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Kuroki, Ryota; Miyazaki, Hiroshi*; Kato, Takashi
Ketsueki Furonteia, 25(2), p.171 - 180, 2015/02
no abstracts in English
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：25.51(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.
Saegusa, Jun; Kurikami, Hiroshi; Yasuda, Ryo; Kurihara, Kazuo; Arai, Shigeki; Kuroki, Ryota; Matsuhashi, Shimpei; Ozawa, Takashi; Goto, Hiroaki; Takano, Takao; et al.
Health Physics, 104(3), p.243 - 250, 2013/03
Times Cited Count：3 Percentile：25.73(Environmental Sciences)After the Nuclear accident on March 2011, water discharge from many outdoor swimming pools in the Fukushima prefecture was suspended out of concern that radiocesium in the pool water would flow into farmlands. We have reviewed the existing flocculation method for decontaminating pool water and established a practical decontamination method by demonstrating the process at several pools in the Fukushima prefecture.
Matsuhashi, Shimpei; Kurikami, Hiroshi; Yasuda, Ryo; Takano, Takao; Seko, Noriaki; Naganawa, Hirochika; Kuroki, Ryota; Saegusa, Jun
JAEA-Testing 2011-007, 189 Pages, 2012/07
JAEA-Testing-2011-007.pdf:46.74MB
Because of TEPCO Fukushima Dai-ichi Nuclear Power Plant accident due to the Great East Japan Earthquake, a huge amount of radioactive materials was widely dispersed and precipitated into the environment. Swimming pools in Fukushima prefectures were contaminated with the radioactives. We JAEA carried out several demonstration tests to decontaminate the radioactives and discharge the pool water safely. We concluded the results obtained from the tests as "Guide for decontaminating swimming pool at school" and released it quickly. Following this, we also released the guide in English. This manuscript, as an experimental report of the swimming pool water decontamination, is consisted from the guide in Japanese and English prepared.
-like spin resonance in the iron-based nodal superconductor BaFe
(As
P
) observed using inelastic neutron scatteringIshikado, Motoyuki; Nagai, Yuki; Kodama, Katsuaki; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Wakimoto, Shuichi; Nakamura, Hiroki; Machida, Masahiko; Suzuki, Katsuhiro*; et al.
Physical Review B, 84(14), p.144517_1 - 144517_5, 2011/10
Times Cited Count：26 Percentile：70.69(Materials Science, Multidisciplinary)We performed inelastic neutron scattering on a powder sample of iron-based superconductor BaFe(AsP) with 
= 30 K. Although this system is expected to have line nodes in its superconducting order parameter, we have observed spin resonance at the same scattering vector as that appeared in the -wave iron-based superconductors without line nodes. Moreover, the resonance enhancement, which can be a measure of the area of sign reversal between the hole and electron Fermi surfaces (FSs), is comparable to those without line nodes. These facts indicate that the sign reversal between the FSs is still dominant in this system, and the line nodes should create only limited area of sign-reversal on a single FS. Hence the system can hold higher Tc than the other iron-based superconductors with nodal symmetry, such as LaFePO
and KFeAs (
10 K).
Ito, Takachika*; Suzuki, Shoichi*; Kanaji, Sachiko*; Shiraishi, Hiroshi*; Ota, Shoichiro*; Arima, Kazuhiko*; Tanaka, Go*; Tamada, Taro; Honjo, Eijiro*; Garcia, K. C.*; et al.
Journal of Biological Chemistry, 284(36), p.24289 - 24296, 2009/09
Times Cited Count：23 Percentile：45.4(Biochemistry & Molecular Biology)Both IL-4 and IL-13 can bind to the shared receptor composed of the IL-4 receptor 
chain and the IL-13 receptor -1 chain (IL-13R1); however, the assembly mechanisms of these ligands to the receptor is different, enabling the principal functions of these ligands to be different. We have previously shown that the N-terminal Ig-like domain in IL-13R1, called the D1 domain, is the specific and critical binding unit for IL-13. However, it has still remained obscure which the amino acid has specific binding capacity to IL-13 and why the D1 domain acts as the binding site for IL-13, but not IL-4. To address these questions, in this study, we performed the mutational analyses for the D1 domain, combining the structural data to identify the amino acids critical for binding to IL-13. Mutations of Lys76, Lys77, or Ile78 in c' strand in which the crystal structure showed interact with IL-13 and those of Trp65 and Ala79 adjacent to the interacting site, resulted in significant impairment of IL-13 binding, demonstrating that these amino acids generate the binding site. Furthermore, mutations of Val35, Leu38, or Val42 at N-terminal 
-strand also resulted in loss of IL-13 binding, probably from decrease structural stability. None of the mutations employed here affected IL-4 binding. These results demonstrate that the hydrophobic patch composed of Lys76, Lys77, and Ile78 is the IL-13 recognition site and solidify our understanding that the differential requirements of the D1 domain in IL-13R1 allows the shared receptor to respond differentially to IL-4 and IL-13.
