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Journal Articles

Structure analysis and derivation of deformed electron density distribution of polydiacetylene giant single crystal by the combination of X-ray and neutron diffraction data

Tashiro, Koji*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Ohara, Takashi; Hanesaka, Makoto*; Yoshizawa, Yoshinori*; Yamamoto, Hiroko*; Niimura, Nobuo*; Tanaka, Ichiro*; Kurihara, Kazuo*; et al.

Macromolecules, 51(11), p.3911 - 3922, 2018/06

 Times Cited Count:4 Percentile:16.38(Polymer Science)

Journal Articles

Development of magnetic sensors for JT-60SA

Takechi, Manabu; Matsunaga, Go; Sakurai, Shinji; Sasajima, Tadayuki; Yagyu, Junichi; Hoshi, Ryo*; Kawamata, Yoichi; Kurihara, Kenichi; JT-60SA Team; Nishikawa, T.*; et al.

Fusion Engineering and Design, 96-97, p.985 - 988, 2015/10

 Times Cited Count:9 Percentile:63.44(Nuclear Science & Technology)

Journal Articles

Evaluation of the resolvable capacity of Bragg reflections for a new diffractometer at J-PARC/MLF designed for protein crystals with large unit cells

Tomoyori, Katsuaki; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota

JPS Conference Proceedings (Internet), 8, p.036004_1 - 036004_6, 2015/09

We aim to build a high-resolution neutron time-of-flight diffractometer for biomacromolecules at the Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex (J-PARC) that allows the collection of neutron diffraction data from crystals with unit cells of $$approx$$ 250 ${AA}$;. Considering both the flux and pulse width necessary to realize data collection covering a minimum d-spacing of 2.0 ${AA}$; and with a unit cell constant of $$approx$$ 250 ${AA}$; we chose a decoupled moderator (DM) as the appropriate source for this high-resolution diffractometer. We considered a simple instrumentation model that includes a moderator, neutron guide, sample size, and neutron detector; we then investigated its spot separation performance and estimated the instrumental parameters for the design of a new diffractometer for protein crystals with large unit cells at J-PARC/MLF. It is preferable to extend the total flight path to resolve Bragg reflections for protein crystals with large unit cells as the scattering angle increases. Meanwhile, to ensure resolvable detection capacity at the middle scattering angle region (2$$theta$$$$approx$$ 90$$^{circ}$$), it is necessary to restrict the angular divergence. In the case of $$theta$$$$_{m}$$ $$approx$$ 0.2$$^{circ}$$, scattering angles from around 2$$theta$$$$approx$$90$$^{circ}$$ to higher backscattering angles are more efficient for protein crystals with large unit cells ($$>$$250 ${AA}$) with a resolution of 2.0 ${AA}$.

Journal Articles

The Cauchy-condition surface (CCS) method for plasma equilibrium shape reproduction

Kurihara, Kenichi; Itagaki, Masafumi*; Miyata, Yoshiaki; Nakamura, Kazuo*; Urano, Hajime

Purazuma, Kaku Yugo Gakkai-Shi, 91(1), p.10 - 47, 2015/01

no abstracts in English

Journal Articles

Background elimination using the SNIP algorithm for Bragg reflections from a protein crystal measured by a TOF single-crystal neutron diffractometer

Tomoyori, Katsuaki; Hirano, Yu; Kurihara, Kazuo; Tamada, Taro

Journal of Physics; Conference Series, 664, p.072049_1 - 072049_7, 2015/00

 Times Cited Count:4 Percentile:82.98

In neutron protein crystallography, it should be also emphasized that the weak Bragg reflections due to the large unit cells may be buried beneath the strong background caused by the incoherent scattering of hydrogen atoms. Therefore, the background estimation from the source is more reliable to improve the accuracy of Bragg integral intensity. We propose the adoption of Statistics-sensitive Nonlinear Iterative Peak-clipping (SNIP) algorithm for background estimation, which can eliminate the background from the source spectrum as well as statistically enhance low peaks. In addition, it was recently reported that the Landau and Vavilov distributions, which are used to describe the energy loss of charged particles traversing a thin absorber were found to be in excellent agreement with the observed TOF profile. I show that it may be beneficial to establish a profile-fitting method with the combined use of the Landau/Vavilov functions to faithfully reproduce the TOF peak shape and a SNIP background evaluation algorithm to eliminate statistical fluctuations.

