SKPDB: A structural database of shikimate pathway enzymes

Background: The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.Description: The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.Conclusions: The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/. © 2010 Arcuri et al; licensee BioMed Central Ltd.

Structural studies of Helicase NS3 variants from Hepatitis C virus genotype 3 in virological sustained responder and non-responder patients

Background. About 130 million people are infected with the hepatitis C virus (HCV) worldwide, but effective treatment options are not yet available. One of the most promising targets for antiviral therapy is nonstructural protein 3 (NS3). To identify possible changes in the structure of NS3 associated with virological sustained response or non-response of patients, a model was constructed for each helicase NS3 protein coding sequence. From this, the goal was to verify the interaction between helicases variants and their ligands. Findings. Evidence was found that the NS3 helicase portion of non-responder patients contained substitutions in its ATP and RNA binding sites. K210E substitution can cause an imbalance in the distribution of loads, leading to a decrease in the number of ligations between the essential amino acids required for the hydrolysis of ATP. W501R substitution causes an imbalance in the distribution of loads, leading and forcing the RNA to interact with the amino acid Thr269, but not preventing binding of ribavirin inhibitor. Conclusions. Useful information is provided on the genetic profiling of the HCV genotype 3, specifically the coding region of the NS3 protein, improving our understanding of the viral genome and the regions of its protein catalytic site. © 2010 Rahal et al; licensee BioMed Central Ltd.

Structural characterization of a new dextran with a low degree of branching produced by Leuconostoc mesenteroides FT045B dextransucrase

This paper offers the physical and chemical characterization of a new dextran produced by Leuconostoc mesenteroides FT045B. The chemical structure was determined by Fourier Transform Infrared spectroscopy and 1H Nuclear Magnetic Resonance spectroscopy. The dextran was hydrolyzed by endodextranase; the products were analyzed using thin layer chromatography and compared with those of commercial B-512F dextran. The number-average molecular weight and degree of polymerization of the FT045B dextran were determined by the measurement of the reducing value using the copper bicinchoninate method and the measurement of total carbohydrate using the phenol-sulfuric acid method. The data revealed that the structure of the dextran synthesized by FT045B dextran sucrase is composed of d-glucose residues, containing 97.9% α-(1,6) linkages in the main chains and 2.1% α-(1,3) branch linkages compared with the commercial B-512F dextran, which has 95% α-(1,6) linkages in the main chains and 5% α-(1,3) branch linkages. © 2012 Elsevier Ltd. All rights reserved.

Influence of optimized lubrication-cooling and minimum quantity lubrication on the cutting forces, on the geometric quality of the surfaces and on the micro-structural integrity of hardened steel parts

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural elements of spiralling inflation

Includes bibliography

Ultra-structural mapping of sugarcane bagasse after oxalic acid fiber expansion (OAFEX) and ethanol production by Candida shehatae and Saccharomyces cerevisiae

Background: Diminishing supplies of fossil fuels and oil spills are rousing to explore the alternative sources of energy that can be produced from non-food/feed-based substrates. Due to its abundance, sugarcane bagasse (SB) could be a model substrate for the second-generation biofuel cellulosic ethanol. However, the efficient bioconversion of SB remains a challenge for the commercial production of cellulosic ethanol. We hypothesized that oxalic-acid-mediated thermochemical pretreatment (OAFEX) would overcome the native recalcitrance of SB by enhancing the cellulase amenability toward the embedded cellulosic microfibrils. Results: OAFEX treatment revealed the solubilization of hemicellulose releasing sugars (12.56 g/l xylose and 1.85 g/l glucose), leaving cellulignin in an accessible form for enzymatic hydrolysis. The highest hydrolytic efficiency (66.51%) of cellulignin was achieved by enzymatic hydrolysis (Celluclast 1.5 L and Novozym 188). The ultrastructure characterization of SB using scanning electron microscopy (SEM), atomic force microscopy (AFM), Raman spectroscopy, Fourier transform-near infrared spectroscopy (FT-NIR), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) revealed structural differences before and after OAFEX treatment with enzymatic hydrolysis. Furthermore, fermentation mediated by C. shehatae UFMG HM52.2 and S. cerevisiae 174 showed fuel ethanol production from detoxified acid (3.2 g/l, yield 0.353 g/g; 0.52 g/l, yield, 0.246 g/g) and enzymatic hydrolysates (4.83 g/l, yield, 0.28 g/g; 6.6 g/l, yield 0.46 g/g). Conclusions: OAFEX treatment revealed marked hemicellulose degradation, improving the cellulases ability to access the cellulignin and release fermentable sugars from the pretreated substrate. The ultrastructure of SB after OAFEX and enzymatic hydrolysis of cellulignin established thorough insights at the molecular level. © 2013 Chandel et al; licensee BioMed Central Ltd.

The thermal, rheological and structural properties of cassava starch granules modified with hydrochloric acid at different temperatures

Starch is arguably one of the most actively investigated biopolymer in the world. In this study, the native (untreated) cassava starch granules (Manihot esculenta, Crantz) were hydrolyzed by standard hydrochloric acid solution at different temperatures (30 °C and 50 °C) and the hydrolytic transformations were investigated by the following techniques: simultaneous thermogravimetry-differential thermal analysis (TG-DTA), differential scanning calorimetry (DSC), as well as non-contact atomic force microscopy (NC-AFM), X-ray diffraction (XRD) powder patterns, and rapid viscoamylographic analysis (RVA). After the treatment with hydrochloric acid at different temperatures, the thermal stability, a gradual loss of pasting properties (viscosity), alterations in the gelatinization enthalpy (ΔHgel), were observed. The use of NC-AFM and XRD allowed the observation of the surface morphology and topography of the starch granules and changes in crystallinity of the granules, respectively. © 2012 Elsevier B.V. All rights reserved.

