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Journal Articles

Development of a technique for high pressure neutron diffraction at 40 GPa with a Paris-Edinburgh press

Hattori, Takanori; Sano, Asami; Machida, Shinichi*; Abe, Jun*; Funakoshi, Kenichi*; Arima, Hiroshi*; Okazaki, Nobuo*

High Pressure Research, 39(3), p.417 - 425, 2019/06

AA2019-0119.pdf:1.79MB

 Times Cited Count:9 Percentile:77.94(Physics, Multidisciplinary)

We have developed a technique for neutron diffraction experiments at pressures up to 40 GPa using a Paris-Edinburgh press at the PLANET beamline in J-PARC. To increase the maximum accessible pressure, the diameter of the dimple for sample chamber at the top of the sintered diamond anvils is sequentially reduced from 4.0 mm to 1.0 mm. As a result, the maximum pressure increased and finally reached 40 GPa. By combining this technique with the beam optics which defines the gauge volume, diffraction patterns sufficient for full-structure refinements are obtainable at such pressures.

Journal Articles

What can we do with the high-pressure neutron diffractometer PLANET?

Hattori, Takanori; Sano, Asami; Machida, Shinichi*; Abe, Jun*; Funakoshi, Kenichi*; Okazaki, Nobuo*

Nihon Kessho Gakkai-Shi, 59(6), p.301 - 308, 2017/12

PLANET is a neutron beamline dedicated to high-pressure experiments. Combining the intense neutron source of J-PARC and high-pressure devices designed for time-of-flight powder neutron diffraction enables precise structure analysis of crystal, liquid and amorphous solids over wide pressure and temperature region of 0-20 GPa and 77-2000K. This beamline is effective for various studies in geophysics, planetary science, physics and chemistry. This paper overviews the beamline and introduces recent results obtained at PLANET.

Journal Articles

Materials and Life Science Experimental Facility at the Japan Proton Accelerator Research Complex, 3; Neutron devices and computational and sample environments

Sakasai, Kaoru; Sato, Setsuo*; Seya, Tomohiro*; Nakamura, Tatsuya; To, Kentaro; Yamagishi, Hideshi*; Soyama, Kazuhiko; Yamazaki, Dai; Maruyama, Ryuji; Oku, Takayuki; et al.

Quantum Beam Science (Internet), 1(2), p.10_1 - 10_35, 2017/09

Neutron devices such as neutron detectors, optical devices including supermirror devices and $$^{3}$$He neutron spin filters, and choppers are successfully developed and installed at the Materials Life Science Facility (MLF) of the Japan Proton Accelerator Research Complex (J-PARC), Tokai, Japan. Four software components of MLF computational environment, instrument control, data acquisition, data analysis, and a database, have been developed and equipped at MLF. MLF also provides a wide variety of sample environment options including high and low temperatures, high magnetic fields, and high pressures. This paper describes the current status of neutron devices, computational and sample environments at MLF.

Journal Articles

Overview of high-pressure neutron beamline, PLANET, and practical aspects of the experiments

Hattori, Takanori; Sano, Asami; Arima, Hiroshi*; Funakoshi, Kenichi*; Abe, Jun*; Machida, Shinichi*; Okazaki, Nobuo*; Ouchi, Keiichi*; Inamura, Yasuhiro

Koatsuryoku No Kagaku To Gijutsu, 26(2), p.89 - 98, 2016/06

PLANET is a high-pressure neutron beamline constructed at pulsed-neutron source in Materials and Life Science Facility (MLF) in J-PARC. The six-axis multi-anvil press designed for time of flight (TOF) neutron diffraction experiments enables routine data collection at high pressures and high temperatures up to 10 GPa and 2000 K, respectively. To obtain clean data, the beamline is equipped with the incident slits and receiving collimators that eliminate parasitic scattering from the high-pressure cell. The high performance of the diffractometer for the resolution ($$Delta d/d$$ $$sim$$ 0.6%) and the accessible d-spacing range (0.2 - 8.4 ${AA}$) together with low-parasitic scattering characteristics enables precise structure determination of crystals and liquids under high pressure and temperature conditions.

