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井上 倫太郎*; 小田 隆; 中川 洋; 富永 大輝*; 池上 貴久*; 小沼 剛*; 岩瀬 裕希*; 川北 至信; 佐藤 衛*; 杉山 正明*
Biophysical Journal, 124(3), p.540 - 548, 2025/02
被引用回数：2 パーセンタイル：82.06(Biophysics)Intrinsically disordered proteins (IDPs) show structural changes stimulated by changes in external conditions. This study aims to reveal the temperature dependence of the structure and the dynamics of the intrinsically disordered region of the helicase-associated endonuclease for fork-structured DNA, one of the typical IDPs, using an integrative approach. Small-angle X-ray scattering (SAXS) and circular dichroism (CD) studies revealed that the radius of gyration and ellipticity at 222 nm remained constant up to 313-323 K, followed by a decline above this temperature range. NMR studies revealed the absence of a promotion of the 
-helix. As a result, SAXS, CD, and NMR data strongly suggest that these temperature-dependent structural changes were primarily due to a reduction in the content of the polyproline II (PPII) helix. Moreover, quasielastic neutron scattering studies revealed a slight change in the activation energy in a similar temperature range. Considering the concept of glass transition, it is posited that dynamical cooperativity between the PPII helix and water may play a significant role in these structural changes. The findings suggest that internal dynamics are crucial for regulating the structure of IDPs, highlighting the importance of considering dynamical cooperativity in future studies of protein behavior under varying temperature conditions.
井上 倫太郎*; 長田 裕也*; 富永 大輝*; 佐藤 宗太*; 川北 至信; 山脇 大昇*; 守島 健*; 杉野目 道紀*; 杉山 正明*
Journal of Chemical Physics, 161(5), p.054905_1 - 054905_8, 2024/08
The side chain dynamics of poly(quinoxaline-2,3-diyl)s (PQXs) are expected to influence their conformation. To investigate these dynamics experimentally, quasielastic neutron scattering (QENS) was performed for PQXs in deuterated tetrahydrofuran (THF-
) and deuterated 1,1,2-trichloroethane/THF (1,1,2-TCE-
/THF-), in which they formed right-handed and left-handed helical structures, respectively. The mean-square displacement of the PQX side chains in 1,1,2-TCE-/THF- was lower than that in THF-. Furthermore, QENS complementary studies and molecular dynamics simulations unraveled a coupling between the main-chain and side chain dynamics of PQXs, suggesting the possibility of controlling the main-chain helical chirality through the dynamics of chiral side chains. These insights present a novel strategy for the design of synthetic helical macromolecules with precise chirality control.
菊地 龍弥*; 川北 至信; 中島 健次; 河村 聖子; 稲村 泰弘
Journal of Molecular Liquids, 385, p.121868_1 - 121868_10, 2023/09
We investigated the diffusion dynamics of liquid benzene as a basic molecular liquid. Quasielastic neutron scattering (QENS) was utilized to elucidate the overall behavior of molecular diffusion in liquid benzene. Mode distribution analysis, which does not require specific model assumptions and can describe molecular dynamics by QENS as a distribution of Lorentz functions, revealed that the diffusion of benzene molecules is represented by three dynamic modes. The Q-dependencies of the scattering intensity and the relaxation time were analyzed using diffusion models constructed to match each dynamic mode. (1) The slowest mode is translational diffusion, described as continuous diffusion rather than jump diffusion. (2) The intermediate-speed mode is rotational diffusion, which is due to the three-dimensional reorientation of benzene molecules with a jump angle of approximately 90
. (3) The fastest mode involves local fluctuations, which may originate from translational oscillations and librations of the benzene crystal. The overall picture of the diffusion dynamics and characteristics of the individual modes were clarified without using a model, which is a new approach in the field of diffusion dynamics of molecular liquids.
