Measurement of the transverse asymmetry of rays in the Sn()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

https://doi.org/10.1103/PhysRevC.106.064601

no abstracts in English

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

https://doi.org/10.1021/acs.chemmater.1c03450

Absence of ferromagnetism in MnBiTe/BiTe 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

https://doi.org/10.1103/PhysRevB.103.205405

Discovery of a selective Cs binding site of a -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

https://www.saga-ls.jp/main/1007.html#gsc.tab=0

no abstracts in English

Interaction of double-stranded DNA with polymerized PprA protein from

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

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

https://doi.org/10.1002/pro.2519

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.

Crystal growth procedure of HIV-1 protease-inhibitor KNI-272 complex for neutron structural analysis at 1.9 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

https://doi.org/10.1021/cg100054s

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.

Crystal structures of the wild type and A20V-mutant for the anti freeze protein AFP6 derived from Japanese fish Zoarces elongatus Kner

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

no journal, , 

Antifreeze proteins can interfere with growing of ice and are focused from the viewpoint of the basic principles and practical applications in science and technology. Previously, it was found that most of the mutant nfeAFP6s showed similar activity to that of the wild type nfeAFP6 whereas A20V-mutant nfeAFP6 showed strong anti-freezing activity. In this study, crystal structures of the wild type and the A20V-mutant AFPs were determined to 1.2 and 1.8 resolution, respectively, by X-ray crystallography to investigate the difference of hydration structure around the essential area. The side chain of Val20 in A20V-mutant faces to the side chain Gln9, and make van der Waals interactions with Gln9 and Thr18. We found the locations of some bound water molecules at the mutated region in A20V-mutant were different from those in wild type. These observations may illustrate the complexity of what hydration structure constitutes to an ice-binding and anti-freezing activity.

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 resolution, respectively. The both complex structures showed that Asn25 forms hydrogen bond with carbonyl group of inhibitor.

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 - or -subunits. In order to understand the biological function of the alpha catalytic subunit of CK2 (CK2), we aim to analyze the structure of CK2 including information of the hydrogen and hydrating water molecule by neutron crystallography. The gene coding CK2 was inserted into pET24a and expressed in . 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 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 resolution.

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