Kabumoto, Hiroshi; Nakagawa, Sohei; Matsuda, Makoto
JAEA-Conf 2022-002, 146 Pages, 2023/03
"The 34th Meeting for Tandem Accelerators and their Associated Technologies" was held on July 21-22, 2022 organized by Nuclear Science Research Institute of the Japan Atomic Energy Agency. This meeting was held only on-line for preventing the spread of COVID-19 infection. The purpose of this meeting is contribution of development for related technology and of management of facilities through exchange of information among the researchers and engineers using and operating electrostatics accelerator facilities like tandem accelerators. There were 25 presentations which contains current status report of facility, technical development of accelerator, research of application. The total number of participants was a hundred, from 26 universities, research organizations and industries. This meeting consisted of only oral session, a poster session was not carried out because of on-line meeting. This proceeding compiles the contents of report papers in the meeting.
Nakagawa, Hiroshi; Yamamoto, Naoki*
Life (Internet), 13(2), p.318_1 - 318_15, 2023/02
Incoherent neutron scattering and terahertz spectroscopy have approximately the same energy range of measurement. Since both techniques are used to study the dynamics of proteins and hydrated water, it is important to review the advantages and disadvantages of both techniques and the relevant literature. To the best of our knowledge, there is no review of both methods, and we believe that this review is of high value.
Kabumoto, Hiroshi; Matsuda, Makoto; Nakamura, Masahiko; Ishizaki, Nobuhiro; Kutsukake, Kenichi; Otokawa, Yoshinori; Asozu, Takuhiro; Matsui, Yutaka; Nakagawa, Sohei; Abe, Shinichi
Proceedings of 19th Annual Meeting of Particle Accelerator Society of Japan (Internet), p.1109 - 1113, 2023/01
no abstracts in English
Sogabe, Tomochika*; Nakagawa, Hiroshi; Yamada, Takeshi*; Koseki, Shigenobu*; Kawai, Kiyoshi*
Biophysical Journal, 121(20), p.3874 - 3882, 2022/10
The purpose of this study was to clarify the glass transition behavior of bacteria () as a function of water activity (). Mechanical relaxation was investigated at 298 K, and the mechanical ( at which mechanical glass transition occurs at 298 K) was determined to be 0.667. Temperature-dependency of mean square displacement was investigated by inelastic neutron scattering. From the linear fitting, two dynamical transition temperatures (low and high-) were determined. There was a minor effect of on the low- except for the anhydrous sample. The high- largely increased with the decrease in . The dynamical determined by high- (0.688) was slightly higher than the mechanical because of the difference in the measurement time-scale. The high- was converted to the glass transition temperature (), and anhydrous was estimated to be 411 K. Bacterial inactive-active transition was discussed according to the glass transition behavior.
Tominaga, Taiki*; Nakagawa, Hiroshi; Sahara, Masae*; Oda, Takashi*; Inoue, Rintaro*; Sugiyama, Masaaki*
Life (Internet), 12(5), p.675_1 - 675_9, 2022/05
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 (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; Matsuo, Tatsuhito*
Hamon, 32(1), p.12 - 15, 2022/02
To elucidate, predict, and control the biological functions of proteins, it is important to clarify their solution structure and dynamics. Small-angle scattering is one of effective methods for examining the changes in their structures and dynamics due to their binding with target molecules under physiological conditions, although its resolution is lower than that of crystallography, which provides structural information at atomic resolution. In addition, neutron spin echo is the only technique that can measure the conformational dynamics of proteins in the Q-region, which is covered by small-angle scattering. In this paper, we will introduce some of our recent studies using small-angle scattering and neutron spin echo.
Matsuo, Tatsuhito*; Nakagawa, Hiroshi
Hamon, 32(1), p.8 - 11, 2022/02
Incoherent neutron scattering is a powerful tool to investigate the dynamics of biomolecules and water. In this article, a new dynamical model called Matryoshka model is first described, which provides detailed information on the motions contained in the phospholipid molecules based on the scattering spectra. In the latter half of the article, a relationship between water activity and water mobility, and the effects of pressure and hydration on protein dynamics are discussed. These studies demonstrate the advancement of analytical methods which provide ever more detailed information for elucidating the mechanism of biological functions.
