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Abstract: Nipah and Hendra viruses are emergent paramyxoviruses, causing disease characterized by rapid onset and high mortality rates, resulting in their classification as Biosafety Level 4 pathogens. Their attachment glycoproteins are essential for the recognition of the cell-surface receptors ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3). Here we report crystal structures of both Nipah and Hendra attachment glycoproteins in complex with human EFNB2. In contrast to previously solved paramyxovirus attachment complexes, which are mediated by sialic acid interactions, the Nipah and Hendra complexes are maintained by an extensive protein-protein interface, including a crucial phenylalanine side chain on EFNB2 that fits snugly into a hydrophobic pocket on the viral protein. By analogy with the development of antivirals against sialic acid binding viruses, these results provide a structural template to target antiviral inhibition of protein-protein interactions.
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Jan 2008
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Abstract: The polydentate ligand 2,4,6-tris(dipyridin-2-ylamino)-1,3,5-triazine (dpyatriz) in combination with the Cu(ClO4)2/CuX2 salt mixtures (X? = Cl?, Br?, or N3?) leads to the formation of molecular coordination aggregates with formulas [Cu3Cl3(dpyatriz)2](ClO4)3 (2), [Cu3Br3(dpyatriz)2](ClO4)3 (3), and [Cu4(N3)4(dpyatriz)2(DMF)4(ClO4)2](ClO4)2 (4). These complexes consist of two dpyatriz ligands bridged via coordination to CuII and disposed either face-to-face in an eclipsed manner (2 and 3) or parallel and mutually shifted in one direction. The copper ions complete their coordination positions with Cl? (2), Br? (3), or N3?, ClO4?, and N,N-dimethylformamide (DMF) (4) ligands. All complexes crystallize together with noncoordinate ClO4? groups that display anion···? interactions with the triazine rings. These interactions have been studied by means of high level ab initio calculations and the MIPp partition scheme. These calculations have proven the ClO4?···[C3N3] interactions to be favorable and have revealed a synergistic effect from the combined occurrence of ??? stacking of triazine rings and the interaction of these moieties with perchlorate ions, as observed in the experimental systems.
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May 2008
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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: 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: The Solar system as we know it formed some 4.5 billion years ago. Our understanding of the timescales of planet formation, the material make-up of the Earth, and deep planetary processes has improved dramatically with advances in several broad, largely separate, areas of science - cosmochemistry, extreme conditions and seismology, and the simulation of planetary growth and mixing. This issue brings together scientists from all disciplines in order to reconcile views on the internal structure and early chemical evolution of the Earth and the relationship with the formation of the moon.
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Nov 2008
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Abstract: The development of the capability to engineer the surface properties of materials to match specific requirements demands high quality surface characterization techniques. The ideal tool should provide chemically specific structural characterization as well as surface sensitivity and depth profiling. Ideally the characterization method should also be applicable to systems both with and without long range order. X-ray absorption spectroscopy fine structure, when using the standard transmission detection system, provides all this information with the significant exception of surface sensitivity. In contrast, by detecting the reflected instead of the transmitted beam, it encompasses all these requirements because when the incident beam impinges onto a sample surface at glancing angles, in conditions close to the total reflection, only the outermost regions of the system under study are sampled. Such a technique provides information about the local structure as a function of depth as well as thin layer structure in the case of layered samples. Although it is potentially the ideal tool to study surface modified materials, experimental difficulties have hampered its widespread use in the fields of surface and materials sciences. As a solution to the experimental challenges, we provide a detailed description of an appropriate experimental station, the sample requirements, the measuring protocols, and software routines needed to optimize the collection of the data. To illustrate the capabilities of the technique the results obtained for a model multilayer sample are presented and analyzed under the total external reflection approximation.
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Jan 2007
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Abstract: Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus (bsh2) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius, may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.
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Sep 2009
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Abstract: Signal-regulatory protein alpha (SIRP alpha) is a myeloid membrane receptor that interacts with the membrane protein CD47, a marker of self. We have solved the structure of the complete extracellular portion of SIRP alpha, comprising three immunoglobulin superfamily domains, by x-ray crystallography to 2.5 Å resolution. These data, together with previous data on the N-terminal domain and its ligand CD47 (possessing a single immunoglobulin superfamily domain), show that the CD47-SIRP alpha interaction will span a distance of around 14 nm between interacting cells, comparable with that of an immunological synapse. The N-terminal (V-set) domain mediates binding to CD47, and the two others are found to be constant (C1-set) domains. C1-set domains are restricted to proteins involved in vertebrate antigen recognition: T cell antigen receptors, immunoglobulins, major histocompatibility complex antigens, tapasin, and beta2-microglobulin. The domains of SIRP alpha (domains 2 and 3) are structurally more similar to C1-set domains than any cell surface protein not involved in antigen recognition. This strengthens the suggestion from sequence analysis that SIRP is evolutionarily closely related to antigen recognition proteins.
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Jul 2009
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Abstract: The high-pressure evolution of the cubic perovskite NH4MnCl3 has been studied in the 0-6 GPa range by angle-dispersive x-ray diffraction. A structural phase transition has been found at low pressure (P-C= 0.4 GPa), in agreement with previous reports. The high-pressure phase has been refined in the tetragonal P4/mbm and orthorhombic Pbnm space groups. In either case, the structure can be described in terms of a tilted perovskite model (one tilt a(0)a(0)c(+) and two tilts a(+)b(-)b(-), respectively). The average tilting under pressure has been estimated from the lattice parameters. The P-V relation has been fitted by a Murnaghan Equation-of-State with K-0=29(2) GPa and K-0'=9(1).
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Mar 2010
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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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