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Investigation of membrane binding mechanism of peripheral membrane protein based on solid state NMR using magnetically aligned membrane bilayers at room temperature

Research Project

Project/Area Number 22570126
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionInstitute for Molecular Science

Principal Investigator

NISHIMURA Katsuyuki  分子科学研究所, 物質分子科学研究領域, 准教授 (00334631)

Co-Investigator(Renkei-kenkyūsha) TANIO Michikazu  分子科学研究所, 物質分子科学研究領域, 特任助教 (10416662)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2011: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2010: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords生物科学 / 構造生物化学 / 膜タンパク質 / 固体NMR / 配向試料 / バイセル / 膜表在性 / PLCδ1 / PHドメイン / 開発 / PLC-δ1
Research Abstract

Phospholipase C (PLC) binds to phosphatidylinositol 4,5-bisphosphate (PIP_2) in the cell membrane through the pleckstrin homology (PH) domain, and hydrolyzes PIP_2 to produce two second messengers, diacylglycerol and inositol 1,4,5-triphosphate (IP_3), by the catalytic domain. In this study, lipid binding mechanism of human PLC-δ1 PH domain (hPH) was explored. First, the contributions of the α2-helix to the IP_3 binding activity and thermal stability of the hPH domain were investigated by developed approach based on Native-PAGE methods. Then, linked local structural changes of hPH induced by the IP_3 binding were detected by solution NMR. It was found that intra molecular interaction network in hPH controls its ligand binding. Furthermore, through the analyses of solid state NMR, it was also found that hPH induces inhomogeneous structure after binding to a surface of PIP_2 embedded lipid bilayers and implied that hPH is finally inserted to lipid bilayers irreversibly.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (35 results)

All 2013 2012 2011 2010 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results) Presentation (23 results) Remarks (3 results)

  • [Journal Article] Difference in the structures of alanine tri- and tetra-peptides with antiparallel β-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW2013

    • Author(s)
      T. Asakura, K. Yazawa, K. Horiguchi, F. Suzuki, Y. Nishiyama, K. Nishimura, H. Kaji
    • Journal Title

      Biopolymers

      Volume: 101 Issue: 1 Pages: 13-20

    • DOI

      10.1002/bip.22241

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Intramolecular allosteric interaction in the phospholipase C-δ1 pleckstrin homology domain2013

    • Author(s)
      M.Tanio, K.Nishimura
    • Journal Title

      Biochim. Biophys. Acta

      Volume: 1834 Issue: 6 Pages: 1034-1043

    • DOI

      10.1016/j.bbapap.2013.01.034

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Determination of accurate ^1H positions of alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution ^1H solid state NMR and GIPAW chemical shift calculation2012

    • Author(s)
      K. Yazawa, F. Suzuki, Y. Nishiyama, T. Ohata, A. Aoki, K. Nishimura, H. Kaji, and T. Asakura
    • Journal Title

      Chem. Comm

      Volume: 48 Issue: 91 Pages: 11199-11201

    • DOI

      10.1039/c2cc36300c

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of the phospholipase C-δ1 pleckstrin homology domain using Native polyacrylamide gel electrophoresis2012

    • Author(s)
      M. Tanio, and K. Nishimura
    • Journal Title

      Anal. Biochem

      Volume: 431 Issue: 2 Pages: 106-114

    • DOI

      10.1016/j.ab.2012.09.012

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and orientation of bovine lactoferrampin in the bacterial membrane as revealed by Solid-State NMR and molecular dynamics simulation.2012

    • Author(s)
      Atsushi Tsutsumi, Namsrai Javkhlantugs, Atsushi Kira, Masako Umeyama, Izuru Kawamura, Kazuyoshi Ueda and Akira Naito
    • Journal Title

      Biophycal. Journal

      Volume: 103 Issue: 8 Pages: 1735-1743

    • DOI

      10.1016/j.bpj.2012.09.010

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] 2^H quadrupolar Carr-Purcell-Meiboom- Gill NMR for paramagnetic solids2011

