Revealing an origin of temperature-dependent structural change in intrinsically disordered proteins

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

https://doi.org/10.1016/j.bpj.2024.12.022

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.

Local atomic structures and lattice dynamics of inverse colossal barocaloric ammonium thiocyanate

Zhang, Z.*; Gong, W.; 川北 至信; 他9名*

Physical Review Materials (Internet), 7(12), p.125402_1 - 125402_9, 2023/12

https://doi.org/10.1103/PhysRevMaterials.7.125402

NHSCN exhibits successive phase transitions from monoclinic to orthorhombic, and then to tetragonal. The former phase transition is accompanied by an inverse colossal barocaloric effect and a huge negative thermal expansion. This transition is complicated by the possibly coexisting orientational disorder of NH and SCN, and the mechanism is still unclear. Here, NHSCN is investigated using high-resolution neutron powder diffraction, pair distribution function analysis, and Raman scattering. Both the average and local structural analysis indicate that only NH is orientationally disordered in the orthorhombic phase and SCN becomes subsequently disordered in the tetragonal phase. Both temperature-induced and pressure-induced hardening behaviors of SCN related vibrations are observed, which leads to the breakage of hydrogen bonds-linked NH with SCN and further facilitates phase transition. Our findings provide a solid standing point of atomic structures and dynamics, on which the scenario of the phase transition and the associated physical properties is established.

Direct observation of concentration fluctuations in Au-Si eutectic liquid by small-angle neutron scattering

坂口 佳史*; 高田 慎一; 川北 至信; 藤村 由希; 近藤 啓悦

Journal of Physics; Condensed Matter, 35(41), p.415403_1 - 415403_11, 2023/10

https://doi.org/10.1088/1361-648X/ace577

It is well-known that eutectic gold-silicon (Au-Si) alloys exhibit anomalous melting point depression, which is more than 1000 C from the melting point of elemental Si (1414 C). The melting point depression in eutectic alloys is generally explained in terms of a decrease of the free energy by mixing. However, it is difficult to understand the anomalous melting point depression only from the stability of the homogeneous mixing. Some researchers suggest that there are concentration fluctuations in the liquids, where the atoms are inhomogeneously mixed. In this paper, we measure the small-angle neutron scattering (SANS) of AuSi (eutectic composition) and AuSi (off-eutectic composition) at temperatures from room temperature to 900 C in both solid and liquid states to observe such concentration fluctuations directly.

Quasielastic neutron scattering probing H dynamics in the H conductors LaHO

玉造 博夢; 福井 慧賀*; 飯村 壮史*; 本田 孝志*; 多田 朋史*; 村上 洋一*; 山浦 淳一*; 倉本 義夫*; 佐賀山 基*; 山田 武*; et al.

Physical Review B, 107(18), p.184114_1 - 184114_8, 2023/05

https://doi.org/10.1103/PhysRevB.107.184114

Using an incoherent quasi-elastic neutron scattering (QENS) technique, we investigate H dynamics in a series of oxyhydrides LaHO that exhibit characteristic high H conductivity. In the end member LaH ( = 0), two kinds of H dynamics are identified: the jump diffusion and the localized motion. The jump length in the jump diffusion mode increases with increasing . The localized motion is identified as a jump between the two inequivalent sites. These dynamics are corroborated by our molecular dynamical simulations. Our QENS data suggest that similar H dynamics occurs also in oxyhydrides LaHO ( 0), whose H concentration dependence is consistent with the previous measurement of ionic conductivity. We also discuss the possibility that LaHO is an example of H ion conductors governed by the concerted migration mechanism. The identified H dynamics is a key to understanding the anomalous hydrogen concentration dependence of the diffusion coefficient in lanthanum hydrides, which has been a longstanding mystery in this compound.