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

Approaches to characterization of nuclear material for establishment of nuclear forensics

Okazaki, Hiro; Sumi, Mika; Sato, Mitsuhiro; Kayano, Masashi; Kageyama, Tomio; Martinez, P.*; Xu, N.*; Thomas, M.*; Porterfield, D.*; Colletti, L.*; et al.

Kaku Busshitsu Kanri Gakkai (INMM) Nihon Shibu Dai-35-Kai Nenji Taikai Rombunshu (Internet), 9 Pages, 2015/01

The quality control section of Plutonium Fuel Development Center (PFDC) in Japan Atomic Energy Agency has been analyzing isotopic compositions and content of plutonium and uranium as well as impurity and physics of nuclear materials in the process of MOX fuel fabrication for accountancy purpose as well as process control purposes. These analytical techniques are also effective for nuclear forensics to identify the source, history, and route of the material by determining a composition and chemical property of it. Therefore, PFDC cooperates with Los Alamos National Laboratory which has broad experience and established measurement skill for nuclear forensics, and evaluates the each method, procedure, and analytical data toward R&D of characterizing a nuclear fuel for forensics purposes. This paper describes the approaches to develop characterization techniques of nuclear fuel for nuclear forensic purpose at PFDC.

Journal Articles

Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from ${it Ralstonia}$ sp. A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis

Arimori, Takao*; Kawamoto, Noriko*; Shinya, Shoko*; Okazaki, Nobuo*; Nakazawa, Masami*; Miyatake, Kazutaka*; Fukamizo, Tamo*; Ueda, Mitsuhiro*; Tamada, Taro

Journal of Biological Chemistry, 288(26), p.18696 - 18706, 2013/07

 Times Cited Count:22 Percentile:58.33(Biochemistry & Molecular Biology)

Chitinase C from ${it Ralstonia}$ sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptideglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu141 acts as a catalytic acid, and that Asp226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases.

Journal Articles

Substrate recognition mechanism of a glycosyltrehalose trehalohydrolase from ${it sulfolobus solfataricus}$ KM1

Okazaki, Nobuo; Tamada, Taro; Feese, M. D.*; Kato, Masaru*; Miura, Yutaka*; Komeda, Toshihiro*; Kobayashi, Kazuo*; Kondo, Keiji*; Blaber, M.*; Kuroki, Ryota

Protein Science, 21(4), p.539 - 552, 2012/04

 Times Cited Count:3 Percentile:7.91(Biochemistry & Molecular Biology)

Journal Articles

A Structural mechanism for dimeric to tetrameric oligomer conversion in ${it Halomonas}$ sp. nucleoside diphosphate kinase

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Protein Science, 21(4), p.498 - 510, 2012/04

 Times Cited Count:15 Percentile:39.86(Biochemistry & Molecular Biology)

In order to clarify the oligomer state of nucleoside diphosphate kinase (NDK) from moderately halophilic ${it Halomonas}$ sp. 593 (HaNDK), the crystal structure of HaNDK was determined by X-ray crystallography. The crystal structures of the wild-type HaNDK and the mutant HaNDK (E134A) showed a dimer and a tetramer, respectively. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Journal Articles

Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from ${it Thermus thermophilus}$ HB8

Okazaki, Nobuo; Adachi, Motoyasu; Tamada, Taro; Kurihara, Kazuo; Oga, Takushi*; Kamiya, Nobuo*; Kuramitsu, Seiki*; Kuroki, Ryota

Acta Crystallographica Section F, 68(1), p.49 - 52, 2012/01

 Times Cited Count:1 Percentile:20.29(Biochemical Research Methods)

Journal Articles

Crystallization and preliminary X-ray diffraction studies of the catalytic domain of a novel chitinase, a member of GH family 23, from the moderately thermophilic bacterium ${it Ralstonia}$ sp. A-471

Okazaki, Nobuo; Arimori, Takao; Nakazawa, Masami*; Miyatake, Kazutaka*; Ueda, Mitsuhiro*; Tamada, Taro

