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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
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
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)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)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)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
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
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 -lactamase from sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr 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- 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.
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 . 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 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 M. This result implies that DNA-bound PprA aids association of the termini of damaged DNAs, which is regulated by the concentration of PprA.
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 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.
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.
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)Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Shimizu, Tetsuya*; Yamazaki, Yoichi*; Kuroki, Ryota; Niimura, Nobuo*; Kataoka, Mikio*
no journal, ,
Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*; Shimizu, Nobutaka*; Yamazaki, Yoichi*; Kataoka, Mikio*
no journal, ,
Ohara, Takashi; Adachi, Motoyasu; Shimizu, Rumi; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*
no journal, ,
no abstracts in English
Ohara, Takashi; Adachi, Motoyasu; Shimizu, Rumi; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*
no journal, ,
no abstracts in English
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.
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
Matsumoto, Fumiko; Adachi, Motoyasu; Shimizu, Rumi; Meguro, Mizue; Arai, Shigeki; Tamada, Taro; Kato, Takashi; Kuroki, Ryota
no journal, ,
Shimizu, Rumi; Adachi, Motoyasu; Kuroki, Ryota; Yamashita, Michi*; Morimoto, Satoshi*
no journal, ,
no abstracts in English