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Hirota, Yuki*; Tominaga, Taiki*; Kawabata, Takashi*; Kawakita, Yukinobu; Matsuo, Yasumitsu*
Bioengineering (Internet), 10(5), p.622_1 - 622_17, 2023/05
Times Cited Count:3 Percentile:38.17(Biotechnology & Applied Microbiology)Hirota, Yuki*; Tominaga, Taiki*; Kawabata, Takashi*; Kawakita, Yukinobu; Matsuo, Yasumitsu*
Bioengineering (Internet), 9(10), p.599_1 - 599_17, 2022/10
Times Cited Count:3 Percentile:28.36(Biotechnology & Applied Microbiology)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:1 Percentile:12.64(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 DO was lower than that of a sample cell coated with regular water (H
O). 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 D
O buffer and the sample container. Consequently, high quality information on protein dynamics could be extracted from dilute protein solutions.
Furuike, Yoshihiko*; Ouyang, D.*; Tominaga, Taiki*; Matsuo, Tatsuhito*; Mukaiyama, Atsushi*; Kawakita, Yukinobu; Fujiwara, Satoru*; Akiyama, Shuji*
Communications Physics (Internet), 5(1), p.75_1 - 75_12, 2022/04
Times Cited Count:5 Percentile:58.65(Physics, Multidisciplinary)Tominaga, Taiki*; Sahara, Masae*; Kawakita, Yukinobu; Nakagawa, Hiroshi; Yamada, Takeshi*
Journal of Applied Crystallography, 54(6), p.1631 - 1640, 2021/12
Times Cited Count:5 Percentile:54.32(Chemistry, Multidisciplinary)Nogami, Satoshi*; Kadota, Kazunori*; Uchiyama, Hiromasa*; Arima-Osonoi, Hiroshi*; Iwase, Hiroki*; Tominaga, Taiki*; Yamada, Takeshi*; Takata, Shinichi; Shibayama, Mitsuhiro*; Tozuka, Yuichi*
International Journal of Biological Macromolecules, 190, p.989 - 998, 2021/11
Times Cited Count:9 Percentile:51.10(Biochemistry & Molecular Biology)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:6 Percentile:36.18(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.
Matsuura, Masato*; Yamada, Takeshi*; Tominaga, Taiki*; Kobayashi, Makoto*; Nakagawa, Hiroshi; Kawakita, Yukinobu
JPS Conference Proceedings (Internet), 33, p.011068_1 - 011068_6, 2021/03
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.
Tominaga, Taiki*; Kobayashi, Makoto*; Yamada, Takeshi*; Matsuura, Masato*; Kawakita, Yukinobu; Kasai, Satoshi*
JPS Conference Proceedings (Internet), 33, p.011095_1 - 011095_5, 2021/03
A vertical movement type of sample changer for the neutron spectrometer BL02, J-PARC MLF was developed for our top-loading type cryostat. The sample changer, termed as "PEACE", can control reproducibility of the irradiated position using guides made of polyether ether ketone. The variation between the background scattering profiles of three sample positions was found to be less than plus minus 1.6%. This result is reasonable, considering the deviation of sample position of less than plus minus 0.3 mm from the vertical axis.
Tominaga, Taiki*; Kawakita, Yukinobu; Nakagawa, Hiroshi; Yamada, Takeshi*; Shibata, Kaoru
JPS Conference Proceedings (Internet), 33, p.011086_1 - 011086_5, 2021/03
We developed a quartz double cylindrical sample cell optimized for a backscattering neutron spectrometer, especially for BL02 (DNA), MLF in J-PARC. A quartz glass tube, with one end closed, is shaved to obtain a wall thickness of 0.55 mm. The inner tube is properly centered using a protrusion into the outer tube such that the interstice between the outer and inner tubes keeps constant. This quartz cell can be used for samples that should not be in contact with the aluminum surface. We verified cell's background effect between the quartz cell and Al cell by QENS measurements using DO buffer. The elastic intensity profiles of the buffer in a low Q region were identical between both quartz cell and Al cell (A1070). In a high Q region, however, the profiles were different caused by the first sharp diffraction peak of quartz glass. For this region the data should be analyzed by consideration of absorption correction and diffraction in individual thickness of quartz cell.
Tominaga, Taiki*; Sahara, Masae*; Kawakita, Yukinobu; Nakagawa, Hiroshi; Shimamoto, Naonobu*
JPS Conference Proceedings (Internet), 33, p.011094_1 - 011094_5, 2021/03
In quasielastic neutron scattering studies, aluminum or aluminum alloys are frequently employed as sample cells. With the increasing incident-neutron flux, the research area currently continues to expand; thus, obtaining data has become quicker than ever for dilute conditions. One such area is the water-containing systems. In this study, we investigated the effect of temperature on Al and found that even in a low temperature atmosphere, Al corrosion can occur. This was attributed to the different thermal expansion coefficients of Al as a base substrate and Al oxide as a passivating film.
