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Cross-scale analysis of temperature compensation in the cyanobacterial circadian clock system

古池 美彦*; Ouyang, D.*; 富永 大輝*; 松尾 龍人*; 向山 厚*; 川北 至信; 藤原 悟*; 秋山 修志*

Communications Physics (Internet), 5, p.75_1 - 75_12, 2022/04

Circadian clock proteins often reveal temperature-compensatory responses that counteract temperature influences to keep their enzymatic activities constant over a physiological range of temperature. This temperature-compensating ability at the reaction level is likely crucial for circadian clock systems, to which the clock proteins are incorporated, to achieve the system-level temperature compensation of the oscillation frequency. Nevertheless, temperature compensation is yet a puzzling phenomenon, since side chains that make up the clock proteins fluctuate more frequently due to greater thermal energy at higher temperature. Here, we investigated temperature influences on the dynamics of KaiC, a temperature-compensated enzyme (ATPase) that hydrolyzes ATP into ADP in the cyanobacterial circadian clock system, using quasielastic neutron scattering. The frequency of picosecond to subnanosecond incoherent local motions in KaiC was accelerated by a factor of only 1.2 by increasing the temperature by 10$$^{circ}$$C. This temperature insensitivity of the local motions was not necessarily unique to KaiC, but confirmed also for a series of temperature-sensitive mutants of KaiC and proteins other than clock-related proteins. Rather, the dynamics associated with the temperature-compensatory nature of the reaction- and system-level was found in global diffusional motions, which was suggested to regulate the temperature dependence of ATPase activity and dephosphorylation process presumably through changes in the hexamer conformation of KaiC. The spatiotemporal scale at which cross-scale causality of the temperature sensitivity is established is finite, and extends down to picosecond to subnanosecond dynamics only in a very limited part of KaiC, not in its entire part.


High temperature gas-cooled reactors

武田 哲明*; 稲垣 嘉之; 相原 純; 青木 健; 藤原 佑輔; 深谷 裕司; 後藤 実; Ho, H. Q.; 飯垣 和彦; 今井 良行; et al.

High Temperature Gas-Cooled Reactors; JSME Series in Thermal and Nuclear Power Generation, Vol.5, 464 Pages, 2021/02



Segmental motions of proteins under non-native states evaluated using quasielastic neutron scattering

藤原 悟*; 松尾 龍人*; 杉本 泰伸*; 柴田 薫

Journal of Physical Chemistry Letters (Internet), 10(23), p.7505 - 7509, 2019/12

 被引用回数:0 パーセンタイル:0.01(Chemistry, Physical)

無秩序なポリペプチド鎖のダイナミクスの特性評価は、本質的に無秩序状態なタンパク質およびフォールディングプロセスに関連する非ネイティブ状態下のタンパク質の挙動を解明するために必要である。本研究では、小角X線散乱測定データと動的光散乱測定データと組み合わせて準弾性中性子散乱測定データから、タンパク質のセグメント運動と分子全体の拡散および局所側鎖運動を評価する方法を独自に開発した。そしてこの方法を、非フォールディング状態およびメルトグロビュール(MG)状態のタンパク質RNase Aに適用し、セグメント運動から生じる拡散係数を評価し、非フォールディング状態とMG状態で異なる値をとることを明らかにした。またこの方法で得られた値は、蛍光現象を用いた別の測定技術を使用して得られた値と一致していることも確認できた。これらの研究成果は、この方法の、さまざまな無秩序状態でのタンパク質の挙動を特徴付ける実行可能性だけでなく、有用性も示している。


Dynamic properties of human $$alpha$$-synuclein related to propensity to amyloid fibril formation

藤原 悟*; 河野 史明*; 松尾 龍人*; 杉本 泰伸*; 松本 友治*; 成田 哲博*; 柴田 薫

Journal of Molecular Biology, 431(17), p.3229 - 3245, 2019/08

 被引用回数:3 パーセンタイル:27.91(Biochemistry & Molecular Biology)



Revising the 4${it f}$ symmetry in CeCu$$_{2}$$Ge$$_{2}$$; Soft X-ray absorption and hard X-ray photoemission spectroscopy

荒谷 秀和*; 中谷 泰博*; 藤原 秀紀*; 川田 萌樹*; 金井 惟奈*; 山神 光平*; 藤岡 修平*; 濱本 諭*; 久我 健太郎*; 木須 孝幸*; et al.