Hydrogen dynamics in hydrated chitosan by quasi-elastic neutron scattering

廣田 夕貴*; 富永 大輝*; 川端 隆*; 川北 至信; 松尾 康光*

Bioengineering (Internet), 9(10), p.599_1 - 599_17, 2022/10

https://doi.org/10.3390/bioengineering9100599

Chitosan, which is an environmentally friendly and highly bio-producible material, is a potential proton-conducting electrolyte for use in fuel cells. Thus, to microscopically elucidate proton transport in hydrated chitosan, we employed the quasi-elastic neutron scattering (QENS) technique. QENS analysis showed that the hydration water, which was mobile even at 238 K, moved significantly more slowly than the bulk water, in addition to exhibiting jump diffusion. Furthermore, upon increasing the temperature from 238 to 283 K, the diffusion constant of water changed increased from to cm/s. It was also found that a portion of the hydrogen atoms in chitosan undergo a jump-diffusion motion similar to that of the hydrogen present in water. Moreover, QENS analysis revealed that the activation energy for the jump-diffusion of hydrogen in chitosan and in the hydration water was 0.30 eV, which is close to the value of 0.38 eV obtained from the temperature-dependent proton conductivity results. Overall, it was deduced that a portion of the hydrogen atoms in chitosan dissociate and protonate the interacting hydration water, resulting in the chitosan exhibiting proton conductivity.

Revealing the ion dynamics in LiGePS by quasi-elastic neutron scattering measurements

堀 智*; 菅野 了次*; Kwon, O.*; 加藤 祐樹*; 山田 武*; 松浦 直人*; 米村 雅雄*; 神山 崇*; 柴田 薫; 川北 至信

Journal of Physical Chemistry C, 126(22), p.9518 - 9527, 2022/06

https://doi.org/10.1021/acs.jpcc.2c01748

Understanding Li-ion conduction in superionic conductors accelerates the development of new solid electrolytes to enhance the charge-discharge performances of all-solid-state batteries. We performed a quasi-elastic neutron scattering study on a model superionic conductor (LiGePS, LGPS), to reveal its ion dynamics on an angstrom-scale spatial range and a pico-to-nanosecond temporal range. The observation of spectra at 298 K confirmed the high lithium diffusivity. The obtained diffusion coefficient was in the order of 10 cms at temperatures 338 K and was higher than the reported diffusion coefficient over a longer time scale, as determined by the pulse-field gradient nuclear magnetic resonance method. This difference indicates that there are impediments to ionic motion over a longer time scale. The dynamic behavior of the Li ions was compared with that observed for the LiPSO phase, which possesses the same crystal structure type, but a lower ionic conductivity. The LGPS phase possessed a high lithium mobility over a distance of 10 , as well as a larger fraction of mobile Li ions, thereby indicating that these features enhance lithium conduction over a longer spatial scale, which is important in all-solidstate batteries.

Evaluation of sample cell materials for aqueous solutions used in quasi-elastic neutron scattering measurements

富永 大輝*; 佐原 雅恵*; 川北 至信; 中川 洋; 山田 武*

Journal of Applied Crystallography, 54(6), p.1631 - 1640, 2021/12

https://doi.org/10.1107/S1600576721009687

For quasi-elastic neutron scattering (QENS) studies, sample cells made of pure or alloyed aluminum are frequently employed. Although the Al surface is protected by a passivating film, this film is not robust. Therefore, when the sample is an aqueous solution, chemical interactions between the Al surface and sample, promoted by corrosive entities such as chloride ions and certain conditions of pH, can compromise the integrity of the cell and interfere with the experiment. In this study, the corrosion susceptibilities of Al and its alloys were investigated by subjecting them to various treatments; the results were compared with those of other candidate materials with low chemical reactivity. This work showed that alloys with higher Al content and boehmite-coated surfaces are resistant to corrosion. In particular, for Al, the resistance is due to a reduction in the contact area achieved by reducing the surface roughness. QENS measurements of empty sample cells made of these materials revealed two results: (1) the profile of the cell fabricated with a copper-free Al alloy showed a minor dependence on the scattering vector magnitude and (2) reducing the real surface area of Al effectively suppresses its scattering intensity, while boehmite coating strengthens the scattering. Cells fabricated with Mo, Nb and single-crystal sapphire can be used as alternatives to Al because of their low scattering intensity and reduced dependence on .

