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Journal Articles

Measurement of the transverse asymmetry of $$gamma$$ rays in the $$^{117}$$Sn($$n,gamma$$)$$^{118}$$Sn reaction

Endo, Shunsuke; Okudaira, Takuya*; Abe, Ryota*; Fujioka, Hiroyuki*; Hirota, Katsuya*; Kimura, Atsushi; Kitaguchi, Masaaki*; Oku, Takayuki; Sakai, Kenji; Shima, Tatsushi*; et al.

Physical Review C, 106(6), p.064601_1 - 064601_7, 2022/12

 Times Cited Count:1 Percentile:54.36(Physics, Nuclear)

no abstracts in English

Journal Articles

Evaluation of analyzing power of gamma-ray polarimeter

Endo, Shunsuke; Shizuma, Toshiyuki*; Zen, H.*; Taira, Yoshitaka*; Omer, M.; Kawamura, Shiori*; Abe, Ryota*; Okudaira, Takuya*; Kitaguchi, Masaaki*; Shimizu, Hirohiko*

UVSOR-49, P. 38, 2022/08

Journal Articles

Repeatable photoinduced insulator-to-metal transition in yttrium oxyhydride epitaxial thin films

Komatsu, Yuya*; Shimizu, Ryota*; Sato, Ryuhei*; Wilde, M.*; Nishio, Kazunori*; Katase, Takayoshi*; Matsumura, Daiju; Saito, Hiroyuki*; Miyauchi, Masahiro*; Adelman, J. R.*; et al.

Chemistry of Materials, 34(8), p.3616 - 3623, 2022/04

 Times Cited Count:6 Percentile:73.76(Chemistry, Physical)

Journal Articles

Bayesian sparse modeling of extended X-ray absorption fine structure to determine interstitial oxygen positions in yttrium oxyhydride epitaxial thin film

Kumazoe, Hiroyuki*; Igarashi, Yasuhiko*; Iesari, F.*; Shimizu, Ryota*; Komatsu, Yuya*; Hitosugi, Taro*; Matsumura, Daiju; Saito, Hiroyuki*; Iwamitsu, Kazunori*; Okajima, Toshihiko*; et al.

AIP Advances (Internet), 11(12), p.125013_1 - 125013_5, 2021/12

 Times Cited Count:1 Percentile:8.23(Nanoscience & Nanotechnology)

Journal Articles

Absence of ferromagnetism in MnBi$$_2$$Te$$_4$$/Bi$$_2$$Te$$_3$$ down to 6 K

Fukasawa, Takuro*; Kusaka, Shotaro*; Sumida, Kazuki; Hashizume, Mizuki*; Ichinokura, Satoru*; Takeda, Yukiharu; Ideta, Shinichiro*; Tanaka, Kiyohisa*; Shimizu, Ryota*; Hitosugi, Taro*; et al.

Physical Review B, 103(20), p.205405_1 - 205405_6, 2021/05

 Times Cited Count:7 Percentile:67.62(Materials Science, Multidisciplinary)

Journal Articles

Epitaxial thin film growth of europium dihydride

Komatsu, Yuya*; Shimizu, Ryota*; Wilde, M.*; Kobayashi, Shigeru*; Sasahara, Yuki*; Nishio, Kazunori*; Shigematsu, Kei*; Otomo, Akira*; Fukutani, Katsuyuki; Hitosugi, Taro*

Crystal Growth & Design, 20(9), p.5903 - 5907, 2020/09

Journal Articles

Discovery of a selective Cs$$^{+}$$ binding site of a $$beta$$-lactamase from the halophile by anomalous X-ray diffraction

Arai, Shigeki; Shibazaki, Chie; Shimizu, Rumi; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Kyushu Shinkurotoronko Kenkyu Senta Nempo, 2014, p.17 - 19, 2016/03

no abstracts in English

Journal Articles

Structure of a highly acidic $$beta$$-lactamase from the moderate halophile ${it Chromohalobacter}$ sp.560 and the discovery of a Cs$$^{+}$$-selective binding site

Arai, Shigeki; Yonezawa, Yasushi*; Okazaki, Nobuo*; Matsumoto, Fumiko*; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu*; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide*; et al.

Acta Crystallographica Section D, 71(3), p.541 - 554, 2015/03

 Times Cited Count:7 Percentile:50.91(Biochemical Research Methods)

The crystal structure of halophilic $$beta$$-lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr$$^{2+}$$ and Cs$$^{+}$$ ions were identified by anomalous X-ray diffraction. The location of one Cs$$^{+}$$ specific binding site was identified on HaBLA even in the presence of 9-fold molar excess of Na$$^{+}$$ (90 mM Na$$^{+}$$ /10 mM Cs$$^{+}$$). This Cs$$^{+}$$ binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs$$^{+}$$ by the cation-$$pi$$ interaction. The observation of a selective and high-affinity Cs$$^{+}$$ binding site provides important information that is useful for designing artificial Cs$$^{+}$$ binding sites useful in bioremediation of radioactive isotopes.

