Structural & chemical study of molecular crystals based on precise positions of hydrogen atoms by single-crystal neutron diffraction

Ohara, Takashi

Nihon Kessho Gakkai-Shi, 64(2), p.132 - 139, 2022/05

https://doi.org/10.5940/jcrsj.64.132

no abstracts in English

Fine structural analysis using single crystal neutron diffraction

Kaneko, Koji

Nihon Kessho Gakkai-Shi, 61(4), p.237 - 242, 2019/12

https://doi.org/10.5940/jcrsj.61.237

Two protonation states and structural features of a bilin reductase PcyA revealed by neutron crystallography

Unno, Masayoshi*; Sugishima, Masakazu*; Wada, Kei*; Hagiwara, Yoshinori*; Kusaka, Katsuhiro*; Tamada, Taro; Fukuyama, Keiichi*

Nihon Kessho Gakkai-Shi, 57(5), p.297 - 303, 2015/10

https://doi.org/10.5940/jcrsj.57.297

Bilin compounds are fundamentally important for oxygenic photosynthetic organisms, because they are utilized as pigments for photosynthesis (phycobilins) and photoreceptors (phytochromobilin). Phycocyanobilin (PCB), a phycobilin, comprises the chromophore of algal phytochromes and the core phycobiliprotein antennae of cyanobacteria and red algae. PCB is biosynthesized by a member of the ferredoxin-dependent bilin reductase family, phycocyanobilin:ferredoxin oxidoreductase (PcyA). In the present study, we determined the neutron crystal structure of PcyA in complex with its substrate biliverdin (BV). This neutron structure revealed the protonation state of BV and the surrounding residues. We found that two forms of BV, neutral BV and protonated BVH, were coupled with the two conformation/protonation states of the essential residue Asp105. Further, His88 and His74 near BV were singly protonated and were connected with an intervening hydronium ion. Neutron analysis also revealed how X-ray irradiation of the PcyA-BV crystal altered the structure of the PcyA-BV complex.

Study of semiconductor growth mechanism using in situ synchrotron X-ray diffraction

Takahashi, Masamitsu

Nihon Kessho Seicho Gakkai-Shi, 42(3), p.201 - 209, 2015/10

AA2015-0739.pdf:0.82MB

https://doi.org/10.19009/jjacg.42.3_201

Structural study on hydrogen-metal systems using X-rays and neutrons

Machida, Akihiko

Nihon Kessho Gakkai-Shi, 57(1), p.34 - 40, 2015/02

https://doi.org/10.5940/jcrsj.57.34

This article reports the recent structural studies on hydrogen-metal systems using X-rays and neutrons. We have focused on the interactions between interstitial hydrogen atoms and their surrounding metal atoms. The hydrogen-metal interactions provide the important knowledge to develop the high performance hydrogen absorbing alloys. The X-ray and neutron diffraction are complementary methods to investigate the structural changes of metals induced by the absorbing hydrogen atoms. As a typical example, pressure-induced phase separation of lanthanum di-hydride are described.

Seven cysteine-deficient mutants depict interplay between thermal and chemical stabilities of individual cysteine residues in MAP kinase JNK1

Nakaniwa, Tetsuko*; Kuroki, Ryota; Kinoshita, Takayoshi*

Nihon Kessho Gakkai-Shi, 55(3), p.197 - 202, 2013/06

https://doi.org/10.5940/jcrsj.55.197

To characterize the role of cysteine residues on the structure, function and stability of JNK1, we prepared and evaluated the wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The solvent exposed cysteine residues did not influence biological function and mutating these residues raised the thermal stability because of newly formed hydrogen bonds and of higher hydration as speculated by the mutant structures. The surface cysteine involved in the molecular surface hydrophobic pocket did not affect biological function; although a moderate thermal destabilization was observed. Cysteines in the loosely-assembled hydrophobic environment moderately contributed to thermal stability and the mutations of these cysteines had negligible effect on enzyme activity. The other cysteines are involved in the tightly-filled hydrophobic core and mutation of these residues conferred the adverse effects on the thermal stability and enzyme activity.

Structure of enzyme-inhibitor complex determined by neutron crystallography

Tamada, Taro; Adachi, Motoyasu; Kurihara, Kazuo; Kuroki, Ryota

Nihon Kessho Gakkai-Shi, 55(1), p.47 - 51, 2013/02

https://doi.org/10.5940/jcrsj.55.47

Neutron crystallography enables us to identify the accurate hydrogen positions in proteins, which play important roles in many chemical reactions in living system. Here we show our results of neutron structure determination of enzymes in complex with its inhibitors which corresponds to transition state analogues. Neutron structure analysis elucidated the detail catalytic reaction of each enzyme by direct observation of hydrogen atoms. Furthermore we would like to introduce a new neutron beam line for neutron structural biology planned at MLF in J-PARC.

Effects of randomness and frustration on the relaxor nature in Pb(InNb)O

Owada, Kenji

Nihon Kessho Gakkai-Shi, 54(3), p.147 - 154, 2012/06

https://doi.org/10.5940/jcrsj.54.147

It is well known that B-site randomness contributes to the appearance of relaxor phenomena in the lead-based complex perovskite Pb(B'B'')O. But the microscopic mechanism of the effect of B-site randomness on the systems has not been understood yet. Among the Pb(B'B'')O systems, Pb(InNb)O (PIN) has drawn much attention because it can be in the antiferroelectric (AFE), ferroelectric (FE), or relaxor state depending on B-site randomness. We review the recent progress in our understanding of the effect of B-site randomness on PIN from the experimental viewpoint. As a conclusion of the arguments, we also introduce the frustration mechanism in Pb(B'B'')O.

The Existence of ferroelectric ice on icy bodies in space; A Neutron diffraction study

Fukazawa, Hiroshi

Nihon Kessho Gakkai-Shi, 52(4), p.219 - 225, 2010/08

https://doi.org/10.5940/jcrsj.52.219

The complex behavior of water and the unusual properties of ferroelectric ice XI continue to attract much interest. Whether ice in the space exists as ice XI, is an important question, because long range electrostatic forces caused by the ferroelectricity might be an important factor for planet formation. From neutron diffraction experiments, we found the temperature and pressure conditions for the transformation of the largest fraction of ice into ferroelectric ice. It suggests that myriad big icy-bodies, which exist as dwarf planets and Kuiper Belt Object, consist of thick ferroelectric-ice surface. Furthermore, we report spectral and vibrational properties of ferroelectric ice investigated by inelastic neutron scattering and infrared absorption measurements. Because the spectral properties of ferroelectric ice are clearly different from those of ordinary ice, the distinct ferroelectric ice in the universe is detectable using infrared telescopes and planetary exploration.

Pressure-induced structural transition and long-period structures of rare-earth metal hydrides

Machida, Akihiko; Watanuki, Tetsu; Aoki, Katsutoshi

Nihon Kessho Gakkai-Shi, 51(6), p.320 - 326, 2009/12

https://doi.org/10.5940/jcrsj.51.320

Pressure-induced structural transition of rare-earth metal hydride, YH, has been investigated by synchrotron radiation X-ray diffraction experiments. We observed the pressure-induced structural transformation from the hexagonal metal lattice into an fcc one through an intermediate state, which appears in the wide pressure span of 1222 Gather obtained X-ray diffraction patterns in the intermediate state are represented by long-period structures, e.g. 27, of the yttrium metal lattice. These long-period structures are interpreted in terms of the periodic arrangements of hexagonal-type and fcc-type stacking layers of the yttrium metals. Such structural transition is considered to be characteristic for rare-earth metal hydride.