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Journal Articles

Data collection for dilute protein solutions via a neutron backscattering spectrometer

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:0 Percentile:0.01(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 D$$_{2}$$O was lower than that of a sample cell coated with regular water (H$$_{2}$$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$$_{2}$$O buffer and the sample container. Consequently, high quality information on protein dynamics could be extracted from dilute protein solutions.

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:1 Percentile:35.05(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:2 Percentile:9.06(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

Experimental investigation of the glass transition of polystyrene thin films in a broad frequency range

Inoue, Rintaro*; Kanaya, Toshiji*; Yamada, Takeshi*; Shibata, Kaoru; Fukao, Koji*

Physical Review E, 97(1), p.012501_1 - 012501_6, 2018/01

 Times Cited Count:8 Percentile:68.86(Physics, Fluids & Plasmas)

In this study, we investigate the $$alpha$$ process of a polystyrene thin film using inelastic neutron scattering (INS), dielectric relaxation spectroscopy (DRS), and thermal expansion spectroscopy (TES). The DRS and TES measurements exhibited a decrease in glass transition temperature ($$T_{rm g}$$) with film thickness. On the other hand, an increase in $$T_{rm g}$$ was observed in INS studies. In order to interpret this contradiction, we investigated the temperature dependence of the peak frequency ($$f_{rm m}$$) of the $$alpha$$ process probed by DRS and TES. The experiments revealed an increase in the peak frequency ($$f_{rm m}$$) with decreasing film thickness in the frequency region. This observation is consistent with the observed decrease in $$T_{rm g}$$ with thickness. The discrepancy between INS and DRS or TES descriptions of the $$alpha$$ process is likely to be attributed to a decrease in the apparent activation energy with film thickness and reduced mobility, due to the impenetrable wall effect.

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:3 Percentile:33.81(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:11 Percentile:66.99(Chemistry, Multidisciplinary)

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

Temperature-dependent nano-scale dynamics of PVA physical gel

Takahashi, Nobuaki; Nishida, Koji*; Inoue, Rintaro*; Ogawa, Hiroki*; Kanaya, Toshiji*; Nagao, Michihiro*

NSL News Letter, 2007-4, p.155 - 157, 2007/04

We have studied dynamics of poly(vinyl alcohol) (PVA) gel in a mixture of deuterated dimethyl sulfoxide (DMSO-d$$_{6}$$) and D$$_{2}$$O (60/40 by volume) during heating process from 25$$^{circ}$$C to 80$$^{circ}$$C using neutron spin-echo (NSE) techniques.

Journal Articles

Neutron spin-echo studies on poly(vinyl alcohol) gels during melting process

Takahashi, Nobuaki; Nishida, Koji*; Tsubouchi, Tsuyoshi*; Ogawa, Hiroki*; Inoue, Rintaro*; Kanaya, Toshiji*; Nagao, Michihiro*

ISSP Activity Report on Neutron scattering Research; Experimental Reports (CD-ROM), 13, 2 Pages, 2006/00

no abstracts in English

Journal Articles

Neutron spin-echo studies on crossover from single chain motion to collective dynamics

Kanaya, Toshiji; Takahashi, Nobuaki; Inoue, Rintaro*; Matsuba, Go*; Nishida, Koji*; Nagao, Michihiro*

ISSP Activity Report on Neutron scattering Research; Experimental Reports (CD-ROM), 13, 1 Pages, 2006/00

Journal Articles

Thermal neutron spin-echo studies on dynamics of a glass-forming polymer in a high ${it Q}$ range

Kanaya, Toshiji*; Kakurai, Kazuhisa; Tsukushi, Itaru*; Inoue, Rintaro*; Watanabe, Hiroshi*; Nishi, Masakazu*; Nakajima, Kenji; Takemura, Kazuhiro*; Furuya, Hidemine*

Journal of the Physical Society of Japan, 74(12), p.3236 - 3240, 2005/12

 Times Cited Count:5 Percentile:37.96(Physics, Multidisciplinary)

We performed thermal neutron spin echo measurements on a glass-forming polymer, deuterated polybutadiene (-[CD$$_{2}$$-CD=CD-CD$$_{2}$$]$$_{n}$$-; PB-d$$_{6}$$), in a high ${it Q}$ range up to 3.5$AA $^{-1}$$ covering the first and second peaks of the structure factor S(${it Q}$), and evaluated the decay rate $$Gamma$$(${it Q}$) of the coherent intermediate scattering function as a function of ${it Q}$. In contrast to the previous experimental findings on the first peak of S(${it Q}$) at ${it Q}$ = 1.5$AA $^{-1}$$, no "de Gennes" type narrowing was observed on the second peak at ${it Q}$ = 2.9$AA $^{-1}$$. This novel finding indicates that the narrowing is hidden by the distinct motions of the soft -CD$$_{2}$$-CD$$_{2}$$- and =CD-CD$$_{2}$$- units and the self-motions of the rigid and soft units in the ${it Q}$ range around the second peak.

