Genomes and Genes
Japan Synchrotron Radiation Research Institute
Organization: Japan Synchrotron Radiation Research Institute
- Evidence for a correlated insulator to antiferromagnetic metal transition in CrNP A Bhobe
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277 8581, Japan
Phys Rev Lett 104:236404. 2010..Thus, CrN transforms from a correlated insulator to an antiferromagnetic metal, coupled to the magnetostructural transition...
- Assembly and disassembly dynamics of the cyanobacterial periodosomeShuji Akiyama
PRESTO, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama 332 0012, Japan
Mol Cell 29:703-16. 2008..The Kai periodosome is assembled in such a way that KaiA and KaiB are recruited to a C-terminal region of KaiC in a phosphorylation-dependent manner...
- Simulation of charge effects on density maps obtained by high-resolution electron crystallographyTeruhisa Hirai
Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
J Electron Microsc (Tokyo) 56:131-40. 2007..Still, density maps obtained by electron crystallography are expected to show slightly elongated features toward the positively charged atoms...
- A closer look at energy transduction in muscleHirofumi Onishi
Exploratory Research for Advanced Technology Actin Filament Dynamics Project, Japan Science and Technology Agency, c o RIKEN Harima Institute SPring 8 Center, Kouto, Sayo, Hyogo 679 5148, Japan
Proc Natl Acad Sci U S A 104:12714-9. 2007....
- Structural insights of HutP-mediated regulation of transcription of the hut operon in Bacillus subtilisThirumananseri Kumarevel
Biometals Laboratory and Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
Biophys Chem 128:1-12. 2007..This analysis clearly demonstrates that the first base in the UAG motifs is not important for the function and is consistent with our previous observations...
- Crowded surfaces change annealing dynamics of actin filamentsDavid Popp
ERATO Actin Filament Dynamics Project, Japan Science and Technology Corporation, c o RIKEN Harima Institute at Spring 8, Kouto, Sayo, Hyogo, 679 5148, Japan
J Mol Biol 368:365-74. 2007..This implicates that dynamic rearrangement of actin filaments by annealing near the leading edge of the cell, could change physical parameters like the mechanical response and contribute significantly to cell motility...
- Electronic structure of DNA nucleobases and their dinucleotides explored by soft X-ray spectroscopyYoshihisa Harada
RIKEN SPring 8 Center, 1 1 1 Kouto Sayo cho Sayo gun Hyogo 679 5148, Japan, National Institute for Materials Science, 1 2 1 Sengen Tsukuba Ibaraki 305 0047, Japan
J Phys Chem A 110:13227-31. 2006....
- Separation of a phosphorylated histidine protein using phosphate affinity polyacrylamide gel electrophoresisSeiji Yamada
Biometal Science Laboratory, RIKEN SPring 8 Center, Harima Institute, Kouto 1 1 1, Sayo, Hyogo 679 5148, Japan
Anal Biochem 360:160-2. 2007
- Molecular determination by electron microscopy of the actin filament end structureAkihiro Narita
ERATO Actin Filament Dynamics Project, Japan Science and Technology Agency c o RIKEN, Sayo, Hyogo 679 5148, Japan
J Mol Biol 365:480-501. 2007..This is the first method for elucidating the detailed 3D structures at the end of the actin filament...
- A structural origin of latency relaxation in frog skeletal muscleNaoto Yagi
SPring 8 JASRI, Kouto, Sayo, Hyogo 679 5198, Japan
Biophys J 92:162-71. 2007..The simultaneous spacing change of the 14.3-nm myosin meridional reflection with the LR suggests that detachment of myosin heads that are bound to actin in the resting muscle is the cause of the LR...
- Fast tomography using quasi-monochromatic undulator radiationKentaro Uesugi
SPring 8 JASRI, Sayo, Hyogo 679 5198, Japan
J Synchrotron Radiat 13:403-7. 2006..Beam-hardening effects were not significant. This technique may be useful in studying time-dependent structural changes of soft materials such as polymers and biological samples...