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:6 Percentile:23.97(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.
Nakano, Shota*; Konno, Soken*; Tomita, Naoto*; Matsuba, Go*; Tominaga, Taiki*; Takata, Shinichi
Microsystem Technologies, 22(1), p.57 - 63, 2016/01
Times Cited Count:3 Percentile:19.97(Engineering, Electrical & Electronic)We studied the structural formation process of polyacrylonitrile (PAN) gelation in a wide-spatial scale with the small and wide angle neutron scattering in MLF, J-PARC. In micron-scale structure, light transmittance and gelation time were evaluated. The presence of water in the mixed solvent accelerated the phase separation and gelation. In the opaque-gel case, we observed the nanometer-scaled correlation of crystalline cross-linking points and smooth boundary of two micron-scaled phases due to liquid-liquid phase separation. The correlation length is independent of the annealing time, then the cross-linking point exists locally and micro-gelation occurs during phase separation. By contrast, in the transparent-gel case, the correlation length was found to increase throughout the gelation process, and the entanglements of the polymer chains play a role similar to that of cross-linking points.
Takata, Shinichi; Suzuki, Junichi*; Oishi, Kazuki*; Iwase, Hiroki*; Shinohara, Takenao; Oku, Takayuki; Nakatani, Takeshi; Inamura, Yasuhiro; Ito, Takayoshi*; Tominaga, Taiki*; et al.
no journal, ,
The small and wide angle neutron scattering instrument, , was installed at the
15 in the Materials and Life Science Experimental Facility,
, of
.
is designed for efficient measurement in wide-q range by using of the wide wavelength and the four detector banks which cover small-, middle-, high-, and backward-angle. At the present stage, 1,216
s are mounted on
, where the number is about 50% of the installable total
s number. On beam commissioning started in January 2012, and user program began in March 2012. The software of data reduction has newly developed and some sample environment devices such as a sample changer, tension tester, and refrigerator have been improved. In this presentation, we present the current status of
about the new software, sample environment devices, and the results on some samples to show the instrument performance of
.
Tominaga, Taiki; Takata, Shinichi; Suzuki, Junichi*; Seto, Hideki; Aizawa, Kazuya; Arai, Masatoshi
no journal, ,
no abstracts in English
Tominaga, Taiki; Suzuki, Junichi*; Takata, Shinichi; Shinohara, Takenao; Oku, Takayuki; Nakatani, Takeshi; Inamura, Yasuhiro; Suzuya, Kentaro; Aizawa, Kazuya; Arai, Masatoshi; et al.
no journal, ,
no abstracts in English
Tominaga, Taiki; Takata, Shinichi; Seto, Hideki; Suzuki, Junichi*; Aizawa, Kazuya; Arai, Masatoshi
no journal, ,
no abstracts in English
Tominaga, Taiki; Takata, Shinichi; Suzuki, Junichi*; Shinohara, Takenao; Oku, Takayuki; Oishi, Kazuki*; Nakatani, Takeshi; Inamura, Yasuhiro; Iwase, Hiroki*; Ito, Takayoshi*; et al.
no journal, ,
no abstracts in English
Nakagawa, Hiroshi; Saio, Tomohide*; Sugiyama, Masaaki*; Inoue, Rintaro*; Tominaga, Taiki*
no journal, ,
The neutron associate elastic scattering device installed in large strength pulse neutron J-PARC is effective for the analysis of the protein dynamics of the pico second - nanosecond. It will show the importance of the QENS experiment of the protein using J-PARC to clarify how the dynamics of the space scale are related with cooperative dynamics of the whole protein affecting creature function expression then. On the other hand, for the structural biology to discuss a function based on a tertiary structure, it is difficult to relate a function to structure dynamics only from QENS spectrum. It is effective to quote molecular simulation so that structure discusses the information of dynamics to relate a function to structure scientifically. I suggest that I visualize the hierarchical structure of protein dynamics in atom resolving power by the MD-Neutron method which fused by a neutron dispersion experiment and molecules simulation while utilizing various technique of the structural biology in this announcement from different angles. In addition, about MurD which is multi-domain protein, I discuss a function of the protein from the dynamic structure that a couple did between the hierarchies of the scale between the different space-time.
Tominaga, Taiki; Takata, Shinichi; Suzuki, Junichi*; Shinohara, Takenao; Oku, Takayuki; Nakatani, Takeshi; Inamura, Yasuhiro; Suzuya, Kentaro; Aizawa, Kazuya; Arai, Masatoshi; et al.
no journal, ,
no abstracts in English