Journal Articles

Accurate structure analyses of polymer crystals on the basis of wide-angle X-ray and neutron diffractions

Tashiro, Koji*; Hanesaka, Makoto*; Yamamoto, Hiroko*; Wasanasuk, K.*; Jayaratri, P.*; Yoshizawa, Yoshinori*; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; et al.

Kobunshi Rombunshu, 71(11), p.508 - 526, 2014/11

 Times Cited Count:6 Percentile:23.96(Polymer Science)

The crystal structure analysis of various polymer substances has been reviewed on the basis of wide-angle high-energy X-ray and neutron diffraction data. The progress in structural analytical techniques of polymer crystals have been reviewed at first. The structural models proposed so far were reinvestigated and new models have been proposed for various kinds of polymer crystals including polyethylene, poly(vinyl alcohol), poly(lactic acid) and its stereocomplex etc. The hydrogen atomic positions were also clarified by the quantitative analysis of wide-angle neutron diffraction data, from which the physical properties of polymer crystals have been evaluated theoretically. The bonded electron density distribution has been estimated for a polydiacetylene single crystal on the basis of the so-called X-N method or by the combination of structural information derived from X-ray and neutron diffraction data analysis. Some comments have been added about future developments in the field of structure-property relationship determination.

Journal Articles

Single crystal diffractometers for bio-macromolecules using neutrons at steady-state reactor sources

Kurihara, Kazuo; Tamada, Taro

Hamon, 24(3), p.190 - 199, 2014/08

In order to overcome low flux of neutron sources as well as weak diffraction intensity from bio-macromolecule crystals, several devices have been developed in neutron biological crystallography. Elastically bent Si monochromator has contributed the increase of incident beam intensity, and neutron imaging plate (NIP) has provided large detecting area. In particular, the successful development of the NIP made a breakthrough in this research field. Additionally, recent advances in techniques for cryogenic temperature measurement, growth of large crystal and sample deuteration have made a contribution to efficient measurement performance. Currently, a total of six diffractometers for bio-macromolecule are available at research reactors in the world. Neutron crystallography is on the verge of becoming a prevalent method for structural study on bio-macromolecules.

Journal Articles

High-resolution crystal structure of copper amine oxidase from ${it Arthrobacter globiformis}$; Assignment of bound diatomic molecules as O$$_{2}$$

Murakawa, Takeshi*; Hayashi, Hideyuki*; Sunami, Tomoko; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Suzuki, Mamoru*; Tanizawa, Katsuyuki*; Okajima, Toshihide*

Acta Crystallographica Section D, 69(12), p.2483 - 2494, 2013/12

 Times Cited Count:13 Percentile:68.03(Biochemical Research Methods)

The crystal structure of a Cu amine oxidase from ${it Arthrobacter globiformis}$ was determined at 1.08 ${AA}$ resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight $$sim$$200) as a cryoprotectant. The final crystallographic $$R$$-factor and $$R$$$$_{rm free}$$ value are 13.0% and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior including the active site, which resulted in the marked reduction of the overall ${it B}$ factor and consequently led to a sub-atomic resolution structure for a relatively large protein with a monomer molecular weight of $$sim$$70,000. About 40% of all the presumed hydrogen atoms were observed as clear electron densities in the $$F$$$$_{rm o}$$ - $$F$$$$_{rm c}$$ difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site that contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely molecular oxygen, are bound to the protein, one of which is located in the region that has been previously proposed as an entry route for the substrate dioxygen from the central cavity of the dimer interface to the active site.

Journal Articles

Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors

Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Tomoyori, Katsuaki; Ohara, Takashi; Katagiri, Masaki*; Kurihara, Kazuo; Tanaka, Ichiro*; Niimura, Nobuo*

Journal of Synchrotron Radiation, 20(6), p.994 - 998, 2013/11

 Times Cited Count:34 Percentile:85.22(Instruments & Instrumentation)

The IBARAKI biological crystal diffractometer, iBIX, is a high-performance time-of-flight neutron single-crystal diffractometer for elucidating mainly the hydrogen, protonation and hydration structures of biological macromolecules in various life processes. Since the end of 2008, iBIX has been available to user's experiments supported by Ibaraki University. Since August 2012, an upgrade of the 14-existing detectors has begun and 16 new detectors have been installed for iBIX. The total measurement efficiency of the present diffractometer has been impoved by one order of magnitude from the previous one with the increasing of accelerator power. In December 2012, commissioning of the new detectors was successful, and collection of the diffraction dataset of ribonucrease A as a standard protein was attempted in order to estimate the performance of the upgraded iBIX in comparison with previous results. The resolution of diffraction data, equivalence among intensities of symmetry-related reflections and reliability of the refined structure have been improved dramatically. iBIX is expected to be one of the highest-performance neutron single-crystal diffractometers for biological macromolecules in the world.