- Stable top-up operation at SPring-8Hitoshi Tanaka
Japan Synchrotron Radiation Research Institute SPring 8, Sayo cho, Sayo gun, Hyogo 679 5198, Japan
J Synchrotron Radiat 13:378-91. 2006..The process of achieving highly stabilized top-up operation at SPring-8 and its utility for user experiments are described...
- Tissue-equivalent TL sheet dosimetry system for X- and gamma-ray dose mappingN Nariyama
Japan Synchrotron Radiation Research Institute, Mikazuki, Sayo, Hyogo 679 5198, Japan
Radiat Prot Dosimetry 120:136-9. 2006..Irradiation using synchrotron radiation between 10 and 100 keV and (60)Co gamma rays showed that the TL sheet dosimetry system was promising for radiation dose mapping for various purposes...
- Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffractionHiroyuki Iwamoto
Research Institute Research and Utilization Division, SPring 8, Japan Synchrotron Radiation, Sayo gun, Hyogo 679 5198, Japan
Proc Biol Sci 273:677-85. 2006....
- Effect of short-range forces on the length distribution of fibrous cytoskeletal proteinsDavid Popp
ERATO Actin Filament Dynamics Project, Japan Science and Technology Corporation, RIKEN Harima Institute, SPring 8, Sayo, Hyogo, Japan
Biopolymers 89:711-21. 2008....
- Mail-in data collection at SPring-8 protein crystallography beamlinesNobuo Okazaki
Japan Synchrotron Radiation Research Institute SPring 8, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5198, Japan
J Synchrotron Radiat 15:288-91. 2008..This system is now in routine operation and is contributing to high-throughput beamline operation...
- Structure of putative CutA1 from Homo sapiens determined at 2.05 A resolutionBagautdin Bagautdinov
Protein Structure Analysis Team, RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 64:351-7. 2008..6 kDa and contains 135 amino-acid residues. In order to obtain clues to the possible function of HsCutA1, its crystal structure was compared with those of other CutA1 and PII proteins...
- Fast x-ray recordings reveal dynamic action of contractile and regulatory proteins in stretch-activated insect flight muscleHiroyuki Iwamoto
Research and Utilization Division, SPring 8, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
Biophys J 99:184-92. 2010..The observed rates of the attachment/detachment of myosin heads and the motion of tropomyosin are fast enough for the thin-filament regulatory system to control each SA event in fast-beating insects...
- Amino acids and glycine ethyl ester as new crystallization reagents for lysozymeLen Ito
Japan Synchrotron Radiation Research Institute SPring 8, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 66:750-4. 2010..A discussion of the crystallization of HEWL using these reagents as precipitating agents is given...
- [SPring-8 structural biology beamline]Takashi Kumasaka
Japan Synchrotron Radiation Research Institute, Hyogo, Japan
Yakugaku Zasshi 130:649-55. 2010..Although the high brilliance severely damages protein samples, the users can estimate the degree of the damage and plan best data collection strategy...
- Temperature gradient analyzers for compact high-resolution X-ray spectrometersD Ishikawa
Materials Dynamics Laboratory, RIKEN SPring 8 Center, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
J Synchrotron Radiat 17:12-24. 2010..In some cases the application of a temperature gradient can improve the energy resolution even with a single-element detector...
- Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometryTatsuya Yamamoto
Biometal Science Laboratory, RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hongo 679 5148, Japan
J Biol Chem 285:5646-52. 2010....
- New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)Jeyaraman Jeyakanthan
National Synchrotron Radiation Research Center, 101 Hsin Ann Road, Hsinchu Science Park, Hsinchu 30076, Taiwan
Acta Crystallogr Sect F Struct Biol Cryst Commun 65:978-86. 2009..Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK...
- Crystal structure of a new cyan fluorescent protein and its hue-shifted variantsAkihiro Kikuchi
Biometal Science Laboratory, RIKEN SPring 8 Center, 1 1 1, Kouto, Sayo, Hyogo 679 5148, Japan
Biochemistry 48:5276-83. 2009..Moreover, the structural comparison suggests that an additional water molecule buried in the space between the Ala158 residue and the chromophore phenolate is also responsible for the chromophore polarization...