Physical Review B, 98(12), p.121113_1 - 121113_6, 2018/09


 被引用回数:3 パーセンタイル:24.8(Materials Science, Multidisciplinary)

We present a detailed study on the $$4f$$ ground state symmetry of the pressure-induced superconductor CeCu$$_2$$Ge$$_2$$ probed by soft X-ray absorption and hard X-ray photoemission spectroscopy. The revised Ce $$4f$$ ground states are determined as $$|{Gamma_7}rangle=sqrt{0.45}|{J_{z}=pm frac{5}{2}}rangle - sqrt{0.55}|{mp frac{3}{2}}rangle$$ with $$Sigmamathchar`-{rm type}$$ in-plane rotational symmetry. This gives an in-plane magnetic moment consistent with the antiferromagnetic moment as reported in neutron measurements. Since the in-plane symmetry is the same as that for the superconductor CeCu$$_2$$Si$$_2$$, we propose that the charge distribution along the $$c$$-axis plays an essential role in driving the system into a superconducting phase.


Difference in the hydration water mobility around F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

松尾 龍人; 荒田 敏昭*; 小田 俊郎*; 中島 健次; 河村 聖子; 菊地 龍弥; 藤原 悟

Biochemistry and Biophysics Reports (Internet), 6, p.220 - 225, 2016/07

Hydration water is essential for a protein to perform its biological function properly. In this study, the dynamics of hydration water around F-actin and myosin subfragment-1 (S1), which are the partner proteins playing a major role in various cellular functions related to cell motility, was characterized by incoherent quasielastic neutron scattering (QENS). The QENS spectra of hydration water around F-actin and S1 provided the translational diffusion coefficient, the residence time, and the rotational correlation time. The differences in these parameters indicate a significant difference in mobility of the hydration water between S1 and F-actin: S1 has the typical hydration water, the mobility of which is reduced compared with that of bulk water, while F-actin has the unique hydration water, the mobility of which is close to that of bulk water rather than the typical hydration water around proteins.


Dynamical behavior of human $$alpha$$-synuclein studied by quasielastic neutron scattering

藤原 悟; 荒木 克哉*; 松尾 龍人; 八木 寿梓*; 山田 武*; 柴田 薫; 望月 秀樹*

PLOS ONE (Internet), 11(4), p.e0151447_1 - e0151447_17, 2016/04

 被引用回数:18 パーセンタイル:67.4(Multidisciplinary Sciences)

Filamentous aggregates (amyloid fibrils) of the protein $$alpha$$-synuclein ($$alpha$$-Syn) are related to the pathogenesis of Parkinson's disease. To understand the pathogenesis mechanism of this disease, the mechanism of the amyloid fibril formation of $$alpha$$-Syn must be elucidated. As a first step toward this ultimate goal, dynamical behavior of $$alpha$$-Syn in the monomeric and the fibril states was investigated using quasielastic neutron scattering (QENS). Analysis of the QENS spectra of solution samples of $$alpha$$-Syn shows that diffusive global motions are observed in the monomeric state but largely suppressed in the fibril state. However, the amplitude of the side chain motion is shown to be larger in the fibril state than in the monomeric state. This implies that significant solvent space exists within the fibrils, which is attributed to the $$alpha$$-Syn molecules within the fibrils having a distribution of conformations. The larger amplitude of the side chain motion in the fibril state than in the monomeric state implies that the fibril state is entropically favorable.


A Technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography

茶竹 俊行*; 藤原 悟

Acta Crystallographica Section D; Structural Biology (Internet), 72(1), p.71 - 82, 2016/01

 被引用回数:3 パーセンタイル:31.37(Biochemical Research Methods)

A technique for the determination of the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography has been developed and evaluated using ribonuclease A. In this technique, the contrast map between the D$$_{2}$$O-solvent and H$$_{2}$$O-solvent crystals is calculated using subtraction in real space. The present technique can thus utilize all the amplitudes of the neutron structure factors for both of the D$$_{2}$$O-solvent and H$$_{2}$$O solvent crystals. The neutron D/H contrast maps clearly demonstrate powerful detectability of the H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at a medium resolution (1.8 AA ). Moreover, water molecules can be categorized into three types according to their tendency for rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. Combination of this technique with the conventional neutron structure determination protocols thus makes more precise and efficient determination of the D atom positions in proteins possible.


