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Abstract: Hydrophilic carotenoids, unusual members of an intrinsically hydrophobic family, and their radical ions are important reactants. An all-optical method for generating singly charged radical ions of a hydrophilic carotenoid (Car) is described. It relies on photolyzing an aqueous mixture of Car and a photoionizable auxiliary solute (A), and making conditions conducive to the capture, by Car, of the hydrated electron (e?aq) or the positive hole in A?+ or both. When A is Trolox (TOH), only e?aq can be captured, since TOH?+ deprotonates too rapidly to be a hole donor; when A is Trolox methyl ether (TOMe), both Car?? and Car?+ are formed, since TOMe?+ lives long enough to transfer its positive hole to Car; formation of Car?? is prevented under aerobic conditions.
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Aug 2009
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Abstract: Bacteria are abundant in many natural and engineered environments where they are thought to exert important controls on the cycling, mobility, bioavailability, and toxicity of metal contaminants. In order to probe their role in moderating the behavior of lanthanides, pH-dependent adsorption edges of 13 individual lanthanides and yttrium to the Gram-negative bacterium Pantoea agglomerans were used to generate discrete site surface complexation constants. The calculated surface complexation constants were compared with stability constants estimated using linear free energy relationships based on a number of hydroxyl-containing ligands. The experimental data suggests that lanthanide adsorption edges below pH 6.5 are consistent with adsorption to phosphate groups for the light and some of the middle lanthanides (La to Gd), whereas some of the middle and heavy lanthanides appear to favor carboxyl co-ordination (Tb to Yb), although exceptions occur in each grouping. The experimentally derived surface complexation constants for carboxyl coordination were of similar magnitude to stability constants estimated from linear free energy correlations using fulvic acid stability constants. The implication is that the adsorption of lanthanides to bacterial surfaces could be modeled reasonably well using lanthanide stability constants for natural organic matter, except perhaps at low pH where phosphate binding dominates.
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Jan 2010
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Abstract: This study was designed to combine surface complexation modelling of macroscopic adsorption data with X-ray Absorption Spectroscopic (XAS) measurements to identify lanthanide sorption sites on the bacterial surface. The adsorption of selected representatives for light (La and Nd), middle (Sm and Gd) and heavy (Er and Yb) lanthanides was measured as a function of pH, and biomass samples exposed to 4 mg/L lanthanide at pH 3.5 and 6 were analysed using XAS. Surface complexation modelling was consistent with the light lanthanides adsorbing to phosphate sites, whereas the adsorption of middle and heavy lanthanides could be modelled equally well by carboxyl and phosphate sites. The existence of such mixed mode coordination was confirmed by Extended X-ray Absorption Fine Structure (EXAFS) analysis, which was also consistent with adsorption to phosphate sites at low pH, with secondary involvement of carboxyl sites at high adsorption density (high pH). Thus, the two approaches yield broadly consistent information with regard to surface site identity and lanthanide coordination environment. Furthermore, spectroscopic analysis suggests that coordination to phosphate sites is monodentate at the metal/biomass ratios used. Based oil the best-fitting pK(a) site, we infer that the phosphate sites are located on N-acetylglucosamine phosphate, the most likely polymer on gram-negative cells with potential phosphate sites that deprotonate around neutral pH.
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Jan 2009
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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: The first layered iron borate, Fe5O5(B6O10(OH)(3)] center dot nH(2)O, has been prepared by the boric acid flux method, Its structure, determined by single crystal X-ray diffraction, contains a double FeO6-octahedral layer and an unusual [B6O13] chain. The rigid and cambered [B6O13] Chains bend the octahedral layers, resulting in a wave-like and sandwiched structure. Crystallographic study indicates the structural modulation is mainly from the [B6O13] chains because of the insertion of water molecules in between. Nevertheless, FeO6 layers in the average structure, which are well separated by borate chains, is still a reasonable model to understand the two-dimensional magnetism. The strong antiferromagnetic interactions and the complex Fe3+-net suggest a possible geometrically magnetic frustration, which may be the reason for the second-order temperature-induced magnetic transition at similar to 125 K. The condensed Fe3+ layers and the relatively low redox potential at about 1.25 V versus Li+/Li show its potentials as an anodic material.
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Oct 2009
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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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Simone
Weyand
,
Tatsuro
Shimamura
,
Shunsuke
Yajima
,
Shunichi
Suzuki
,
Osman
Mirza
,
Kuakarun
Krusong
,
Liz
Carpenter
,
Nicholas G.
Rutherford
,
Jonathan M.
Hadden
,
John
O'reilly
,
Pikyee
Ma
,
Massoud
Saidjam
,
Simon G.
Patching
,
Ryan J.
Hope
,
Halina T.
Norbertczak
,
Peter C. J.
Roach
,
So
Iwata
,
Peter J. F.
Henderson
,
Alexander D.
Cameron
Diamond Proposal Number(s):
[456]
Abstract: The nucleobase–cation–symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuTAa and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.
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Oct 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: 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: We present the design of a synchrotron x-ray beamline (BL-I11) dedicated to powder diffraction experiments, currently under construction at Diamond Light Source (DLS). An in-vaCLIurn Lindulator will provide an intense and highly collimated x-ray Source and with the necessary optics, a high purity beam of low energy-bandpass x-rays in the range 5-30 keV will be delivered at the sample. The diffraction instrument is designed to have the flexibility to house a variety of sample environments and to have two detection systems to collect high quality diffraction data, i.e. multi-analysing crystals for high angular resolution experiments and a fast position sensitive detector for tirne-resolved studies. BL-I11 will be a powerful state-of-the-art dedicated user facility for high resolution (d-space and time) powder diffraction studies of polycrystalline materials under ambient and non-ambient conditions.
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Nov 2007
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