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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

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:0 Percentile:0(Materials Science, Multidisciplinary)

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:4 Percentile:40.84(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:31.87(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:14.97(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:73.7(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:142 Percentile:94.89(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

Oral presentation

Interaction between the thrombopoietin receptor extra cellular region and its specific ligand

Matsumoto, Fumiko; Hatanaka, Takaaki*; Adachi, Motoyasu; Shimizu, Rumi; Tamada, Taro; Ito, Yuji*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

X-ray structure analysis of inactivated single-chained HIV-1 protease in complex with inhibitor KNI-272

Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota; Moriya, Keisuke*; Kidokoro, Shunichi*; Hidaka, Koshi*; Tsuda, Yuko*; Kiso, Yoshiaki*

no journal, , 

Human immune deficiency virus protease-I (HIV-PR) is one of the important drug target proteins for the acquired immune deficiency syndrome. In this study, we designed the two single chain derivatives of wild-type and A17 type HIV-PRs in which the catalytic residue of Asp25 was placed with Asn25 to inactivate the enzyme. The tertiary structure of sc-HIV-PR of wild-type and A17 type were determined by X-ray crystallography to 1.1 and 1.5 ${AA}$ resolution, respectively. The both complex structures showed that Asn25 forms hydrogen bond with carbonyl group of inhibitor.

Oral presentation

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

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

no journal, , 

We have already succeeded in creation of the de novo designed protein (Symfoil) exhibiting the threefold symmetrical $$beta$$-trefoil fold based on the human acidic fibroblast growth factor. Based on the Symfoil protein, we created Symfoil-II having the three repeats. The Symfoil-II protein was expressed in Eschericha coli as soluble protein, and purified by metal affinity chromatography using nickel-chelated agarose. The Symfoil-II was further purified by anion-exchange column chromatography after removing the HisTag by proteolysis. Symfoil-II was crystallized in 0.1 M Tris-HCl buffer (pH7.0) containing 1.8 M ammonium sulfate as precipitant at 20$$^{circ}$$C. The X-ray diffraction data was collected to 1.9 ${AA}$ resolution using a Rigaku R-AXIS VII diffractometer. The crystal belongs to a monoclinic space group C2. The refined crystal structure of Symfoil-II showed three fold symmetry as is observed in other Symfoils.

Oral presentation

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

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

no journal, , 

We have already succeeded in creation of the de novo designed protein (Symfoil) exhibiting the threefold symmetrical $$beta$$-trefoil fold based on the human acidic fibroblast growth factor. Based on the Symfoil protein, we created Symfoil-II having the three repeats. The Symfoil-II protein was expressed in Eschericha coli as soluble protein, and purified by metal affinity chromatography using nickel-chelated agarose. The Symfoil-II was further purified by anion-exchange column chromatography after removing the HisTag by proteolysis. Symfoil-II was crystallized in 0.1 M Tris-HCl buffer (pH7.0) containing 1.8 M ammonium sulfate as precipitant at 20$$^{circ}$$C. The X-ray diffraction data was collected to 1.9${AA}$ resolution using a Rigaku R-AXIS VII diffractometer. The crystal belongs to a monoclinic space group C2. The refined crystal structure of Symfoil-II showed three fold symmetry as is observed in other Symfoils.

Oral presentation

Preparation of large volume casein kinase-2 crystals for neutron diffraction experiment

Shibazaki, Chie; Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota

no journal, , 

Casein kinase 2(CK2) is one of the ubiquitous Ser/Thr kinases and is involved in the cell cycle and the survival and proliferation of cells. CK2 is a heterotetrameric structure comprising two $$alpha$$- or $$alpha$$-subunits. In order to understand the biological function of the alpha catalytic subunit of CK2 (CK2$$alpha$$), we aim to analyze the structure of CK2$$alpha$$ including information of the hydrogen and hydrating water molecule by neutron crystallography. The gene coding CK2$$alpha$$ was inserted into pET24a and expressed in ${it E}$. coli strain BL21DE3, in which the mobile region (330-335) and chemically reactive thiols (Cys147 and Cys220) were removed by amino acid mutation. A total of 150 mg protein was obtained from a 6 L culture, and was used for crystallization trials. The preparation of large crystals was performed using a macro seeding method. Finally, a large crystal with a volume of approximately 2 mm$$^{3}$$ was reproducibly obtained. The crystal was dialyzed in the deuterated reagent and deuterium water, and the preliminary neutron diffraction experiments were carried out at neutron beam line BioDIFF in research reactor FRM-II in Technical University of Munich. The diffraction was successfully observed greater than 1.9 ${AA}$ resolution.

36 (Records 1-20 displayed on this page)