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Journal Articles

Anomalous hydrogen dynamics of the ice VII-VIII transition revealed by high-pressure neutron diffraction

Komatsu, Kazuki*; Klotz, S.*; Machida, Shinichi*; Sano, Asami; Hattori, Takanori; Kagi, Hiroyuki*

Proceedings of the National Academy of Sciences of the United States of America, 117(12), p.6356 - 6361, 2020/03

 Times Cited Count:1 Percentile:100(Multidisciplinary Sciences)

Above 2 GPa the phase diagram of water simplifies considerably and exhibits only two solid phases up to 60 GPa, ice VII and ice VIII. The two phases are related to each other by hydrogen ordering, with the oxygen sub-lattice being essentially the same. Here we present neutron diffraction data to 15 GPa which reveal that the rate of hydrogen-ordering at the ice VII-VIII transition decreases strongly with pressure to reach time scales of minutes at 10 GPa. Surprisingly, the ordering process becomes more rapid again upon further compression. We show that such an unusual change in transition rate can be explained by a slowing-down of the rotational dynamics of water molecules with a simultaneous increase of translational motion of hydrogen under pressure, as previously suspected. The observed crossover in the hydrogen dynamics in ice is likely the origin of various hitherto unexplained anomalies of ice VII in the 10-15 GPa range reported by Raman spectroscopy, X-ray diffraction, and proton conductivity.

Journal Articles

Magnetization dynamics and its scattering mechanism in thin CoFeB films with interfacial anisotropy

Okada, Atsushi*; He, S.*; Gu, B.; Kanai, Shun*; Soumyanarayanan, A.*; Lim, S. T.*; Tran, M.*; Mori, Michiyasu; Maekawa, Sadamichi; Matsukura, Fumihiro*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 144(15), p.3815 - 3820, 2017/04

Journal Articles

Giant cadherins Fat and Dachsous self-bend to organize properly spaced intercellular junctions

Tsukasaki, Yoshikazu*; Miyazaki, Naoyuki*; Matsumoto, Atsushi; Nagae, Shigenori*; Yonemura, Shigenobu*; Tanoue, Takuji*; Iwasaki, Kenji*; Takeichi, Masatoshi*

Proceedings of the National Academy of Sciences of the United States of America, 111(45), p.16011 - 16016, 2014/11

 Times Cited Count:27 Percentile:35.12(Multidisciplinary Sciences)

Journal Articles

Detection of atomic spin labels in a lipid bilayer using a single-spin nanodiamond probe

Kaufmann, S.*; Simpson, D. A.*; Hall, L. T.*; Perunicic, V.*; Senn, P.*; Steinert, S.*; McGuinness, L. P.*; Johnson, B. C.*; Oshima, Takeshi; Caruso, F.*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 110(27), p.10894 - 10898, 2013/07

 Times Cited Count:74 Percentile:7.26(Multidisciplinary Sciences)

Journal Articles

Deep-sea record of impact apparently unrelated to mass extinction in the Late Triassic

Onoue, Tetsuji*; Sato, Honami*; Nakamura, Tomoki*; Noguchi, Takaaki*; Hidaka, Yoshihiro*; Shirai, Naoki*; Ebihara, Mitsuru*; Osawa, Takahito; Hatsukawa, Yuichi; Toh, Yosuke; et al.

Proceedings of the National Academy of Sciences of the United States of America, 109(47), p.19134 - 19139, 2012/11

 Times Cited Count:27 Percentile:28.78(Multidisciplinary Sciences)

