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Open Access
Abstract: The transient complex between cytochrome f and plastocyanin from the cyanobacterium Nostoc sp. PCC 7119 has been analysed by X-ray Absorption Spectroscopy in solution, using both proteins in their oxidized and reduced states. Fe K-edge data mainly shows that the atypical metal coordination geometry of cytochrome f, in which the N-terminal amino acid acts as an axial ligand of the heme group, remains unaltered upon binding to its redox partner, plastocyanin. This fact suggests that cytochrome f provides a stable binding site for plastocyanin and minimizes the reorganization energy required in the transient complex formation, which could facilitate the electron transfer between the two redox partners.
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Jan 2007
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Abstract: We use thermal diffuse scattering of x rays to visualize the lens-shaped portions of the Fermi surface in metallic zinc. Our interpretation of the nature of the observed scattered intensity anomalies is supported by the incorporation of inelastic x-ray scattering measurements as well as ab initio calculations of the electronic structure and lattice dynamics. Our work demonstrates that thermal diffuse scattering complements well-established techniques and is a powerful tool in its own right for studying the shape of the Fermi surface through the associated electron-phonon coupling.
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Aug 2009
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Jan 2008
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Abstract: For the initiation of DNA replication, dsDNA is unwound by helicases. Primases then recognize specific sequences on the template DNA strands and synthesize complementary oligonucleotide primers that are elongated by DNA polymerases in leading- and lagging-strand mode. The bacterial plasmid RSF1010 provides a model for the initiation of DNA replication, because it encodes the smallest known primase RepB? (35.9 kDa), features only 1 single-stranded primase initiation site on each strand (ssiA and ssiB, each 40 nt long with 5?- and 3?-terminal 6 and 13 single-stranded nucleotides, respectively, and nucleotides 7–27 forming a hairpin), and is replicated exclusively in leading strand mode. We present the crystal structure of full-length dumbbell-shaped RepB? consisting of an N-terminal catalytic domain separated by a long ?-helix and tether from the C-terminal helix-bundle domain and the structure of the catalytic domain in a specific complex with the 6 5?-terminal single-stranded nucleotides and the C7–G27 base pair of ssiA, its single-stranded 3?-terminus being deleted. The catalytic domains of RepB? and the archaeal/eukaryotic family of Pri-type primases share a common fold with conserved catalytic amino acids, but RepB? lacks the zinc-binding motif typical of the Pri-type primases. According to complementation studies the catalytic domain shows primase activity only in the presence of the helix-bundle domain. Primases that are highly homologous to RepB? are encoded by broad-host-range IncQ and IncQ-like plasmids that share primase initiation sites ssiA and ssiB and high sequence identity with RSF1010.
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Apr 2009
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Abstract: We show that Fe nanoislands capped with Al, Pd, and Pt protecting layers include an alloy at the interface with the capping layer, which explains the previously known capping layer dependence on the interparticle magnetic coupling. Vibrating sample magnetometry results, for instance, are evidencing a reduction in the magnetization measured under a magnetic field of 15 mT, which is larger in the case of the Al capping and which is due to the presence of a magnetically dead interface alloy. This reduction is also observed at the atomic level using x-ray magnetic circular dichroism measurements, showing a capping layer dependence of the Fe magnetic-moment reduction that is similar for the Pd and Pt capping, and stronger for the Al capping. The trend in the magnetic properties as a function of the capping layer is explained in the light of x-ray photoemission spectroscopy results that evidence the formation of alloys at the interface between the Fe nanoislands and the capping layers. The present results highlight the strong influence of interface alloying in systems of reduced dimensionality. In particular, it is shown that the magnetic properties are strongly affected at both the atomic and macroscopic level.
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Jan 2008
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Abstract: We report a thermodynamic investigation of the adsorption of saturated and unsaturated (cis- and trans-) alkyl amides onto the surface of graphite from their pure liquids and from binary mixtures. We identify the formation of solid monolayers of the amides at temperatures when the bulk materials are liquid. The extent of this presolidification is much more extensive than other related materials, indicating that these amide layers are significantly more stable. The monolayer stability is found to be greatest for saturated amides. In addition, the stability of unsaturated amides is extremely sensitive to the location of the double bonds in the alkyl chain of the molecules, and trans isomers are found to be more stable than cis. We also address the preferential adsorption and mixing behavior of amide mixtures and amides mixed with other species coadsorbed onto graphite from binary solution. The results indicate that the amide molecules appear to be adsorbed with their principal axis parallel to the graphite surface and that amides are found to be strongly preferentially adsorbed with respect to alkanes. Interestingly the amides appear to mix rather better than might have been expected. There is also evidence of a number of other transitions in the adsorbates.
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Feb 2008
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Abstract: Medium energy ion scattering has been used to investigate the possible interdiffusion of Co and V at the Co/V interface in the Co/V/MgO(1 0 0) system at room temperature and after annealing in the temperature range from 100 to 500 °C. The Co and V composition and structure as a function of depth has been studied using two-dimensional maps of the scattered ion energy versus scattering angle and with the corresponding projections onto the angle axis over a small energy range (angle spectrum) and onto the energy axis over a small scattering angle range (energy spectrum). At room temperature only limited interdiffusion at the Co/V interface can be inferred from the analysis of the experimental data, while at 300 °C and higher drastic changes are observed at the Co/V interface in terms of sharpness and composition. Furthermore, a structural change is observed after annealing at 500 °C as a consequence of the V and/or Co interdiffusion.
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Jan 2008
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Abstract: An experimental setup has been developed to perform soft x-ray coherent scattering at beamline ID08 of the European Synchrotron Radiation Facility. An intense coherent beam was obtained by filtering the primary beam with the monochromator and a circular pinhole. A pinhole holder with motorized translations was installed inside the UHV chamber of the diffractometer. The scattered intensity was recorded in reflection geometry with a back-illuminated charge coupled device camera. As a demonstration we report experimental results of resonant magnetic scattering using coherent beam. The degree of coherence is evaluated, and it is shown that, while the vertical coherence is much higher than the horizontal one at the source, the situation is reversed at the diffractometer. The intensity of the coherent beam is also discussed.
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Sep 2007
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Abstract: The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeon Methanothermobacter thermautotrophicus is described at 2.65 angstrom resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme.
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May 2010
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Abstract: The adsorption behaviour of Fe on the tenfold surface of the decagonal quasicrystal Al72.6Ni10.5Co16.9 has been studied using scanning tunnelling microscopy, low energy electron diffraction (LEED), Auger electron spectroscopy (AES) and x-ray magnetic circular dichroism (XMCD). The results show the growth of a disordered film up to a coverage of 9 MLE (monolayer equivalent) after which polycrystalline island growth is observed. These islands are interconnected, and the LEED pattern indicates that they preferentially align along five directions. The AES results indicate that the film is composed of Fe intermixed with the substrate elements. The XMCD results point to an induced magnetic moment for Co and Ni in the intermixed layer/interface region.
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Jan 2008
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