- Evaluation of enamel crystallites in subsurface lesion by microbeam X-ray diffractionN Yagi
Japan Synchrotron Radiation Research Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5198, Japan
J Synchrotron Radiat 16:398-404. 2009..As these diffraction methods provide structural information in the nanometre range, they are useful for investigating the mechanism of the mineral loss in early caries lesion at a nanometre level...
- Orbital hybridization and magnetic coupling of the A-site Cu spins in CaCu3B4O12 (B = Ti, Ge, and Sn) perovskitesM Mizumaki
Japan Synchrotron Radiation Research Institute JASRI, Sayo cho Sayo gun, Hyogo 679 5198, Japan
Inorg Chem 48:3499-501. 2009....
- Microangiography system for investigation of metabolic syndrome in rat model using synchrotron radiationKeiji Umetani
Japan Synchrotron Radiation Research Institute, Sayo gun, Hyogo, Japan
Conf Proc IEEE Eng Med Biol Soc 2008:2693-6. 2008..We assessed the magnitude of coronary artery vasorelaxation before and after administration of drugs that modulate endothelial control of the coronary arteries in the rat model...
- Structural model of the Rev regulatory protein from equine infectious anemia virusYungok Ihm
Department of Physics and Astronomy, Iowa State University, Ames, IA, USA
PLoS ONE 4:e4178. 2009..Our predicted structure should increase understanding of structure-function relationships in Rev and may provide a basis for the design of new therapies for lentiviral diseases...
- On the ability of 8-bromoadenosine triphosphate to support contractility of vertebrate skeletal muscle fibersHiroyuki Iwamoto
Research and Utilization Division, SPring 8, Japan Synchrotron Radiation Research Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5198, Japan
J Muscle Res Cell Motil 29:45-55. 2008....
- Crystallization and preliminary X-ray crystallographic analysis of full-length yeast tropomyosin 2 from Saccharomyces cerevisiaeVladimir Meshcheryakov
ERATO Actin Filament Dynamics Project, Japan Science and Technology Agency, c o RIKEN Harima Institute SPring 8 Center, Sayo, Hyogo 679 5148, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 64:528-30. 2008..8, b = 49.9, c = 104.0 A, alpha = gamma = 90.0, beta = 124.0 degrees and two molecules in the asymmetric unit. A complete native X-ray diffraction data set was collected to 3.5 A resolution using synchrotron radiation...
- Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereusHideo Ago
Structural Biophysics Laboratory, RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
J Biol Chem 281:16157-67. 2006..In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate...
- Silicon avalanche photodiodes for direct detection of X-raysAlfred Q R Baron
SPring 8 JASRI, Hyogo, Japan
J Synchrotron Radiat 13:131-42. 2006..Data from several APD arrays are also presented, as is a detailed description of an integrated package system. Tables are included comparing commercially available devices, including arrays...
- Direct observation of photolysis-induced tertiary structural changes in hemoglobinShin ichi Adachi
RIKEN Harima Institute SPring 8, 1 1 1 Kouto, Mikazuki, Sayo, Hyogo 679 5148, Japan
Proc Natl Acad Sci U S A 100:7039-44. 2003..Our results establish that the structural basis of the low affinity of the T state is radically different between the subunits, because of differences in the packing and chemical tension at the hemes...
- [X-ray refraction contrast imaging]Katsuhito Yamazaki
Japan Synchrotron Radiation Research Institute, Japan
Igaku Butsuri 22:8-12. 2002
- Structural dissection of alkaline-denatured pepsinYuji O Kamatari
Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, Oxford OX1 3QT, UK
Protein Sci 12:717-24. 2003..This study demonstrates that the structure of pepsin in the I(P) state is significantly more complex than that of a fully folded C-terminal lobe connected to an unstructured N-terminal lobe...
- Chimeric sensory kinases containing O2 sensor domain of FixL and histidine kinase domain from thermophileHideyuki Kumita
RIKEN Harima Institute SPring 8, 1 1 1 Koto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
Biochim Biophys Acta 1646:136-44. 2003....
- Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolutionNobuo Kamiya
RIKEN Harima InstituteSPring 8, Kouto 1 1 1, Mikazuki cho, Sayou gun, Hyogo 679 5148, Japan
Proc Natl Acad Sci U S A 100:98-103. 2003..In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions...
