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Iwata, Mitsunao*; Sugiyama, Yuichi*; Murata, Yoshinori*; Takaya, Shigeru
Defect and Diffusion Forum, 326-328, p.578 - 582, 2012/04
Times Cited Count：0 Percentile：0.01(Nanoscience & Nanotechnology)no abstracts in English
S states from 
Si(
He, 
)SSetoodehnia, K.*; Chen, A. A.*; Komatsubara, Tetsuro*; Kubono, Shigeru*; Binh, D. N.*; Carpino, J. F.*; Chen, J.*; Hashimoto, Takashi*; Hayakawa, Takehito; Ishibashi, Yoko*; et al.
Physical Review C, 83(1), p.018803_1 - 018803_4, 2011/01
Times Cited Count：12 Percentile：60.75(Physics, Nuclear)The structure of proton-unbound S states strongly determines the thermonuclear 
P(
, )S reaction rate at temperatures characteristic of explosive hydrogen burning in classical novae and type I X-ray bursts. Specifically, the rate had been previously predicted to be dominated by two low-lying, unobserved, levels in the 
=4.7-4.8 MeV region, with spin and parity assignments of 3
and 2. In recent experimental work, two candidate levels were observed with energies of 4.699 MeV and 4.814 MeV, but no experimental information on their spins and parities was obtained. We have performed an in-beam -ray spectroscopy study of S with the Si(He, )S reaction. The spin and parities were inferred from a comparison to the known decay schemes of the corresponding mirror states.
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
Times Cited Count：4 Percentile：48.31(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 
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 
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) obtained by this method diffracted to beyond 3.5 
resolution.
resolutionShimizu, 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：72.02(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.
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：111 Percentile：90.72(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 resolution and X-ray crystallography at 1.4 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.
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 .
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 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.
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
Sugiyama, Yuichi*; Iwata, Mitsunao*; Murata, Yoshinori*; Takaya, Shigeru
no journal, ,
no abstracts in English
Sugiyama, Yuichi*; Iwata, Mitsunao*; Murata, Yoshinori*; Takaya, Shigeru
no journal, ,
no abstracts in English
Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro*; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari*; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.
no journal, ,
In this study, we determined crystal structures of HIV-1 protease complexed with inhibitor by neutron and X-ray crystallography. Finally, we refined the structures to R-factor of 17.3% and free R-factor 20.3% by neutron crystallography and to R-factor of 10.4 % and free R-factor 12.4% by X-ray crystallography. The result shows that Asp 25 residue is protonated and Asp 125 is deprotonated. These information is important to resolve catalytic mechanism and design of new potent inhibitor.
Iwata, Mitsunao*; Sugiyama, Yuichi*; Murata, Yoshinori*; Takaya, Shigeru
no journal, ,
Microstructural states of metallic materials can be expressed by system free energy, and the estimation of the system free energy is useful for damage analysis of the materials. In this study, change with creep time in the system free energy of the FG-HAZ in 9Cr heat resistant ferritic steels is estimated on the basis of a series of experiments such as chemical analysis by using extracted residues, X-ray diffraction, and scanning transmission observations. The change in the system free energy is expressed quantitatively by rate constants depending on applied stress. It is observed that the steel ruptures when the applied stress exceeds the allowable stress. The relationship between allowable stress and system free energy makes it possible to predict the rupture time in the long term.
