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Journal Articles

Structural phase transition in cobalt oxyfluoride Co$$_{3}$$Sb$$_{4}$$O$$_{6}$$F$$_{6}$$ observed by high-resolution synchrotron and neutron diffraction

Shimono, Seiya*; Ishibashi, Hiroki*; Nagayoshi, Yusuke*; Ikeno, Hidekazu*; Kawaguchi, Shogo*; Hagihara, Masato; Torii, Shuki*; Kamiyama, Takashi*; Ichihashi, Katsuya*; Nishihara, Sadafumi*; et al.

Journal of Physics and Chemistry of Solids, 163, p.110568_1 - 110568_7, 2022/04

https://doi.org/10.1016/j.jpcs.2021.110568
 Times Cited Count：1 Percentile：14.38(Chemistry, Multidisciplinary)

Journal Articles

Structural and functional characterization of the ${it Geobacillus}$ copper nitrite reductase; Involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner

Fukuda, Yota*; Koteishi, Hiroyasu*; Yoneda, Ryohei*; Tamada, Taro; Takami, Hideto*; Inoue, Tsuyoshi*; Nojiri, Masaki

Biochimica et Biophysica Acta; Bioenergetics, 1837(3), p.396 - 405, 2014/03

https://doi.org/10.1016/j.bbabio.2014.01.004
 Times Cited Count：15 Percentile：46.96(Biochemistry & Molecular Biology)

The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium ${it Geobacillus kaustophilus}$ HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3${AA}$ and 1.8${AA}$, respectively. Both structures show a striking resemblance with the overall structure of the well-known CuNiRs composed of two Greek key $$beta$$-barrel domains; however, a remarkable structural difference was found in the N-terminal region. The unique region has one $$beta$$-strand and one $$alpha$$-helix extended to the northern surface of the type-1 copper site. The superposition of the ${it Geobacillus}$ CuNiR model on the electron-transfer complex structure of CuNiR with the redox partner cytochrome ${it c$_{551}$}$ in other denitrifier system led us to infer that this region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the ${it Geobacillus}$ system. Furthermore, electron-transfer kinetics experiments using N-terminal residue-deleted mutant and the redox partner, ${it Geobacillus}$ cytochrome ${it c$_{551}$}$, were carried out. These structural and kinetics studies demonstrate that that region is directly involved in the specific partner recognition.

Journal Articles

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of GK0767, the copper-containing nitrite reductase from Geobacillus kaustophilus

Fukuda, Yota*; Tamada, Taro; Takami, Hideto*; Suzuki, Shinichiro*; Inoue, Tsuyoshi*; Nojiri, Masaki

Acta Crystallographica Section F, 67(6), p.692 - 695, 2011/06

https://doi.org/10.1107/S1744309111013297
 Times Cited Count：9 Percentile：67.68(Biochemical Research Methods)

Journal Articles

Growth of large protein crystals by a large-scale hanging-drop method

Kakinouchi, Keisuke*; Nakamura, Tsutomu*; Tamada, Taro; Adachi, Hiroaki*; Sugiyama, Shigeru*; Maruyama, Mihoko*; Takahashi, Yoshinori*; Takano, Kazufumi*; Murakami, Satoshi*; Inoue, Tsuyoshi*; et al.

Journal of Applied Crystallography, 43(4), p.937 - 939, 2010/08

https://doi.org/10.1107/S0021889810015967
 Times Cited Count：4 Percentile：48.29(Chemistry, Multidisciplinary)

A method for growing large protein crystals is described. In this method, a cut pipette tip is used to hang large-scale droplets (maximum volume 200 $$mu$$l) consisting of protein and precipitating agents. A crystal grows at the vapor-liquid interface; thereafter the grown crystal can be retrieved by droplet-droplet contact both for repeated macroseeding and for mounting crystals in a capillary. Crystallization experiments with peroxiredoxin of ${it Aeropyrum pernix}$ K1(thioredoxin peroxidase, ApTPx) and hen egg white lysozyme demonstrated that this large-scale hanging-drop method could produce a large-volume crystal very effectively. A neutron diffraction experiment confirmed that an ApTPx crystal (6.2 mm$$^{3}$$) obtained by this method diffracted to beyond 3.5 ${AA}$ resolution.

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

https://doi.org/10.1021/cg100054s
 Times Cited Count：11 Percentile：71.95(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

Crystallization and preliminary neutron diffraction studies of HIV-1 protease cocrystallized with inhibitor KNI-272

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

https://doi.org/10.1107/S1744309108029679
 Times Cited Count：17 Percentile：77.84(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$$^{3}$$ 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 ${AA}$ resolution in space group P2(1)2(1)2, with unit-cell parameters a = 59.5, b = 87.4, c = 46.8 ${AA}$.

Journal Articles

Neutron spin-echo studies on crossover from single chain motion to collective dynamics

Kanaya, Toshiji; Takahashi, Nobuaki; Inoue, Rintaro*; Matsuba, Go*; Nishida, Koji*; Nagao, Michihiro*

ISSP Activity Report on Neutron scattering Research; Experimental Reports (CD-ROM), 13, 1 Pages, 2006/00

Oral presentation

The 1.3 ${AA}$ structure of copper nitrite reductase from thermophilic denitrifer

Fukuda, Yota*; Tamada, Taro; Takami, Hideto*; Inoue, Tsuyoshi*; Nojiri, Masaki

no journal, , 

Denitrification is known as anaerobic respiration in which nitrogenous compounds (NO$$_{2}$$$$^{-}$$ or NO$$_{3}$$$$^{-}$$) are used as terminal electron acceptors. Copper-containing nitrite reductase (CuNIR) catalyzes the one electron reduction of nitrite to nitric oxide (NO), which is the key step in the denitrification pathway. Here, we report the structure analysis of CuNIR from thermophilic ${it Geobacillus kaustophilus}$ HTA426(${it Gk}$NIR) at 1.3 ${AA}$ resolution. ${it Gk}$NIR folds a homo-trimeric structure, having two copper binding sites per a monomeric unit as well as other CuNIRs. There are main characteristics of ${it Gk}$NIR in two loops (tower loop and extra loop regions) and the N-terminal region. The additional N-terminal $$alpha$$-helix is positioned in the vicinity of the tower loop. These characteristic structures found in ${it Gk}$NIR structure suggest evolutionary diversity of CuNIR and play a key role in functioning in the particular environment where ${it G. kaustophilus}$ inhabits.

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