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Journal Articles

$^{57}$ Fe polarization dependent synchrotron Mssbauer spectroscopy using a diamond phase plate and an iron borate nuclear Bragg monochromator

Mitsui, Takaya; Imai, Yasuhiko*; Masuda, Ryo*; Seto, Makoto*; Mibu, Ko*

Journal of Synchrotron Radiation, 22(2), p.427 - 435, 2015/03

https://doi.org/10.1107/S1600577514028306

Times Cited Count：10 Percentile：50.53(Instruments & Instrumentation)

Journal Articles

Momentum-resolved resonant inelastic X-ray scattering on a single crystal under high pressure

Yoshida, Masahiro*; Ishii, Kenji; Jarrige, I.*; Watanuki, Tetsu; Kudo, Kazutaka*; Koike, Yoji*; Kumagai, Kenichi*; Hiraoka, Nozomu*; Ishii, Hirofumi*; Tsuei, K.-D.*; et al.

Journal of Synchrotron Radiation, 21(1), p.131 - 135, 2014/01

https://doi.org/10.1107/S1600577513028944

Times Cited Count：3 Percentile：19.34(Instruments & Instrumentation)

Journal Articles

High-speed classification of coherent X-ray diffraction Patterns on the K computer for high-resolution single biomolecule imaging

Tokuhisa, Atsushi*; Arai, Junya*; Jochi, Yasumasa*; Ono, Yoshiyuki*; Kameyama, Toyohisa*; Yamamoto, Keiji*; Hatanaka, Masayuki*; Gerofi, B.*; Shimada, Akio*; Kurokawa, Motoyoshi*; et al.

Journal of Synchrotron Radiation, 20(6), p.899 - 904, 2013/11

https://doi.org/10.1107/S0909049513022152

Times Cited Count：5 Percentile：29.65(Instruments & Instrumentation)

Journal Articles

Creation and structure determination of an artificial protein with three complete sequence repeats

Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota; Blaber, M.

Journal of Synchrotron Radiation, 20(6), p.953 - 957, 2013/11

https://doi.org/10.1107/S0909049513022164

Times Cited Count：2 Percentile：13.4(Instruments & Instrumentation)

Symfoil-4P is a protein exhibiting the threefold symmetrical beta-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine-glycine sequences of Symfoil-4P are replaced with glutamine-glycine (Symfoil-QG) or serine-glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Symfoil-QG and II crystals gave 1.5 and 1.1, resolution, respectively. The refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils.

Journal Articles

Crystal structure of endo-1,4--glucanase from

Arimori, Takao*; Ito, Akihiro*; Nakazawa, Masami*; Ueda, Mitsuhiro*; Tamada, Taro

Journal of Synchrotron Radiation, 20(6), p.884 - 889, 2013/11

https://doi.org/10.1107/S0909049513021110

Times Cited Count：16 Percentile：66.2(Instruments & Instrumentation)

The saccharification process is essential for bioethanol production from woody biomass including celluloses. Cold-adapted cellulase, which has sufficient activity at low temperature ( 293 K), is capable of reducing heating costs during the saccharification process and is suitable for simultaneous saccharification and fermentation. Endo-1,4--glucanase from the earthworm Eisenia fetida (EF-EG2) belonging to glycoside hydrolase family 9 has been shown to have the highest activity at 313 K, and also retained a comparatively high activity at 283 K. The recombinant EF-EG2 was purified expressed in Pichia pastoris, and then grew needle-shaped crystals with dimensions of 0.02 0.02 1 mm. The crystals belonged to the space group P3221 with unit-cell parameters of = =136 , = 55.0 ,. The final model of EF-EG2, including 435 residues, two ions, seven crystallization reagents and 696 waters, was refined to a crystallographic -factor of 14.7% (free -factor of 16.8%) to 1.5 , resolution. The overall structure of EF-EG2 has an (/) $_{6}$ barrel fold which contains a putative active-site cleft and a negatively charged surface. This structural information helps us understand the catalytic and cold adaptation mechanisms of EF-EG2.

Journal Articles

Crystal structure of UDP-glucose:anthocyanidin 3--glucosyltransferase from

Hiromoto, Takeshi; Honjo, Eijiro*; Tamada, Taro; Noda, Hisanobu*; Kazuma, Kohei*; Suzuki, Masahiko*; Kuroki, Ryota

Journal of Synchrotron Radiation, 20(6), p.894 - 898, 2013/11

https://doi.org/10.1107/S0909049513020712

Times Cited Count：36 Percentile：86.4(Instruments & Instrumentation)

Flowers of the butterfly pea () accumulate a group of polyacylated anthocyanins, named ternatins, in their petals. The first step in ternatin biosynthesis is the transfer of glucose from UDP-glucose to anthocyanidins such as delphinidin, a reaction catalyzed in by UDP-glucose:anthocyanidin 3--glucosyltransferase (3GT-A; AB185904). To elucidate the structure-function relationship of 3GT-A, recombinant 3GT-A was expressed in and its tertiary structure was determined to 1.85 , resolution by using X-ray crystallography. The structure of 3GT-A shows a common folding topology, the GT-B fold, comprised of two Rossmann-like // domains and a cleft located between the N- and C-domains containing two cavities that are used as binding sites for the donor (UDP-Glc) and acceptor substrates. By comparing the structure of 3GT-A with that of the flavonoid glycosyltransferase GT1 from red grape () in complex with UDP-2-deoxy-2-fluoro glucose and kaempferol, locations of the catalytic His-Asp dyad and the residues involved in recognizing UDP-2-deoxy-2-fluoro glucose were essentially identical in 3GT-A, but certain residues of GT1 involved in binding kaempferol were found to be substituted in 3GT-A. These findings are important for understanding the differentiation of acceptor-substrate recognition in these two enzymes.

