OHNUKI, Jun

写真a

Affiliation

Faculty of Science and Engineering, Waseda Research Institute for Science and Engineering

Job title

Junior Researcher(Assistant Professor)

Education 【 display / non-display

  • 2010.04
    -
    2016.03

    Waseda university   Graduate School of Advanced Science and Engineering   Department of Pure and Applied Physics  

  • 2006.04
    -
    2010.03

    Waseda university   School of Science and Engineering   Deptarment of Physics  

Degree 【 display / non-display

  • Waseda university   Doctor of Philosophy

Research Experience 【 display / non-display

  • 2016.04
    -
    2019.03

    Waseda university   Department of Physics, School of Advanced Science and Engineering   Research Associate

Professional Memberships 【 display / non-display

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    Biophysical Society

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    The Biophysical Society of Japan

 

Research Areas 【 display / non-display

  • Biophysics, chemical physics and soft matter physics

  • Biophysics

Research Interests 【 display / non-display

  • 生体分子間相互作用

  • 分子動力学シミュレーション

  • 分子機械

  • 分子モーター

  • アロステリー

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Papers 【 display / non-display

  • Coupling of Redox and Structural States in Cytochrome P450 Reductase Studied by Molecular Dynamics Simulation

    Mikuru Iijima, Jun Ohnuki, Takato Sato, Masakazu Sugishima, Mitsunori Takano

    Scientific Reports   9   9341  2019.12  [Refereed]

     View Summary

    Cytochrome P450 reductase (CPR) is the key protein that regulates the electron transfer from NADPH to various heme-containing monooxygenases. CPR has two flavin-containing domains: one with flavin adenine dinucleotide (FAD), called FAD domain, and the other with flavin mononucleotide (FMN), called FMN domain. It is considered that the electron transfer occurs via FAD and FMN (NADPH → FAD → FMN → monooxygenase) and is regulated by an interdomain open-close motion. It is generally thought that the structural state is coupled with the redox state, which, however, has not yet been firmly established. In this report, we studied the coupling of the redox and the structural states by full-scale molecular dynamics (MD) simulation of CPR (total 86.4 μs). Our MD result showed that while CPR predominantly adopts the closed state both in the oxidized and reduced states, it exhibits a tendency to open in the reduced state. We also found a correlation between the FAD-FMN distance and the predicted FMN-monooxygenase distance, which is embedded in the equilibrium thermal fluctuation of CPR. Based on these results, a physical mechanism for the electron transfer by CPR is discussed.

    DOI

  • Reply: Hydrophobic surface enhances electrostatic interaction in water

    J Ohnuki, T Sato, T Sasaki, K Umezawa, M Takano

    Physical Review Letters   123 ( 4 ) 049602  2019.07  [Refereed]

    DOI

  • Hydrophobic surface enhances electrostatic interaction in water

    T Sato, T Sasaki, J Ohnuki, K Umezawa, M Takano

    Physical Review Letters   121 ( 20 ) 206002  2018.11  [Refereed]

     View Summary

    A high dielectric constant is one of the peculiar properties of liquid water, indicating that the electrostatic interaction between charged substances is largely reduced in water. We show by molecular dynamics simulation that the dielectric constant of water is decreased near the hydrophobic surface. We further show that the decrease in the dielectric constant is due to both the decreased water density and the reduced water dipole correlation in the direction perpendicular to the surface. We finally demonstrate that electrostatic interaction in water is actually strengthened near the hydrophobic surface.

    DOI

  • Long-range coupling between ATP-binding and lever-arm regions in myosin via dielectric allostery

    Takato Sato, Jun Ohnuki, Mitsunori Takano

    JOURNAL OF CHEMICAL PHYSICS   147 ( 21 ) 215101  2017.12  [Refereed]

     View Summary

    A protein molecule is a dielectric substance, so the binding of a ligand is expected to induce dielectric response in the protein molecule, considering that ligands are charged or polar in general. We previously reported that binding of adenosine triphosphate (ATP) to molecular motor myosin actually induces such a dielectric response in myosin due to the net negative charge of ATP. By this dielectric response, referred to as "dielectric allostery," spatially separated two regions in myosin, the ATP-binding region and the actin-binding region, are allosterically coupled. In this study, from the statistically stringent analyses of the extensive molecular dynamics simulation data obtained in the ATP-free and the ATP-bound states, we show that there exists the dielectric allostery that transmits the signal of ATP binding toward the distant lever-arm region. The ATP-binding-induced electrostatic potential change observed on the surface of the main domain induced a movement of the converter subdomain from which the lever arm extends. The dielectric response was found to be caused by an underlying large-scale concerted rearrangement of the electrostatic bond network, in which highly conserved charged/polar residues are involved. Our study suggests the importance of the dielectric property for molecular machines in exerting their function. Published by AIP Publishing.