    • Author(s)
      T. Iijima, and K. Nishimura
    • Journal Title

      Chem. Phys. Lett

      Volume: 514 Pages: 181-186

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] ^2H quadrupolar Carr-Purcell-Meiboom-Gill NMR for paramagnetic solids2011

    • Author(s)
      T.Iijima, K.Nishimura
    • Journal Title

      Chemical Physics Letters

      Volume: 514 Issue: 1-3 Pages: 181-186

    • DOI

      10.1016/j.cplett.2011.08.058

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular -Dynamics Simulation2010

    • Author(s)
      S. Toraya, N. Javkhlantugs, D. Mishima, K. Nishimura, K. Ueda, and A. Naito
    • Journal Title

      Biophys. J

      Volume: 99

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation2010

    • Author(s)
      S.TORAYA, N.JAVKHLANTUGS, D.MISHIMA, K.NISHIMURA, K.UEDA, A.NAITO
    • Journal Title

      Biophysical Journal

      Volume: 99 Pages: 3282-3289

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] NMR and Native-PAGE analyses of the phospholipase C-δ1 pleckstrin homology domain2012

    • Author(s)
      M. Tanio, and K. Nishimura
    • Organizer
      第51回NMR討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子の1^H精密位置決定~超高速MAS1H固体NMRによる1H DQMAS測定とGIPAW化学シフト計算~2012

    • Author(s)
      矢澤宏次、鈴木不律、西山裕介、西村勝之、梶弘典、朝倉哲郎
    • Organizer
      第51回NMR討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] The short α2-helix of the phospholipase C-δ1 pleckstrin homology domain contributes to stable IP_3 binding2012

    • Author(s)
      M. Tanio, K. Nishimura
    • Organizer
      第50回日本生物物理学会年会
    • Related Report
      2012 Final Research Report
  • [Presentation] 脂質二重膜上におけるDef6 PH ドメインの高次構造の解析2012

    • Author(s)
      N. Tokuda, M. Tanio, K. Nishimura, T. Kohno, D. Yokogawa, T. Ikegami, S. Tuzi
    • Organizer
      第50回日本生物物理学会年会
    • Related Report
      2012 Final Research Report
  • [Presentation] 1^H固体NMRの新時代 ~1^Hの位置からみるペプチドおよびタンパク質の分子間構造解析~2012

    • Author(s)
      矢澤宏次、杉本真理、西山裕介、西村勝之、鈴木不律、梶弘典、朝倉哲郎
    • Organizer
      第61回高分子討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] 高分解能1^H 固体NMR を用いた家蚕絹結晶部モデルペプチドの分子間構造解析"2012

    • Author(s)
      大畑卓也,矢澤宏次,青木昭宏,西山裕介,西村勝之,朝倉哲郎
    • Organizer
      第61回高分子討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] The short τ2-helix of the phospholipase C-χ1 pleckstrin homology domain stabilizes the protein-IP_3 interaction2012

    • Author(s)
      M. Tanio, and K. Nishimura
    • Organizer
      第12回日本蛋白質科学会年
    • Related Report
      2012 Final Research Report
  • [Presentation] “1H固体NMRの新時代 ~1Hの位置からみるペプチドおよびタンパク質の分子間構造解析~“2012

    • Author(s)
      矢澤宏次、杉本真理、西山裕介、西村勝之、鈴木不律、梶弘典、朝倉哲郎
    • Organizer
      第61回高分子討論会
    • Place of Presentation
      名古屋工業大学 (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] The short alpha2-helix of the phospholipase C-delta1 pleckstrin homology domain stabilizes the protein-IP3 interaction2012

    • Author(s)
      Michikazu Tanio, and Katsuyuki Nishimura
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場 (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 高分解能1H 固体NMR を用いた家蚕絹結晶部モデルペプチドの分子間構造解析2012

    • Author(s)
      大畑卓也、矢澤宏次、青木昭宏、西山裕介、西村勝之、朝倉哲郎
    • Organizer
      第61回高分子討論会
    • Place of Presentation
      名古屋工業大学 (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] The short α2-helix of the phospholipase C-δ1 pleckstrin homology domain contributes to stable IP3 binding2012

