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Journal Articles

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

 Times Cited Count:0 Percentile:0.01(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.

Journal Articles

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

 Times Cited Count:0 Percentile:0(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.

Journal Articles

Nanostructural characterization of oleyl acid phosphate in poly-$$alpha$$-olefin using small-angle X-ray scattering

Oba, Yojiro; Motokawa, Ryuhei; Hino, Masahiro*; Adachi, Nozomu*; Todaka, Yoshikazu*; Inoue, Rintaro*; Sugiyama, Masaaki*

Chemistry Letters, 49(7), p.823 - 825, 2020/07

 Times Cited Count:0 Percentile:0(Chemistry, Multidisciplinary)

Journal Articles

Solution neutron scattering

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.

Journal Articles

Imaging measurement of neutron attenuation by small-angle neutron scattering using soller collimator

Oba, Yojiro; Shinohara, Takenao; Sato, Hirotaka*; Onodera, Yohei*; Hiroi, Kosuke; Su, Y.; Sugiyama, Masaaki*

Journal of the Physical Society of Japan, 87(9), p.094004_1 - 094004_5, 2018/09

 Times Cited Count:0 Percentile:0(Physics, Multidisciplinary)

no abstracts in English

JAEA Reports

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.

Journal Articles

Energy-resolved small-angle neutron scattering from steel

Oba, Yojiro*; Morooka, Satoshi; Oishi, Kazuki*; Suzuki, Junichi*; Takata, Shinichi; Sato, Nobuhiro*; Inoue, Rintaro*; Tsuchiyama, Toshihiro*; Gilbert, E. P.*; Sugiyama, Masaaki*

Journal of Applied Crystallography, 50(2), p.334 - 339, 2017/04

 Times Cited Count:2 Percentile:26.99(Chemistry, Multidisciplinary)

Journal Articles

Novel neutron scattering techniques using neutron transmission spectra

Oba, Yojiro*; Morooka, Satoshi; Sato, Hirotaka*; Sato, Nobuhiro*; Inoue, Rintaro*; Sugiyama, Masaaki*

Hamon, 26(4), p.170 - 173, 2016/11

Journal Articles

Magnetic scattering in the simultaneous measurement of small-angle neutron scattering and Bragg edge transmission from steel

Oba, Yojiro*; Morooka, Satoshi; Oishi, Kazuki*; Sato, Nobuhiro*; Inoue, Rintaro*; Adachi, Nozomu*; Suzuki, Junichi*; Tsuchiyama, Toshihiro*; Gilbert, E. P.*; Sugiyama, Masaaki*

Journal of Applied Crystallography, 49(5), p.1659 - 1664, 2016/10

 Times Cited Count:9 Percentile:63.8(Chemistry, Multidisciplinary)

Journal Articles

High-efficiency contact grating fabricated on the basis of a Fabry-Perot type resonator for terahertz wave generation

Yoshida, Fumiko; Nagashima, Keisuke; Tsubouchi, Masaaki; Ochi, Yoshihiro; Maruyama, Momoko; Sugiyama, Akira

Japanese Journal of Applied Physics, 55(1), p.012201_1 - 012201_5, 2016/01

 Times Cited Count:6 Percentile:37.08(Physics, Applied)

Journal Articles

Development of hydrogen behavior simulation code system

Terada, Atsuhiko; Matsumoto, Masaaki*; Sugiyama, Hitoshi*; Kamiji, Yu; Hino, Ryutaro

Proceedings of 6th International Conference on Hydrogen Safety (ICHS 2015) (CD-ROM), 11 Pages, 2015/10

To improve the safety performance of the Nuclear Power Station, especially on the hydrogen safety under severe accident conditions, a simulation code system has been developed to analyze hydrogen behavior including diffusion, combustion, explosion and structural integrity evaluation. This developing system consists of CFD and FEM tools in order to support various hydrogen user groups consisting of students, researchers and engineers. Preliminary analytical results obtained with above mentioned tools, especially with open source codes including buoyancy turbulent model and condensation model, agreed well with the existing test data.

Journal Articles

Yb:YAG thin-disk chirped pulse amplification laser system for intense terahertz pulse generation

Ochi, Yoshihiro; Nagashima, Keisuke; Maruyama, Momoko; Tsubouchi, Masaaki; Yoshida, Fumiko; Kono, Nanase; Mori, Michiaki; Sugiyama, Akira

Optics Express (Internet), 23(11), p.15057 - 15064, 2015/06

 Times Cited Count:20 Percentile:79.2(Optics)

We have developed a 1 kHz repetition picosecond laser system dedicated for intense terahertz (THz) pulse generation. The system comprises a chirped pulse amplification laser equipped with a Yb:YAG thin-disk amplifier. At room temperature, the Yb:YAG thin-disk regenerative amplifier provides pulses having energy of over 10 mJ and spectral bandwidth of 1.2 nm. The pulse duration achieved after passage through a diffraction grating pair compressor was 1.3 ps. By employing this picosecond laser as a pump source, THz pulses having a peak frequency of 0.3 THz and 4 $$mu$$J of energy were generated by means of optical rectification in an Mg-doped LiNbO$$_{3}$$ crystal.