Structures of the troponin core domain containing the cardiomyopathy-causing mutants studied by small-angle X-ray scattering

松尾 龍人; 武田 壮一*; 小田 俊郎*; 藤原 悟

Biophysics and Physicobiology (Internet), 12, p.145 - 158, 2015/12

Troponin (Tn), consisting of three subunits, TnC, TnI, and TnT, is a protein that plays a major role in regulation of muscle contraction. Various mutations of Tn cause familial hypertrophic cardiomyopathy. Here we focus on the mutations E244D and K247R of TnT, which induce an increase in the maximum tension of cardiac muscle without changes in Ca$$^{2+}$$-sensitivity, and carried out small-angle X-ray scattering experiments on the Tn core domain containing the wild type subunits and those containing the mutant TnT in the absence and presence of Ca$$^{2+}$$. Changes in the overall shape induced by the mutations were detected for the first time by the changes in the radius of gyration and the maximum dimension between the wild type and the mutants. Analysis by model calculations shows that TnC adopts a dumbbell structure regardless of the mutations, and that the mutations change the distributions of the conformational ensembles so that the flexible N- and C-terminal regions of TnT become close to the center of the whole molecule.


Internal dynamics of F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

松尾 龍人; 荒田 敏昭*; 小田 俊郎*; 中島 健次; 河村 聖子; 菊地 龍弥; 藤原 悟

Biochemical and Biophysical Research Communications, 459(3), p.493 - 497, 2015/04

 被引用回数:4 パーセンタイル:16.86(Biochemistry & Molecular Biology)

Various biological functions related to cell motility are driven by the interaction between the partner proteins, actin and myosin. To obtain insights into how this interaction occurs, the internal dynamics of F-actin and myosin subfragment-1 (S1) were characterized by quasielastic neutron scattering measurements on the solution samples of F-actin and S1. Contributions of the internal motions of the proteins to the scattering spectra were separated from those of the global macromolecular diffusion. Analysis of the spectra arising from the internal dynamics showed that the correlation times of the atomic motions were about two times shorter for F-actin than for S1, suggesting that F-actin fluctuates more rapidly than S1. It was also shown that the fraction of the immobile atoms is larger for S1 than for F-actin. These results suggest that F-actin actively facilitates the binding of myosin by utilizing the more frequent conformational fluctuations than those of S1.



田代 孝二*; 塙坂 真*; 山元 博子*; Wasanasuk, K.*; Jayaratri, P.*; 吉澤 功徳*; 田中 伊知朗*; 新村 信雄*; 日下 勝弘*; 細谷 孝明*; et al.

高分子論文集, 71(11), p.508 - 526, 2014/11

 被引用回数:5 パーセンタイル:22.7(Polymer Science)



Difference in hydration structures between F-actin and myosin subfragment-1 detected by small-angle X-ray and neutron scattering

松尾 龍人; 荒田 敏昭*; 小田 俊郎*; 藤原 悟

Biophysics, 9, p.99 - 106, 2013/07

Hydration structures around F-actin and myosin subfragment-1 (S1), which play central roles as counterparts in muscle contraction, were investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The radius of gyration of S1 was evaluated to be 41.3 $$pm$$ 1.1 ${AA}$ for SAXS, 40.1 $$pm$$ 3.0 ${AA}$ for SANS in H$$_{2}$$O, and 37.8 $$pm$$ 0.8 ${AA}$ for SANS in D$$_{2}$$O, respectively. The values of the cross-sectional radius of gyration of F-actin were 25.4 $$pm$$ 0.03 ${AA}$ for SAXS, 23.4 $$pm$$ 2.4 ${AA}$ for SANS in H$$_{2}$$O, and 22.6 $$pm$$ 0.6 ${AA}$ for SANS in D$$_{2}$$O, respectively. Analysis showed that the hydration shell of S1 has the average density 10-15% higher than bulk water, being the typical hydration shell, while the hydration shell of F-actin has the average density more than 19% higher than bulk water, indicating that F-actin has a denser, unusual hydration structure. The results indicate a difference in the hydration structures around F-actin and S1.