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

https://doi.org/10.1107/S0909049513021845

Times Cited Count：35 Percentile：85.81(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

https://doi.org/10.1107/S090904951302075X

Times Cited Count：6 Percentile：34.1(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 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

Sagittal focusing of synchrotron radiation X-rays using a winged crystal

Nisawa, Atsushi*; Yoneda, Yasuhiro; Ueno, Go*; Murakami, Hironori*; Okajima, Yuka*; Yamamoto, Kenichiro*; Semba, Yasunori*; Uesugi, Kentaro*; Tanaka, Yoshihito*; Yamamoto, Masaki*; et al.

Journal of Synchrotron Radiation, 20(2), p.219 - 225, 2013/03

https://doi.org/10.1107/S0909049512049813

Times Cited Count：12 Percentile：54.93(Instruments & Instrumentation)

A Si(111) winged crystal has been designed to minimize anticlastic bending and improve sagittal focusing efficiency. The crystal was thin with wide stiffening wings. The length-to-width ratio of the crystal was optimized by finite element analysis, and the optimal value was larger than the "golden value". The analysis showed that the slope error owing to anticlastic bending is less than the Darwin width. The X-rays were focused two-dimensionally using the crystal and a tangentially bent mirror. The observed profiles of the focal spot agreed well with the results of a ray-tracing calculation in the energy range from 8 to 17.5 keV. X-ray diffraction measurements with a high signal-to-noise ratio using this focusing system were demonstrated for a small protein crystal.

Journal Articles

An X-ray diffraction study on a single rod outer segment from frog retina

Yagi, Naoto*; Matsuo, Tatsuhito; Ota, Noboru*

Journal of Synchrotron Radiation, 19(4), p.574 - 578, 2012/07

https://doi.org/10.1107/S0909049512018535

Times Cited Count：1 Percentile：7.17(Instruments & Instrumentation)

X-ray diffraction patterns were recorded from isolated single rod outer segments of frog. The outer segments in Ringer's solution were exposed to a 6 m microbeam (15 keV) at the BL40XU beamline, SPring-8. The diffraction pattern demonstrated a remarkable regularity in the stacking and flatness of the disk membranes. The electron density profile calculated from the intensity of up to tenth-order reflections showed a pair of bilayers that comprise a disk membrane. The structure of the disk membrane and the changes in the profile on swelling generally agreed with previous reports. Radiation damage was significant with an irradiation of 5 10 $^{5}$ Gy which is much lower than the known damaging dose on proteins at the liquid-nitrogen temperature.

Journal Articles

Performance upgrade in the JAEA actinide science beamline BL23SU at SPring-8 with a new twin-helical undulator

Saito, Yuji; Fukuda, Yoshihiro; Takeda, Yukiharu; Yamagami, Hiroshi; Takahashi, Sunao*; Asano, Yoshihiro*; Hara, Toru*; Shirasawa, Katsutoshi*; Takeuchi, Masao*; Tanaka, Takashi*; et al.

Journal of Synchrotron Radiation, 19(3), p.388 - 393, 2012/05

https://doi.org/10.1107/S0909049512006772

Times Cited Count：95 Percentile：96.88(Instruments & Instrumentation)

The soft X-ray beamline BL23SU at SPring-8 has undergone an upgrade with a twin-helical undulator of in-vacuum type to enhance the experimental capabilities of the end stations. The new light source with a fast helicity-switching operation allows not only the data throughput but also the sensitivity in X-ray magnetic circular dichroism (XMCD) to be improved. The operational performance and potential are described by presenting XMCD results of paramagnetic -US $_{2}$ measured with a 10 T superconducting magnet.

Journal Articles

MFM and PEEM observation of micrometre-sized magnetic dot arrays fabricated by ion-microbeam irradiation in FeRh thin films

Aiko, Kazuma*; Toki, Atsushi*; Matsui, Toshiyuki*; Iwase, Akihiro*; Sato, Takahiro; Takano, Katsuyoshi*; Koka, Masashi; Saito, Yuichi; Kamiya, Tomihiro; Okochi, Takuo*; et al.