Journal Articles

Hydrogen-bond network and pH sensitivity in human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro*; Niimura, Nobuo*

Journal of Synchrotron Radiation, 20(6), p.834 - 837, 2013/11

 Times Cited Count:5 Percentile:30.27(Instruments & Instrumentation)

Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm$$^{3}$$ for four months. The neutron crystal structure solved at 2.0 ${AA}$ revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

Journal Articles

Neutron and X-ray crystallographic analysis of the human $$alpha$$-thrombin-bivalirubin complex at pD 5.0; Protonation states and hydration structure of the enzyme-product complex

Yamada, Taro*; Kurihara, Kazuo; Onishi, Yuki*; Tamada, Taro; Tomoyori, Katsuaki; Masumi, Kenji*; Tanaka, Ichiro*; Kuroki, Ryota; Niimura, Nobuo*

Biochimica et Biophysica Acta; Proteins and Proteomics, 1834(8), p.1532 - 1538, 2013/08

 Times Cited Count:15 Percentile:45.92(Biochemistry & Molecular Biology)

The protonation states and hydration structures of the $$alpha$$-thrombin-bivalirubin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8 ${AA}$, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25 ${AA}$ resolution. The complex represents a model of the enzyme-product (EP) complex of $$alpha$$-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for D$$delta$$1 and D$$epsilon$$2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen O$$gamma$$ of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the O$$gamma$$ atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.

Journal Articles

Neutron and X-ray crystallographic analysis of ${it Achromobacter}$ protease I at pD 8.0; Protonation states and hydration structure in the free-form

Onishi, Yuki*; Yamada, Taro*; Kurihara, Kazuo; Tanaka, Ichiro*; Sakiyama, Fumio*; Masaki, Takeharu*; Niimura, Nobuo*

Biochimica et Biophysica Acta; Proteins and Proteomics, 1834(8), p.1642 - 1647, 2013/08

 Times Cited Count:7 Percentile:21.99(Biochemistry & Molecular Biology)

The structure of the free-form of ${it Achromobacter}$ protease I (API) at pD 8.0 was refined by simultaneous use of single crystal X-ray and neutron diffraction data sets to investigate the protonation states of key catalytic residues of the serine protease. Occupancy refinement of the catalytic triad in the active site of API free-form showed that ca. 30% of the imidazole ring of H57 and ca. 70% of the hydroxyl group of S194 were deuterated. This observation indicates that a major fraction of S194 is protonated in the absence of a substrate. The protonation state of the catalytic triad in API was compared with the bovine $$beta$$-trypsin-BPTI complex. The comparison led to the hypothesis that close contact of a substrate with S194 could lower the acidity of its hydroxyl group, thereby allowing H57 to extract the hydrogen from the hydroxyl group of S194. H210, which is a residue specific to API, does not form a hydrogen bond with the catalytic triad residue D113. Instead, H210 forms a hydrogen bond network with S176, H177 and a water molecule. The close proximity of the bulky, hydrophobic residue W169 may protect this hydrogen bond network, and this protection may stabilize the function of API over a wide pH range.

Journal Articles

Decontamination of outdoor school swimming pools in Fukushima after the nuclear accident in March 2011

Saegusa, Jun; Kurikami, Hiroshi; Yasuda, Ryo; Kurihara, Kazuo; Arai, Shigeki; Kuroki, Ryota; Matsuhashi, Shimpei; Ozawa, Takashi; Goto, Hiroaki; Takano, Takao; et al.

Health Physics, 104(3), p.243 - 250, 2013/03

 Times Cited Count:3 Percentile:26.98(Environmental Sciences)

After the Nuclear accident on March 2011, water discharge from many outdoor swimming pools in the Fukushima prefecture was suspended out of concern that radiocesium in the pool water would flow into farmlands. We have reviewed the existing flocculation method for decontaminating pool water and established a practical decontamination method by demonstrating the process at several pools in the Fukushima prefecture.