Matsumura, Hiroyoshi*; Adachi, Motoyasu; Sugiyama, Shigeru*; Okada, Shino*; Yamakami, Megumi*; Tamada, Taro; Hidaka, Koshi*; Hayashi, Yoshio*; Kimura, Toru*; Kiso, Yoshiaki*; et al.
Acta Crystallographica Section F, 64(11), p.1003 - 1006, 2008/11
Times Cited Count：17 Percentile：77.92(Biochemical Research Methods)This paper reports the crystallization and preliminary neutron diffraction measurements of HIV-1 protease, a potential target for anti-HIV therapy, complexed with an inhibitor (KNI-272). The aim of this neutron diffraction study is to obtain structural information about the H atoms and to determine the protonation states of the residues within the active site. The crystal was grown to a size of 1.4 mm
by repeated macroseeding and a slow-cooling method using a two-liquid system. Neutron diffraction data were collected at room temperature using a BIX-4 diffractometer at the JRR-3 research reactor of the Japan Atomic Energy Agency (JAEA). The data set was integrated and scaled to 2.3 
resolution in space group P2(1)2(1)2, with unit-cell parameters a = 59.5, b = 87.4, c = 46.8 .
Honjo, Eijiro; Kuroki, Ryota; Kobori, Hiroshi*; Takakura, Hikaru*; Yahata, Kazuhide*; Sone, Takefumi*; Imamoto, Fumio*; Moriyama, Tatsuya*
Tampakushitsu Seisei To Toriatsukai No Kotsu, p.135 - 178, 2007/10
Protein expression and purification are important techniques for protein scientists. Especially in the field of molecular biology, the researchers often requires for some know-how on protein handling based on biochemical information. This book is aimed at introducing an overview of recombinant protein expression and purification, and furthermore providing experimental know-how about the selection of analytical reagents or instruments.
Yamada, Hidenori*; Tamada, Taro; Kosaka, Megumi*; Miyata, Kohei*; Fujiki, Shinya*; Tano, Masaru*; Moriya, Masayuki*; Yamanishi, Mamoru*; Honjo, Eijiro; Tada, Horiko*; et al.
Protein Science, 16(7), p.1389 - 1397, 2007/07
Times Cited Count：39 Percentile：59.61(Biochemistry & Molecular Biology)In an attempt to control protein incorporation in a crystal lattice, a leucine zipper-like hydrophobic interface (comprising four leucine residues) was introduced into a helical region (helix 2) of the human pancreatic ribonuclease 1 (RNase 1) that was predicted to form a suitable crystallization interface. Although crystallization of wild type RNase 1 has not yet been reported, the RNase 1 mutant having four leucines (4L-RNase 1) was successfully crystallized under several different conditions. The crystal structures were subsequently determined by X-ray crystallography by molecular replacement using the structure of bovine RNase A. The overall structure of 4L-RNase 1 is quite similar to that of the bovine RNase A, and the introduced leucine residues formed the designed crystal interface. To further characterize the role of the introduced leucine residues in crystallization of RNase 1, the number of leucines was reduced to three or two (3L- and 2L-RNase 1, respectively). Both mutants crystallized and a similar hydrophobic interface as in 4L-RNase 1 was observed. A related approach to engineer crystal contacts at helix 3 of RNase 1 (N4L-RNase 1) was also evaluated. N4L-RNase 1 also successfully crystallized, and formed the expected hydrophobic packing interface. These results suggest that appropriate introduction of a leucine zipper-like hydrophobic interface can promote intra molecular symmetry for more efficient protein crystallization in crystal lattice engineering efforts.
Ishikado, Motoyuki; Nagai, Yuki; Kodama, Katsuaki; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Mizuno, Fumio; Wakimoto, Shuichi; Nakamura, Hiroki; Machida, Masahiko; et al.
no journal, ,
Three years have passed since the discovery of iron-based superconductors, its maximum superconducting transition temperature () is 55 K, resulting in second highest material system next to cuprate high- superconductors. Among various material systems in iron-based superconductors, we have systematically studied on LaFeAsO
F
(
=28 K) of first discovered system and BaFe(As,P) which have recently attracted tremendous attention by the discovery of line nodes in its order parameter. In the session, we present recent results on "spin fluctuation and superconductivity on LaFePO
", and "symmetry of order parameter on BaFe(As,P) by inelastic neutron scattering" studied by the chopper spectrometer 4SEASONS (J-PARC).
