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Tominaga, Taiki*; Nakagawa, Hiroshi; Sahara, Masae*; Oda, Takashi*; Inoue, Rintaro*; Sugiyama, Masaaki*
Life (Internet), 12(5), p.675_1 - 675_9, 2022/05
Times Cited Count：0 Percentile：0.01(Biology)The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D
O was lower than that of a sample cell coated with regular water (HO). In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the DO buffer and the sample container. Consequently, high quality information on protein dynamics could be extracted from dilute protein solutions.
Nakagawa, Hiroshi; Saio, Tomohide*; Nagao, Michihiro*; Inoue, Rintaro*; Sugiyama, Masaaki*; Ajito, Satoshi; Tominaga, Taiki*; Kawakita, Yukinobu
Biophysical Journal, 120(16), p.3341 - 3354, 2021/08
Times Cited Count：4 Percentile：38.66(Biophysics)A multi-domain protein can have various conformations in solution. Interactions with other molecules result in the stabilization of one of the conformations and change in the domain dynamics. SAXS, a well-established experimental technique, can be employed to elucidate the conformation of a multi-domain protein in solution. NSE spectroscopy is a promising technique for recording the domain dynamics in nanosecond and nanometer scale. Despite the great efforts, there are still under development. Thus, we quantitatively removed the contribution of diffusion dynamics and hydrodynamic interactions from the NSE data via incoherent scattering, revealing the differences in the domain dynamics of the three functional states of a multi-domain protein, MurD. The differences among the three states can be explained by two domain modes.
Inoue, Rintaro*; Oda, Takashi*; Nakagawa, Hiroshi; Tominaga, Taiki*; Saio, Tomohide*; Kawakita, Yukinobu; Shimizu, Masahiro*; Okuda, Aya*; Morishima, Ken*; Sato, Nobuhiro*; et al.
Scientific Reports (Internet), 10, p.21678_1 - 21678_10, 2020/12
Times Cited Count：3 Percentile：13.48(Multidisciplinary Sciences)Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, both low flux of neutron beam and absence of analytical procedure for extracting the internal dynamics from iQENS profile have been obstacles for studying it under physiological condition (in solution). Thanks to the recent development of neutron source, spectrometer and computational technique, they enable us to decouple internal dynamics, translational and rotational diffusions from the iQENS profile. The internal dynamics of two proteins: globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution were studied. It was found that the average relaxation rate of IDP was larger than that of GDP. Through the detailed analyses on their internal dynamics, it was revealed that the fraction of mobile H atoms in IDP was much higher than that in GDP. Interestingly, the fraction of mobile H atoms was closely related to the fraction of H atoms on highly solvent exposed surfaces. The iQENS study presented that the internal dynamics were governed by the highly solvent exposed amino acid residues depending upon protein molecular architectures.
Sugiyama, Masaaki*; Inoue, Rintaro*; Nakagawa, Hiroshi; Saio, Tomohide*
Hamon, 30(1), p.16 - 25, 2020/02
Neutron has distinct features as a scattering probe to analyze structure and dynamics of biological macromolecules. The theme of this review is to try to describe how we did/do utilize them. And "How we should utilize them more effectively in the trend of integrative structural biology?" with solution scattering.
Sugiyama, Jun*; Umegaki, Izumi*; Nozaki, Hiroshi*; Higemoto, Wataru; Hamada, Koji*; Takeshita, Soshi*; Koda, Akihiro*; Shimomura, Koichiro*; Ninomiya, Kazuhiko*; Kubo, Kenya*
Physical Review Letters, 121(8), p.087202_1 - 087202_5, 2018/08
Times Cited Count：18 Percentile：74.47(Physics, Multidisciplinary)Sugiyama, Masaaki*; Nakagawa, Hiroshi; Inoue, Rintaro*; Kawakita, Yukinobu
JAEA-Review 2017-024, 40 Pages, 2017/12
JAEA-Review-2017-024.pdf:8.69MB
Now-a-days, promotion of life science by utilizing neutron (neutrons biology) is highly demanded in our country, following installation and improvement of high quality and intensity neutron sources at J-PARC and JRR-3. Aiming at accelerating development of neutrons biology in our country, an international workshop "Neutron biology for next generation" was held as a J-PARC Workshop at Ibaraki Quantum Beam Research Center from 22 March to 23 March in 2017. In the workshop, latest instruments, new-fashioned methodologies, recent scientific results and future perspectives were extensively discussed by domestic neutron instrumental scientists and domestic/foreign neutron biologists. This is a report of the workshop summarized by organizers.
and reference compound ThCd; Studied by the de Haas-van Alphen effectHirose, Yusuke*; Miura, Yasunao*; Tsutsumi, Hiroki*; Yoshiuchi, Shingo*; Oya, Masahiro*; Sugiyama, Kiyohiro*; Takeuchi, Tetsuya*; Yamagami, Hiroshi*; Yamamoto, Etsuji; Haga, Yoshinori; et al.
