Name

OHNUKI, Jun

Official Title

Junior Researcher(Assistant Professor)

Affiliation

(Waseda Research Institute for Science and Engineering)

Contact Information

Mail Address

Mail Address
j.ohnuki.825@aoni.waseda.jp

URL

Grant-in-aids for Scientific Researcher Number
90777989
ORCID ID
0000-0002-7351-3427

Educational background・Degree

Educational background

2006/04 -2010/03 Waseda university School of Science and Engineering Deptarment of Physics
2010/04 -2016/03 Waseda university Graduate School of Advanced Science and Engineering Department of Pure and Applied Physics

Degree

Doctor of Philosophy Coursework Waseda university Biophysics

Career

2016/04-2019/03Waseda universityDepartment of Physics, School of Advanced Science and EngineeringResearch Associate

Academic Society Joined

The Biophysical Society of Japan

Biophysical Society

Paper

Reply: Hydrophobic surface enhances electrostatic interaction in water

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

Physical Review Letters Peer Review Yes 123(4) p.0496022019/07-2019/07

DOIlink

Detail

Publish Classification:Research paper (scientific journal)

Coupling of redox and structural states in cytochrome P450 reductase studied by molecular dynamics simulation

M Iijima, J Ohnuki, T Sato, M Sugishima, M Takano

Scientific Reports Peer Review Yes 9p.93412019/06-2019/06

DOIlink

Detail

Publish Classification:Research paper (scientific journal)

Outline: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.

Hydrophobic surface enhances electrostatic interaction in water

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

Physical Review Letters Peer Review Yes 121(20) p.2060022018/11-2018/11

DOIlink

Detail

Publish Classification:Research paper (scientific journal)

Outline: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.

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

J Ohnuki, A Yodogawa, M Takano

Cytoskeleton Peer Review Yes 74(12) p.504 - 5112017/12-2017/12

DOI

Detail

Publish Classification:Research paper (scientific journal) ISSN:19493584

Outline:© 2017 Wiley Periodicals, Inc. 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.

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

T Sato, J Ohnuki, M Takano

Journal of Chemical Physics Peer Review Yes 147(21) p.2151012017/12-2017/12

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Detail

Publish Classification:Research paper (scientific journal) ISSN:00219606

Outline:© 2017 Author(s). 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.

Over-destabilization of protein-protein interaction in generalized Born model and utility of energy density integration cutoff

Y Mizuhara, D Parkin, K Umezawa, J Ohnuki, M Takano

Journal of Physical Chemistry B Peer Review Yes 121(18) p.4669 - 46772017/05-2017/05

DOI

Detail

Publish Classification:Research paper (scientific journal) ISSN:15206106

Outline:© 2017 American Chemical Society. The generalize Born (GB) model is frequently used in MD simulations of biomolecular systems in aqueous solution. The GB model is usually based on the so-called Coulomb field approximation (CFA) for the energy density integration. In this study, we report that the GB model with CFA overdestabilizes the long-range electrostatic attraction between oppositely charged molecules (ionic bond forming two-helix system and kinesin-tubulin system) when the energy density integration cutoff, r max , which is used to calculate the Born energy, is set to a large value. We show that employing large r max , which is usually expected to make simulation results more accurate, worsens the accuracy so that the attraction is changed into repulsion. It is demonstrated that the overdestabilization is caused by the overestimation of the desolvation penalty upon binding that originates from CFA. We point out that the overdestabilization can be corrected by employing a relatively small cutoff (r max = 10-15 Å), affirming that the GB models, even with CFA, can be used as a powerful tool to theoretically study the protein-protein interaction, particularly on its dynamical aspect, such as binding and unbinding.

Intrinsic disorder accelerates dissociation rather than association

K Umezawa, J Ohnuki, J Higo, M Takano

Proteins: Structure, Function and Bioinformatics Peer Review Yes 84(8) p.1124 - 11332016/08-2016/08

DOI

Detail

Publish Classification:Research paper (scientific journal) ISSN:08873585

Outline:© 2016 Wiley Periodicals, Inc.The intrinsically disordered protein (IDP) has distinct properties both physically and biologically: it often becomes folded when binding to the target and is frequently involved in signal transduction. The physical property seems to be compatible with the biological property where fast association and dissociation between IDP and the target are required. While fast association has been well studied, fueled by the fly-casting mechanism, the dissociation kinetics has received less attention. We here study how the intrinsic disorder affects the dissociation kinetics, as well as the association kinetics, paying attention to the interaction strength at the binding site (i.e., the quality of the “fly lure”). Coarse-grained molecular dynamics simulation of the pKID-KIX system, a well-studied IDP system, shows that the association rate becomes larger as the disorder-inducing flexibility that was imparted to the model is increased, but the acceleration is marginal and turns into deceleration as the quality of the fly lure is worsened. In contrast, the dissociation rate is greatly enhanced as the disorder is increased, indicating that intrinsic disorder serves for rapid signal switching more effectively through dissociation than association.

Dielectric allostery of protein: Response of myosin to ATP binding

T Sato, J Ohnuki, M Takano

Journal of Physical Chemistry B Peer Review Yes 120(51) p.13047 - 130552016/12-2016/12

DOI

Detail

Publish Classification:Research paper (scientific journal) ISSN:15206106

Outline:© 2017 American Chemical Society. Protein uses allostery to execute biological function. The physical mechanism underlying the allostery has long been studied, with the focus on the mechanical response by ligand binding. Here, we highlight the electrostatic response, presenting an idea of “dielectric allostery”. We conducted molecular dynamics simulations of myosin, a motor protein with allostery, and analyzed the response to ATP binding which is a crucial step in force-generating function, forcing myosin to unbind from the actin filament. We found that the net negative charge of ATP causes a large-scale, anisotropic dielectric response in myosin, altering the electrostatic potential in the distant actin-binding region and accordingly retracting a positively charged actin-binding loop. A large-scale rearrangement of electrostatic bond network was found to occur upon ATP binding. Since proteins are dielectric and ligands are charged/polar in general, the dielectric allostery might underlie a wide spectrum of functions by proteins.

Piezoelectric allostery of protein

J Ohnuki, T Sato, M Takano

Physical Review E Peer Review Yes 94(1) p.0124062016/07-2016/07

DOI

Detail

Publish Classification:Research paper (scientific journal) ISSN:24700045

Outline:© 2016 American Physical Society.Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins.

Criticality of electrostatic network in an allosteric protein

J Ohnuki, M Takano

Proceedings of Waseda AICS Symposium and the 14th Slovenia-Japan Seminar Peer Review Yes B11p.161 - 1642015/03-2015/03

Detail

Publish Classification:Research paper (international conference proceedings) ISSN:2187204X

On-campus Research System

Special Research Project

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?

2017Collaborator:高野 光則

Research Results Outline: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...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。

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

2018Collaborator:高野 光則

Research Results Outline: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...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。

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

2018Collaborator:高野 光則

Research Results Outline: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...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。