- Interactions of a lysozyme-monomethoxypolyethylene glycol conjugate with lipopolysaccharides and lipid bilayers and effects of conjugate on gram-negative bacteriaYuichi Nodake
Division of Bioresource and Bioenvironmental Sciences, Graduate School of Kyushu University, Fukuoka, Japan
Biosci Biotechnol Biochem 66:1848-52. 2002..mPEG-lysozyme may perturb the outer membrane of Gram-negative microorganisms, gaining itself access to the peptidoglycan layers of the bacterium...
- [Development of high-throughput automatic protein crystallization and observation system]Mitsuaki Sugahara
Tanpakushitsu Kakusan Koso 47:1026-32. 2002
- States of thin filament regulatory proteins as revealed by combined cross-linking/X-ray diffraction techniquesHiroyuki Iwamoto
Life and Environment Division, Japan Synchrotron Radiation Research Institute, Hyogo 679 5198, Japan
J Mol Biol 317:707-20. 2002....
- Picometer-scale dynamical x-ray imaging of single DNA moleculesY C Sasaki
Biomedical Group, Japan Synchrotron Radiation Research Institute, SPring 8, Mikazuki, Hyogo 679 5198, Japan
Phys Rev Lett 87:248102. 2001..DXT can obtain information about the dynamics of single molecules through a quantitative analysis, since the signals from DXT are independent of the chemical conditions...
- Cross-bridge and calcium behavior in ferret papillary muscle in different thyroid statesN Yagi
Department of Pharmacology, Tohoku University School of Medicine, Sendai, 980 8575 Japan
Jpn J Physiol 51:319-26. 2001..In hyperthyroidism, the cross-bridge movement significantly preceded tension development, suggesting that hyperthyroid myosin (V1) has a longer latency period between the shift to the vicinity of the thin filament and force development...
- Fixed-height exit bender of synchrotron X-rays above 40 keVY Yoneda
Japan Atomic Energy Research Institute JAERI, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
J Synchrotron Radiat 8:18-21. 2001..The flux density of the focused beam measured at 40 keV was 15 times higher than that of the unfocused beam. The height deviation of the focused beam throughout the measured energy range was within +/- 0.15 mm...
- The shapes and sizes of two domains of tropomodulin, the P-end-capping protein of actin-tropomyosinT Fujisawa
Laboratory for Structural Biochemistry, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki, Sayo, Hyogo 679 5148, Japan
FEBS Lett 498:67-71. 2001....
- Time-resolved two-dimensional X-ray diffraction study of the effect of shortening on activation of contracting skeletal muscleH Iwamoto
Experimental Research Division, SPring 8, JASRI, Hyogo, Japan
Pflugers Arch 439:646-9. 2000....
- [The structure and function of nicotinic acetylcholine receptor]Atsuo Miyazawa
Tanpakushitsu Kakusan Koso 49:1-10. 2004
- Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallographyTadashi Nakai
RIKEN Harima Institute SPring 8, 1 1 1 Kouto, Mikazuki, Sayo gun, Hyogo 679 5148, Japan
J Mol Biol 337:1011-33. 2004..MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively...
- Crystal structure of purine nucleoside phosphorylase from Thermus thermophilusTahir H Tahirov
Highthroughput Factory, RIKEN Harima Institute, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
J Mol Biol 337:1149-60. 2004..The obtained experimental data suggest that the catalytic properties of the T.thermophilus enzyme are reminiscent of the trimeric rather than hexameric purine nucleoside phosphorylases...
- Structure and function of NADPH-cytochrome P450 reductase and nitric oxide synthase reductase domainTakashi Iyanagi
Biometal Science Laboratory, RIKEN Harima Institute SPring8, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
Biochem Biophys Res Commun 338:520-8. 2005..In addition, a new model for the redox-linked conformational changes during the catalytic cycle for both CPR and NOS reductase domain is also discussed...
- Morphometric deformations of small airways and alveoli under quasi-static inflation processToshihiro Sera
Japan Synchrotron Radiation Research Institute JASRI SPring 8, Hyogo, Japan
J Physiol Anthropol Appl Human Sci 24:465-8. 2005..8%, range: 0.36-0.89) than larger airways (45.2%, range: 0.40-0.57). These results indicated that the airway did not deformed in same manner and that these morphological differences characterized the heterogeneous lung function...