Nakagawa, Hiroshi; Appavou, M.-S.*; Wuttke, J.*; Zamponi, M.*; Holderer, O.*; Schrader, T.*; Richter, D.*; Doster, W.*
Joint Annual Report 2021 of the MLZ and FRM II, P. 55, 2022/00
-casein undergoes a reversible endothermic self-association with increasing temperature, forming micelles of limited size. We characterize the structural flexibility in terms of nano-second molecular motions. We report on two relaxation processes on a nano-second and a sub-nano-second time scale for -casein in solution. Both processes are analyzed by Brownian Oscillator model, by which the spring constant can be defined in the isotropic parabolic potential. The slower process seems a characteristic feature of the unfolded structure, and dividing the relaxation time by the solvent viscosity removes most of the temperature dependence, indicating that indicates, the process involves density fluctuations of the solvent. The faster process has a smaller amplitude and requires hydration water. The flexibility of a -casein monomer is preserved in the micelle.
Aguribaio, 6(1), p.44 - 46, 2021/12
In order to understand the macroscopic physical properties that characterize the quality of food, such as shelf life and texture, it is important to understand the relationship between microscopic information on the nanostructure and hydration state of food molecules and macroscopic observables. The elucidation of the complex hierarchical structure of food molecules from nano to micro scale and the interaction and hydration state within the molecular structure is one of the central themes in food physics. Small-angle neutron scattering and quasi-elastic scattering methods can be used to analyze molecular structures and molecular motions on such spatial scales.
Nakagawa, Hiroshi; Appavou, M.-S.*; Wuttke, J.*; Zamponi, M.*; Holderer, O.*; Schrader, T. E.*; Richter, D.*; Doster, W.*
Biophysical Journal, 120(23), p.5408 - 5420, 2021/12
Casein proteins are characterized by its extended structural features and its dynamics, which are different from those of typical folded proteins, due to a large number of proline residues. We were able to describe the unique structural dynamics by Orenstein-Uhlenbeck Brownian oscillator model by several types of QENS experiments with wide time-scales. The characterized dynamics also allowed us to discuss the effective sequestration of calcium phosphate in terms of its unique dynamical structure. The biological role of the physical processes of the proteins on the nanosecond order on the biological functions is presented.
Yamamoto, Naoki*; Nakanishi, Masahiro*; Rajan, R.*; Nakagawa, Hiroshi
Biophysics and Physicobiology (Internet), 18, p.284 - 288, 2021/12
Water is an indispensable solvent for living things. 60% of our body is composed of water, the lack of which causes lots of fatal problems. It has also been known that protein function is performed only when it accompanies water molecules around the surface, i.e. hydration water molecules. Therefore, it is essential to understand how water and biological component interact with each other in the view point of structure and dynamics. Freezing is a fundamental and simple phenomenon of water, and thus can be used as a probe for the purpose. Furthermore, preservation of cells and proteins under low temperature is crucial for numerous applications, which in turn triggers a myriad of undesirable consequences because of the freezing.
Tominaga, Taiki*; Sahara, Masae*; Kawakita, Yukinobu; Nakagawa, Hiroshi; Yamada, Takeshi*
Journal of Applied Crystallography, 54(6), p.1631 - 1640, 2021/12
Nakagawa, Hiroshi; Tamada, Taro*
Frontiers in Chemistry (Internet), 9, p.738077_1 - 738077_7, 2021/10
Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules interact with a protein surface via hydrogen bonding. Here, we examined the hydration structure and hydrogen bonding state of a globular protein, staphylococcal nuclease, at various hydration levels in a crystalline state by all-atom molecular dynamics simulation. The hydrophobic residue surface was found to be more hydrated than the hydrophilic residue surface, but both were uniformly hydrated in response to increased water content. In addition, the hydrogen bonds in hydrated water have a tetrahedral structure, which is not much different from the structure of bulk water. The hydrogen bonding structure is compatible with the results of neutron crystallography. The simulations are useful for analyzing the hydration structure and hydrogen bonding state in the crystalline state, and will greatly assist in the further analysis of the information obtained from crystal structure analysis.
Teion Seibutsu Kogakkai-Shi, 67(2), p.129 - 133, 2021/10
Water activity is an indication of the microbial growth, enzymatic activity, preservation, and quality of foods. The water activity of glycerol-water mixtures can be controlled by changing its ratio. In this study, the diffusive dynamics of water were investigated at various water activities by incoherent quasi-elastic neutron scattering. It was found that water activity dependent diffusive water dynamics is correlated with the water sorption isotherm.