The 34 million year (My) interval of the Late Triassic is marked by the formation of several large impact structures on Earth. As with the Chicxulub impact event at the Cretaceous/Paleogene boudary, the Late Triassic impact events have been considered a factor in biotic extinction events in the Late Triassic (e.g., the Triassic/Jurassic boundary). However, the causal link between these impact events and a mass extinction event in the Late Triassic remains controversial because of a lack of stratigraphic records of their ejecta deposits. Here we report evidence for an impact event (platinum group elements anomaly, nickel-rich magnetite and microspherules) deposited within a Paleo-Pacific basin in the middle Norian (Upper Triassic) deep-sea sediment in Japan. This includes anomalously high abundances of iridium, up to 41.5 parts per billion (ppb), in the ejecta deposit, which suggests that the iridium anomaly may be found on a global scale. The middle Norian age of the ejecta deposit suggests that the impact event that produced the 100-km-wide Manicouagan crater in Canada8 is most likely related to its deposition. Our analysis of siliceous microfossils shows no evidence of a mass extinction event across the impact event horizon, and no contemporaneous faunal turnover is seen in other marine fossils. However, such an event has been reported among terrestrial tetrapods and floras in North America. We therefore hypothesize that the Manicouagan impact caused the catastrophic collapse of terrestrial ecosystems near the impact site, but not within the marine realm.

Journal Articles

Ion-beam irradiation, gene identification, and marker-assisted breeding in the development of low-cadmium rice

Ishikawa, Satoru*; Ishimaru, Yasuhiro*; Igura, Masato*; Kuramata, Masato*; Abe, Tadashi*; Senoura, Takeshi*; Hase, Yoshihiro; Arao, Tomohito*; Nishizawa, Naoko*; Nakanishi, Hiromi*

Proceedings of the National Academy of Sciences of the United States of America, 109(47), p.19166 - 19171, 2012/11

 Times Cited Count:210 Percentile:0.35(Multidisciplinary Sciences)

Rice (${it Oryza sativa}$ L.) is one of major sources of dietary intake of cadmium (Cd) for the human. However, the reliable technique to reduce substantially rice Cd contamination has not been offered so far. Here, we report the ion-beam irradiated rice mutants that do not nearly accumulate Cd in the grains and the mutant gene responsible for the Cd limitation. We found three mutants in which a favorable low-Cd trait is expressed by the different mutations on the same gene (${it OsNRAMP5}$), and the transporter encoded by the mutant gene ${it osnramp5}$ had a defective function of root Cd influx. The mutants adapted well in the Cd-polluted paddy fields by exhibiting nearly non-detectable Cd concentrations in their grains in accordance with no adverse economic traits. The DNA marker has been developed to breed new cultivars carrying ${it osnramp5}$. Our findings would be useful for greatly reducing the Cd level of paddy rice.

Journal Articles

Electronic inhomogeneity in a Kondo lattice

Bauer, E. D.*; Yang, Y.-F.*; Capan, C.*; Urbano, R. R.*; Miclea, C. F.*; Sakai, Hironori; Ronning, F.*; Graf, M. J.*; Balatsky, A. V.*; Movshovich, R.*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 108(17), p.6857 - 6861, 2011/04

 Times Cited Count:34 Percentile:15.81(Multidisciplinary Sciences)

Here, we report a manifestation of electronic inhomogeneity in a strongly correlated $$f$$-electron system, using CeCoIn$$_5$$ as an example. A thermodynamic analysis of its superconductivity, combined with nuclear quadrupole resonance measurements, shows that nonmagnetic impurities (Y, La, Yb, Th, Hg, and Sn) locally suppress unconventional superconductivity, generating an inhomogeneous electronic "Swiss cheese" due to disrupted periodicity of the Kondo lattice. Our analysis may be generalized to include related systems, suggesting that electronic inhomogeneity should be considered broadly in Kondo lattice materials.

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:98 Percentile:8.56(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.

Journal Articles

Low-barrier hydrogen bond in photoactive yellow protein

Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*; Shimizu, Nobutaka*; Yamazaki, Yoichi*; Kataoka, Mikio*

Proceedings of the National Academy of Sciences of the United States of America, 106(2), p.440 - 444, 2009/01

 Times Cited Count:131 Percentile:5.17(Multidisciplinary Sciences)

Journal Articles

Mutational reconstructed ferric chelate reductase confers enhanced tolerance in rice to iron deficiency in calcareous soil

Ishimaru, Yasuhiro*; Kim, S.*; Tsukamoto, Takashi*; Oki, Hiroyuki*; Kobayashi, Takanori*; Watanabe, Satoshi; Matsuhashi, Shimpei; Takahashi, Michiko*; Nakanishi, Hiromi*; Mori, Satoshi*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 104(18), p.7373 - 7378, 2007/05