Oral presentation

Analysis of protein domain dynamics studied by neutron/X-ray scattering and MD simulation

Nakagawa, Hiroshi; Saio, Tomohide*; Sugiyama, Masaaki*; Inoue, Rintaro*; Nagao, Michihiro*

no journal, , 

It is necessary for the understanding of structure polymorphism of various molecules and interacting protein and the plastic molecules base to clarify the fluctuation of the domain as the mer. In this study, I targeted protein MurD consisting of three domains and a ligand was in a free state and analyzed domain exercise by the quantum beam dispersion method using X-rays and the neutron and the correlation structure analytical method that fused of the molecules simulation about an ATP-binding state, three states of the Compound1-binding state. By the solution small angle scattering experiment, I showed that the solution structure of the 3 state was different. In addition, I showed good agreement with the dispersion profile obtained from the molecular simulation and confirmed that I could discuss solution structure in atom resolving power from experimental data of the low resolving power. I extracted a domain campaign in conjunction with the function from the chief ingredient analysis of the molecular simulation result. Furthermore, a result to suggest what a fluctuation and a couple of the amino acid residue that this domain campaign participated in the combination with interaction molecules of MurD did was provided. By the method that fused by an experiment method of dynamic solution structure analysis including a neutron spin echo and technique of the calculation science in addition to small angle scattering, I visualize domain exercise of protein in atom resolving power and, in the announcement, argue by a function of the protein from the dynamic structure that a couple did between the hierarchies of different space scale.

Oral presentation

Analysis of solution structure of multi-domain protein

Nakagawa, Hiroshi; Saio, Tomohide*; Sugiyama, Masaaki*; Inoue, Rintaro*

no journal, , 

It is necessary to check a structural change of the protein on the domain scale to predict the interaction with the target molecule and interaction between the protein based on tertiary structure information of the protein at the atom level. In addition, it is necessary for the understanding of structure polymorphism of various molecules and interacting protein and the plastic molecules base to clarify the fluctuation of the domain as the mer. It becomes the important problem how you elucidate flexibility of such a protein structure in the next-generation structural biology. In this study, I analyze a change of the multi-domain protein structure by the quantum beam dispersion method using X-rays and the neutron and the correlation structure analytical method that fused of the molecular simulation. In addition, I analyze the local structure of the active site of the protein in conjunction with a domain structure by quoting molecular simulation. I mediate between a solution dispersion experiment of the low resolving power and two experiment information of the crystal structure of the atom resolving power that has been already untied by a computer technology and elucidate the protein interaction that plural domains weave in wide space resolving power to be able to foresee the whole complex from an atom level.

Oral presentation

Characterization of microstructures in steels using small-angle X-ray scattering

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

no journal, , 

no abstracts in English

Oral presentation

Correlative protein dynamics in the hierarchical structure by MD-Neutron analysis

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.

Oral presentation

QENS of protein solutions measured by the TOF near backscattering spectrometer DNA

Nakagawa, Hiroshi; Saio, Tomohide*; Oda, Takashi*; Sato, Mamoru*; Inoue, Rintaro*; Sugiyama, Masaaki*; Tominaga, Taiki*; Kawakita, Yukinobu

no journal, , 

Protein is thermally fluctuating in solution, and the dynamics is essential for its biological functions. A protein has hierarchal structure and dynamics in temporal and spatial scale. In this work, QENS of a multi-domain protein, MurD, were measured by the TOF near backscattering spectrometer DNA in order to observe the internal motions. Hef is classified as an intrinsically disordered protein, which lost the rigid folded domain structure, and then have a more flexible structure than a folded protein. We will discuss the data treatment and analytical method of QENS of protein solutions, and characteristic dynamical features of folded rigid and disordered flexible proteins in the presentation.

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