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Elucidation of polymerization mechanism of ion channels and its physiological significance

Research Project

Project/Area Number 17K17768
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field General physiology
Biophysics
Research InstitutionKanazawa University (2018-2019)
University of Fukui (2017)

Principal Investigator

Sumikama Takashi  金沢大学, ナノ生命科学研究所, 特任助教 (30579412)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywordsイオンチャネル / 細胞膜 / 分子動力学法 / シミュレーション / 分子動力学 / タンパク質 / 膜 / 相互作用 / 膜挿入 / トキシン / チャネル / 多量体形成
Outline of Final Research Achievements

The insertion process of monomers of ion channels to membranes and the mechanism of eventual multimeric formation of them are still unknown. In this study, we aimed to reveal them by using the molecular dynamics simulation. The insertion process of the polytheonamide B, one of the smallest ion channel, was clarified at the molecular level. Though the multimeric formation mechanism was not investigated, it was confirmed that the recently suggested electronic continuum correction is significant for precisely describing ion-protein and ion-lipid interaction.

Academic Significance and Societal Importance of the Research Achievements

イオンチャネルがいかにその機能を発揮するかを調べることは、生理的・生物物理学的に重要であるだけでなく、イオンチャネルは神経や筋肉の動きを支配する分子の一つであり、その機能の欠陥による様々な病気が知られているため、社会的にも意義深いものと考える。また、簡便なelectronic continuum correction法がイオンとタンパク質や脂質分子の相互作用の大幅な改善につながることは、今度のシミュレーションにとって不可欠な知識となっていくと考える。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (38 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (1 results) Journal Article (9 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 7 results,  Open Access: 4 results) Presentation (27 results) (of which Int'l Joint Research: 7 results,  Invited: 11 results) Remarks (1 results)

  • [Int'l Joint Research] Aalto University(フィンランド)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Induced-Fit Pathway Accelerated Binding of Agitoxin-2 to A K+ Channel Imaged by HS-AFM2020

    • Author(s)
      Sumino Ayumi、Sumikama Takashi、Uchihashi Takayuki、Oiki Shigetoshi
    • Journal Title

      Biophysical Journal

      Volume: 118 Issue: 3 Pages: 236a-236a

    • DOI

      10.1016/j.bpj.2019.11.1392

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computing Atomic Force Microscopy Images of Chromosomes using Polymer Simulation2020

    • Author(s)
      Sumikama Takashi、Foster Adam S.、Fukuma Takeshi
    • Journal Title

      Biophysical Journal

      Volume: 118 Issue: 3 Pages: 619a-619a

    • DOI

      10.1016/j.bpj.2019.11.3341

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit2019

    • Author(s)
      A. Sumino,T. Sumikama,T. Uchihashi,S. Oiki
    • Journal Title

      Science Advances

      Volume: 5 Issue: 7 Pages: 1-10

    • DOI

      10.1126/sciadv.aax0495

    • NAID

      120006649788

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Queueing arrival and release mechanism for K+ permeation through a potassium channel2019

    • Author(s)
      Takashi Sumikama, Shigetoshi Oiki
    • Journal Title

      The Journal of Physiological Sciences

      Volume: 69 Pages: 919-930

    • NAID

      120006715810

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computed Atomic Force Microscopy Images of Chromosomes by Calculating Forces with Oscillating Probes2019

    • Author(s)
      Sumikama Takashi、Foster Adam. S.、Fukuma Takeshi
    • Journal Title

      The Journal of Physical Chemistry C

      Volume: 124 Issue: 3 Pages: 2213-2218

    • DOI

      10.1021/acs.jpcc.9b10263

    • NAID

      120006780310

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Origins of Heat Evolution in Mixing Water and Dimethyl Sulfoxide2018

    • Author(s)
      Mizuno Kazuko、Sumikama Takashi、Tarnai Yoshinori、Tani Masahiko
    • Journal Title

      International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz2018)

      Volume: - Pages: 1-2

    • DOI

      10.1109/irmmw-thz.2018.8509894

    • NAID

      120006602138

    • Related Report
      2018 Research-status Report
  • [Journal Article] Capturing the Freeze-Drying Dynamics of NaCl Nanoparticles Using THz Spectroscopy2018

    • Author(s)
      Ajito Katsuhiro、Ueno Yuko、Kim Jae-Young、Sumikama Takashi
    • Journal Title

      Journal of the American Chemical Society

      Volume: 140 Issue: 42 Pages: 13793-13797

    • DOI

      10.1021/jacs.8b07828

    • NAID

      120006602137

    • Related Report
      2018 Research-status Report
  • [Journal Article] Entrance of Channel Determines Ion Permeation Rate through the Kv1.2 Channel2018

    • Author(s)
      炭竈 享司、老木 成稔
    • Journal Title

      Seibutsu Butsuri

      Volume: 58 Issue: 1 Pages: 012-016

    • DOI

      10.2142/biophys.58.012

    • NAID

      130006322043

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study2018

    • Author(s)
      Kalathingal Mahroof、Sumikama Takashi、Mori Toshifumi、Oiki Shigetoshi、Saito Shinji
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 20 Issue: 5 Pages: 3334-3348

    • DOI

      10.1039/c7cp06299k

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Toward elucidating a relation between computed atomic force microscopy image and actual structure using machine learning2020

    • Author(s)
      Takashi Sumikama, Niko Oinonen, Fedor Urtev, Adam. S. Foster, Takeshi Fukuma
    • Organizer
      The 1st International Conference on Big Data and Machine Learning in Microscopy
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computing Atomic Force Microscopy Images of Chromosomes Using Polymer Simulation2020

