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Abstract: There has been great interest recently in peptide amphiphiles and block copolymers containing biomimetic peptide sequences due to applications in bionanotechnology. We investigate the self-assembly of the peptide-PEG amphiphile FFFF-PEG5000 containing the hydrophobic sequence of four phenylalanine residues conjugated to PEG of molar mass 5000. This serves as a simple model peptide amphiphile. At very low concentration, association of hydrophobic aromatic phenylalanine residues occurs, as revealed by circular dichroism and UV/vis fluorescence experiments. A critical aggregation concentration associated with the formation of hydrophobic domains is determined through pyrene fluorescence assays. At higher concentration, defined ?-sheets develop as revealed by FTIR spectroscopy and X-ray diffraction. Transmission electron microscopy reveals self-assembled straight fibril structures. These are much shorter than those observed for amyloid peptides, the finite length may be set by the end cap energy due to the hydrophobicity of phenylalanine. The combination of these techniques points to different aggregation processes depending on concentration. Hydrophobic association into irregular aggregates occurs at low concentration, well-developed ?-sheets only developing at higher concentration. Drying of FFFF-PEG5000 solutions leads to crystallization of PEG, as confirmed by polarized optical microscopy (POM), FTIR and X-ray diffraction (XRD). PEG crystallization does not disrupt local ?-sheet structure (as indicated by FTIR and XRD). However on longer lengthscales the ?-sheet fibrillar structure is perturbed because spherulites from PEG crystallization are observed by POM.
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May 2009
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Abstract: We measured coherent x-ray diffraction (CXD) on zeolite microcrystals in order to gain information on internal density distribution and to learn more about the strain developed during the synthesis and attachment process on the substrate. From the distortion and asymmetry of the diffraction pattern on the (020) Bragg peak, the strain field distribution is estimated. We inverted the diffraction patterns from a less strained crystal to obtain the three-dimensional image of the shape and internal strain fields using the error reduction and hybrid input–output phase retrieval algorithms. We also show a few examples of characteristic distortion modes relevant to CXD of zeolites.
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Mar 2010
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Abstract: NGFI-B is a ligand-independent orphan nuclear receptor of the NR4A subfamily that displays important functional differences with its homolog Nurr1. In particular, the NGFI-B ligand-binding domain (LBD) exhibits only modest activity in cell lines in which the Nurr1 LBD strongly activates transcription. To gain insight into the structural basis for the distinct activation potentials, we determined the crystal structure of the NGFI-B LBD at 2.4-Å resolution. Superimposition with the Nurr1 LBD revealed a significant shift of the position of helix 12, potentially caused by conservative amino acids exchanges in helix 3 or helix 12. Replacement of the helix 11–12 region of Nurr1 with that of NGFI-B dramatically reduces the transcriptional activity of the Nurr1 LBD. Similarly, mutation of Met414 in helix 3 to leucine or of Leu591 in helix 12 to isoleucine (the corresponding residues found in NGFI-B) significantly affects Nurr1 transactivation. In comparison, swapping the helix 11–12 region of Nurr1 into NGFI-B results in a modest increase of activity. These observations reveal a high sensitivity of LBD activity to changes that influence helix 12 positioning. Furthermore, mutation of hydrophobic surface residues in the helix 11–12 region (outside the canonical co-activator surface constituted by helices 3, 4, and 12) severely affects Nurr1 transactivation. Together, our data suggest that a novel co-regulator surface that includes helix 11 and a specifically positioned helix 12 determine the cell type-dependent activities of the NGFI-B and the Nurr1 LBD.
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Feb 2005
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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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Abstract: The crystal structure of VEGF-E was solved by the sulfur single-wavelength anomalous dispersion method (S-SAD) using highly redundant low-resolution data collected at a wavelength of 1.7 Å with an estimated anomalous signal of 1.5%. 11 sulfur sites, nine out of 16 disulfide bonds and two out of 12 methionines could be located in the asymmetric unit using data truncated at a resolution of 4.1 Å; however, none of the common diffraction data-quality indicators for SAD allowed clear discrimination between successful and unsuccessful resolution cutoffs. The high solvent content of 75% allowed efficient density modification to be performed and an unbiased electron-density map of good quality to be generated. This study demonstrates the strength of S-¬SAD for phasing using accurate highly redundant data at low resolution.
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Nov 2006
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Abstract: By cunningly diffracting X-rays twice from an exploding nanometre-scale sphere, holographic images can be made of a tiny system evolving at lightning speed. The technique could be used to picture atomic dynamics.