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
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.
Saio, Tomohide*; Hiramatsu, Soya*; Asada, Mizue*; Nakagawa, Hiroshi; Shimizu, Kazumi*; Kumeta, Hiroyuki*; Nakamura, Toshikazu*; Ishimori, Koichiro*
Biophysical Journal, 120(15), p.2943 - 2951, 2021/08
A rigid double-arm lanthanide tag was utilized in electron paramagnetic resonance spectroscopy to measure the distance between two specific points on a protein, and conformational states and distribution of a multi-domain protein enzyme MurD was investigated. Although the previous crystallographic and NMR studies have reported the three distinct conformational states of MurD, our data unveiled that the protein exists in much more variety of conformational states in the absence of the ligand. Given the fact that MurD is one of the potent drug target for infectious diseases, the finding in this study will provide important structural basis for drug development.
Aguribaio, 5(6), p.537 - 539, 2021/06
Water activity is a thermodynamic quantity that evaluates the preservation and quality of food, defined as the ratio of the vapor pressure of food and pure water. On the other hand, the state of water in food is only qualitatively explained by bound water and free water classified by water sorption isothermal properties, and there are many ambiguities in the relationship between physicochemical properties of water and water activity. Neutron scattering can be used to analyze molecular mobility and hydration structure, and is a useful technique for investigating the physicochemical state of water in food and the interaction between food and water.
Nakagawa, Hiroshi; Matsuo, Tatsuhito*
Jikken Igaku, 39(10), p.1667 - 1673, 2021/06
X-ray and neutron scattering are methods to reveal the structural state, assembly state, and intermolecular interactions of biomolecules in solution. Synchrotron X-rays provide highly accurate solution scattering data in a short time. Deuterated labeling can be used to make specific molecules invisible in neutron beams, allowing us to selectively observe only the molecules of interest in a molecular population. Neutron beams with energies comparable to thermal fluctuations are also suitable for measuring molecular motion. Although its application to the analysis of phase separation phenomena is currently limited, it is an effective method for analyzing phase separation states on the nano- to meso-scale and for studying the liquid-liquid phase separation.
Miura, Daisuke*; Kumada, Takayuki; Sekine, Yurina; Motokawa, Ryuhei; Nakagawa, Hiroshi; Oba, Yojiro; Ohara, Takashi; Takata, Shinichi; Hiroi, Kosuke; Morikawa, Toshiaki*; et al.
Journal of Applied Crystallography, 54(2), p.454 - 460, 2021/04
We developed a spin-contrast-variation neutron powder diffractometry technique that extracts the structure factor of hydrogen atoms, namely, the contribution of hydrogen atoms to a crystal structure factor. Crystals of L-glutamic acid were dispersed in a dpolystyrene matrix containing 4-methacryloyloxy-2,2,6,6,-tetramethyl-1-piperidinyloxy (TEMPO methacrylate) to polarize their proton spins dynamically. The intensities of the diffraction peaks of the sample changed according to the proton polarization, and the structure factor of the hydrogen atoms was extracted from the proton-polarization dependent intensities. This technique is expected to enable analyses of the structures of hydrogen-containing materials that are difficult to determine with conventional powder diffractometry.
Nakagawa, Hiroshi; Yonetani, Yoshiteru*; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya*; Inamura, Yasuhiro; Kataoka, Mikio*; Kono, Hidetoshi*
JPS Conference Proceedings (Internet), 33, p.011101_1 - 011101_6, 2021/03
Hydration water dynamics were measured by quasi-elastic neutron scattering with HnO/DO contrast for two DNA dodecamers, 5'CGCGCGCG'3 and 5'CGCGCGCG'3, which have been computationally shown to be structurally rigid and flexible, respectively. The dynamical transitions of the hydration water as well as DNA were observed for both sequences at approximately 240 K. Above the transition temperature, the mean square displacements of the hydration water for the rigid sequence were smaller than those for the flexible one. Furthermore, the relaxation time of the hydration water was longer in the rigid DNA than in the flexible DNA. We suggest that hydration water dynamics on the picosecond timescale are associated with sequence-dependent deformability of DNA.