Expression of the hepatitis C virus structural proteins in mammalian cells induces morphology similar to that in natural infection

Like many positive-strand RNA viruses, replication of the hepatitis C virus (HCV) is associated with cytoplasmic membrane rearrangements. However, it is unclear which HCV Proteins induce these ultrastructural features. This work examined the morphological changes induced by expression of the HCV structural proteins, core, E1 and E2, expressed from a Semliki Forest Virus (SFV) recombinant RNA replicon. Electron microscopy of cells expressing these proteins showed cytoplasmic vacuoles containing membranous and electron-dense material that were distinct from the type I cytoplasmic vacuoles induced during SFV replicon replication. Immunogold labelling showed that the core and E2 proteins localized to the external and internal membranes of these vacuoles. At times were also associated with some of the internal amorphous material. Dual immunogold labelling with antibodies raised against the core protein and against an endoplasmic reticulum (ER)-resident protein (protein disulphide isomerase) showed that the HCV-induced vacuoles were associated with ER-labelled membranes. This report has identified an association between the HCV core and E2 proteins with induced cytoplasmic vacuoles which are morphologically similar to those observed in HCV-infected liver tissue, suggesting that the HCV structural proteins may be responsible for the induction of these vacuoles during HCV replication in vivo.

Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.

Structural characterization of the N-terminal autoregulatory sequence of phenylalanine hydroxylase

Phenylalanine hydroxylase (PAH) is activated by its substrate phenylalanine, and through phosphorylation by cAMP-dependent protein kinase at Ser 16 in the N-terminal autoregulatory sequence of the enzyme. The crystal structures of phosphorylated and unphosphorylated forms of the enzyme showed that, in the absence of phenylalanine, in both cases the N-terminal 18 residues including the phosphorylation site contained no interpretable electron density. We used nuclear magnetic resonance (NMR) spectroscopy to characterize this N-terminal region of the molecule in different stages of the regulatory pathway. A number of sharp resonances are observed in PAH with an intact N-terminal region, but no sharp resonances are present in a truncation mutant lacking the N-terminal 29 residues. The N-terminal sequence therefore represents a mobile flexible region of the molecule. The resonances become weaker after the addition of phenylalanine, indicating a loss of mobility. The peptides corresponding to residues 2-20 of PAH have different structural characteristics in the phosphorylated and unphosphorylated forms, with the former showing increased secondary structure. Our results support the model whereby upon phenylalanine binding, the mobile N-terminal 18 residues of PAH associate with the folded core of the molecule; phosphorylation may facilitate this interaction.

Synthesis and structural properties of patellamide a derivatives and their copper(II) compounds

The synthesis, characterization and copper(II) coordination chemistry of three new cyclic peptide ligands, PatJ(1) (cyclo-(Ile -Thr- (Gly)Thz-lle-Thr(Gly)Thz)), PatJ(2) (cyclo-(Ile-Thr(Gly)Thz-(D)-Ile-Thr-(Gly)Thz)), and PatL (cyclo-(Ile-Ser-(Gly)Thz-Ile-Ser(Gly)Thz)) are reported. All of these cyclic peptides and PatN (cyclo-(Ile-Ser(Gly)Thz-Ile-Thr-(Gly)Thz)) are derivatives of patellamide A and have a [24]azacrown-8 macrocyclic structure. All four synthetic cyclic peptides have two thiazole rings but, in contrast to patellamide A, no oxazoline rings. The molecular structure of PatJ1, determined by X-ray crystallography, has a saddle conformation with two close-to-co-parallel thiazole rings, very similar to the geometry of patellamide D. The two coordination sites of PatJ1 with thiazole-N and amide-N donors are each well preorganized for transition metal ion binding. The coordination of copper(II) was monitored by UV/Vis spectroscopy, and this reveals various (meta)stable mono- and dinuclear copper(II) complexes whose stoichiometry was confirmed by mass spectra. Two types of dinuclear copper(II) complexes, [Cu-2(H4L)(OH2)(n)](2+) (n = 6, 8) and [Cu-2(H4L)(OH2)(n)] (n=4, 6; L=PatN, PatL, PatJ1, PatJ2) have been identified and analyzed structurally by EPR spectroscopy and a combination of spectra simulations and molecular mechanics calculations (MM-EPR). The four structures are similar to each other and have a saddle conformation, that is, derived from the crystal structure of PatJ(1) by a twist of the two thiozole rings. The small but significant structural differences are characterized by the EPR simulations.