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Aug 2007
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Abstract: We report on the capillary flow behaviour of thermotropic liquid crystal mixtures containing 4-n-octyl-4?-cyanobiphenyl (8CB) and 4-n-pentyl-4?-cyanobiphenyl (5CB). The liquid crystal mixtures are studied in the Nematic (N) and Smectic (SA) phases at room temperature. Polarised optical microscopy (POM), rheology and simultaneous X-ray diffraction (XRD)/capillary flow experiments are performed to characterise the system.
Polarised optical microscopy reveals a dramatic change in optical texture when the 5CB content is increased from 20 to 30% in the mixtures. X-ray diffraction results show that the system goes through a SA–N phase transition, such that the mixtures are smectic for 10–20% 5CB and nematic for 30–90% 5CB. Smectic mixtures flow with the layers aligned along the flow direction (mesogens perpendicular to flow) while nematic mixtures flow with the mesogens aligned in the flow direction. Simultaneous XRD/shear flow experiments show that the SA–N transition is independent of the flow rate in the range 1–6 ml min?1.
The correlation length of the liquid crystal order decreases with increasing 5CB content. Rheology is used to prove that the correlation length behaviour is related to a reduction in the viscosity of the mixture.
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Apr 2009
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Abstract: Bacillus anthracis, the causative agent of anthrax, has been targeted by the Oxford Protein Production Facility to validate high-throughput protocols within the Structural Proteomics in Europe project. As part of this work, the structures of an alanine racemase (BA0252) in the presence and absence of the inhibitor (R)-1-aminoethylphosphonic acid (L-Ala-P) have determined by X-ray crystallography to resolutions of 2.1 and 1.47 Å, respectively. Difficulties in crystallizing this protein were overcome by the use of reductive methylation. Alanine racemase has attracted much interest as a possible target for anti-anthrax drugs: not only is D-alanine a vital component of the bacterial cell wall, but recent studies also indicate that alanine racemase, which is accessible in the exosporium, plays a key role in inhibition of germination in B. anthracis. These structures confirm the binding mode of L-Ala-P but suggest an unexpected mechanism of inhibition of alanine racemase by this compound and could provide a basis for the design of improved alanine racemase inhibitors with potential as anti-anthrax therapies.
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Apr 2008
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Abstract: Context. Silicate dust grains exist in a wide range of astronomical environments and understanding the effect of these on grain structure is of great interest, particularly the effect of thermal annealing on amorphous silicates as a possible route to the formation of crystalline grains. Although laboratory simulations have largely focussed on IR-spectroscopic measurements, since these relate directly to observational data, laboratory synchrotron techniques such as X-ray absorption spectroscopy (XAS) and X-ray scattering are becoming increasingly routine in the analysis of recovered materials. With the increasing prospect of performing astronomical XAS observations, there is much to be gained from applying these techniques to laboratory analogues.
Aims. Diagnostic markers for medium-range order and the effect of thermal annealing on these in amorphous silicates of differing Mg content are characterised using synchrotron X-ray methods.
Methods. Three synthetic amorphous silicates with high, medium and low Mg:Si ratios were annealed at varying temperatures up to 1300 K. X-ray Absorption Near Edge Structure (XANES) spectra at the Si and Mg K-shell absorption edges and X-ray scattering patterns for low values of the X-ray scattering wavevector were recorded for these along with comparative data for commercially produced amorphous SiO2 and mineral samples of forsterite, enstatite and quartz.
Results. XANES features due to short- and medium-range structure are identified at both Mg and Si edges and a new temperature dependent behaviour observed in the medium-range structure surrounding Mg and Si. Based on changes to the morphological details of the XANES spectra, the medium-range structure changes between an enstatite-like and forsterite-like coordination with increasing temperature and appears to correlate directly with Mg content. Low wavevector X-ray scattering features were also found to be diagnostic of the type of medium-range structural ordering. However, these features depend on whether the relative arrangement of clusters of medium-range structure exhibit semi-periodic ordering over the longer-range, which can vary with annealing.
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Jun 2008
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Abstract: New World arenaviruses, which cause severe hemorrhagic fever, rely upon their envelope glycoproteins for attachment and fusion into their host cell. Here we present the crystal structure of the Machupo virus GP1 attachment glycoprotein, which is responsible for high-affinity binding at the cell surface to the transferrin receptor. This first structure of an arenavirus glycoprotein shows that GP1 consists of a novel alpha/beta fold. This provides a blueprint of the New World arenavirus attachment glycoproteins and reveals a new architecture of viral attachment, using a protein fold of unknown origins.
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Jan 2009
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