Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution

Small-angle X-ray scattering (SAXS) and elastic and quasi-elastic neutron scattering techniques were used to investigate the high-pressure-induced changes on interactions, the low-resolution structure and the dynamics of lysozyme in solution. SAXS data, analysed using a global-fit procedure based on a new approach for hydrated protein form factor description, indicate that lysozyme completely maintains its globular structure up to 1500 bar, but significant modi. cations in the protein-protein interaction potential occur at approximately 600-1000 bar. Moreover, the mass density of the protein hydration water shows a clear discontinuity within this pressure range. Neutron scattering experiments indicate that the global and the local lysozyme dynamics change at a similar threshold pressure. A clear evolution of the internal protein dynamics from diffusing to more localized motions has also been probed. Protein structure and dynamics results have then been discussed in the context of protein-water interface and hydration water dynamics. According to SAXS results, the new configuration of water in the first hydration layer induced by pressure is suggested to be at the origin of the observed local mobility changes.

Three-dimensional structure of tropism-switching Bordetella bacteriophage.

Bacteriophage BPP-1, which infects Bordetella species, can switch its specificity by mutations to the ligand-binding surface of its major tropism-determinant protein, Mtd. This targeted mutagenesis results from the activity of a phage-encoded diversity-generating retroelement. Purified Mtd binds its receptor with low affinity, yet BPP-1 binding and infection of Bordettella cells are efficient because of high-avidity binding between phage-associated Mtd and its receptor. Here, using an integrative approach of three-dimensional (3D) structural analyses of the entire phage by cryo-electron tomography and single-prticle cryo-electron microscopy, we provide direct localization of Mtd in the phage and the structural basis of the high-avidity binding of the BPP-1 phage. Our structure shows that each BPP-1 particle has a T = 7 icosahedral head and an unusual tail apparatus consisting of a short central tail "hub," six short tail spikes, and six extended tail fibers. Subtomographic averaging of the tail fiber maps revealed a two-lobed globular structure at the distal end of each long tail fiber. Tomographic reconstructions of immuno-gold-labeled BPP-1 directly localized Mtd to these globular structures. Finally, our icosahedral reconstruction of the BPP-1 head at 7A resolution reveals an HK97-like major capsid protein stabilized by a smaller cementing protein. Our structure represents a unique bacteriophage reconstruction with its tail fibers and ligand-binding domains shown in relation to its tail apparatus. The localization of Mtd at the distal ends of the six tail fibers explains the high avidity binding of Mtd molecules to cell surfaces for initiation of infection.

Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone

Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Peduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthelemy, M., Prigent, Y., Salomon, R. A., Farias, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.

High-Temperature Workability of Thixocast A356 Aluminum Alloy

The present work highlights the role of globular microstructure on the workability of A356 aluminum alloy at elevated temperature. The hot deformation behavior was studied by isothermal hot compression tests in the temperature range 573 K to 773 K (300 A degrees C to 500 A degrees C) and strain rate range of 0.001 to 10 s(-1). The flow stress data obtained from the tests were used to estimate the strain rate sensitivity and strain rate hardening. Flow stress analysis of the alloy shows that the effect of temperature on strain hardening is more significant at lower strain levels and strain rate sensitivity is independent of strain. The results also reveal that the flowability of conventionally cast alloy increases after changing the dendritic microstructure into a globular structure through semisolid processing route. Thixocast alloy exhibits lower yield strength and higher elongation at elevated temperature in comparisons to conventionally cast values. This property has an important implication toward thixo-forming at an elevated temperature. (C) The Minerals, Metals & Materials Society and ASM International 2015

Improvement of heat-induced gel properties of porcine plasma

L'objectiu és millorar els gels de plasma porcí induïts per calor a pH àcid utilitzant transglutaminasa microbiana (MTGasa). El tractament millora textura i CRA dels gels a pH 5,5, però les millores no són suficients per recuperar les pèrdues degut a l'acidificació. L'estructura globular de les proteïnes dificulta l'atac enzimàtic. La reactivitat de l'enzim no millora amb l'addició de cisteïna a plasma amb MTGasa. El tractament del plasma amb MTGasa sota alta pressió (HP) millora la duresa dels gels. No obstant, la CRA només millora lleugerament. La duresa es pot incrementar mantenint les solucions de plasma pressuritzat sota refrigeració, encara que no millora la CRA. Es pot concloure que les pèrdues en la textura dels gels de plasma induïts per calor a pH àcid es poden recuperar parcialment tractant amb MTGasa, especialment afegint cisteïna o sota HP. Encara que la CRA només es veu lleugerament millorada en el segon cas.