    DOI

  • Electrostatic balance between global repulsion and local attraction in reentrant polymerization of actin

    Jun Ohnuki, Akira Yodogawa, Mitsunori Takano

    CYTOSKELETON   74 ( 12 ) 504 - 511  2017.12  [Refereed]

     View Summary

    Actin polymerization depends on the salt concentration, exhibiting a reentrant behavior: the polymerization is promoted by increasing KCl concentration up to 100 mM, and then depressed by further increase above 100 mM. We here investigated the physical mechanism of this reentrant behavior by calculating the polymerization energy, defined by the electrostatic energy change upon binding of an actin subunit to a filament, using an implicit solvent model based on the Poisson-Boltzmann (PB) equation. We found that the polymerization energy as a function of the salt concentration shows a non-monotonic reentrant-like behavior, with the minimum at about 100 mM (1:1 salt). By separately examining the salt concentration effect on the global electrostatic repulsion between the like-charged subunits and that on the local electrostatic attraction between the inter-subunit ionic-bond-forming residues in the filament, we clarified that the reentrant behavior is caused by the change in the balance between the two opposing electrostatic interactions. Our study showed that the non-specific nature of counterions, as described in the mean-field theory, plays an important role in the actin polymerization. We also discussed the endothermic nature of the actin polymerization and mentioned the effect of ATP hydrolysis on the G-F transformation, indicating that the electrostatic interaction is widely and intricately involved in the actin dynamics.

    DOI

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Misc 【 display / non-display

  • 26aXZC-11 Contribution of loop region and electrostatic interaction to binding of kinesin to microtuble

    Mizuhara Y., Ohnuki J., Umezawa K., Takano M.

    Meeting abstracts of the Physical Society of Japan   68 ( 1 ) 419 - 419  2013.03

    CiNii

Awards 【 display / non-display

  • 若手招待講演賞

    2020.09   日本生物物理学会   非リボソーム分子機械によるペプチド合成の静電的ラチェット機構

    Winner: 大貫 隼

  • 第 9 期アーリーバードプログラム 若手研究者奨励賞

    2020.03   早稲田大学理工学術院総合研究所  

    Winner: 大貫 隼

Specific Research 【 display / non-display

  • 圧電アロステリーによるメカノトランスダクション:結合エネルギー解析による定量化

    2018   高野 光則

     View Summary

    筋収縮や細胞内物質輸送はミオシンとアクチン繊維から成るタンパク質複合体が駆動する。申請者らはこれまでミオシン、アクチンに力学的入力を与えると圧電的な分子内情報伝達(アロステリー)が生じることを明らかにし、これがミオシン-アクチン間結合制御および力発生をもたらす示唆を得た。本研究では、この静電応答が分子間結合に与える影響を解明するため、まず分子動力学計算により結合自由エネルギーに対する静電相互作用の寄与の定量化を試みた。結合自由エネルギーの定量化には今後さらなる調査が必要であるが、ポテンシャルエネルギー解析と結合領域解析から、静電相互作用が分子間結合の安定化に確かに寄与することが示された。

  • 圧電アロステリーによるメカノトランスダクションの定量解析

    2018   高野 光則

     View Summary

    真核細胞に最も多く含まれるタンパク質アクチンは、アデノシン三リン酸の加水分解という化学的入力を分子間相互作用変化へと変換するケモトランスダクション、さらに張力という力学的入力を分子間相互作用へと変換するメカノトランスダクションを行い、自身の重合・脱重合を制御することで細胞運動を駆動する。本研究では化学的入力、力学的入力に対するアクチンの応答を大規模分子動力学計算により調査し、アクチンの誘電性・圧電性に起因した分子内情報伝達機構(アロステリー)が存在することを発見した。そしてこの静電的応答が分子間結合を制御できることを相互作用エネルギー解析から示した。

  • 蛋白質の圧電効果が外力依存的な分子間相互作用変化をもたらすのか?

    2017   高野 光則

     View Summary

    アクチンフィラメントが張力に応答してミオシン、コフィリンといったアクチン結合蛋白質との相互作用を変化させる物理機構を明らかにするため、アクチンフィラメントに張力を課した分子動力学(MD)シミュレーションを実施した。その結果、張力によってアクチン分子表面の静電ポテンシャルが変化することが示され、アクチンフィラメントに圧電性が備わっていることを明らかにした。さらに、MDシミュレーションで得られたアクチンフィラメントの構造集団を基に、アクチン結合蛋白質との複合体を構築し、分子間の静電相互作用エネルギーがアクチンフィラメントの圧電応答によって変化することを捉えることができた。