1. SPring-8の現状／PRESENT STATUS OF SPring-8
Report of the Proposal Review Committee on the 14th Public Research Term 2004B
Interim Evaluation of Macromolecular Assemblies Beamline (BL44XU)
The Experiments in the 13th Research Period (2004A) at the Public Beamlines of SPring-8
Call for the Beam Time Application for the Public Beamlines at SPring-8
Call for the Beam Time Application for Nanotechnology Experiments
The Experiments in the 12th Research Period (2003B) at the Public Beamlines of SPring-8
Current Status of RIKEN Coherent Soft X-ray Spectroscopy Beamline (BL17SU)
Laser Electron Photons and Quark Nuclear Physics LEPS−BL33LEP−Pentaquark
愛媛大学 地球深部ダイナミクス研究センター Geodynamics Research Center, Ehime University
- Carbonates are important constituents of marine sediments and play an important role in the long-term recycling of carbon in the Earth’s deep interior via subduction of oceanic plates. We studied the stability of magnesite, the major carbonate in the mantle, by in situ X-ray diffraction measurements using a combination of laser-heated diamond anvil cell (LHDAC) and synchrotron radiation at BL10XU. We found that magnesite is stable at pressure up to ~115 GPa, at temperatures of ~ 2100 - 2200K, whereas it transforms to a new phase at higher pressures. The diffraction data of the new phase, magnesiteⅡ, are reasonably indexed on the basis of an orthorhombic system, yielding a density of 5.2 g/cm3 at 119 GPa, at room temperature. The present results suggest that magnesite and its high-pressure form are the major hosts for carbon throughout the most parts of the Earth’s lower mantle.
A Study of an Unusual Glass Prepared by the Containerless Method – Glass Formation at the Limit of Insufficient Network Formers –
（財）高輝度光科学研究センター 利用研究促進部門Ⅰ Materials Science Division, JASRI、日本原子力研究所 中性子利用研究センター Neutron Science Research Center, Japan Atomic Energy Research Institute、東京理科大学 基礎工学部 Faculty of Industrial Science and Technology, Tokyo University of Science
- Inorganic glasses normally exhibit a network of interconnected covalent-bonded structural elements that has no long-range order. In silicate glasses the network formers are based on SiO4-tetrahedra of which the interconnectivity is realized by sharing the oxygen atoms at the corners. Conventional wisdom then implies that alkaline and alkaline-earth orthosilicate materials cannot be vitrified because they do not contain sufficient network forming SiO2 to establish the needed interconnectivity. We have studied a bulk magnesium orthosilicate glass obtained by levitation melting- and-cooling. We find that the role of network former is largely taken on by corner- and edge-sharing ionic magnesium species that adopt 4-, 5- and 6-coordination with oxygen.
Study on Element-and Site-Specific Vibrational Densities of States Using Nuclear Resonant Inelastic Scattering
Role of Cyanobacterial Circadian Clock Protein KaiA as Revealed by Crystal Structure
名古屋大学 遺伝子実験施設 Center for Gene Research, Nagoya University、京都大学大学院 薬学研究科 Graduate School of Pharmaceutical Sciences, Kyoto University、京都大学大学院 薬学研究科 Graduate School of Pharmaceutical Sciences, Kyoto University、名古屋大学 遺伝子実験施設 Center for Gene Research, Nagoya University
- KaiA, KaiB, and KaiC constitute the circadian clock machinery in cyanobacteria. KaiA activates kaiBC expression while KaiC represses it. Here we demonstrated that KaiA is composed of three functional domains : the N-terminal amplitude-amplifier domain, the central period-adjuster domain, and the C-terminal clock-oscillator domain. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation, and generating circadian oscillations. The 1.8 Å X-ray crystal structure of the C-terminal clock-oscillator domain of KaiA from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 shows that residue His270, located at the center of a KaiA dimer concavity, is essential to KaiA function. KaiA binding to KaiC likely occurs via the concave surface. Based on the structure, we could predict the structural roles of the residues that affected circadian oscillations.
