Title

      Biochemistry

      Volume: 53 Pages: 1742–1752

    • DOI

      10.1021/bi401341g

    • Peer Reviewed
  • [Journal Article] Interaction of water with G-quadruplex loop contributes to the binding energy of G-quadruplex to protein2012

    • Author(s)
      S. Nagatoishi and N. Sugimoto
    • Journal Title

      Mol. BioSyst.

      Volume: 8 Pages: 2766–2770

    • DOI

      10.1039/C2MB25234A

    • Peer Reviewed
  • [Journal Article] Structural and functional characterization of RecG helicase under dilute and molecular crowding conditions2012

    • Author(s)
      S. Saxena, S. Nagatoishi, D. Miyoshi and N. Sugimoto
    • Journal Title

      J. Nucleic acids

      Volume: 2012 Pages: 392039

    • DOI

      10.1155/2012/392039

    • Peer Reviewed
  • [Presentation] 生命分子相互作用解析 : ITCとSPR2014

    • Author(s)
      長門石曉・津本浩平
    • Organizer
      日本薬学会第134年会
    • Place of Presentation
      くまもと県民交流会館パレアホール(熊本県熊本市)
    • Year and Date
      2014-03-30
  • [Presentation] 天然変性型蛋白質の機能制御へ向けた核酸結合蛋白質YB-1の物理化学的解析2013

    • Author(s)
      長門石曉・田邊裕美子・西方敬人・杉本直己・津本浩平
    • Organizer
      第7回バイオ関連化学シンポジウム
    • Place of Presentation
      名古屋大学東山キャンパス(愛知県名古屋市)
    • Year and Date
      2013-09-28
  • [Presentation] 分子間相互作用をミクロに捕らえる表面プラズモン共鳴法と熱測定の活用2013

    • Author(s)
      長門石曉・津本浩平
    • Organizer
      第17回コロイド・界面フォーラム
    • Place of Presentation
      KKR江の島ニュー向洋(神奈川県藤沢市)
    • Year and Date
      2013-07-18
  • [Presentation] 癌関連蛋白質Y-box binding protein 1の物理化学的手法を用いた機能解析2013

    • Author(s)
      田邊裕美子・長門石曉、西方敬人、杉本直己、津本浩平
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取市)
    • Year and Date
      2013-06-12
  • [Presentation] Y-box binding protein 1(YB-1)の物性とDNA結合メカニズムの解析2013

    • Author(s)
      田邊裕美子・長門石曉・西方敬人・杉本直己・津本浩平
    • Organizer
      日本化学会第93春季年会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス(草津市)
    • Year and Date
      2013-03-22
  • [Presentation] Physicochemical studies of YB-1 functions and structures2013

    • Author(s)
      Satoru Nagatoishi, Yumiko Tanabe, Kouhei Tsumoto
    • Organizer
      Biophysical Society 58th Annual Meeting
    • Place of Presentation
      Moscone Center (San Francisco, CA)
    • Year and Date
      2013-02-18
  • [Presentation] Effects of a thymine residue deletion in TT loops on thrombin-‐TBA recognition interactions : a crystallographic study2012

    • Author(s)
      Irene Russo Krauss, Andrea Pica, Antonello Merlino, Satoru Nagatoishi, Naoki Sugimoto, Lelio Mazzarella and Filomena Sica
    • Organizer
      CONFORMATIONAL DIVERSITY AND APPLICATIONS OF G-QUADRUPLEXES
    • Place of Presentation
      Spain
    • Year and Date
      20121006-08
  • [Presentation] Thermodynamics and hydration effects on the interaction between DNA G-quadruplex and thrombin2012

    • Author(s)
      Satoru Nagatoishi, Naoki Sugimoto
    • Organizer
      The Second Asian Chemical Biology Conference, ACBC2012
    • Place of Presentation
      Okinawa
    • Year and Date
      20120704-06
  • [Book] 「等温滴定型カロリメトリー」ぶんせき2012

    • Author(s)
      長門石曉・津本浩平
    • Publisher
      日本分析化学会
  • [Remarks]

    • URL

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

URL: 

Published: 2015-06-25  

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