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.

Antiferromagnetism and phase stability of CrMnFeCoNi high-entropy alloy

Zhu, L.*; He, H.*; Naeem, M.*; Sun, X.*; Qi, J.*; Liu, P.*; Harjo, S.; 中島 健次; Li, B.*; Wang, X.-L.*

Physical Review Letters, 133(12), p.126701_1 - 126701_6, 2024/09

https://doi.org/10.1103/PhysRevLett.133.126701

It has long been suspected that magnetism could play a vital role in the phase stability of multi- component high-entropy alloys. However, the nature of the magnetic order, if any, has remained elusive. Here, by using elastic and inelastic neutron scattering, we demonstrate evidence of antiferromagnetic order below 80 K and strong spin fluctuations persisting to room temperature in a single-phase face-centered cubic (fcc) CrMnFeCoNi high-entropy alloy. Despite the chemical complexity, the magnetic structure in CrMnFeCoNi can be described as -Mn-like, with the magnetic moments confined in alternating (001) planes and pointing toward the 111 direction. Combined with first-principles calculation results, it is shown that the antiferromagnetic order and spin fluctuations help stabilized the fcc phase in CrMnFeCoNi high-entropy alloy.

Organization of malonamides from the interface to the organic bulk phase

Micheau, C.; 上田 祐生; 元川 竜平; 阿久津 和宏*; 山田 悟史*; 山田 雅子*; Moussaoui, S. A.*; Makombe, E.*; Meyer, D.*; Berthon, L.*; et al.

Journal of Molecular Liquids, 401, p.124372_1 - 124372_12, 2024/05

https://doi.org/10.1016/j.molliq.2024.124372

Supramolecular organization of amphiphilic extractant molecules is involved in metal cation selectivity and separation kinetics during solvent extraction. The relationship between extractant associates/aggregates formed in the organic bulk phase and at the liquid-liquid interface is poorly understood even though it affects the extraction mechanism. The nanoscopic structures of the extraction systems N,N,N',N'-tetrahexylmalonamide (THMA) in toluene and N,N'-dibutyl-N,N'-dimethyl-2-tetradecylmalonamide (DBMA) in n-heptane, used for either Pd(II) or Nd(III) selective extraction from an acidic aqueous phase, were examined. These systems present markedly different affinity for Pd(II) and Nd(III), and extraction kinetics. Extractant organization in the organic bulk phase and at the interface were compared by small-angle X-ray scattering, interfacial tension, and neutron reflectivity. THMA in toluene forms small associates in the organic bulk phase and accumulates in a diffuse layer at the interface, decreasing Pd(II) coordination probability and resulting in slow extraction. DBMA in n-heptane forms large aggregates and a compact, dense interfacial layer, resulting in rapid Pd(II) and Nd(III) extraction. Thus, Pd(II) extraction is driven by interfacial coordination alone, whereas the incorporation of Nd(III) into the core of large aggregates governs Nd(III) extraction in the interfacial layer. These results suggest that the interface should be described as a nanoscale interphase containing a high extractant concentration compared with the organic bulk phase.

Quantum critical behavior of the hyperkagome magnet MnCoSi

山内 宏樹; Sari, D. P.*; 安井 幸夫*; 坂倉 輝俊*; 木村 宏之*; 中尾 朗子*; 大原 高志; 本田 孝志*; 樹神 克明; 井川 直樹; et al.

Physical Review Research (Internet), 6(1), p.013144_1 - 013144_9, 2024/02

https://doi.org/10.1103/PhysRevResearch.6.013144

-Mn-type family alloys Mn have three-dimensional antiferromagnetic (AFM) corner-shared triangular network. The antiferromagnet MnRhSi shows magnetic short-range order (SRO) over a wide temperature range of approximately 500 K above the Nel temperature = 190 K. MnCoSi has the smallest lattice parameter and the lowest in the family compounds. The quantum critical point (QCP) from AFM to the quantum paramagnetic state is expected near a cubic lattice parameter of 6.15 of MnCoSi is only 140 K, quantum critical behavior is observed in MnCoSi as the enhancement of the electronic specific heat coefficient . We study how the magnetic SRO appears in MnCoSi by using neutron scattering, SR, and physical property measurements. The experimental results show that the neutron scattering intensity of the magnetic SRO does not change much regardless of the suppressed magnetic moment in the long-range magnetic ordered state compared to those of MnRhSi. The initial asymmetry drop ratio of SR above becomes small, and the magnetic SRO temperature is suppressed to 240 K. The results suggest that the MnCoSi is close to the QCP in the Mn system.

