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Abstract: Magnetite, Fe(3)O(4), displays a highly complex low-temperature crystal structure that may be charge and orbitally ordered. Many of the recent experimental claims of such ordering rely on resonant soft x-ray diffraction at the oxygen K and iron L edges. We have reexamined this system and undertaken soft x-ray diffraction experiments on a high-quality single crystal. Contrary to previous claims in the literature, we show that the intensity observed at the Bragg forbidden (001/2)(c) reflection can be explained purely in terms of the low-temperature structural displacements around the resonant atoms. This does not necessarily mean that magnetite is not charge or orbitally ordered but rather that the present sensitivity of resonant soft x-ray experiments does not allow conclusive demonstration of such ordering.
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May 2009
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Diamond Proposal Number(s):
[316]
Open Access
Abstract: The mechanism by which nucleotide-binding domains (NBDs) of ABC transporters power the transport of substrates across cell membranes is currently unclear. Here we report the crystal structure of an NBD, FbpC, from the Neisseria gonorrhoeae ferric iron uptake transporter with an unusual and substantial domain swap in the C-terminal regulatory domain. This entanglement suggests that FbpC is unable to open to the same extent as the homologous protein MalK. Using molecular dynamics we demonstrate that this is not the case: both NBDs open rapidly once ATP is removed. We conclude from this result that the closed structures of FbpC and MalK have higher free energies than their respective open states. This result has important implications for our understanding of the mechanism of power generation in ABC transporters, because the unwinding of this free energy ensures that the opening of these two NBDs is also powered.
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Sep 2009
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Abstract: We use optical-pump terahertz-probe spectroscopy to investigate the near-threshold behavior of the photoinduced insulator-to-metal (IM) transition in vanadium dioxide thin films. Upon approaching Tc a reduction in the fluence required to drive the IM transition is observed, consistent with a softening of the insulating state due to an increasing metallic volume fraction (below the percolation limit). This phase coexistence facilitates the growth of a homogeneous metallic conducting phase following superheating via photoexcitation. A simple dynamic model using Bruggeman effective medium theory describes the observed initial condition sensitivity.
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Nov 2007
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Abstract: With one or two exceptions, biological materials are “soft”, meaning that they combine viscous and elastic elements. This mechanical behavior results from self-assembled supramolecular structures that are stabilized by noncovalent interactions. It is an ongoing and profound challenge to understand the self-organization of biological materials. In many cases, concepts can be imported from soft-matter physics and chemistry, which have traditionally focused on materials such as colloids, polymers, surfactants, and liquid crystals. Using these ideas, it is possible to gain a new perspective on phenomena as diverse as DNA condensation, protein and peptide fibrillization, lipid partitioning in rafts, vesicle fusion and budding, and others, as discussed in this selective review of recent highlights from the literature.
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May 2007
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Abstract: Over the past 30 years the literature has burgeoned with bioremediation approaches to heavy metal removal from wastes. The price of base and precious metals has dramatically increased. With the resurgence of nuclear energy uranium has become a strategic resource. Other ‘non-carbon energy’ technologies are driven by the need to reduce CO2 emissions. The ‘New Biohydrometallurgy’ we describe unites these drivers by the concept of conversion of wastes into new materials for environmental applications. The new materials, fashioned, bottom-up, into nanomaterials under biocontrol, can be termed ‘Functional Bionanomaterials’. This new discipline, encompassing waste treatment along with nanocatalysis or other applications, can be summarized as ‘Environmental Bionanotechnology’. Several case histories illustrate the scope and potential of this concept.
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May 2009
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Jan 2010
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Abstract: We show that double-resonance spectra recorded during the simultaneous absorption of x-ray and microwave (MW) photons are a fingerprint of the perturbed electronic configuration of atomic species driven to ferromagnetic resonance. X-ray absorption measurements performed as a function of x-ray energy and polarization over the Fe?L 2,3 edges of single-crystal yttrium-iron garnet reveal MW-induced multiplet features related to angular momentum transfer from the MW field to localized Fe?3d magnetic sublevels. O?K -edge absorption spectra demonstrate the formation of dynamic 2p -orbital magnetization components at O sites coupled to the Fe magnetic moments at tetrahedral and octahedral sites. These results are compared with double-resonance x-ray absorption spectra of Permalloy, showing that the MW transition probability is distributed according to the hybridization character of the 3d states and proportional to the unperturbed unoccupied magnetic density of states of metals and insulators.