Physica Status Solidi (B), 250(3), p.642 - 645, 2013/03
Times Cited Count：4 Percentile：20.56(Physics, Condensed Matter)Onuki, Yoshichika; Settai, Rikio*; Takeuchi, Tetsuya*; Sugiyama, Kiyohiro*; Honda, Fuminori*; Haga, Yoshinori; Yamamoto, Etsuji; Matsuda, Tatsuma; Tateiwa, Naoyuki; Aoki, Dai*; et al.
Journal of the Physical Society of Japan, 81(Suppl.B), p.SB001_1 - SB001_18, 2012/12
and CePtSiHirose, Yusuke*; Nishimura, Naoto*; Honda, Fuminori*; Sugiyama, Kiyohiro*; Hagiwara, Masayuki*; Kindo, Koichi*; Takeuchi, Tetsuya*; Yamamoto, Etsuji; Haga, Yoshinori; Matsuura, Masato*; et al.
Journal of the Physical Society of Japan, 80(2), p.024711_1 - 024711_12, 2011/02
Times Cited Count：7 Percentile：47.32(Physics, Multidisciplinary)Ara, Kuniaki; Sugiyama, Kenichiro*; Kitagawa, Hiroshi*; Nagai, Masahiko*; Yoshioka, Naoki*
Journal of Nuclear Science and Technology, 47(12), p.1165 - 1170, 2010/12
Times Cited Count：11 Percentile：59.22(Nuclear Science & Technology)A study on the chemical reactivity control of sodium utilizing the atomic interaction of sodium with suspended nanoparticles was carried out. The atomic interaction between nanoparticles and sodium atoms were estimated by theoretical calculations and verified by fundamental physical properties measurements. Results showed the atomic bond of the sodium atom and the nanoparticle atom was significantly larger than that of the sodium atoms, when the transition metals that have the property of large electronegativity are applied as nanoparticles. From the theoretical calculation results, it was suggested that charge transfer occurs from the sodium atom to the nanoparticle atom. The fundamental physical properties of sodium with suspended nanoparticles were examined in comparison with that of sodium to verify the change of the atomic interaction. From the experimental results, it became clear that the surface tension becomes larger and the evaporation rate becomes smaller. These changes in fundamental physical properties were measured to verify the stability of the atomic interaction under the conditions of wide temperature range and the phase transformation from solid phase to liquid phase.
Ara, Kuniaki; Sugiyama, Kenichiro*; Kitagawa, Hiroshi*; Nagai, Masahiko*; Yoshioka, Naoki*
Journal of Nuclear Science and Technology, 47(12), p.1171 - 1181, 2010/12
Times Cited Count：10 Percentile：56.32(Nuclear Science & Technology)A study was conducted on the control of the chemical reactivity of sodium utilizing the atomic interaction between sodium and nanoparticles. The authors reported in a previous paper that the atomic interaction between sodium and nanoparticles increases and has the potential to suppress chemical reactivity. In this paper, the authors examined the released reaction heat and the reaction behavior. As a result, it was confirmed that the released reaction heat and the reaction rate decreased. From the results of experimental studies, it is clear that the suppressions of chemical reactivity are caused by a change in the sodium evaporation rate and fundamental physical properties such as surface tension which originate in the change in the atomic interaction between sodium and nanoparticle atoms. The suppression of chemical reactivity applying to FBR coolant was estimated for the case of sodium combustion and sodium-water reaction. It was confirmed that the concept of suspending nanoparticles into sodium has high potential for the suppression of chemical reactivity. Applicability as coolant to the FBR was investigated, including not only the chemical reaction properties but also the aspects of heat transfer and operation.