3. 最近の研究から／FROM LATEST RESEARCH
Crystal Structures of Bacterial Lipoprotein Localization Factors, LolA and LolB
理化学研究所 播磨研究所 Harima Institute, RIKEN、京都大学 大学院理学研究科 Graduate School of Science, Kyoto University
- Five Lol proteins are involved in the lipoprotein transport in Gram-negative bacteria. Crystal structures of a lipoprotein-specific periplasmic chaperone, LolA, and an outer membrane lipoprotein receptor, LolB from Escherichia coli were determined using diffraction data collected at the beamlines of SPring-8. Despite their dissimilar amino acid sequences (identity ~ 8%), the structures of LolA and LolB are strikingly similar to each other. Both have a hydrophobic cavity consisting of an unclosed β-barrel and an α-helical lid. The cavity represents a possible binding site for the lipid moiety of lipoproteins. However, the structural differences in size and shape of hydrophobic inner spaces between LolA and LolB are highly connected to the functional differences between two proteins. Furthermore, these structural differences between two proteins provide significant insights into the molecular mechanisms underlying the energy-independent transfer of lipoproteins from LolA to LolB, and from LolB to the outer membrane.
The Precise Structure Determination of High Performance Thermoelectric Material, Zn4Sb3, by Synchrotron Powder Diffraction.
名古屋大学 工学研究科 Department of Applied Physics, Nagoya University
- The precise crystal structure of Zn4Sb3, which is one of the most efficient thermoelectric materials, has been determined by combination of Maximum Entropy Method and Rietveld analysis using synchrotron-radiation powder diffraction at SPring-8. The structure contains significant disorder with zinc atoms distributed over multiple positions. The crystal structure of Zn4Sb3 in present study allows a general explanation of the electric transport properties which explains the remarkable thermoelectric figure of merit.
− 超伝導から量子コンピュータまで −
Possibility of New Nano Devices Using Nano Clusters Colored by Silicon Isotopes
−From Superconductors to Quantum Computers −
大阪市立大学大学院 理学研究科 Graduate School of Science, Osaka City University、慶應義塾大学 理工学部 Faculty of Science and Technology, Keio University、名古屋大学大学院 工学研究科 Graduate School of Engineering, Nagoya University、広島大学大学院 工学研究科 Graduate School of Engineering, Hiroshima University
- VIth group elements like C, Si, Ge and Sn make clusters consisting of pentagonal and/or hexagonal plolyhedra. A avarious crystals having hierachical structure can be constructed on a basis of these clusters. Recent strong demand from the field of isotope engineering for semiconductors has spurred on efforts that have led to the successful separation of stable Si isotopes. The combination of nano clusters and pure isotopes may open a new field of materials science. The present paper describnes, as such examples, the clarification of superconducting mechanism of the first discovered silicon-network Si46 superconductor. An approach of all silicon quantum computors using 28Si isotope is also demonstrated.
− 単結晶窒化ガリウム育成の新手法 −
Congruent Melting of Gallium Nitride at High Pressure and Its Application to Single Crystal Growth
日本原子力研究所 関西研究所 放射光科学研究センター Synchrotron Radiation Research Center, Kansai Research Establishment, JAERI、スプリングエイトサービス㈱ SPring-8 Service Co., Ltd
- The decomposition and melting behaviors of GaN under high pressures and temperatures were studied by in situ x-ray diffraction experiments using a large volume multi-anvil high-pressure apparatus at beamline BL14B1. GaN decomposed into Ga melt and N2 at lower pressures than 5.5 GPa. At pressures above 6.0 GPa, however, congruent melting of GaN occurred around 2220 ℃, and decreasing the temperature allowed the GaN melt to crystallize to the original structure. Single crystals of GaN were formed by cooling the melt slowly under high pressures and were recovered at ambient conditions. The present results have great potential in providing high quality bulk single crystals of GaN, which are desirable substrates for fabricating optoelectronic devices.
大阪大学 蛋白質研究所 Institute for Protein Research, Osaka University
- The photosynthetic unit of oxygenic photosynthesis is organized as two large multimolecular membrane complexes, photosystem II (PSII) and photosystem I (PSI). The two photosystems operate in series linked by a third multiprotein complex called the cytochrome b6f complex. The cytochrome b6f complex is a membrane-spanning protein complex embedded in a thylakoide membrane of photosynthetic organisms. The b6f complex arranges the electron transfer between plastoquinol reduced by PSII and an electron carrier protein plastocyanin that connects to PSI. The structure of the b6f complex from cyanobacterium M. laminosus was solved at 3.0 Å resolution by isomorphous replacement method and multiwavelength anomalous diffraction from native iron atoms. The crystal structures of the cytochrome b6f complex complete the description of the architecture of the oxygenic photosynthetic electron transport chain, since three-dimensional structures have been provided for two photosystems.