Journal Articles

Interaction of double-stranded DNA with polymerized PprA protein from ${it Deinococcus radiodurans}$

Adachi, Motoyasu; Hirayama, Hiroshi; Shimizu, Rumi; Sato, Katsuya; Narumi, Issey*; Kuroki, Ryota

Protein Science, 23(10), p.1349 - 1358, 2014/10

 Times Cited Count:9 Percentile:25.73(Biochemistry & Molecular Biology)

Pleiotropic protein promoting DNA repair A (PprA) is a key protein that facilitates the extreme radioresistance of ${it Deinococcus radiodurans}$. To clarify the role of PprA in the radioresistance mechanism, the interaction between recombinant PprA expressed in Escherichia coli with several double-stranded DNAs was investigated. In a gel-shift assay, the band shift of supercoiled pUC19 DNA caused by the binding of PprA showed a bimodal distribution, which was promoted by the addition of 1 mM Mg, Ca, or Sr ions. The dissociation constant of the PprA-supercoiled pUC19 DNA complex, calculated from the relative portions of shifted bands, was 0.6 $$mu$$M with a Hill coefficient of 3.3 in the presence of 1 mM Mg acetate. This indicates that at least 281 PprA molecules are required to saturate a supercoiled pUC19 DNA, which is consistent with the number of bound PprA molecules estimated by the UV absorption of the PprA-pUC19 complex purified by gel filtration. This saturation also suggests linear polymerization of PprA along the dsDNA. On the other hand, the bands of linear dsDNA and nicked circular dsDNA that eventually formed PprA complexes did not saturate, but created larger molecular complexes when the PprA concentration was greater than 1.3 $$mu$$M. This result implies that DNA-bound PprA aids association of the termini of damaged DNAs, which is regulated by the concentration of PprA.

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

 Times Cited Count:2 Percentile:13.23(Instruments & Instrumentation)

Symfoil-4P is a ${it de novo}$ 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 ${it Eschericha coli}$ 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${AA}$, resolution, respectively. The refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils.

Journal Articles

Crystal growth procedure of HIV-1 protease-inhibitor KNI-272 complex for neutron structural analysis at 1.9 ${AA}$ resolution

Shimizu, Noriko*; Sugiyama, Shigeru*; Maruyama, Mihoko*; Takahashi, Yoshinori*; Adachi, Motoyasu; Tamada, Taro; Hidaka, Koshi*; Hayashi, Yoshio*; Kimura, Toru*; Kiso, Yoshiaki*; et al.

Crystal Growth & Design, 10(7), p.2990 - 2994, 2010/06

 Times Cited Count:11 Percentile:72.07(Chemistry, Multidisciplinary)

We report crystal growth of human immunodeficiency virus 1 protease (HIV PR) in a complex with its inhibitor KNI-272 by six different methods. Comparative analysis indicates that top-seeded solution growth (TSSG) and TSSG combined with the floating and stirring technique (TSSG-FAST) are efficient strategies for rapidly obtaining large single crystals and effectively preventing polycrystallization of the seed crystal. Neutron diffraction analysis confirmed that the crystalobtained by TSSG is a high-quality single crystal. Furthermore, crystal shape was observed to be influenced by solution flow, suggesting that the degree of supersaturation significantly affects the crystal growth direction of HIV PR complex. This finding implies that the shape of the HIV PR complex crystal might be controlled by the solution flow rate.

Journal Articles

Low-barrier hydrogen bond in photoactive yellow protein

Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*; Shimizu, Nobutaka*; Yamazaki, Yoichi*; Kataoka, Mikio*

Proceedings of the National Academy of Sciences of the United States of America, 106(2), p.440 - 444, 2009/01

 Times Cited Count:153 Percentile:94.62(Multidisciplinary Sciences)

Oral presentation

Determination of hydrogen positions of photoactive yellow protein

Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Shimizu, Tetsuya*; Yamazaki, Yoichi*; Kuroki, Ryota; Niimura, Nobuo*; Kataoka, Mikio*

no journal, , 

Oral presentation

Direct observation of two distinct types of short hydrogen bond in photoactive yellow protein

Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*; Shimizu, Nobutaka*; Yamazaki, Yoichi*; Kataoka, Mikio*

no journal, , 

Oral presentation

Study of the mechanism of an antifreeze protein from Notched-fin eelpout by mutation and X-ray diffraction

Ohara, Takashi; Adachi, Motoyasu; Shimizu, Rumi; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*

no journal, , 

no abstracts in English

Oral presentation

Study of the mechanism of an antifreeze protein from Notched-fin eelpout by mutation and crystal structure analyses

Ohara, Takashi; Adachi, Motoyasu; Shimizu, Rumi; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*

no journal, , 

no abstracts in English

Oral presentation

Preparation and characterization of two cytokine receptor homologues regions comprising the thrombopoietin receptor extra cellular region

Matsumoto, Fumiko; Adachi, Motoyasu; Shimizu, Rumi; Meguro, Mizue; Tamada, Taro; Kato, Takashi; Kuroki, Ryota

no journal, , 

Thrombopoietin (TPO) is a glycoprotein hormone produced mainly by the liver and the kidney that regulates the production of platelets by the bone marrow. It stimulates the production and differentiation of megakaryocytes, the bone marrow cells that fragment into large numbers of platelets. The extracellular domain consists of 450 amino acid residues of thrombopoietin receptor (soluble TPO-R) contains two repeat of cytokine receptor homologous region, CRH-1 and CRH-2. In this work, we prepare CRH-1domein of TPO-R, and we discover that CRH-1 has binding site of TPO.

Oral presentation

Effect of mutations on the stability and function of anti freeze protein

Shimizu, Rumi; Matsumoto, Fumiko; Arai, Shigeki; Ohara, Takashi; Adachi, Motoyasu; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*

no journal, , 

no abstracts in English

Oral presentation

Activation mechanism of thrombopoietin receptor investigated by its specific ligand and neutralization antibodies

Matsumoto, Fumiko; Adachi, Motoyasu; Shimizu, Rumi; Meguro, Mizue; Arai, Shigeki; Tamada, Taro; Kato, Takashi; Kuroki, Ryota

no journal, , 

Oral presentation

Preparation of recombinant peroxidase metabolizing morphine in the opium poppy

Shimizu, Rumi; Adachi, Motoyasu; Kuroki, Ryota; Yamashita, Michi*; Morimoto, Satoshi*

no journal, , 

no abstracts in English

46 (Records 1-20 displayed on this page)