 Times Cited Count:106 Percentile:6.28(Multidisciplinary Sciences)

Journal Articles

Switch interactions control energy frustration and multiple flagellar filament structures

Kitao, Akio*; Yonekura, Koji*; Yonekura, Saori*; Samatey, F.*; Imada, Katsumi*; Namba, Keiichi*; Go, Nobuhiro

Proceedings of the National Academy of Sciences of the United States of America, 103(13), p.4894 - 4899, 2006/03

 Times Cited Count:43 Percentile:33.83(Multidisciplinary Sciences)

no abstracts in English

Journal Articles

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Proceedings of the National Academy of Sciences of the United States of America, 103(9), p.3135 - 3140, 2006/02

 Times Cited Count:71 Percentile:19.2(Multidisciplinary Sciences)

A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF), and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8${AA}$ resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry via a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different to that between human GCSF and the CRH domain of mouse GCSF-R, but similar to that of the interleukin-6 (IL-6)/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.

Journal Articles

Neutron crystallographic study on rubredoxin from ${it Pyrococcus furiosus}$ by BIX-3, a single-crystal diffractometer for biomacromolecules

Kurihara, Kazuo; Tanaka, Ichiro*; Chatake, Toshiyuki*; Adams, M. W. W.*; Jenney, F. E. Jr.*; Moiseeva, N.*; Bau, R.*; Niimura, Nobuo

Proceedings of the National Academy of Sciences of the United States of America, 101(31), p.11215 - 11220, 2004/08

 Times Cited Count:46 Percentile:36.72(Multidisciplinary Sciences)

The structure of a rubredoxin (Rd) from ${it Pyrococcus furiosus}$, an organism that grows optimally at 100 $$^{circ}$$C, was determined using the neutron single-crystal diffractometer for biological macromolecules (BIX-3) at the JRR-3 reactor of JAERI. Data were collected at room temperature up to a resolution of 1.5 ${AA}$, and the completeness of the data set was 81.9 %. The model contains 306 H atoms and 50 D atoms. A total of 37 hydration water molecules were identified. The model has been refined to final agreement factors of ${it R}$ = 18.6 % and ${it R}$$$_{free}$$ = 21.7 %. Several orientations of the O-D bonds of side chains, whose assignments from X-ray data were previously ambiguous, were clearly visible in the neutron structure. While most backbone N-H bonds had undergone some degree of H/D exchange throughout the molecule, five H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND$$_{3}$$$$^{+}$$ terminus that may contribute to the unusual thermostability of this molecule.

Journal Articles

Computational design of water-soluble analogues of the potassium channel KcsA

Slovic, A. M.*; Kono, Hidetoshi; Lear, J. D.*; Saven, J. G.*; DeGrado, W. F.*

Proceedings of the National Academy of Sciences of the United States of America, 101(7), p.1828 - 1833, 2004/02

 Times Cited Count:74 Percentile:21.46(Multidisciplinary Sciences)

no abstracts in English

Journal Articles

Posttranslational modification of the ${it umuD}$-encoded subunit of ${it Escherichia coli}$ DNA polymerase V regulates its interactions with the $$beta$$ processivity clamp

Sutton, M. D.*; Narumi, Issei; Walker, G. C.*

Proceedings of the National Academy of Sciences of the United States of America, 99(8), p.5307 - 5312, 2002/04

 Times Cited Count:36 Percentile:46.4(Multidisciplinary Sciences)

The ${it Escherichia coli umuDC}$ gene products (PolV) participate in both a DNA damage checkpoint control and translesion DNA synthesis. Interactions of the two ${it umuD}$ gene products, UmuD and UmuD' proteins, with components of the replicative DNA polymerase (PolIII), are important for determining which biological role the ${it umuDC}$ gene products will play. We have shown that UmuD possesses a higher affinity for PolIII $$beta$$ processivity clamp than does UmuD' because of the N-terminal arm of UmuD, much of which is missing in UmuD'. Futhermore, we identified specific amino acid residues of UmuD that crosslink to $$beta$$ with a crosslinker, ${it p}$-azidoiodoacetanilide, defining the domain important for the interaction.

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