Characterisation of an s-type low molecular weight glutenin subunit of wheat and its proline and glutamine-rich repetitive domain

The low molecular weight glutenin subunits (LMW-GS) are major components of the glutenin polymers which determine the elastomeric properties of wheat (Triticum aestivum L.) gluten and dough. They comprise a complex mixture of components and have proved to be difficult to purify for detailed characterisation. The mature LMW subunit proteins comprise two structural domains, with one domain consisting of repeated sequences based on short peptide motifs. DNA sequences encoding this domain and a whole subunit were expressed in Escherichia coli and the recombinant proteins purified. Detailed comparisons by spectroscopy (CD, FT-IR) and dynamic light scattering indicated that the repetitive and non-repetitive domains of the proteins formed different structures with the former having an extended conformation with an equilibrium between poly-L-proline II-like structure and type II’ b-turns, and the latter a more compact globular structure rich in a-helix. Although the structures of these two domains appear to form independently, dynamic light scattering of the whole subunit dissolved in trifluoroethanol(TFE) suggested that they interact, leading to a more compact conformation. These observations may have relevance to the role of the LMW-GS in gluten structure and functionality.

Serum protein layers on parylene-C and silicon oxide: effect on cell adhesion

Among the range of materials used in bioengineering, parylene-C has been used in combination with silicon oxide and in presence of the serum proteins, in cell patterning. However, the structural properties of adsorbed serum proteins on these substrates still remain elusive. In this study, we use an optical biosensing technique to decipher the properties of fibronectin (Fn) and serum albumin adsorbed on parylene-C and silicon oxide substrates. Our results show the formation of layers with distinct structural and adhesive properties. Thin, dense layers are formed on parylene-C, whereas thicker, more diffuse layers are formed on silicon oxide. These results suggest that Fn acquires a compact structure on parylene-C and a more extended structure on silicon oxide. Nonetheless, parylene-C and silicon oxide substrates coated with Fn host cell populations that exhibit focal adhesion complexes and good cell attachment. Albumin adopts a deformed structure on parylene-C and a globular structure on silicon oxide, and does not support significant cell attachment on either surface. Interestingly, the co-incubation of Fn and albumin at the ratio found in serum, results in the preferential adsorption of albumin on parylene-C and Fn on silicon oxide. This finding is supported by the exclusive formation of focal adhesion complexes in differentiated mouse embryonic stem cells (CGR8), cultured on Fn/albumin coated silicon oxide, but not on parylene-C. The detailed information provided in this study on the distinct properties of layers of serum proteins on substrates such as parylene-C and silicon oxide is highly significant in developing methods for cell patterning.

Identifying foldable regions in protein sequence from the hydrophobic signal

Structural genomics initiatives aim to elucidate representative 3D structures for the majority of protein families over the next decade, but many obstacles must be overcome. The correct design of constructs is extremely important since many proteins will be too large or contain unstructured regions and will not be amenable to crystallization. It is therefore essential to identify regions in protein sequences that are likely to be suitable for structural study. Scooby-Domain is a fast and simple method to identify globular domains in protein sequences. Domains are compact units of protein structure and their correct delineation will aid structural elucidation through a divide-and-conquer approach. Scooby-Domain predictions are based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method employs an A*-search to identify sequence regions that form a globular structure and those that are unstructured. On a test set of 173 proteins with consensus CATH and SCOP domain definitions, Scooby-Domain has a sensitivity of 50% and an accuracy of 29%, which is better than current state-of-the-art methods. The method does not rely on homology searches and, therefore, can identify previously unknown domains.

Flow evolution of a metallic slurry during thixoextrusion of an automotive valve

The aim of this work is to characterize a metallic slurry (Al-4.5%Cu) flow during thixoforming of an automotive valve. The necessary globular structure was obtained by first inoculating the alloy with TIBAL (5%Ti, 1%B, Al - rest) at 750.0°C, and then reheating to a state between liquidus and solidus prior to thixoforming. Two metallic slurries, with a solid phase of approximately 86.1 and 78.2 percent, were used to generate different experimental flow patterns during the thixoforming process. The flow of the material into the die was observed for total, and partial displacement (2.7, 5.4, 7.5mm) of the punch. The first displacement shows formation of the valve rod. The patterns at each step of displacement of the punch were preserved by quenching in water, thus revealing the profile of the die fill and microstructural evolution. Degeneration of the globular phase was observed along the piece thixoextruded. Thixoextrusion forces versus time curves were generated for partial and full displacement of the punch. Porosity was visible along the billet prior to thixoforming. However, some areas show that the porosity gradually decreased to zero as the thixoextrusion pressure increased. Turbulent, transient and laminar flow are analyzed in this work.