Activities of the SPring-8 Advisory Committee and the Others in the 2003 Fiscal Year
Proton Pumping Mechanism of Bovine Heart Cytochrome c Oxidase
– X-ray Crystallographical, Molecular Biological and Infrared Spectroscopical Analyses
兵庫県立大学大学院 生命理学研究科 Graduate School of Life Science, University of Hyogo
- Improved X-ray structures of bovine heart cytochrome c oxidase (at 1.8/1.9 Å resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme (heme a) drives the active proton transport from the interior of the mitochondria to Asp51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of heme a, suggests that the channel functions as an effective proton collecting region. The Asp51Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Infrared results indicate that the conformation of Asp51 is controlled only by the oxidation state of heme a. These results indicate that heme a drives the proton pumping process.
Compaction and Structure Formation of Proteins Revealed by Time-Resolved Small Angle X-ray Scattering
大阪大学 蛋白質研究所 Institute for Protein Research, Osaka University、京都大学大学院 工学研究科 Graduate School of Engineering, Kyoto University、（独）理化学研究所 播磨研究所 Harima Institute, RIKEN
- The compaction process in protein folding has not been characterized well due to experimental difficulties. The submillisecond-resolved observation system for small-angle X-ray scattering was developed and applied for the process of apomyoglobin folding. It was demonstrated that the secondary and tertiary structures are largely organized cooperatively; however, the initial folding phase involves a significant collapse of their main chain structures. A common folding mechanism was proposed, in which hydrophobic environments realized by the initial collapse prompts the subsequent formation of helical structures.
Elucidation of the Crystal Structure of the PsbP Protein Involved in the Oxygen Evolution in Photosynthesis
京都大学大学院 生命科学研究科／（独）理化学研究所 播磨研究所 Graduate School of Biostudies, Kyoto University / Harima Institute, RIKEN
- Photosynthesis is a multi-step reaction that utilizes light energy to convert carbon dioxide into sugar and generate oxygen as by-product. The first step of photosynthesis is the oxygen-evolving reaction performed by the protein-pigment complex called “photosystem II”, and PsbP is one of the protein subunits constituting photosystem II. Since PsbP exists only in higher plants and green algae, its existence has been the subject of inquiry in the process of plant evolution. In order to elucidate the origin and function of PsbP from its 3D structure, a high-resolution analysis based on multiple wavelength anomalous dispersion method using the X-ray of SPring-8 was conducted. The result showed that the structure of PsbP was not similar to any known structures in photosystem II from cyanobacteria, primitive organisms doing oxygenic photosynthesis. This research shows one aspect of the evolution of oxygenic photosynthetic organisms.
Meeting on the Results of FY2003 Research Activities by Synchrotron Radiation Research Group of the Nano Technology Researchers Project, MEXT
4. 研究会等報告／WORKSHOP AND COMMITTEE REPORT
RIKEN/BBSRC Joint Symposium : Japan-UK Membrane Protein Structure Biology
−Towards High-throughput Membrane Protein Crystallography and Related Technology−
JAERI International Workshop on“X-Ray Scattering and Electronic Structure”
Joint Workshop by SPring-8 Beamlines and Research Subgroups ;
“X-ray Inelastic Scattering and Materials Science II”
Report of the Joint Symposium on the 17th Annual Meeting of Japan Synchrotron Radiation Society and Synchrotron Radiation Science
26th International Free-Electron Laser Conference and 11th FEL User-Workshop (FEL2004)
5. 談話室・ユーザー便り／OPEN HOUSE･A LETTERS FROM SPring-8 USERS
The 12th SPring-8 Open House -SPring-8 Never Fails to Bring us a Refreshing Surprise!-
“HANDY TIPS AROUND HARIMA SCIENCE GARDEN CITY” will be separately bound from the September 2004 issue (No.5, Vol.9)