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Jun 2009
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S.
Arai
,
I.
Yamato
,
A.
Saijo
,
Y.
Kakinuma
,
Y.
Ishizuka-katsura
,
M.
Toyama
,
T.
Terada
,
M.
Shirouzu
,
S.
Yokoyama
,
S.
Iwata
,
T.
Murata
Diamond Proposal Number(s):
[316]
Abstract: Enterococcus hirae vacuolar ATPase (V-ATPase) is composed of a soluble catalytic domain (V1; NtpA3-B3-D-G) and an integral membrane domain (V0; NtpI-K10) connected by a central and peripheral stalk(s) (NtpC and NtpE-F). Here we examined the nucleotide binding of NtpA monomer, NtpB monomer or NtpD-G heterodimer purified by using Escherichia coli expression system in vivo or in vitro, and the reconstitution of the V1 portion with these polypeptides. The affinity of nucleotide binding to NtpA was 6.6 ?M for ADP or 3.1 ?M for ATP, while NtpB or NtpD-G did not show any binding. The NtpA and NtpB monomers assembled into NtpA3-B3 heterohexamer in nucleotide binding-dependent manner. NtpD-G bound NtpA3-B3 forming V1 (NtpA3-B3-D-G) complex independent of nucleotides. The V1 formation from individual NtpA and NtpB monomers with NtpD-G heterodimer was absolutely dependent on nucleotides. The ATPase activity of reconstituted V1 complex was as high as that of native V1-ATPase purified from the V0V1 complex by EDTA treatment of cell membrane. This in vitro reconstitution system of E. hirae V1 complex will be valuable for characterizing the subunit-subunit interactions and assembly mechanism of the V1-ATPase complex.
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Dec 2009
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Abstract: X-ray crystallography is currently the most successful method for determining the three-dimensional structure of membrane proteins. Nevertheless, growing the crystals required for this technique presents one of the major bottlenecks in this area of structural biology. This is especially true for the alpha-helical type membrane proteins that are of particular interest due to their medical relevance. To address this problem we have undertaken a detailed analysis of the crystallization conditions from 121 alpha-helical membrane protein structures deposited in the Protein Data Bank. This information has been analyzed so that the success of different parameters can be easily compared for different membrane protein families. Concurrent with this analysis, we also present the new sparse matrix crystallization screen MemGold.
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Mar 2008
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Abstract: The self-assembly of PEGylated peptides containing a modified sequence from the amyloid beta peptide, FEK LVFF, has been studied in aqueous solution. PEG molar masses PEG1k, PEG2k, and PEG10k were used in the conjugates. It is shown that the three FFK LVFF-PEG hybrids form fibrils comprising a FFKLVFF core and a PEG corona. The beta-sheet secondary structure of the peptide is retained in the FFK LVFF fibril core. At sufficiently high concentrations, FEK LVFF-PEG1k and FEK LVFF-PEG2k form a nema tic phase, while PEG10k-FEK LVFF exhibits a hexagonal columnar phase. Simultaneous small angle neutron scattering/shear flow experiments were performed to study the shear flow alignment of the nematic and hexagonal liquid crystal phases. On drying, PEG crystallization occurs without disruption of the FFK LVFF beta-sheet structure leading to characteristic peaks in the X-ray diffraction pattern and FTIR spectra. The stability of beta-sheet structures was also studied in blends of FFKLVFF-PEG conjugates with poly(acrylic acid) (PAA). While PEG crystallization is only observed up to 25% PAA content in the blends, the FFK LVFF beta-sheet structure is retained up to 75% PAA.
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Jan 2010
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