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Journal Articles

Analysis of nanostructures and hydration states of foods by neutron scattering and diffraction

Nakagawa, Hiroshi

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.

Journal Articles

Protein hydration and its freezing phenomena; Toward the application for cell freezing and frozen food storage

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. $$sim$$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.

Journal Articles

Hydration and its hydrogen bonding state on a protein surface in the crystalline state as revealed by molecular dynamics simulation

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.

Journal Articles

Molecular dynamics of water and water activity in glycerol-water mixtures

Nakagawa, Hiroshi

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.

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

Conformational ensemble of a multidomain protein explored by Gd$$^{3+}$$ electron paramagnetic resonance

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

 Times Cited Count:0 Percentile:0.01(Biophysics)

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.

Journal Articles

Analysis of water in food by neutron scattering

Nakagawa, Hiroshi

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.

Journal Articles

X-ray scattering $$cdot$$ neutron scattering

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.

Journal Articles

Development of spin-contrast-variation neutron powder diffractometry for extracting the structure factor of hydrogen atoms

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

 Times Cited Count:0 Percentile:0.02(Chemistry, Multidisciplinary)

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.

Journal Articles

Sequence-dependent hydration water dynamics of dodecameric DNA

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 Hn$$_{2}$$O/D$$_{2}$$O contrast for two DNA dodecamers, 5'CGCG$$underline{rm AATT}$$CGCG'3 and 5'CGCG$$underline{rm TTAA}$$CGCG'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.

Journal Articles

Corrosion of aluminum-based containers for neutron studies with aqueous samples under low temperatures

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.

Journal Articles

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

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.

Journal Articles

Quartz cell for a backscattering spectrometer

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 D$$_{2}$$O 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.

Journal Articles

Freezable and unfreezable hydration water; Distinct contributions to protein dynamics revealed by neutron scattering

Yamamoto, Naoki*; Kofu, Maiko; Nakajima, Kenji; Nakagawa, Hiroshi; Shibayama, Naoya*

Journal of Physical Chemistry Letters (Internet), 12(8), p.2172 - 2176, 2021/03

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

Hydration water plays a crucial role for activating the protein dynamics required for functional expression. Yet, the details are not understood about how hydration water couples with protein dynamics. A temperature hysteresis of the ice formation of hydration water is a key phenomenon to understand which type of hydration water, unfreezable or freezable hydration water, is crucial for the activation of protein dynamics. Using neutron scattering, we observed a temperature-hysteresis phenomenon in the diffraction peaks of the ice of freezable hydration water, whereas protein dynamics did not show any temperature hysteresis. These results show that the protein dynamics is not coupled with freezable hydration water dynamics, and unfreezable hydration water is essential for the activation of protein dynamics.

Journal Articles

Introduction to SANS-J and PNO

Kumada, Takayuki; Motokawa, Ryuhei; Nakagawa, Hiroshi; Oba, Yojiro; Sekine, Yurina

Hamon, 31(1), p.5 - 6, 2021/02

no abstracts in English

Journal Articles

Study of protein hydration via neutron scattering

Nakagawa, Hiroshi; Ajito, Satoshi

Teion Seibutsu Kogakkai-Shi, 66(2), p.83 - 92, 2021/02

Hydration and dehydration of bio-macromolecules result in the changes in the structural stabilization and biological functionality. The structure and dynamics of the hydration water are essential to understand the hydration and dehydration processes of the biosystem. Since neutron has wavelength in the order of angstrom and thermal energy, it is able to observe the structures and dynamics of the bio-molecules and hydration water. The large difference in neutron scattering cross-sections between hydrogen and deuterium provides powerful methods for emphasizing the scattering from a bio-macromolecule or hydration water by selective deuteration for hydrated biological materials. Incoherent neutron scattering and small-angle neutron scattering are able to examine the dynamics of the hydration water, and the density and structure of the hydration shell, respectively. The neutron sources, JRR-3 reactor and J-PARC accelerator, are available in Japan. The present review aims to provide the readers with brief descriptions of the neutron scattering methods and the applications to the protein hydration.

Journal Articles

Eco-friendly carboxymethyl cellulose nanofiber hydrogels prepared via freeze cross-linking and their applications

Sekine, Yurina; Nankawa, Takuya; Yunoki, Shunji*; Sugita, Tsuyoshi; Nakagawa, Hiroshi; Yamada, Teppei*

ACS Applied Polymer Materials (Internet), 2(12), p.5482 - 5491, 2020/12

We developed a cross-linking method using freeze concentration and used it to synthesize a new type of carboxymethyl cellulose nanofiber (CMCF) hydrogel with high compressive strength ($$>$$ 80 MPa) and high compressive recoverability. The hydrogels were prepared by adding an aqueous solution of citric acid (CA) to a frozen CMCF sol and then thawing the sol. The reaction between the freeze-concentrated CMCF and CA created a rigid porous structure that reflected the ice crystal structure. Their cross-linked structure has a high stability to compressive stress. Bentonite was immobilized on a CMCF hydrogel by adding bentonite to the CMCF sol before freeze cross-linking. The CMCF-bentonite hydrogel showed high adsorptivity for chemical dyes. The physically cross-linked CMCF hydrogels are non-toxic, metal-free, and simple to prepare, and thus they may be useful as sustainable materials in various fields.

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

Understanding water-mediated DNA damage production by molecular dynamics calculation of solvent accessibility

Yonetani, Yoshiteru*; Nakagawa, Hiroshi

Chemical Physics Letters, 749, p.137441_1 - 137441_5, 2020/06

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

We calculated solvent accessibility of DNA backbone hydrogen sites, H1'-H5' by using molecular dynamics simulation of DNA. The result of accessibility is well correlated with the site-dependent reactivity with OH radicals experimentally reported, indicating that the different DNA-radical reactivity is mainly caused by the difference in the solvent accessibility of each hydrogen site. Compared with the previous calculation with solvent-accessible surface area, the present MD-based counting of molecular access provided a slightly improved result, which suggests importance of more realistic molecular components such as electrostatic interactions and DNA conformational fluctuation.

Journal Articles

Rigidity of protein structure revealed by incoherent neutron scattering

Nakagawa, Hiroshi; Kataoka, Mikio*

Biochimica et Biophysica Acta; General Subjects, 1864(4), p.129536_1 - 129536_6, 2020/04

 Times Cited Count:2 Percentile:45.26(Biochemistry & Molecular Biology)

The rigidity and flexibility of a protein is reflected in its structural dynamics. Studies on protein dynamics often focus on flexibility and softness; this review focuses on protein structural rigidity. The extent of rigidity can be assessed experimentally with incoherent neutron scattering; a method that is complementary to molecular dynamics simulation. This experimental technique can provide information about protein dynamics in timescales of pico- to nanoseconds and at spatial scales of nanometers; these dynamics can help quantify the rigidity of a protein by indices such as force constant, Boson peak, dynamical transition, and dynamical heterogeneity. These indicators also reflect the rigidity of a protein's secondary and tertiary structures. In addition, the indices reveal how rigidity is influenced by different environmental parameters, such as hydration, temperature, pressure, and protein-protein interactions. Hydration affects both rigidity and softness more than other environmental factors. Interestingly, hydration affects harmonic and anharmonic motions in opposite ways. This difference is probably due to the protein's dynamic coupling with water molecules via hydrogen bonding.

234 (Records 1-20 displayed on this page)