(As,P)Ishikado, Motoyuki; Nagai, Yuki; Kodama, Katsuaki; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Wakimoto, Shuichi; Nakamura, Hiroki; Machida, Masahiko; Suzuki, Katsuhiro*; et al.
no journal, ,
In this study, we have performed inelastic neutron scattering measurement on 36g powder sample of optimally-doped BaFe(As,P) whose superconducting order parameter is expected to have line node by Fermi chopper spectrometer 4SEASONS in J-PARC. Unexpectedly, we have observed spin resonance at same 
-position and nearly identical resonance enhancement ration to other iron-based superconducctors with fully-gapped 
-wave. We will discuss about the possible superconducting gap symmetry based on our experimental results.
superconductorsIshikado, Motoyuki; Kodama, Katsuaki; Wakimoto, Shuichi; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Mizuno, Fumio; Nagai, Yuki; Nakamura, Hiroki; Machida, Masahiko; et al.
no journal, ,
Among various iron-based superconductors, we have systematically studied on LaFeAsOF (=28 K) and BaFe(As,P) (=31 K) by the Fermi chopper spectrometer 4SEASONS (J-PARC). We will discuss the possible relation between high- superconductivity and magnetic fluctuation based on our inelastic neutron scattering results.
(As,P) with nodal gap symmetryIshikado, Motoyuki; Kodama, Katsuaki; Wakimoto, Shuichi; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Nagai, Yuki; Nakamura, Hiroki; Machida, Masahiko; Suzuki, Katsuhiro*; et al.
no journal, ,
In this study, we performed inelastic neutron scattering measurement on 36g polycrystalline powder sample of optimally-doped BaFe(AsP) using a Fermi chopper spectrometer 4SEASONS in J-PARC. We observed strong spin resonance at the same -position similar to those of other iron-based superconductors with fully-gapped -wave. We will discuss about the possible superconducting gap symmetry and what causes relatively high-
of this material based on our inelastic neutron scattering results.
(As,P)Ishikado, Motoyuki; Nagai, Yuki; Kodama, Katsuaki; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Mizuno, Fumio; Wakimoto, Shuichi; Nakamura, Hiroki; Machida, Masahiko; et al.
no journal, ,
We report systematic studies on Fe-based superconductors LaFeAsOF (
=28 K) and BaFe(As,P) ( =31 K) by using inelastic neutron scattering measurement.
(As,P) with =30KIshikado, Motoyuki; Nagai, Yuki; Kodama, Katsuaki; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Wakimoto, Shuichi; Nakamura, Hiroki; Machida, Masahiko; Suzuki, Katsuhiro*; et al.
no journal, ,
In this study, we performed inelastic neutron scattering measurement on 36g polycrystalline powder sample of optimally-doped BaFe(As,P) using Fermi chopper spectrometer 4SEASONS in J-PARC. Unexpectedly, we observed spin resonance at the same -position and nearly identical resonance enhancement ratio to other iron-based superconductors with fully-gapped -wave. We will discuss about the possible superconducting gap symmetry based on our inelastic neutron scattering experiment and theoretical calculations.
Ishikado, Motoyuki; Kodama, Katsuaki; Wakimoto, Shuichi; Kajimoto, Ryoichi; Nakamura, Mitsutaka; Inamura, Yasuhiro; Mizuno, Fumio; Nagai, Yuki; Nakamura, Hiroki; Machida, Masahiko; et al.
no journal, ,
We have systematically studied nodal iron-based superconductor LaFePO (=5 K) and BaFe(As,P) (=30 K) by using Fermi chopper spectrometer 4SEASONS (J-PARC) and Triple Axis Spectrometer (TAS-1) at JRR-3. In the session, we will discuss the relation between superconductivity and spin fluctuation.
, expression system while difficult by 
Onishi, Hiromasa*; Mizukami, Makoto*; Hanagata, Hiroshi*; Tokunaga, Masao*; Kuroki, Ryota; Adachi, Motoyasu; Ishikawa, Kazuhiko*; Miyauchi, Akira*
no journal, ,
is one of the remarkable host developing to produce secretory proteins. The proteins above amount of 10g/L have been expressed into the medium using the Brevibacillus expression system as known examples. In addition, there are many examples of expression of proteins derived from bacteria to human proteins and including disulfide bridge. Recently, we succeeded in high-level and secretory expression of protease and cellulase which are not efficiently produced in E. coli expression system.
Hirayama, Hiroshi; Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota
no journal, ,
no abstracts in English
Suzuki, Hiroshi; Akita, Koichi; Tsunori, Mitsuyoshi*; Nezaki, Koji*; Shinohara, Takahiko*; Kuroki, Hiroshi*; Morita, Ichiro*
no journal, ,
no abstracts in English