Acta Crystallographica Section F, 67(4), p.494 - 497, 2011/04

 Times Cited Count:3 Percentile:43.75(Biochemical Research Methods)

Journal Articles

Towards investigation of the inhibitor-recognition mechanisms of drug-target proteins by neutron crystallography

Kuroki, Ryota; Okazaki, Nobuo; Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro

Acta Crystallographica Section D, 66(11), p.1126 - 1130, 2010/11

 Times Cited Count:2 Percentile:32.06(Biochemical Research Methods)

It is generally known that enzymes represent important drug-target proteins. Elucidation of the catalytic function and the molecular-recognition mechanisms of enzymes provides important information for structure-based drug design. Neutron crystallography provides accurate information on the locations of H atoms that are essential in enzymatic function and molecular recognition. Recent examples are described of the structure determination of the drug-target proteins human immunodeficiency virus protease and porcine pancreatic elastase in complex with transition-state analogue inhibitors using the neutron diffractometers for biological crystallography (BIX-3 and BIX-4) installed at the JRR-3 research reactor.

Journal Articles

Neutron diffraction experiments for protein

Kurihara, Kazuo; Okazaki, Nobuo; Kuroki, Ryota

Radioisotopes, 59(4), p.263 - 277, 2010/04

Crystallographic analysis using neutron diffraction allows identification and position determination of light atoms like hydrogen. This method has been used for three-dimensional structure determination of organic compounds as well as macromolecules like protein. Hydrogen atoms in proteins, as well as those in solvent molecules, play significant roles in many naturally occurring processes, such as catalytic function and molecular recognition. In the field of neutron crystallography novel diffractometers and techniques for preparation and crystallization of target samples has been developed to complement the low flux of neutron sources to permit higher measurement performance. In Japan, single-crystal diffractometers named BIX-3 and BIX-4 were constructed with Neutron Imaging Plates as a detector. These diffractometers have contributed to the investigation of hydrogen-related molecular structures; for example, determination of hydrogen atom positions which are difficult to predict based on X-ray structure data, precise configuration of hydrogen bonds, and the orientation degree of freedom of hydration water molecules. On the other hand, a complementary application of neutron diffraction with X-ray diffraction has also been developed. Using a joint structure refinement method with X-ray diffraction data, elucidation of an enzymatic reaction mechanism and observation of a particular atomic configuration including hydrogen atoms were successfully achieved in neutron crystallographic studies of drug-discovery-target proteins. The information obtained from these neutron analyses has been consolidated into a database called Hydrogen and Hydration Database for Biomolecules which permits the analysis of key statistical information. In Japan as well as overseas, efforts to acquire higher measurement performance are now in progress to further investigate mechanisms involving hydrogen atoms, and to increase the application of neutron crystallographic studies.

Journal Articles

Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Kimura, Kaname*; Matsumura, Hiroyoshi*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 106(12), p.4641 - 4646, 2009/03

 Times Cited Count:100 Percentile:91.04(Multidisciplinary Sciences)

To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp25 and Asp125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9 ${AA}$ resolution and X-ray crystallography at 1.4 ${AA}$ resolution. The resulting structural data shows that the catalytic residue Asp25 is protonated and that Asp125 is deprotonated. The proton on Asp25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine group in KNI-272. The deprotonated Asp125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease; and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.

Oral presentation

Development of Hydrogen and Hydration Database for Biomolecules (HHDB)

Okazaki, Nobuo; Ohara, Takashi; Umino, Hisao*; Chatake, Toshiyuki*; Kurihara, Kazuo; Cachau, R. E.*; Blaber, M.*; Niimura, Nobuo*; Kuroki, Ryota

no journal, , 

Oral presentation

Neutron crystal structure analysis of HIV-1 protease complexed with KNI-272

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.