New measurement system based on small-angle neutron scattering for structural analysis of light-responsive materials

岩瀬 裕希*; 赤松 允顕*; 稲村 泰弘; 坂口 佳史*; 森川 利明*; 笠井 聡*; 大内 啓一*; 小林 一貴*; 酒井 秀樹*

Journal of Applied Crystallography, 56(1), p.110 - 115, 2023/02

https://doi.org/10.1107/S1600576722011104

光応答性材料の重要性が高まる中、光照射によって引き起こされる構造変化とその機能との相関を解析することは極めて重要である。このような構造解析には小角散乱(SAS)が有効であるが、SASによって1nm以下のスケールで局所的な分子構造形成や分子反応を定量的に捉えることは困難である。そこで本研究では、光応答性物質における非平衡現象の構造解析を目的として、紫外可視光照射装置、紫外可視分光光度計から構成される新しい試料環境を開発し、中性子小角・広角散乱装置(TAIKAN)に設置することで中性子小角散乱と紫外可視光吸収の同時測定を実現した。この測定手法を用いることで、光応答性分子であるアゾベンゼンを修飾した陽イオン性界面活性剤が水溶液中で形成するミセルが紫外可視光照射によって構造変化する様子をその場観察することを可能とした。その結果、本測定手法によりミセル構造の変化と分子配置の変化の相互作用に関する直接的な情報を提供することが示された。

Rotation of complex ions with ninefold hydrogen coordination studied by quasielastic neutron scattering and first-principles molecular dynamics calculations

大政 義典*; 高木 茂幸*; 戸嶋 健人*; 横山 凱乙*; 遠藤 亘*; 折茂 慎一*; 齋藤 寛之*; 山田 武*; 川北 至信; 池田 一貴*; et al.

Physical Review Research (Internet), 4(3), p.033215_1 - 033215_9, 2022/09

https://doi.org/10.1103/PhysRevResearch.4.033215

Quasielastic neutron scattering (QENS) and neutron powder diffraction of the complex transition metalhydrides LiMoH and LiNbH were measured in a temperature range of 10-300 K to study their structures and dynamics, especially the dynamics of the hydrogen atoms. These hydrides contain unusual ninefold H coordinated complex ions (MoH or NbH) and hydride ions (H). A QENS signal appeared 150 K due to the relaxation of H atoms. The intermediate scattering functions derived from the QENS spectra are well fitted by a stretched exponential function called the Kohlrausch-Williams-Watts functions with a small stretching exponent 0.3-0.4, suggesting a wide relaxation time distribution. The dependence of the elastic incoherent structure factor is reproduced by the rotational diffusion of MH (M = Mo or Nb) anions. The results are well supported by a van Hove analysis for the motion of H atoms obtained using first-principles molecular dynamics calculations. We conclude that the wide relaxation time distribution of the MH rotation is due to the positional disorder of the surrounding Li ions and a unique rotation with MH anion deformation (pseudorotation).

Multipole polaron in the devil's staircase of CeSb

新井 陽介*; 黒田 健太*; 野本 拓也*; Tin, Z. H.*; 櫻木 俊輔*; Bareille, C.*; 明比 俊太朗*; 黒川 輝風*; 木下 雄斗*; Zhang, W.-L.*; et al.

Nature Materials, 21(4), p.410 - 415, 2022/04

https://doi.org/10.1038/s41563-021-01188-9

Low-energy electronic structures of CeSb which shows multiple phase transitions known as devil's staircase were examined by combination of laser angle-resolved photoemission, Raman and neutron scattering spectroscopies. A new type of electron-boson coupling between the mobile electrons and quadrupole CEF-excitations of the 4f orbitals was found. The coupling is exceedingly strong and exhibits anomalous step-like enhancement during the devil's staircase transition, unveiling a new type of quasiparticle, named multipole polaron.

Position-encoded automatic cell elevator for BL02, J-PARC MLF

富永 大輝*; 小林 誠*; 山田 武*; 松浦 直人*; 川北 至信; 笠井 聡*

JPS Conference Proceedings (Internet), 33, p.011095_1 - 011095_5, 2021/03

BB2019-1955.pdf:1.33MB

https://doi.org/10.7566/JPSCP.33.011095

トップローディング型冷凍機用の垂直移動型試料交換機が、J-PARC MLFのBL02に設置された中性子分光器の利用支援のために開発された。PEACEと名付けられたこの試料交換機は、中性子照射位置での試料位置の再現性を、PEEKと呼ぶ物質でできたガイドを利用して制御している。3つの試料位置でのバックグラウンド散乱のプロファイルの変化は1.6%以内であることが分かった。この結果は、垂直軸からの試料位置の偏差が0.3mmであることを考えると妥当である。

Nanoscale relaxation in "Water-in-Salt" and "Water-in-Bisalt" electrolytes

Gonzalz, M. A.*; Borodin, O.*; 古府 麻衣子; 柴田 薫; 山田 武*; 山室 修*; Xu, K.*; Price, D. L.*; Saboungi, M.-L.*

Journal of Physical Chemistry Letters (Internet), 11(17), p.7279 - 7284, 2020/09

https://doi.org/10.1021/acs.jpclett.0c01765

"Water-in-salt" (WIS) and "water-in-bisalt" (WIBS) electrolytes have recently been developed for Li-ion batteries. We report Quasielastic Neutron Scattering (QENS) measurements on solutions of a WIS electrolyte at two concentrations, and a WIBS electrolyte at one concentration. The data were Fourier transformed to obtain experimental intermediate scattering functions (ISFs) and compared with corresponding quantities obtained from Molecular Dynamics (MD) simulations. Both QENS and MD ISFs could be fitted well by a single stretched exponential function to obtain apparent translational diffusion coefficients for the water molecules. The QENS values agree well with the MD simulations for the solutions of a WIS electrolyte at two concentrations, but MD simulations predict a slower relaxation of water compared to QENS for the WIBS electrolyte. Comparison of the incoherent and coherent scattering reveals much faster water dynamics compared with structural relaxation of the ionic framework.

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

https://doi.org/10.1021/acs.jpclett.9b03196

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。