奥地 拓生*; 富岡 尚敬*; Purevjav, N.*; 柴田 薫
Journal of Applied Crystallography, 51, p.1564 - 1570, 2018/12
被引用回数：2 パーセンタイル：18.28(Chemistry, Multidisciplinary)中性子準弾性散乱(QENS)は、鉱物結晶格子内で起こる原子スケール水素拡散プロセスを分析するための新規かつ有効な方法であることが実証されている。この方法は、凝縮体中の拡散性が高い水素原子または水分子の拡散頻度および距離を分析するために敏感であると以前から考えられていた。本論文では、水酸基として結晶格子に結合している非常に遅い運動の水素原子の拡散運動を分析する応用研究の結果が示されている。ブルーサイト鉱物( brucite)、Mg(OH)
では、水素原子の単一の二次元層面内でのジャンプとそれに最も近い次の層へのジャンプの2種類の水素拡散プロセスが観察された。ブルーサイトの結晶構造内で観察されるこれらの拡散プロセスは、層状構造を有する様々な種類の酸化物およびミネラル内で起こる水素拡散現象にQENS測定が適用可能であることを示している。
吉田 亨次*; 井上 拓也*; 鳥越 基克*; 山田 武*; 柴田 薫; 山口 敏男*
Journal of Chemical Physics, 149(12), p.124502_1 - 124502_10, 2018/09
被引用回数：4 パーセンタイル：14.06(Chemistry, Physical)異なる幾つかの、グリシン濃度, pH、および充填率(=グリシン溶液の質量/MCM-41の乾燥質量))をパラメーターとして、メソポーラスシリカ(MCM-41)に閉じ込められたグリシン水溶液の示差走査熱量測定、X線回折および準弾性中性子散乱(QENS)を305-180Kの温度範囲で実施して、グリシン水溶液の熱的挙動, 構造、および動的特性に対する閉じ込め効果を検討した。
首藤 靖幸*; 和泉 篤士*; 萩田 克美*; 山田 武*; 柴田 薫; 柴山 充弘*
Macromolecules, 51(16), p.6334 - 6343, 2018/08
被引用回数：16 パーセンタイル：46.03(Polymer Science)The dynamics of methanol confined in highly cross-linked phenolic resins was investigated using incoherent quasielastic neutron scattering (QENS) and atomistic molecular dynamics (MD) simulations. The QENS analysis for adeuterated phenolic resin and both deuterated and nondeuterated methanol indicated the presence of resin dynamics induced by methanol invasion and confined diffusion of the methanol molecules. QENS results suggested that methanol had a diffusion coefficient of 1.6 
10
cm
/s, which is 1 order of magnitude smaller than the bulk value (2.3 10
cm/s. The MD trajectories also showed that the methanol diffusion was limited by the resin network, consistent with QENS results in terms of the diffusion coefficient and diffusion-like behavior.
川北 至信
no journal, ,
Japan Proton Accelerator Research Complex (J-PARC) provides us high intense pulsed proton beam. At Materials and Life Science Experimental Facility (MLF), currently 830 kW proton beam produces pulsed neutron beam with the reputation rate of 25 Hz from the mercury target. From the coupled moderator, the highest intense pulsed neutron over the world provides us opportunities to survey material and life sciences. Especially, quasi-elastic neutron scattering (QENS) by utilizing DNA time-of-flight back-scattering spectrometer and AMATERAS double disk chopper spectrometer with direct geometry is the best tool to investigate relaxation phenomena in molecular liquids, softmatters and ionic conductors. In this talk, current status of the instruments will be introduced together with several examples of QENS study and analysis on relaxation phenomena, which involve the mode distribution analysis (MDA) of liquid benzene relating to its molecular motion, proton conduction mechanism of chitin and chitosan which are abundant biomatter forming crab shell, Li conduction of battery material and so on. Analysis of Van Hove function, time-space correlation, of coherent QENS for liquid metals will be also introduced if I have enough time.
松浦 直人*; 川北 至信; 山田 武*; 富永 大輝*; 玉造 博夢; 中川 洋; 大内 啓一*
no journal, ,
DNA is a time-of-flight backscattering spectrometer installed at the Materials and Life Science Experimental Facility (MLF) in Japan Proton Accelerator Research Complex (J-PARC), Tokai, Japan. Its purpose is revealing pico to nano second dynamics in a wide field of sciences and industrial applications including soft matter, bio-molecules, chemical molecules, battery, catalyst, and magnetism. A pulse-shaping chopper equipped at the 7.75 m position from the coupled moderator makes this instrument relatively short in the neutron guide length (42 m from the moderator to the sample position). Its maximum rotation speed of 300 Hz provides us fine energy resolutions up to 1.4 micro second for a sample with dimension of 1 cm wide and 1cm tall. Changing phases of the slit opening of the chopper enables us to select energy bands and even to scan a wide energy transfer range with the highest resolution. Two types of analyzer mirrors of Si111 and Si311 cover large momentum transfer ranges of 0.08 to 1.98 
and 1.79 to 3.39 , respectively. Frequently used measurement modes are a high-flux mode without rotating the chopper and a high-resolution mode with 225 Hz. Those provides 12 and 3.6 micro eV energy resolutions for a large sample of 1.4 cm wide and 4 cm tall. The back-coat by neutron absorber such as Gd and GdO for Si analyzer mirrors serves us in realizing extremely high signal-to-noise ratio of 
, which allows us to obtain QENS spectra from a tiny amount of sample or a dilute protein solution. Various conditions of sample environment are available; cryo-furnaces (4 K to 700 K), a 2K cryostat, a top-loading sample stick for applying electric field, a humidity control system, a cryostat with a samples changer for three samples, an inner atmosphere controller for cryo-furnaces and so on. A high temperature furnace up to 1000K, 3.5 Tesla cryo-magnet and a sample changer for 20 samples are under commissioning.