no journal, , 

We have determined a crystal structure of HIV-1 protease by neutron crystallography. The development of HIV-1 protease inhibitors is regarded as a major success of structure-based drug design and contributes to establish highly active anti-retroviral therapy for AIDS. To further understand the catalytic mechanism of HIV-1 protease and interaction between HIV-1 protease and its inhibitor, we have determined the crystal structure of HIV-1 protease in complex with a inhibitor, KNI-272 to 2.3 ${AA}$ resolution by neutron crystallography. Our results indicates that the carbonyl group of allophenylnorstatine (Apns) in KNI-272 forms a significant hydrogen bond with protonated Asp 25, and the hydrogen atom from the hydroxyl group of Apns forms a remarkable hydrogen bond with the deprotonated Asp125. These results show direct evidence that Asp25 provides a proton to carbonyl group of substrate and Asp125 contributes to activate the attacking water molecule as a nucleophile.

Oral presentation

Neutron crystallography for investigation of catalytic mechanism of HIV-1 protease

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Kimura, Kaname*; Matsumura, Hiroyoshi*; et al.

no journal, , 

HIV-1 protease is a dimeric aspartic protease that cleaves the nascent polyproteins of HIV-1 and plays an essential role in viral replication. To further understand the catalytic mechanism of HIV-1 protease, we have determined the crystal structure of HIV-1 protease in complex with a transition state mimetic tripeptide inhibitor, KNI-272 to 1.9 ${AA}$ resolution by neutron crystallography in combination with 1.4 ${AA}$ resolution X-ray diffraction data. Our results indicates that the carbonyl group of allophenylnorstatine in KNI-272 forms a significant hydrogen bond with protonated Asp 25, and the hydrogen atom from the hydroxyl group of Apns forms a remarkable hydrogen bond with the deprotonated Asp125. These results show direct evidence that Asp25 provides a proton to carbonyl group of substrate and Asp125 contributes to activate the attacking water molecule as a nucleophile.

Oral presentation

Development of hydrogen and hydration database for biomolecules (HHDB)

Okazaki, Nobuo; Ohara, Takashi; Umino, Hisao*; Chatake, Toshiyuki*; Kurihara, Kazuo; Cachau, R. E.*; Blaber, M.*; Niimura, Nobuo*; Kuroki, Ryota

no journal, , 

In protein molecules, key energetic contributors are solvation, desolvation and hydrogen bonding. They contribute protein folding, dynamics and molecular recognition. As a result, more elaborate studies of hydrogen atoms will be great help to recognize protein structures and obtain new findings of them. However, we do not have system which dedicated to characterization and analysis of hydrogen bonding. Therefore, we have developed a database for hydrogen and hydration water molecules. That database named Hydrogen and Hydration Database for Biomolecules (HHDB). Hydrogen bond data stored to HHDB use hydrogen atom coordinates determined directly by neutron diffraction and certain extremely high resolution X-ray diffraction. HHDB provides graphical user interface, users can use it through web browser. HHDB can visualize hydrogen atom positions in protein and solvent, and hydrogen bonding interactions. Fig. 1 shows HHDB plot example. In this plot, hydrogen atom is placed at the origin, and each point represents hydrogen bond distance and angle. We are improving the web user interfaces and the performance for usability.

Oral presentation

Structure analysis of HIV-1 protease by neutron diffraction

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.

no journal, , 

no abstracts in English

Oral presentation

Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389

Okazaki, Nobuo; Tamada, Taro; Kato, Masaru*; Miura, Yutaka*; Kobayashi, Kazuo*; Kuroki, Ryota

no journal, , 

We successed crystallization of glycosyltransferase (GTSase) from Sulfolobus shibatae DSM5389, and determined crystal structure with data which was collected at SPring-8 BL41XU. The enzyme has 729 amino acids and five domains. Domain A is major domain which has ($$beta$$/$$alpha$$)8 barrel catalytic domain as in the usual alpha-amylase family enzymes. The catalytic center is located in the center of the ($$beta$$/$$alpha$$)8 barrel. In the near ($$beta$$/$$alpha$$)8 barrel, electric density of Mg$$^{2+}$$ ion is observed. Some hydrogen bonding network is observed, too.

51 (Records 1-20 displayed on this page)