    • Author(s)
      Michikazu Tanio, Katsuyuki Nishimura
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学 (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 脂質二重膜上におけるDef6 PH ドメインの高次構造の解析2012

    • Author(s)
      Naomi Tokuda、Michikazu Tanio、 Katsuyuki Nishimura、Toshiyuki Kohno、Daisuke Yokogawa、Takahisa Ikegami、Satoru Tuzi
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学 (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] NMR and Native-PAGE analyses of the phospholipase C-δ1 pleckstrin homology domain2012

    • Author(s)
      Michikazu Tanio, and Katsuyuki Nishimura
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      ウインクあいち (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 生体分子の1H精密位置決定~超高速MAS1H固体NMRによる1H DQMAS測定とGIPAW化学シフト計算~2012

    • Author(s)
      矢澤宏次、鈴木不律、西山裕介、西村勝之、梶弘典、朝倉哲郎
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      ウインクあいち (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 常磁性ポリ酸の固体95MoNMR2012

    • Author(s)
      飯島隆広、山瀬利博、丹所正孝、清水禎、西村勝之
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      ウインクあいち (愛知県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 1^H spin diffusion solid state NMR analysis of the crystalline structures of alanine oligomers2011

    • Author(s)
      K. Yazawa, K. Miyazawa, T. Ohata, Y. Nishiyama, K. Nishimura, T. Asakura
    • Organizer
      第50回NMR討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] Hydrogen- bonding network and rotational motion of Ser side-chain studied by solid-state NMR2011

    • Author(s)
      T. Kameda, H. Teramoto, D. Hashizume, H. Koshino, K. Nishimura
    • Organizer
      第50回NMR討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] Hydrogen-bonding network and rotational motion of Ser side-chain studied by solid-state NMR2011

    • Author(s)
      Tsunenori Kameda, Hidetoshi Teramoto, Daisuke Hashizume, Hiroyuki Koshino, Katsuyuki Nishimura
    • Organizer
      第50回NMR討論会
    • Place of Presentation
      大さんばしホール(神奈川県)
    • Related Report
      2011 Annual Research Report
  • [Presentation] ^1H spin diffusion solid state NMR analysis of the crystalline structures of alanine oligomers2011

    • Author(s)
      Koji Yazawa, Kenta Miyazawa, Takuya Ohata, Yusuke Nishiyama, Katsuyuki Nishimura, Tetsuo Asakura
    • Organizer
      第50回NMR討論会
    • Place of Presentation
      大さんばしホール(神奈川県)
    • Related Report
      2011 Annual Research Report
  • [Presentation] 不飽和脂質を含有するバイセルに関する固体NMRを用いた研究2010

    • Author(s)
      西村勝之
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2010-11-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] Orientational Properties of New Bicelle Composed of Un-, and Saturated Phosphatidylcholine as Studied by Solid State NMR Spectroscopy2010

    • Author(s)
      西村勝之
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学(宮城県)
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] 不飽和脂質を含有するバイセルに関する固体NMRを用いた研究2010

    • Author(s)
      上釜奈緒子、辻暁、西村勝之
    • Organizer
      第49回NMR討論会
    • Related Report
      2012 Final Research Report
  • [Presentation] Orientational Properties of New Bicelle Composed of Un-, and Saturated Phosphatidylcholine as Studied by Solid State NMR Spectroscopy2010

    • Author(s)
      上釜奈緒子、西村勝之
    • Organizer
      第48回日本生物物理学会年会
    • Related Report
      2012 Final Research Report
  • [Remarks]

    • URL

      http://www.ims.ac.jp/publications/letters67/301.pdf

    • Related Report
      2012 Final Research Report
  • [Remarks] 分子研レターズ67号

    • URL

      http://www.ims.ac.jp/publications/letters67/301.pdf

    • Related Report
      2012 Annual Research Report
  • [Remarks] annual review

    • URL

      http://www.ims.ac.jp/english/know_en/publications/ann_rev_2011/nishimura.pdf

    • Related Report
      2012 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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