Comparative influence of forest management and habitat structural factors on the abundances of hollow-nesting bird species in subtropical Australian eucalypt forest

We examined the impact of single-tree selective logging and fuel reduction bums on the abundance of hollow-nesting bird species at a regional scale in southeastern Queensland, Australia. Data were collected on species abundance and habitat structure of dry sclerophyll production forest at 36 sites with known logging and fire histories. Sixteen bird species were recorded with most being resident, territorial, obligate hollow nesters that used hollows that were either small (18 cm diameter). Species densities were typically low, but combinations of two forest management and three habitat structural variables influenced the abundances of eight bird species in different and sometimes conflicting ways. The results suggest that habitat tree management for biodiversity in production forests cannot depend upon habitat structural characteristics alone. Management histories appear to have independent influence (on some bird species) that are distinguishable from their impacts on habitat structure per se. Rather than managing to maximize species abundances to maintain biodiversity, we may be better off managing to avoid extinctions of populations by identifying thresholds of acceptable fluctuations in populations of not only hollow-nesting birds but other forest dependent wildlife relative to scientifically valid forest management and habitat structural surrogates.

Reversible luminescence thermochromism in dipotassiumsodium tris[dicyanoargentate(I)] and the role of structural phase transitions

As a function of temperature, the layered compound K2Na[Ag(CN)213 displays dramatic variations in luminescence thermochromism with major trend changes occurring around 80 K. In order to understand these interesting optical properties, high-resolution neutron diffraction investigations were performed on a polycrystalline sample of this material in the temperature range from 1.5 to 300 K, and previous synchrotron X-ray data of Larochelle et al. (Solid State Commun. 114, 155 (2000)) were reinterpreted. The corresponding significant structural changes were found to be continuous with an anomalous increase of the monoclinic c-lattice parameter with decreasing temperature, associated with slight reorientations of two inequivalent, approximately linear N-C-Ag-C-N units. In the whole temperature range, the crystal structure is monoclinic with the space group C2/m. Based on the structural results, the major luminescence thermochromism changes around 80 K are attributed to the dominance of a back energy transfer process from low- to high-energy excitons at high temperatures. (E) 2002 Elsevier Science (USA).

Copolymers obtained by the radiation-induced grafting of styrene onto poly(tetrafluoroethylene-co-perfluoropropylvinyl ether) substrates. 1. Preparation and structural investigation

A study has been made to investigate the radiation grafting of styrene onto poly(tetrafluoroethylene-co-perfluoropropylvinyl ether) (PFA) substrates, using the simultaneous irradiation method. Two PFA polymers of different comonomer perfluoropropyl vinyl ether (PPVE) content and degree of crystallinity were used. Effects of grafting conditions such as monomer concentrations, type of solvent, dose rate, and irradiation dose on the grafting yield were investigated. Of the six different solvents used, the most efficient in terms of increasing grafting yield were dichloromethane, benzene, and methanol. The degree of grafting increased with increasing radiation dose up to 500 kGy, stabilizing above this dose. However, the grafting yield decreased with an increase in the dose rate. The grafting of styrene onto the PFA substrates was confirmed by FTIR-ATR and micro-Raman spectroscopy, The increase in the overall grafting yield was accompanied by a proportional increase in the penetration depth of the grafts into the substrate.

RNA trafficking and stabilization elements associate with multiple brain proteins

Two of the best understood somatic cell mRNA cytoplasmic trafficking elements are those governing localization of beta-actin and myelin basic protein mRNAs. These cis-acting elements bind the trans-acting factors fibroblast ZBP-1 and hnRNP A2, respectively. It is not known whether these elements fulfil other roles in mRNA metabolism. To address this question we have used Edman sequencing and western blotting to identify six rat brain proteins that bind the beta-actin element (zipcode). All are known RNA-binding proteins and differ from ZBP-1. Comparison with proteins that bind the hnRNP A2 and AU-rich response elements, A2RE/A2RE11 and AURE, showed that AURE and zipcode bind a similar set of proteins that does not overlap with those that bind A2RE11. The zipcode-binding protein, KSRP, and hnRNP A2 were selected for further study and were shown by confocal immunolluorescence microscopy to have similar distributions in the central nervous system, but they were found in largely separate locations in cell nuclei. In the cytoplasm of cultured oligodendrocytes they were segregated into separate populations of cytoplasmic granules. We conclude that not only may there be families of trans-acting factors for the same cis-acting element, which are presumably required at different stages of mRNA processing and metabolism, but independent factors may also target different and multiple RNAs in the same cell.

