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

Omasa, Yoshinori*; Takagi, Shigeyuki*; Toshima, Kento*; Yokoyama, Kaito*; Endo, Wataru*; Orimo, Shinichi*; Saito, Hiroyuki*; Yamada, Takeshi*; Kawakita, Yukinobu; Ikeda, Kazutaka*; et al.

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

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

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

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

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

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.

Position dependency of the scattered intensity in the time-of-flight backscattering spectrometer DNA

Matsuura, Masato*; Yamada, Takeshi*; Tominaga, Taiki*; Kobayashi, Makoto*; Nakagawa, Hiroshi; Kawakita, Yukinobu

JPS Conference Proceedings (Internet), 33, p.011068_1 - 011068_6, 2021/03

https://doi.org/10.7566/JPSCP.33.011068

The position dependence of the scattered intensity in the time-of-flight backscattering spectrometer DNA was investigated. A periodic structure for both vertical (pixel) and horizontal (PSD) directions was observed. The solar slit and over-bending of an analyzer crystal is discussed as a possible origin of the modulation in the intensity. We have developed software program for the systematic correction of the position-dependent intensity and offset energy for the elastic peak. This corrects the deviation from the true scattering intensity and improve the quality of the data, which includes the energy resolution.

Dynamics of proteins with different molecular structures under solution condition

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

https://doi.org/10.1038/s41598-020-78311-4

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.

Neutron biology for next generation; Report from J-PARC workshop "Neutron Biology for Next Generation"; March 22nd-23rd, 2017, Ibaraki Quantum Beam Research Center

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.

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

Takahashi, Nobuaki; Shibata, Kaoru; Kawakita, Yukinobu; Nakajima, Kenji; Inamura, Yasuhiro; Nakatani, Takeshi; Nakagawa, Hiroshi; Fujiwara, Satoru; Sato, Taku*; Tsukushi, Itaru*; et al.

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

https://doi.org/10.1143/JPSJS.80SB.SB007

Instrumental design of indirect geometry crystal analyzer spectrometer; DNA at J-PARC

Shibata, Kaoru; Takahashi, Nobuaki; Nakagawa, Hiroshi; Fujiwara, Satoru; Kataoka, Mikio; Sato, Taku*; Kawakita, Yukinobu*; Tsukushi, Itaru*

Nihon Kessho Gakkai-Shi, 50(1), p.46 - 50, 2008/02

https://doi.org/10.5940/jcrsj.50.46

The instrumental design of an indirect geometry crystal analyzer spectrometer: DNA which is scheduled to be constructed in the Material and Life Science experimental Facility (MLF) at J-PARC, is reported in this article. This spectrometer is mainly aimed at searching for the high quality inelastic scattering spectra with only several mg order biomolecular sample in the plenty of wide range of energy and momentum transfers.

Remote monitoring of airborne asbestos particles using laser-induced fluorescence imaging

Ozu, Akira; Esaka, Fumitaka; Kawakita, Hiroshi*; Okamoto, Ryuta*; Imaki, Masaharu*; Kobayashi, Takao*

Reviewed and Revised Papers Presented at the 23rd International Laser Radar Conference (ILRC-23), p.107 - 108, 2006/07

We have demonstrated that asbestos particles in air can be visualized with laser-induced fluorescence emitted from asbestos. A ultra-violet (266 nm) laser pulse is used to excite asbestos particles suspended in a closed vessel. The fluorescence emitted from the asbestos in the region where the laser beam passes through is detected with a low-pass optical filter and an image intensified CCD camera with ultra-fast gate shutter. Many asbestos particles in the region are separately visualized on an image. It is possible to derive from the image the number and size of asbestos particles through image data processing. The method described in this study is expected to be useful in real-time monitoring of the concentration of asbestos particle.

Remote particle counter for clean rooms

Ozu, Akira; Okamoto, Ryuta*; Kawakita, Hiroshi*

Kurin Tekunoroji, 16(3), p.56 - 61, 2006/03

In recent years, particle counting devices capable of monitoring particles suspended in air on real-time basis are of considerable practical concern in the fields of semiconductor and large display panel industries. A remote particle counter, which had been developed for monitoring aerosols released in air from nuclear facilities, has been applied to a measurement system for clean rooms used in the fields. It can visualize the particles in narrow space at a distance of 6m and derive the number and size distribution of particles with diameter of above 0.5 microns. By improving the laser energy, sensitivity of the image intensifier camera, and magnification of the zoom lens used in the system, it is possible to detect the particles with diameters of below 0.5 microns. The method and the current performance of the measurement system are described.

Operation and management data for the JRR-3 CNS Facility

Suzuki, Masatoshi; Hazawa, Tomoya; Ishizaki, Yoichi*; Obara, Michio*; Inada, Katsutoshi*; Yonekawa, Mitsunori*; Wakita, Hiroshi*

JAERI-Tech 2004-060, 153 Pages, 2004/09

JAERI-Tech-2004-060.pdf:9.78MB

The cold neutron source (CNS) at JRR-3 was constructed for the purpose of improving the utilization performance of the reactor along the lines of upgrade program. There are two methods for extracting cold neutrons from a reactor, one is to filter a small fraction of cold neutrons in the Maxwellian spectrum of reactor neutrons while the other is to increase the fraction of cold neutron by inserting a cryogenic moderator. The latter is adopted as CNS facilities at almost all cases, and liquid hydrogen and its cooling system are equipped with a cold neutron source at many neutron facilities just like JRR-3. Cold neutrons generated in a cold source are extracted through a neutron guide tube, and are utilized for the purpose of neutron beam experiments such as neutron scattering which study the structures of atoms and molecules in the materials and life science fields. This report summarizes the operation data and the main technical issues which were recorded in the whole operation period from commencement date in 1989 to March 2004.