    • Author(s)
      Takashi Sumikama, Adam. S. Foster, Takeshi Fukuma
    • Organizer
      Biophysical Society 64th Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] KcsA K+チャネルでのイオン選択性の分子機構2020

    • Author(s)
      炭竈享司、三田建一郎、老木成
    • Organizer
      日本生理学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 分子シミュレーションで見る毒の作用機序:海綿由来毒ポリセオナミドの細胞膜への挿入2019

    • Author(s)
      炭竈享司、Mahroof Kalathingal、老木成稔、斉藤真司
    • Organizer
      トキシンシンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 染色体の3D-AFM像と実像の関係の理論的解明2019

    • Author(s)
      炭竈享司、宮澤佳甫、Adam S. Foster、福間剛士
    • Organizer
      日本生物物理学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Computational prediction of 3D-AFM images of chromosomes2019

    • Author(s)
      炭竈享司
    • Organizer
      Joint UBI-NanoLSI workshop "Trends in Molecular Biophysics of Living Cells"
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 間期と分裂期の染色体の3D-AFM像の理論的予測2019

    • Author(s)
      炭竈享司、宮澤佳甫、Adam S. Foster、福間剛士
    • Organizer
      日本分子生物学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 染色体の3D-AFM像の理論予測2019

    • Author(s)
      炭竈享司、福間剛士
    • Organizer
      生物物理学会中部支部会
    • Related Report
      2018 Research-status Report
  • [Presentation] 3D-AFM像の理論予測とHS-AFMの動画解析2019

    • Author(s)
      炭竈享司
    • Organizer
      第2回CREST会議(研究課題名:高速原子間力顕微鏡1分子計測のデータ同化による生体分子4次元構造解析法の開発)
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] KcsAチャネルでのK+とNa+の選択的透過のMDシミュレーションによる再現2018

    • Author(s)
      炭竈享司
    • Organizer
      第3回イオンチャネル研究会チャネルフェニックス
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Computational modeling of chromosomes and carbon nanotubes as a probe of atomic force microscopy2018

    • Author(s)
      炭竈享司、宮澤佳甫、日笠山拓、中山響介、原田昌征、福間剛士
    • Organizer
      Biophysical Society Thematic Meeting on the Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] K+チャネルでのイオンの透過と選択性の誤謬:どこで何を間違えたか?2018

    • Author(s)
      炭竈享司
    • Organizer
      蛋白研研究会「構造情報に基づいた膜イオン輸送タンパク質の生理機能の解明に向けて 」
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Na+イオンはKcsA K+チャネルを遅いが透過する2018

    • Author(s)
      炭竈享司、三田建一郎、老木成稔
    • Organizer
      日本生物物理学会
    • Related Report
      2018 Research-status Report
  • [Presentation] Towards elucidating the physical origin of force in AFM measurements and a method analyzing dynamics observed by HS-AFM2018

    • Author(s)
      炭竈享司
    • Organizer
      WPI-NanoLSI workshop "Trends in Computational Molecular Biophysics"
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] An alternative permeation mechanism through the K+ channel2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      日本生理学会
    • Related Report
      2017 Research-status Report
  • [Presentation] イオンチャネルにおけるノックオン機構は本当に重要か?ーその2ー2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      生物物理学会中部支部会
    • Related Report
      2017 Research-status Report
  • [Presentation] Knock-on is not a canonical mechanism for K+ permeation through potassium channels2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      アメリカ生物物理学会
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Is Knock-on the Canonical Mechanism for the Ion Permeation through a Potassium Channel?2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      新学術領域研究「動的秩序と機能」第6回国際シンポジウム
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] K+チャネルを通る電流のMichaelis-Menten様の飽和の分子論的説明2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      分子シミュレーション討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Water orientation in nanocavity of the Kv1.2 channel and its role in ion permeation: A molecular dynamics study2017

    • Author(s)
      炭竈享司
    • Organizer
      Workshop on Reaction and Structural Dynamics in Condensed Phases
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 何がK+チャネルでのイオンの透過速度を決めるか?:分子動力学シミュレーションによる研究2017

    • Author(s)
      炭竈享司
    • Organizer
      ナノ計測勉強会2017
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Spontaneous exits of ions from the KcsA channel2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      日本生物物理学会
    • Related Report
      2017 Research-status Report
  • [Presentation] K+チャネルでのイオン透過におけるイオンと水分子の相互作用の重要性2017

    • Author(s)
      炭竈享司
    • Organizer
      第2回イオンチャネル研究会チャネル七夕
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 計算科学は膜イオン輸送の実験をどこまで再現できるか?:K+チャネルでのイオン透過2017

    • Author(s)
      炭竈享司
    • Organizer
      蛋白研研究会「膜イオン輸送の学際研究:計算科学から医学まで」
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 分布関数の時間発展で生体内現象を解析する:K+チャネルにおけるイオン透過を例に2017

    • Author(s)
      炭竈享司
    • Organizer
      第16回計算分子化学コロキウム
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] イオンチャネルでのイオン透過を分布関数の時間発展で捉える2017

    • Author(s)
      炭竈享司、老木成稔
    • Organizer
      理論化学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] イオンチャネルを通るイオン透過における水分子の役割:モデルチャネルとK+チャネルを例に2017

    • Author(s)
      炭竈享司
    • Organizer
      福井大学遠赤外領域開発研究センターセミナー
    • Related Report
      2017 Research-status Report
    • Invited
  • [Remarks] サソリ毒ペプチドが効率的にK+チャネルを阻害する仕組みを世界で初めて解明!

    • URL

      https://nanolsi.kanazawa-u.ac.jp/achievements/achievements-7257/

    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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