Coupling of the hydration water dynamics and the internal dynamics of actin detected by quasielastic neutron scattering

藤原 悟; Plazanet, M.*; 小田 俊郎*

Biochemical and Biophysical Research Communications, 431(3), p.542 - 546, 2013/02

 被引用回数:4 パーセンタイル:13.91(Biochemistry & Molecular Biology)

Quasi-elastic neutron scattering experiments of powder samples of F-actin and G-actin, hydrated either with D$$_{2}$$O or H$$_{2}$$O, at hydration ratios of 0.4 and 1.0, were performed. Combined analysis of the quasi-elastic neutron scattering spectra provided the parameters characterizing the water dynamics in the first hydration layer and those outside of the first layer. The translational diffusion coefficients (D$$_{T}$$) of the hydration water in the first layer were found to be 1.2 $$times$$ 10$$^{-5}$$ cm$$^{2}$$/s and 1.7 $$times$$ 10$$^{-5}$$ cm$$^{2}$$/s for F-actin and G-actin, respectively, while that for bulk water was 2.8 $$times$$ 10$$^{-5}$$ cm$$^{2}$$/s. The residence times were 6.6 ps and 5.0 ps for F-actin and G-actin, respectively, while that for bulk water was 0.63 ps. These differences between F-actin and G-actin, indicating that the hydration water around G-actin is more mobile than that around F-actin, are in concert with the results of the internal dynamics of F-actin and G-actin, showing that G-actin fluctuates more rapidly than F-actin. This implies that the dynamics of the hydration water is coupled to the internal dynamics of the actin molecules. The D$$_{T}$$ values of the water molecules outside of the first hydration layer were found to be similar to that of bulk water though the residence times are strongly affected by the first hydration layer. This supports the recent observation on intracellular water that shows bulk-like behavior.



藤原 悟; 中川 洋

波紋, 23(1), p.72 - 80, 2013/02



Dynamics of cardiomyopathy-causing mutant of troponin measured by neutron scattering

松尾 龍人; Natali, F.*; Plazanet, M.*; Zaccai, G.*; 藤原 悟

Journal of the Physical Society of Japan, 82(Suppl.A), p.SA020_1 - SA020_5, 2013/01

 被引用回数:1 パーセンタイル:12.72(Physics, Multidisciplinary)

トロポニンと呼ばれる蛋白質は、心筋の収縮を細胞内カルシウム濃度依存的に調節する。また、トロポニン分子内に起こるさまざまな変異が、肥大型心筋症等の疾患に繋がることが知られている。変異によってトロポニン分子の機能に異常が起こり、疾患へと繋がる。蛋白質が機能するためには、それを構成する原子の熱揺らぎ(ダイナミクス)が必須であると考えられているため、変異によるトロポニンの機能変化がダイナミクスの違いに起因する可能性が考えられる。そこで、変異によるトロポニンのダイナミクス変化を検出するために、野生型及び変異型(K247R)ヒト心筋トロポニンの溶液試料を用いて中性子散乱実験を行った。実験はフランスILLのIN13分光器を用いて行い、280Kから292Kの温度範囲を3Kごとに変化させて弾性散乱強度を測定した。得られたデータから見かけのバネ定数(蛋白質の柔らかさの指標)を計算すると、0.077N/m(野生型), 0.046N/m(変異型)となった。この結果は、変異によりトロポニン分子全体の柔軟性が増大することを示している。分子全体が過度に柔軟になることで、トロポニンのカルシウムシグナル伝達機構が正常に機能しなくなると考えられる。



中川 洋; 藤原 悟

波紋, 22(3), p.268 - 273, 2012/08

Proteins are constantly fluctuating under the influence of environment. These thermal fluctuations, or dynamics, of the proteins at a picosecond time scale are known to be indispensable for functions of the proteins. Neutron inelastic scattering provides a unique tool to directly measure dynamics of the proteins. In particular, since the incoherent neutron scattering cross section of hydrogen is significantly larger than any other atoms commonly found in biological materials, the techniques of incoherent neutron scattering is important for the measurements of the dynamics of the protein, a half of the atoms in which are hydrogen atoms. Furthermore, since a distribution of hydrogen atoms is fairly homogeneous in the protein, the neutron scattering spectra arising from hydrogen atoms in the proteins provides a global view of the protein dynamics. Here, various aspects of three techniques of incoherent neutron scattering: elastic incoherent neutron scattering, quasi-elastic neutron scattering, and inelastic neutron scattering, are briefly described as a basis for application to characterization of the protein dynamics.