Study of polypropylene surface modification by air dielectric barrier discharge operated at two different frequencies

In this work, air dielectric barrier discharge (DBD) operating at the line frequency (60 Hz) or at frequency of 17 kHz was used to improve the wetting properties of polypropylene (PP). The changes in the surface hydrophilicity were investigated by contact angle measurements. The plasma-induced chemical modifications of PP surface were studied by X-ray photoelectron spectroscopy (XPS) and Fourier-transformed infrared spectroscopy (FTIR). The polymer surface morphology and roughness before and after the DBD treatment were analyzed by atomic force microscopy (AFM). To compare the plasma treatment effect at different frequencies the variation of the contact angle is presented as a function of the deposited energy density. The results show that both DBD treatments leaded to formation of water-soluble low molecular weight oxidized material (LMWOM), which agglomerated into small mounts on the surface producing a complex globular structure. However, the 60 Hz DBD process produced higher amount of LMWOM on the PP surface comparing to the 17 kHz plasma treatment with the same energy dose. The hydrophilic LMWOM is weakly bounded to the surface and can be easily removed by polar solvents. After washing the DBD-treated samples in de-ionized water their surface roughness and oxygen content were reduced and the PP partially recovered its original wetting characteristics. This suggested that oxidation also occurred at deeper and more permanent levels of the PP samples. Comparing both DBD processes the 17 kHz treatment was found to be more efficient in introducing oxygen moieties on the surface and also in improving the PP wetting properties. © 2012 Elsevier B.V. All rights reserved.

Continuous production of metal matrix composites from the semisolid state

Continuous strip metal matrix composite (MMC) casting of 0.3 mm diameter hard-drawn stainless steel (316L) wire in a quasi-eutectic SnPb (64Sn36Pb) matrix was performed by a two-roll melt drag processing (TRMDping) method, with the wire being dragged through a semisolid puddle with a fibre contact time of approximately 0.2 s. A slag weir placed at the nozzle contained two wire guide holes: one located near the upper roll, and the other located between the rolls. A successful continuous composite strip casting with good fibre alignment was achieved by inserting and embedding the wire into the matrix using the guide hole between the rolls. Degeneration of eutectic/dendrite structures led to the formation of globular structures. The occurrence and formation mechanisms of cracks, de-lamination and voids in the matrix were discussed. TRMDping is economically viable and has significant benefits over other MMC fabrication methods. © (2013) Trans Tech Publications, Switzerland.

Organic carbon and amino acid concentration of Karelian shungite rocks from the lake Onego area, Russia

The study of amino acids in the Precambrian shungite rocks of Karelia showed that their contents vary within 25-89 µg/g depending on proportions between shungite and mineral components. It was established that the amino acids exhibit an excess of L-enantiomers. In the shungite rocks, they form organomineral complexes with silica and aluminosilicates, being built in the globular structure of shungite matter. There are several sources of amino acids in shungites: secondary synthesis, microbial pollution, and original amino acids of organic matter in shungite rocks.

Semisolid microstructural evolution of AlSi7Mg alloy during partial remelting

Different as-cast microstructures of an AlSi7Mg alloy were produced by controlling the solidification conditions. The as-cast grain size ranged from 1.4 mm to 160 mum and the morphology varied from dendritic to rosette-like to globular. The as-cast materials were then partially remelted and isothermally held at 580degreesC for microstructure evolution. The final microstructure depended on the initial as-cast microstructure and the isothermal holding time. After partial remelting and isothermal holding, coarse-grained dendritic structures were not able to evolve to a globular structure, while structures with medium sized dendritic grains evolved to a globular structure with a relatively large particle size after a long isothermal holding time. Fine-grained structures evolved to well-rounded globular grains within times ranging front 10 min to 5 min as the dendritic nature of the starting structure diminished. An empirical equation has been established to describe the relationship between the evolved microstructure and the as-cast microstructure. (C) 2003 Elsevier B.V. All rights reserved.

A novel supersecondary structure in globular proteins comprising the collagen-like helix and ?-turn

A structure consisting of the polyproline-II or collagen-like helix immediately succeeded by a ?-turn is seen in several synthetic peptides and has been suggested to be the conformational requirement for proline hydroxylation in nascent procollagen. Using a simple algorithm for detecting secondary structures, we have analysed crystal structure data on 40 globular proteins and have found eight examples of the collagen-helix + ?-turn supersecondary structure in 15 proteins that contain the collagen-like helical segments.