Dynamics of water in a catalyst layer of a fuel cell by quasielastic neutron scattering

伊藤 華苗; 山田 武*; 篠原 朗大*; 高田 慎一; 川北 至信

Journal of Physical Chemistry C, 125(39), p.21645 - 21652, 2021/10

https://doi.org/10.1021/acs.jpcc.1c06014

The catalyst layer (CL) in polymer electrolyte fuel cells (PEFCs) plays a critical role in the performance of a PEFC. In this study, we investigate the water dynamics in the CL using quasielastic neutron scattering (QENS) and small-angle neutron scattering. The temperature dependence of the mean square displacement u shows that the freezing of water does not occur at a melting temperature in the Nafion thin film of the CL, suggesting that the water is confined in a smaller region than 15 . The QENS measurements established three kinds of water in the CL: immobile water tightly connected to a sulfonic group, water in a fast mode assigned to free diffusion restricted in a sphere, and water in a slow mode described by a jump diffusion model. Assuming that these three modes were independent, the number of water molecules in each mode was estimated. On discussing the structure and dynamics elucidated in the study, we finally conclude that the coupled model of the fast and slow modes is plausible for describing the diffusion of water confined in the thin Nafion film of the CL.

Conformational dynamics of a multidomain protein by neutron scattering and computational analysis

中川 洋; 齋尾 智英*; 長尾 道弘*; 井上 倫太郎*; 杉山 正明*; 味戸 聡志; 富永 大輝*; 川北 至信

Biophysical Journal, 120(16), p.3341 - 3354, 2021/08

https://doi.org/10.1016/j.bpj.2021.07.001

マルチドメインタンパク質は、溶液中で様々な構造を持つことができる。他の分子との相互作用により、そのうちの1つの構造が安定化し、ドメインダイナミクスが変化することが知られている。マルチドメインタンパク質の溶液中での構造を解明するためには、小角散乱法を用いることができる。中性子スピンエコー法は、ナノ秒・ナノメートルスケールでのドメインダイナミクスを解析するための有望な技術であるが、まだ開発途上である。本研究では、非干渉性散乱を用いて中性子スピンエコー法のデータから拡散運動や流体力学的相互作用の寄与を定量的に除去し、マルチドメインタンパク質MurDの3つの機能状態のドメインダイナミクスの違いを明らかにした。3つの状態間の違いは、2つのドメインモードによって説明できた。

Quartz cell for a backscattering spectrometer

富永 大輝*; 川北 至信; 中川 洋; 山田 武*; 柴田 薫

JPS Conference Proceedings (Internet), 33, p.011086_1 - 011086_5, 2021/03

BB2019-1956.pdf:0.78MB

https://doi.org/10.7566/JPSCP.33.011086

後方散乱型中性子分光器、特にJ-PARC MLFのBL02(DNA)分光器用に最適化された二重円筒型石英試料セルを開発した。一端を閉じられた石英ガラス管を0.55mmの厚みまで削り、内筒を底部の突起によって外筒に同芯になるように挿入する。この石英セルは、標準的に用いられているアルミセルの表面に触れさせたくない試料に用いられる。石英セルと標準アルミセルの容器散乱の効果を重水バッファ試料を使って中性子準弾性散乱実験(QENS)により確かめた。Qが1[1/A]未満の領域では石英セルとアルミ容器の弾性散乱プロファイルはほぼ同一であった。一方Qが1[1/A]以上の領域では、石英ガラスのFSDPのために、プロファイルが異なることが分かった。この領域では、吸収補正や石英セルの個々の厚みの差を考慮した解析が必要である。