Journal Articles

Structure of enzyme-inhibitor complex determined by neutron crystallography

Tamada, Taro; Adachi, Motoyasu; Kurihara, Kazuo; Kuroki, Ryota

Nihon Kessho Gakkai-Shi, 55(1), p.47 - 51, 2013/02

Neutron crystallography enables us to identify the accurate hydrogen positions in proteins, which play important roles in many chemical reactions in living system. Here we show our results of neutron structure determination of enzymes in complex with its inhibitors which corresponds to transition state analogues. Neutron structure analysis elucidated the detail catalytic reaction of each enzyme by direct observation of hydrogen atoms. Furthermore we would like to introduce a new neutron beam line for neutron structural biology planned at MLF in J-PARC.

Journal Articles

Structure and function of $$Delta$$1-tetrahydrocannabinolic acid (THCA) synthase, the enzyme controlling the psychoactivity of ${it Cannabis sativa}$

Shoyama, Yoshinari*; Tamada, Taro; Kurihara, Kazuo; Takeuchi, Ayako*; Taura, Futoshi*; Arai, Shigeki; Blaber, M.*; Shoyama, Yukihiro*; Morimoto, Satoshi*; Kuroki, Ryota

Journal of Molecular Biology, 423(1), p.96 - 105, 2012/10

 Times Cited Count:76 Percentile:89.33(Biochemistry & Molecular Biology)

$$Delta$$1-tetrahydrocannabinolic acid (THCA) synthase catalyzes the oxidative cyclization of cannabigerolic acid (CBGA) into THCA, the precursor of the primary psychoactive agent $$Delta$$1-tetrahydrocannabinol in ${it Cannabis sativa}$. The structure-function relationship of THCA synthase was investigated by X-ray structure determination (2.75 ${AA}$ resolution) and mutational analysis. Specific amino acid residues were identified in the active site of THCA synthase that are involved in the oxidative cyclization of the CBGA substrate.

Journal Articles

Structure of morpholinium tribromoplumbate C$$_{4}$$H$$_{8}$$ONH$$_{2}$$PbBr$$_{3}$$ studied using single-crystal neutron diffraction

Kawasaki, Takuro; Takahashi, Miwako*; Ohara, Takashi*; Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Kurihara, Kazuo

Journal of the Physical Society of Japan, 81(9), p.094602_1 - 094602_6, 2012/09

 Times Cited Count:7 Percentile:47.64(Physics, Multidisciplinary)

Journal Articles

Manufacture of the winding pack and development of key parts for the JT-60SA poloidal field coils

Tsuchiya, Katsuhiko; Kizu, Kaname; Murakami, Haruyuki; Yoshida, Kiyoshi; Kurihara, Kenichi; Hasegawa, Mitsuru*; Kuno, Kazuo*; Nomoto, Kazuhiro*; Horii, Hiroyuki*

IEEE Transactions on Applied Superconductivity, 22(3), p.4202304_1 - 4202304_4, 2012/06

 Times Cited Count:8 Percentile:45.39(Engineering, Electrical & Electronic)

no abstracts in English

Journal Articles

Hydrogen-bond network and pH sensitivity in transthyretin; Neutron crystal structure of human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Tomoyori, Katsuaki*; Tanaka, Ichiro*; et al.

Journal of Structural Biology, 177(2), p.283 - 290, 2012/02

 Times Cited Count:46 Percentile:83.74(Biochemistry & Molecular Biology)

Journal Articles

Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from ${it Thermus thermophilus}$ HB8

Okazaki, Nobuo; Adachi, Motoyasu; Tamada, Taro; Kurihara, Kazuo; Oga, Takushi*; Kamiya, Nobuo*; Kuramitsu, Seiki*; Kuroki, Ryota

Acta Crystallographica Section F, 68(1), p.49 - 52, 2012/01

 Times Cited Count:2 Percentile:33.62(Biochemical Research Methods)

Journal Articles

Eddy current-adjusted plasma shape reconstruction by Cauchy condition surface method on QUEST

Nakamura, Kazuo*; Jiang, Y.*; Liu, X.*; Mitarai, Osamu*; Kurihara, Kenichi; Kawamata, Yoichi; Sueoka, Michiharu; Hasegawa, Makoto*; Tokunaga, Kazutoshi*; Zushi, Hideki*; et al.

Fusion Engineering and Design, 86(6-8), p.1080 - 1084, 2011/10

 Times Cited Count:4 Percentile:33.74(Nuclear Science & Technology)

174 (Records 1-20 displayed on this page)