Al and PrPdAlNakano, Yasunori*; Honda, Fuminori*; Takeuchi, Tetsuya*; Sugiyama, Kiyohiro*; Hagiwara, Masayuki*; Kindo, Koichi*; Yamamoto, Etsuji; Haga, Yoshinori; Settai, Rikio*; Yamagami, Hiroshi*; et al.
Journal of the Physical Society of Japan, 79(2), p.024702_1 - 024702_9, 2010/02
Times Cited Count：17 Percentile：67.51(Physics, Multidisciplinary)Matsumura, Hiroyoshi*; Adachi, Motoyasu; Sugiyama, Shigeru*; Okada, Shino*; Yamakami, Megumi*; Tamada, Taro; Hidaka, Koshi*; Hayashi, Yoshio*; Kimura, Toru*; Kiso, Yoshiaki*; et al.
Acta Crystallographica Section F, 64(11), p.1003 - 1006, 2008/11
Times Cited Count：17 Percentile：77.92(Biochemical Research Methods)This paper reports the crystallization and preliminary neutron diffraction measurements of HIV-1 protease, a potential target for anti-HIV therapy, complexed with an inhibitor (KNI-272). The aim of this neutron diffraction study is to obtain structural information about the H atoms and to determine the protonation states of the residues within the active site. The crystal was grown to a size of 1.4 mm
by repeated macroseeding and a slow-cooling method using a two-liquid system. Neutron diffraction data were collected at room temperature using a BIX-4 diffractometer at the JRR-3 research reactor of the Japan Atomic Energy Agency (JAEA). The data set was integrated and scaled to 2.3 
resolution in space group P2(1)2(1)2, with unit-cell parameters a = 59.5, b = 87.4, c = 46.8 .
Saito, Junichi; Ara, Kuniaki; Sugiyama, Kenichiro*; Kitagawa, Hiroshi*; Nakano, Haruyuki*; Ogata, Kan*; Yoshioka, Naoki*
Proceedings of 16th International Conference on Nuclear Engineering (ICONE-16) (CD-ROM), 4 Pages, 2008/05
no abstracts in English
(R: Rare earth)Hieu, N. V.*; Takeuchi, Tetsuya*; Shishido, Hiroaki*; Tonohiro, Chie*; Yamada, Tsutomu*; Nakashima, Hiroshi*; Sugiyama, Kiyohiro*; Settai, Rikio*; Matsuda, Tatsuma; Haga, Yoshinori; et al.
Journal of the Physical Society of Japan, 76(6), p.064702_1 - 064702_16, 2007/06
Times Cited Count：49 Percentile：84.5(Physics, Multidisciplinary)Saito, Junichi; Ara, Kuniaki; Sugiyama, Kenichiro*; Kitagawa, Hiroshi*; Oka, Nobuki*; Yoshioka, Naoki*
Proceedings of 15th International Conference on Nuclear Engineering (ICONE-15) (CD-ROM), 5 Pages, 2007/04
Liquid sodium is used as the coolant of the fast breeder reactor (FBR), because of its high thermal conductivity and wide temperature range of liquid. However the chemical reactivity with water and oxygen of sodium is very high. So an innovative technology to control the reactivity is desired. The purpose of this study is to reduce the chemical reactivity of liquid sodium by dispersing the nanometer-size metallic particles into liquid sodium. Sub-themes of this study are nanoparticles production, evaluation of reaction control of liquid sodium, and feasibility study to FBR. In this paper, we describe the research program of them.
Sugiyama, Kiyohiro*; Nakashima, Hiroshi*; Aoki, Dai*; Haga, Yoshinori; Yamamoto, Etsuji; Nakamura, Akio; Homma, Yoshiya*; Shiokawa, Yoshinobu*; Kindo, Koichi*; Hagiwara, Masayuki*; et al.
Journal of the Physical Society of Japan, 75(9), p.094707_1 - 094707_6, 2006/09
Times Cited Count：6 Percentile：41.83(Physics, Multidisciplinary)We have measured the high-field magnetization for a transuranium antiferromagnet NpRhGa with two successive antiferromagnetic transition temperatures of 
= 36 and 
= 32 K and an ordered moment of 0.96 
/Np. For the magnetic field along the easy-axis of the [100] direction of the tetragonal structure, the magnetization indicates a metamagnetic transition at 
= 26 T with a sharp step and saturates above 
=38 T, with 0.43 /Np. On the other hand, the hard-axis magnetization for the [001] direction increases linearly and saturates above =28 T, with 0.44 /Np. These magnetization curves were discussed on the basis of reorientation and reduction of the magnetic moment.
