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Neutron Diffraction Analysis of Human Farnesyl Pyrophosphate Synthase in Complex with Bisphosphonate

Research Project

Project/Area Number 25860022
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical pharmacy
Research InstitutionUniversity of Toyama

Principal Investigator

Yokoyama Takeshi  富山大学, 医学薬学研究部(薬学), 助教 (50524162)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords構造生物学 / 中性子結晶構造解析 / 医薬品化学 / 構造活性相関 / プロトン化状態 / pH / リン酸基 / ビスホスホネート / ファルネシル二リン酸合成酵素 / イソペンテニル二リン酸 / 蛋白質科学 / 生物物理学 / リセドロネート / 大型結晶化 / BIODIFF
Outline of Final Research Achievements

Neutron crystal structure of human farnesyl pyrophosphate synthase (FPPS) in complex with risedronate (RIS) was determined, and the protonation state and hydration of RIS were elucidated. The structural analysis revealed that the phosphate groups of RIS were fully deprotonated with the abnormally decreased pKa. In addition, it was suggested that the roles of E93 and D264 consisted of canceling the extra negative charges upon the binding of ligands. This information would be helpful for the development of non-bisphosphonate FPPS inhibitors.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (19 results)

All 2016 2015 2014 2013

All Journal Article (8 results) (of which Peer Reviewed: 8 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (11 results) (of which Invited: 1 results)

  • [Journal Article] Structural stabilization of transthyretin by a new compound, 6-benzoyl-2-hydroxy-1H-benzo[de]isoquinoline-1,3(2H)-dione2015

    • Author(s)
      Yokoyama T, Takaki S, Chosa K, Sato T, Suico MA, Teranishi Y, Shuto T, Mizuguchi M, Kai H
    • Journal Title

      J Pharmacol Sci.

      Volume: 129 Issue: 4 Pages: 240-243

    • DOI

      10.1016/j.jphs.2015.09.006

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Yokoyama T, Kosaka Y, Mizuguchi M2015

    • Author(s)
      Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids
    • Journal Title

      J Med Chem

      Volume: 58 Issue: 18 Pages: 7400-7408

    • DOI

      10.1021/acs.jmedchem.5b00893

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Yokoyama T, Mizuguchi M, Ostermann A, Kusaka K, Niimura N, Schrader TE, Tanaka I2015

    • Author(s)
      Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase
    • Journal Title

      J Med Chem

      Volume: 58 Issue: 18 Pages: 7549-7556

    • DOI

      10.1021/acs.jmedchem.5b01147

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Discovery of γ-Mangostin as an Amyloidogenesis Inhibitor.2015

    • Author(s)
      Yokoyama T, Ueda M, Ando Y, Mizuguchi M.
    • Journal Title

      Sci Rep

      Volume: 5 Issue: 1 Pages: 13570-13570

    • DOI

      10.1038/srep13570

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inhibitory Activities of Propolis and its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin2014

    • Author(s)
      Yokoyama, T.; Kosaka, Y.; Mizuguchi, M
    • Journal Title

      Journal of Medicinal Chemistry

      Volume: 57 Issue: 21 Pages: 8928-8935

    • DOI

      10.1021/jm500997m

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate.2014

    • Author(s)
      Yokoyama T, Ostermann A, Mizuguchi M, Niimura N, Schrader TE, Tanaka I.
    • Journal Title

      Acta Crystallogr F Struct Biol Commun.

      Volume: 70 Issue: 4 Pages: 470-472

    • DOI

      10.1107/s2053230x14004087

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystal structures of human transthyretin complexed with glabridin.2014

    • Author(s)
      Yokoyama T, Kosaka Y, Mizuguchi M.
    • Journal Title

      J Med Chem.

      Volume: 57 Issue: 3 Pages: 1090-1096

    • DOI

      10.1021/jm401832j

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Hydrogen-bond network and pH sensitivity in human transthyretin2013

    • Author(s)
      T. Yokoyama, M. Mizuguchi, Y. Nabeshima, K. Kusaka, T. Yamada, T. Hosoya, T. Ohhara, K. Kurihara, I. Tanaka, N. Niimura
    • Journal Title

      J. Synchrotron Radiat.

      Volume: 2013 Issue: 6 Pages: 834-837

    • DOI

      10.1107/s090904951302075x

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] トランスサイレチン型アミロイドーシスの治療を目指した構造生物学的研究2016

    • Author(s)
      横山武司
    • Organizer
      第1051回金曜セミナーおよび第4回neutrons in biology研究会
    • Place of Presentation
      東海
    • Year and Date
      2016-03-25
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 天然物の結合によるヒトトランスサイレチンの構造変化2015

    • Author(s)
      横山武司
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Structural insight into the interaction between Death-associated protein kinase 1 and natural flavonoids2015

    • Author(s)
      小坂友人,水口峰之,横山武司
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 創薬標的タンパク質の中性子結晶構造解析および天然物阻害剤との相互作用解析2015

    • Author(s)
      横山武司
    • Organizer
      2015年度第一回水和ナノ構造研究会
    • Place of Presentation
      塩原
    • Year and Date
      2015-09-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] プロポリスとその有効成分CAPE のトランスサイレチンアミロイド線維形成阻害効果2015

    • Author(s)
      小坂友人,横山武司,水口峰之
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      徳島
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] γ-マンゴスチンはトランスサイレチンのアミロイド線形成を阻害する2015

    • Author(s)
      横山武司,水口峰之
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      徳島
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] FPPS-ビスホスホネート複合体におけるプロトン化状態の変化と水和構造2015

    • Author(s)
      横山武司
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      徳島
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] FPPS-ビスホスホネート複合体におけるプロトン化状態の変化と水和構造2015

    • Author(s)
      横山武司
    • Organizer
      第8回iBIX研究会
    • Place of Presentation
      東海村
    • Year and Date
      2015-01-28
    • Related Report
      2014 Research-status Report
  • [Presentation] Neutron crystal structure of human FPPS complexed with risedronate2014

    • Author(s)
      Takeshi Yokoyama, Andreas Ostermann, Mineyuki Mizuguchi, Nobuo Niimura, Tobias Schrader, Ichiro Tanaka
    • Organizer
      XXIII Congress and General Assembly International Union of Crystallography
    • Place of Presentation
      カナダ
    • Year and Date
      2014-08-01 – 2014-08-08
    • Related Report
      2014 Research-status Report
  • [Presentation] トランスサイレチンとグラブリジンの複合体結晶構造解析2014

    • Author(s)
      小坂友人、横山武司、水口峰之
    • Organizer
      第14回日本蛋白質科学会
    • Place of Presentation
      横浜
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Research-status Report
  • [Presentation] ファルネシル二リン酸合成酵素の中性子結晶構造解析2014

    • Author(s)
      横山武司、オスターマン アンドレアス、水口峰之、新村信雄、シュレイダー トビアス、田中伊知朗
    • Organizer
      第14回日本蛋白質科学会
    • Place of Presentation
      横浜
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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