氏名

オオヌキ ジュン

大貫 隼

職名

次席研究員(研究院講師) (https://researchmap.jp/7000017497/)

所属

(理工学術院総合研究所)

連絡先

メールアドレス

メールアドレス
j.ohnuki.825@aoni.waseda.jp

URL等

研究者番号
90777989
ORCID ID
0000-0002-7351-3427

学歴・学位

学歴

2006年04月-2010年03月 早稲田大学 理工学部 物理学科
2010年04月-2016年03月 早稲田大学 先進理工学研究科 物理学及応用物理学専攻

学位

修士(理学) 課程 早稲田大学 生物物理学

経歴

2016年04月-早稲田大学先進理工学部物理学科助手

所属学協会

日本生物物理学会

Biophysical Society

研究分野

キーワード

蛋白質、アロステリー、分子モーター、分子機械、分子動力学シミュレーション、生体分子間相互作用

科研費分類

生物学 / 生物科学 / 生物物理学

数物系科学 / 物理学 / 生物物理・化学物理・ソフトマターの物理

論文

Hydrophobic surface enhances electrostatic interaction in water

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

Physical Review Letters査読有りin press2018年11月-2018年11月 

link

詳細

掲載種別:研究論文(学術雑誌)

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

J Ohnuki, A Yodogawa, M Takano

Cytoskeleton査読有り74(12)p.504 - 5112017年12月-2017年12月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:19493584

概要:© 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査読有り147(21)p.2151012017年12月-2017年12月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:00219606

概要:© 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査読有り121(18)p.4669 - 46772017年05月-2017年05月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:15206106

概要:© 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査読有り84(8)p.1124 - 11332016年08月-2016年08月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:08873585

概要:© 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査読有り120(51)p.13047 - 130552016年12月-2016年12月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:15206106

概要:© 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査読有り94(1)p.0124062016年07月-2016年07月 

DOI

詳細

掲載種別:研究論文(学術雑誌)ISSN:24700045

概要:© 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査読有りB11p.161 - 1642015年03月-2015年03月 

詳細

掲載種別:研究論文(国際会議プロシーディングス)ISSN:2187204X

学内研究制度

特定課題研究

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年度共同研究者:高野 光則

研究成果概要: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...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

2018年度共同研究者:高野 光則

研究成果概要: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...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

2018年度共同研究者:高野 光則

研究成果概要: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...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。