, TbRhIn, DyRhIn, and HoRhInHieu, N. V.*; Shishido, Hiroaki*; Takeuchi, Tetsuya*; Thamizhavel, A.*; Nakashima, Hiroshi*; Sugiyama, Kiyohiro*; Settai, Rikio*; Matsuda, Tatsuma; Haga, Yoshinori; Hagiwara, Masayuki*; et al.
Journal of the Physical Society of Japan, 75(7), p.074708_1 - 074708_6, 2006/07
Times Cited Count：18 Percentile：67.26(Physics, Multidisciplinary)We grew single crystals of NdRhIn, TbRhIn, DyRhIn, and HoRhIn with the tetragonal crystal structure and measured the magnetic susceptibility and magnetization. NdRhIn is an antiferromagnet with a Neel temperature 
= 11.6 K. Below , magnetization reveals two metamagnetic transitions at Hm1 = 70 kOe and Hm2 = 93 kOe for the magnetic field along the [001] direction. The saturation moment of 2.5 
/Nd is in good agreement with the staggered Nd moment determined by the neutron diffraction experiment. These metamagnetic transitions correspond to the change of the magnetic structure. TbRhIn, DyRhIn and HoRhIn are found to be antiferromagnets with = 47.3, 28.1, and 15.8 K, respectively. The magnetization curves of these compounds are also quite similar to those of NdRhIn, revealing two metamagnetic transitions. The magnetic structures in magnetic fields are proposed by considering the exchange interactions based on the crystal structure.
B and GdRhBObiraki, Yoshiko*; Nakashima, Hiroshi*; Galatanu, A.*; Matsuda, Tatsuma; Haga, Yoshinori; Takeuchi, Tetsuya*; Sugiyama, Kiyohiro*; Kindo, Koichi*; Hagiwara, Masayuki*; Settai, Rikio*; et al.
Journal of the Physical Society of Japan, 75(6), p.064702_1 - 064702_8, 2006/06
Times Cited Count：4 Percentile：32.33(Physics, Multidisciplinary)We succeeded in growing single crystals of ferromagnets NdRhB and GdRhB with the hexagonal structure, and measured the electrical resistivity, specific heat, magnetic susceptibility and magnetization. From these measurements, the Curie temperature 
is determined as =10.2 K in NdRhB and TC=93 K in GdRhB. The magnetic moments of about 2.5 in NdRhB and 7.7 in GdRhB are oriented in the basal plane. The crystalline electric field scheme is proposed for NdRhB on the basis of the experimental results of Schottky anomaly in the specific heat and anisotropic susceptibility and magnetization. The Fermi surface in NdRhB is very similar to that in a non-4 f reference compound LaRhB, possessing the quasi-one dimensional electronic character.
NiGeThamizhavel, A.*; Nakashima, Hiroshi*; Obiraki, Yoshiko*; Nakashima, Miho*; Matsuda, Tatsuma; Haga, Yoshinori; Sugiyama, Kiyohiro*; Takeuchi, Tetsuya*; Settai, Rikio*; Hagiwara, Masayuki*; et al.
Journal of the Physical Society of Japan, 74(10), p.2843 - 2848, 2005/10
Times Cited Count：14 Percentile：59.33(Physics, Multidisciplinary)Single crystals of a pressure-induced superconductor CeNiGe have been successfully grown by the flux method. The anisotropic magnetic properties due to the orthorhombic crystal structure have been studied precisely by the electrical resistivity, specific heat, magnetic susceptibility, and high-field magnetization measurements. The results of these measurements confirmed two antiferromagnetic transitions at T
=5.0 K and T
=4.3 K. The electronic specific heat coefficient obtained from the low-temperature specific heat data amounts to 90 mJ/K
mol Ce. The high-field magnetization for H //[100] shows four magnetic transitions at 11.8, 12.9, 17.5 and 23.9 T with a saturation moment of 0.73 /Ce at 1.3 K. We have also performed the crystalline electric field (CEF) analysis on the magnetic susceptibility and magnetization to understand the magnetocrystalline anisotropy, where the splitting energies of two excited doublets in the CEF scheme are estimated to be 140 and 576 K, respectively.