Repetition Rate Multiplication: RRM, an advanced measuring method planed for the backscattering instrument, ${it DNA}$ at the MLF, J-PARC

高橋 伸明; 柴田 薫; 川北 至信; 中島 健次; 稲村 泰弘; 中谷 健; 中川 洋; 藤原 悟; 佐藤 卓*; 筑紫 格*; et al.

Journal of the Physical Society of Japan, 80(Suppl.B), p.SB007_1 - SB007_4, 2011/12

 被引用回数:5 パーセンタイル:41.54(Physics, Multidisciplinary)

A TOF-BSS named ${it DNA}$ has been under construction on BL02 in the MLF of J-PARC. We have estimated expected performances of several candidates under realistic neutron source parameters at MLF. The expected neutron intensity under comparable energy resolutions of the ${it DNA}$-type is 2.6 times higher than that of the BASIS-type. Consequently, we have chosen the CM with pulse-shaping device for ${it DNA}$. Pulse-shaping is a good technique from a view point of a variability of resolution. On the other hand, a neutron energy band passing through the pulse-shaping chopper is limited and thus scanning range with one phase of the chopper is narrow. Of course, ${it DNA}$ also can access larger energy transfers by appropriate phasing of the pulse-shaping chopper. In addition, ${it DNA}$ will be able to utilize Repetition Rate Multiplication (RRM). RRM is essentially a way to employ multiple pulse-shaped incident neutron beams to effectively increase neutron counting time to more efficiently measure the inelastic region. In this presentation we will show the chopper sequence and introduce the RRM mode of the forthcoming backscattering spectrometer ${it DNA}$ in detail.


Event structure and double helicity asymmetry in jet production from polarized $$p + p$$ collisions at $$sqrt{s}$$ = 200 GeV

Adare, A.*; Afanasiev, S.*; Aidala, C.*; Ajitanand, N. N.*; Akiba, Y.*; Al-Bataineh, H.*; Alexander, J.*; Aoki, K.*; Aphecetche, L.*; Armendariz, R.*; et al.

Physical Review D, 84(1), p.012006_1 - 012006_18, 2011/07

 被引用回数:25 パーセンタイル:72.31(Astronomy & Astrophysics)

重心エネルギー200GeVでの縦偏極陽子陽子衝突からのジェット生成のイベント構造と二重非対称($$A_{LL}$$)について報告する。光子と荷電粒子がPHENIX実験で測定され、イベント構造がPHYTIAイベント生成コードの結果と比較された。再構成されたジェットの生成率は2次までの摂動QCDの計算で十分再現される。測定された$$A_{LL}$$は、一番低い横運動量で-0.0014$$pm$$0.0037、一番高い横運動量で-0.0181$$pm$$0.0282であった。この$$A_{LL}$$の結果を幾つかの$$Delta G(x)$$の分布を仮定した理論予想と比較する。


Identified charged hadron production in $$p + p$$ collisions at $$sqrt{s}$$ = 200 and 62.4 GeV

Adare, A.*; Afanasiev, S.*; Aidala, C.*; Ajitanand, N. N.*; 秋葉 康之*; Al-Bataineh, H.*; Alexander, J.*; 青木 和也*; Aphecetche, L.*; Armendariz, R.*; et al.

Physical Review C, 83(6), p.064903_1 - 064903_29, 2011/06

 被引用回数:156 パーセンタイル:99.42(Physics, Nuclear)

200GeVと62.4GeVでの陽子陽子の中心衝突からの$$pi, K, p$$の横運動量分布及び収量をRHICのPHENIX実験によって測定した。それぞれエネルギーでの逆スロープパラメーター、平均横運動量及び単位rapidityあたりの収量を求め、異なるエネルギーでの他の測定結果と比較する。また$$m_T$$$$x_T$$スケーリングのようなスケーリングについて示して陽子陽子衝突における粒子生成メカニズムについて議論する。さらに測定したスペクトルを二次の摂動QCDの計算と比較する。



藤原 悟

生物物理, 51(3), p.138 - 139, 2011/06


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