Journal Articles

Development of hydrogen behavior simulation code system; Outline of code system and validation using existing data

Terada, Atsuhiko; Matsumoto, Masaaki*; Sugiyama, Hitoshi*; Kamiji, Yu; Kadowaki, Satoshi*; Hino, Ryutaro

Proceedings of 23rd International Conference on Nuclear Engineering (ICONE-23) (DVD-ROM), 6 Pages, 2015/05

In the Fukushima Daiichi Nuclear Power Station (NPS) accident, hydrogen was generated by oxidation reaction of the cladding and water etc, then leaked into the NPS building, and finally led to occurrence of hydrogen explosion in the building. This resulted in serious damage to the environment. To improve the safety performance of the NPS, especially on the hydrogen safety under severe accident conditions, a simulation code system has been developed to analyze hydrogen behaviors including diffusion, combustion, explosion and structural integrity evaluation. This developing system consists of CFD and FEM tools in order to support various hydrogen user groups of students, researchers and engineers. Preliminary calculated results obtained with above mentioned tools, damage of piping induced by hydrogen combustion, agreed well with existing test data.

Journal Articles

Small-angle neutron scattering for biology; Application of SANS to biological study

Endo, Hitoshi; Sugiyama, Masaaki*; Inoue, Rintaro*

Hamon, 22(3), p.258 - 267, 2012/08

In this text, the authors introduce two powerful techniques and one developing one for Small-Angle Neutron Scattering (SANS). The most fascinating feature of neutron as a scattering probe is its isotope effect in hydrogen. The first topic is concerning about recent progress on Contrast Variation Method: the author shows how to apply the contrast variation method to protein-mineral complex system and analyze the data. The second is concerning about deuteration-labeling: the author shows kinetics analysis in quaternary structure of homo-oligomeric protein with this technique. The final topic is concerning about the next generation analysis: an analysis method coupling SANS with neutron spin echo for dynamics of tertiary structure of protein.

Journal Articles

New development in nanostructure analysis by smaller-angle neutron scattering instrument of J-PARC

Suzuki, Junichi; Shinohara, Takenao; Takata, Shinichi; Oku, Takayuki; Suzuya, Kentaro; Aizawa, Kazuya; Arai, Masatoshi; Otomo, Toshiya*; Sugiyama, Masaaki*

Nihon Kessho Gakkai-Shi, 50(1), p.24 - 28, 2008/02

no abstracts in English

JAEA Reports

Summary of fuel safety research meeting 2005; March 2-3, 2005, Tokyo

Fuketa, Toyoshi; Nakamura, Takehiko; Nagase, Fumihisa; Nakamura, Jinichi; Suzuki, Motoe; Sasajima, Hideo; Sugiyama, Tomoyuki; Amaya, Masaki; Kudo, Tamotsu; Chuto, Toshinori; et al.

JAEA-Review 2006-004, 226 Pages, 2006/03

JAEA-Review-2006-004.pdf:34.43MB

Fuel Safety Research Meeting 2005, which was organized by the Japan Atomic Energy Agency was held on March 2-3, 2005 at Toshi Center Hotel, Tokyo. The purposes of the meeting are to present and discuss the results of experiments and analyses on reactor fuel safety and to exchange views and experiences among the participants. The technical topics of the meeting covered the status of fuel safety research activities, fuel behavior under Reactivity Initiated Accident (RIA) and Loss of coolant accident (LOCA) conditions, high fuel behavior, and radionuclide release under severe accident conditions. This summary contains all the abstracts and sheets of viewgraph presented in the meeting.

Journal Articles

RIA-simulating experiments on high burnup PWR fuel rods with advanced cladding alloys

Sugiyama, Tomoyuki; Fuketa, Toyoshi; Ozawa, Masaaki*; Nagase, Fumihisa

Proceedings of 2004 International Meeting on LWR Fuel Performance, p.544 - 550, 2004/09

Two pulse irradiation experiments simulating reactivity initiated accidents were performed on high burnup ($$sim$$60 GWd/t) PWR UO$$_2$$ rods with advanced cladding alloys. Test OI-10 was performed on an MDA cladded rod with large-grain ($$sim$$25 $$mu$$m) fuel pellets with a peak fuel enthalpy condition of 435 J/g, and resulted in a peak residual hoop strain of 0.7%. On the other hand, Test OI-11 on a ZIRLO cladded rod with conventional pellets resulted in a fuel failure at a fuel enthalpy of 500 J/g due to the pellet-cladding mechanical interaction (PCMI). A long axial split was generated on the cladding over the active length. The fuel pellets were fragmented and dispersed into the coolant water. The fuel enthalpy at failure is higher than the PCMI failure criterion of 209 J/g at the corresponding burnup. The experimental results suggest that the rods with improved corrosion resistance have much safety margin against the PCMI failure compared to the conventional Zircaloy-4 rod.

Journal Articles

Characteristics of a dye laser amplifier transversely pumped by copper vapor lasers with a two-dimensional calculation model

Sugiyama, Akira; *; Kato, Masaaki; Maruyama, Yoichiro

Applied Optics, 36(24), p.5849 - 5854, 1997/08

 Times Cited Count:3 Percentile:23.5(Optics)

no abstracts in English

JAEA Reports

Sum frequency and second harmonics generation of copper vapor laser by nonlinear crystals

Sugiyama, Akira; Ozu, Akira; Kato, Masaaki; Maruyama, Yoichiro

JAERI-Research 96-050, 21 Pages, 1996/10

JAERI-Research-96-050.pdf:0.63MB

no abstracts in English

Journal Articles

Characteristics of a pressure-tuned single-mode dye laser oscillator pumped by a copper

Sugiyama, Akira; ; Kato, Masaaki; Maruyama, Yoichiro; Arisawa, Takashi

Opt. Eng., 35(4), p.1093 - 1097, 1996/04

 Times Cited Count:17 Percentile:67.43(Optics)

no abstracts in English

73 (Records 1-20 displayed on this page)