Negative ion electrospray mass spectra of caerulein peptides: an aid to structural determination

MS/MS data derived from the [M-H](-) ions of desulfated caerulein peptides provide (i) sequencing information from a combination of alpha, beta and gamma backbone cleavages, and (ii) identification of specific amino acid side chains by side-chain cleavages [e.g. Ser (-CH2O), Thr (-CH3CHO) and Asp (-H2O)] (fragmentations having no counterparts in positive ion spectra). In addition, delta and/or gamma backbone cleavage ions from Asp residues identify the position of these residues in the peptide. In contrast, neither delta nor gamma cleavage ions are observed from either the Gln2 residue nor from Phe residues. Full structural information can be obtained from a consideration of the positive and negative ion MS/MS data in concert. Copyright (C) 2002 John Wiley Sons, Ltd.

Single mode Lamb waves in composite laminated plates generated by piezoelectric transducers

The technique of permanently attaching piezoelectric transducers to structural surfaces has demonstrated great potential for quantitative non-destructive evaluation and smart materials design. For thin structural members such as composite laminated plates, it has been well recognized that guided Lamb wave techniques can provide a very sensitive and effective means for large area interrogation. However, since in these applications multiple wave modes are generally generated and the individual modes are usually dispersive, the received signals are very complex and difficult to interpret. An attractive way to deal with this problem has recently been introduced by applying piezoceramic transducer arrays or interdigital transducer (IDT) technologies. In this paper, the acoustic wave field in composite laminated plates excited by piezoceramic transducer arrays or IDT is investigated. Based on dynamic piezoelectricity theory, a discrete layer theory and a multiple integral transform method, an analytical-numerical approach is developed to evaluate the input impedance characteristics of the transducer and the surface velocity response of the plate. The method enables the quantitative evaluation of the influence of the electrical characteristics of the excitation circuit, the geometric and piezoelectric properties of the transducer array, and the mechanical and geometrical features of the laminate. Numerical results are presented to validate the developed method and show the ability of single wave mode selection and isolation. The results show that the interaction between individual elements of the piezoelectric array has a significant influence on the performance of the IDT, and these effects can not be neglected even in the case of low frequency excitation. It is also demonstrated that adding backing materials to the transducer elements can be used to improve the excitability of specific wave modes. (C) 2002 Elsevier Science Ltd. All rights reserved.

Structural changes in mixed Langmuir-Blodgett films upon nanoparticle formation

The formation of CdS nanoparticles by reacting mixed Langmuir-Blodgett films of arachidic acid and either octadecylamine or dimethyldioctadecylammonium nitrate on a cadmium-containing subphase with hydrogen sulfide gas has resulted in the identification of a number of structural changes, observed using grazing incidence X-ray diffraction. In the case of octadecylamine, the structure after reaction is a hexagonal close-packed array of surfactant-stabilized nanoclusters, with a lattice constant of a = 17.65 Angstrom. In both octadecylamine and dimethyldioctadecylammonium nitrate films, the presence of a unit cell tilted at 38degrees to the plane of the substrate was found. Despite these changes, the average nanoparticle size was unaffected by the addition of either second component to the film.

Structural and surface property changes of macadamia nut-shell char upon activation and high temperature treatment

Structural and surface property changes of macadamia nut-shell (MNS) char upon activation and high temperature treatment (HTT) were studied by high-resolution nitrogen adsorption, diffuse reflectance infra-red Fourier transform spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption. It is found that activation of MNS char can be divided into the low extent activation which may involve the reactions of internal oxygen-containing groups and leads to the formation of comparatively uniform micropores, and the high extent activation which induces reactions between carbon and activating gas and produces a large amount of micropores. The surface functional groups (SFGs) basically increase with the increase of activation extent, but high extent activation preferentially increases the amount of -C-O and -C=O. HTT in air for a short tithe at a high temperature (1173 K) greatly increases the micropore volume and the amounts of SFGs. By appropriately choosing the activation and HTT conditions, it is possible to control both the textural structure and the type and amounts of SFG. (C) 2002 Published by Elsevier Science Ltd.

Effect of a control burn on lizards and their structural environment in a eucalypt open-forest

The composition of an open-forest lizard assemblage in eastern Australia was examined before and after a low-intensity controlled fire and concurrently compared with that in an adjoining unburnt area. The effect of fire on the available structural environment and the habitat used by two focal species, Carlia vivax and Lygisaurus foliorum, was also examined. Lizard species richness was unaffected by the controlled burn as was the abundance of most species. C. vivax was the only species to display a significant reduction in abundance after fire. While the low-intensity fire resulted in significant changes to the available structural environment, there were no compensatory shifts in the habitat preferences of either C. vivax or L. foliorum. The reduction in abundance of C. vivax was congruent with this species' avoidance of burnt areas. C. vivax displayed a non-random preference for ground cover and litter cover, which were reduced in burnt areas. Changes in the availability of preferred structural habitat features are likely to contribute to changes in the abundance of some lizard species. Therefore, even low-intensity disturbances can have an impact on lizard assemblages if critical habitat features are lost or become limiting.