Journal of Synchrotron Radiation, 19(2), p.223 - 226, 2012/03

https://doi.org/10.1107/S0909049511054057

Times Cited Count：7 Percentile：37.06(Instruments & Instrumentation)

Journal Articles

Grazing-incidence synchrotron-radiation $^{57}$ Fe-Mssbauer spectroscopy using a nuclear Bragg monochromator and its application to the study of magnetic thin films

Mitsui, Takaya; Masuda, Ryo*; Seto, Makoto; Suharyadi, E.*; Mibu, Ko*

Journal of Synchrotron Radiation, 19(2), p.198 - 204, 2012/03

https://doi.org/10.1107/S0909049511049958

Times Cited Count：19 Percentile：67.13(Instruments & Instrumentation)

An energy-domain grazing-incidence $^{57}$ Fe-Mssbauer spectroscopy(E-GIMS) with synchrotron radiation (SR) has been developed to studysurface and interface structures of thin films. A high-brilliant $^{57}$ Fe-Mssbauer radiation, filtered from SR by a $^{57}$ FeBO $_{3}$ single crystal nuclear Bragg monochromator (NBM), allows us to perform the conventional Mssbauer spectroscopy (MS) for the dilute $^{57}$ Fe in a mirror-like film in any bunch-mode operation of SR. Theoretical and experimental study of the specular reflections from isotope-enriched ( $^{57}$ Fe: 95%) and natural-abundance ( $^{57}$ Fe: 2%) iron thin films has been carried out to clarify the basic features of coherent interference between electronic and nuclear resonant scattering of $^{57}$ Fe-Mo"ssbauer radiation in thin films. Moreover, a new surface and interface sensitive method has been developed by the combination of SR based E-GIMS and $^{57}$ Fe-probe layer technique, which enables us to probe interfacial complex magnetic structures in thin film with atomic-scale depth resolution.

Journal Articles

Application of magnetic Compton scattering for spin-specific magnetic hysteresis measurement

Agui, Akane; Sakurai, Hiroshi*; Tamura, Takuro*; Kurachi, Toshitaka*; Tanaka, Masahito*; Adachi, Hiromichi*; Kawata, Hiroshi*

Journal of Synchrotron Radiation, 17(3), p.321 - 324, 2010/05

https://doi.org/10.1107/S090904951000292X

Times Cited Count：16 Percentile：60.33(Instruments & Instrumentation)

An application of magnetic Compton scattering as a new tool to measure a spin-specific magnetic hysteresis loop was introduced and demonstrated its validity. The applied magnetic field dependence of the integrated intensity of magnetic Compton scattering spectra was interpreted as the spin-specific hysteresis in this study.

Journal Articles

Mutagenesis of the crystal contact of acidic fibroblast growth factor

Honjo, Eijiro; Tamada, Taro; Adachi, Motoyasu; Kuroki, Ryota; Meher, A.*; Blaber, M.*

Journal of Synchrotron Radiation, 15(3), p.285 - 287, 2008/05

https://doi.org/10.1107/S0909049508004470

Times Cited Count：5 Percentile：29.93(Instruments & Instrumentation)

We attempt to improve a crystal contact of human acidic fibroblast growth factor (haFGF1) to control the crystal growth because haFGF crystallizes only as a thin-plate form. X-ray crystal analysis of haFGF showed that side chain Glu81, located at a crystal contact between haFGF molecules related by crystallographic symmetry, were in close proximity, suggesting that charge-repulsion may disrupt suitable crystal-packing interaction. To investigate whether the Glu residue affects crystal packing, we constructed haFGF mutants. Although crystals of Ala, Val and Leu mutants were grown as a thin-plate form by the same precipitant (formate) as wild type, crystals of Ser and Thr mutants were grown as a more bulky form. X-ray structural analysis of Ser and Thr mutants determined at 1.5 resolution revealed that hydroxyl groups of Ser and Thr were linked by hydrogen bonds mediated by formate used as a precipitant.

Journal Articles

High-temperature and high-pressure SCC device for synchrotron radiation diffraction experiments and application using an austenitic stainless steel

Yamamoto, Atsushi*; Nakahigashi, Shigeo*; Terasawa, Michitaka*; Mitamura, Toru*; Akiniwa, Yoshiaki*; Yamada, Takayuki*; Liu, L.*; Shobu, Takahisa; Tsubakino, Harushige*

Journal of Synchrotron Radiation, 13(1), p.14 - 18, 2006/01

https://doi.org/10.1107/S0909049505038288

Times Cited Count：5 Percentile：29.95(Instruments & Instrumentation)

Suppressing the stress corrosion cracking (SCC) by reducing the carbon content in austenitic stainless steels is apparently not effective on core shrouds used in boiling water reactors in Japan: trans-granular cracking was found in the shrouds. To clarify the mechanism of the cracking, in situ stress measurements on specimens under stretched conditions in hot water have been attempted in the present study. In situ experiments have been carried out at SPring-8. The SUS316L steel specimen was placed in the in situ device. Sapphire windows were used for the light path in the device. A sufficient diffracted beam intensity was obtained through two sapphire windows and water. The side-inclination method was used for measuring the stress exerted on the specimen. A 2 sin $^{2}$ plot showed that a tensile stress was induced. The measured stress value is considered to be the summation of stresses owing to pre-straining, in situ loading and residual stress owing to surface grinding.