- A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAINaoki Kunishima
Highthroughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Sayo gun, Hyogo 679 5148, Japan
J Mol Biol 352:212-28. 2005....
- X-ray microdiffraction and conventional diffraction from frozen-hydrated biological specimensHiroyuki Iwamoto
Research and Utilization Division, SPring 8, Japan Synchrotron Radiation Research Institute, Hyogo 679 5198, Japan
J Synchrotron Radiat 12:479-83. 2005..The quick-freezing of biological specimens has also been proven useful in reducing the specimen volume in the beam in conventional diffraction recordings...
- Pure-type superconducting permanent-magnet undulatorTakashi Tanaka
RIKEN SPring 8, Koto 1 1 1, Mikazuki, Sayo, Hyogo 679 5148, Japan
J Synchrotron Radiat 12:442-7. 2005..Experiments were performed to demonstrate the principle of the proposed scheme and the results have been found to be very promising...
- Structural changes of actin-bound myosin heads after a quick length change in frog skeletal muscleNaoto Yagi
Japan Synchrotron Radiation Research Institute, SPring 8, Kouto, Sayo gun, Hyogo
Biophys J 89:1150-64. 2005..2 nm(-1) are not readily explained by a simple axial swing of cross-bridges. Intensity changes of the actin-based layer lines at 1/36 and 1/5.9 nm(-1) are not explained by it either, suggesting a structural change in actin molecules...
- Localized morphometric deformations of small airways and alveoli in intact mouse lungs under quasi-static inflationToshihiro Sera
Japan Synchrotron Radiation Research Institute SPring 8 JASRI, SPring 8, 1 1 1, Kouto, Mikazuki, Sayo, Hyogo 679 5198, Japan
Respir Physiol Neurobiol 147:51-63. 2005..The volume behavior for the small airways was not similar to that of the lung volume. These results indicated that all airways did not behave homogenously...
- Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemiaTadashi Nakai
RIKEN Harima Institute at SPring 8, Mikazuki, Sayo, Hyogo, Japan
EMBO J 24:1523-36. 2005..These results provide insights into the molecular basis of nonketotic hyperglycinemia...
- Position and orientation of phalloidin in F-actin determined by X-ray fiber diffraction analysisToshiro Oda
Max Planck Institute for Medical Research, Department of Biophysics, Heidelberg, Germany
Biophys J 88:2727-36. 2005..The method of analysis developed in this study is applicable for the determination of binding positions of other drugs, such as jasplakinolide and dolastatin 11...
- X-ray structural study of noncrystalline regenerated Bombyx mori silk fibroinHiroyuki Saitoh
Institute of Materials Science, University of Tsukuba, Tsukuba 305 8573, Japan
Int J Biol Macromol 34:317-23. 2004..X-ray diffraction should be a useful technique to understand the structural characteristics of noncrystalline organic materials...
- EPR studies of 5-bromouracil crystal after irradiation with X rays in the bromine K-edge regionAkinari Yokoya
Synchrotron Radiation Research Center, Japan Atomic Energy Research Institute, Hyogo 679 5148, Japan
Radiat Res 162:469-73. 2004..EPR signals were not detectable with gamma irradiation at liquid nitrogen temperature...
- [Synchrotron X-ray small-angle scattering measurement]Tetsuro Fujisawa
Tanpakushitsu Kakusan Koso 49:1687-92. 2004
- A large-area CMOS imager as an X-ray detector for synchrotron radiation experimentsNaoto Yagi
SPring 8 JASRI, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5198, Japan
J Synchrotron Radiat 11:347-52. 2004..Its relatively low price (about 30,000 US dollars) makes it a unique option in the choice of detectors...
- Single- and double-strand breaks in solid pBR322 DNA induced by ultrasoft X-rays at photon energies of 388, 435 and 573 eVA Yokoya
Department of Synchrotron Radiation Research, Japan Atomic Energy Research Institute, Hyogo
J Radiat Res 40:145-58. 1999....