Phylogenetic and structural studies of a novel equine papillomavirus identified from aural plaques

Papillomaviruses (PVs) infect a wide range of animal species and show great genetic diversity. To date, excluding equine sarcoids, only three species of PVs were identified associated with lesions in horses: Equus caballus papillomavirus 1 (EcPV1-cutaneous), EcPV2 (genital) and EcPV3 (aural plaques). In this study, we identified a novel equine PV from aural plaques, which we designated EcPV4. Cutaneous samples from horses with lesions that were microscopically diagnosed as aural plaques were subjected to DNA extraction, amplification and sequencing. Rolling circle amplification and inverse PCR with specific primers confirmed the presence of an approximately 8. kb circular genome. The full-length EcPV4 L1 major capsid protein sequence has 1488 nucleotides (495 amino acids). EcPV4 had a sequence identity of only 53.3%, 60.2% and 51.7% when compared with the published sequences for EcPV1, EcPV2 and EcPV3, respectively. A Bayesian phylogenetic analysis indicated that EcPV4 clusters with EcPV2, but not with EcPV1 and EcPV3. Using the current PV classification system that is based on the nucleotide sequence of L1, we could not define the genus of the newly identified virus. Therefore, a structural analysis of the L1 protein was carried out to aid in this classification because EcPV4 cause lesion similar to the lesion caused by EcPV3. A comparison of the superficial loops demonstrated a distinct amino acid conservation pattern between EcPV4/EcPV2 and EcPV4/EcPV3. These results demonstrate the presence of a new equine PV species and that structural studies could be useful in the classification of PVs. © 2012 Elsevier B.V.

Thermal, rheological, and structural behaviors of natural and modified cassava starch granules, with sodium hypochlorite solutions

The use of chemically modified starches is widely accepted in various industries, with several applications. In this research, natural cassava starch granules were treated with standard sodium hypochlorite solution at 0.8, 2.0, and 5.0 g Cl/100 g starch. The native and modified starch samples were investigated by means of the following techniques: simultaneous thermogravimetry-differential thermal analysis, which allowed us to verify the thermal decomposition associated with endothermic or exothermic phenomena; and differential scanning calorimetry that was used to determine gelatinization enthalpy as well as the rapid viscoamylographic analysis that provided the pasting temperature and viscosity. By means of non-contact-atomic force microscopy method and X-ray powder patterns diffractometry, it was possible to observe the surface morphology, topography of starch granules, and alterations in the granules' crystallinity. © 2012 Akadémiai Kiadó, Budapest, Hungary.

The effects of water molecules on the electronic and structural properties of peptide nanotubes

The self-assembly of short amino acid chains appears to be one of the most promising strategies for the fabrication of nanostructures. Their solubility in water and the possibility of chemical modification by targeting the amino or carboxyl terminus give peptide-based nanostructures several advantages over carbon nanotube nanostructures. However, because these systems are synthesized in aqueous solution, a deeper understanding is needed on the effects of water especially with respect to the electronic, structural and transport properties. In this work, the electronic properties of l-diphenylalanine nanotubes (FF-NTs) have been studied using the Self-Consistent Charge Density-Functional-based Tight-Binding method augmented with dispersion interaction. The presence of water molecules in the central hydrophilic channel and their interaction with the nanostructures are addressed. We demonstrate that the presence of water leads to significant changes in the electronic properties of these systems decreasing the band gap which can lead to an increase in the hopping probability and the conductivity. © the Owner Societies 2013.

A theoretical and experimental study to unequivocal structural assignment of tetrahydroquinoline derivatives

The tetrahydroquinoline derivatives can be easily synthesized through Povarov reaction and have several important biological activities. This work describes a comparative study for the unequivocal assignment of molecular structure of different tetrahydroquinoline derivatives, through a complete analysis of NMR 1D and 2D NMR spectra (1H, 13C, COSY, HSQC, and HMBC), and the correlation this data with theoretical calculations of energy-minimization and chemical shift (δ), employing the theory level of DFT/B3LYP with set of the cc-pVDZ basis. For these derivatives the experimental analyses and the theoretical model adopted were sufficient to obtain a good description of its structures, and these results can be used to assign the structure of various others tetrahydroquinoline derivatives. © 2013 Springer Science+Business Media New York.

Structural characteristics of P123-modified supercritical drying and hydrophobic ambient pressure drying aerogels

Supercritical drying (SCD) and hydrophobic ambient pressure drying (APD) aerogels were prepared from hydrolysis of tetraethoxysilane in solutions of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (P123) in the range of composition below the threshold for the ordered mesoporous silica precipitation. APD was carried out after silylation of wet gels with trimethylchlorosilane (TMCS) or hexamethyldisilazane (HMDZ). The samples were analyzed by small-angle X-ray scattering and nitrogen adsorption. Wet gels are formed by mass-fractal domains, with fractal dimension close to 2, and larger pores superposing the pores belonging to the fractal structure in case of high P123 concentrations. Aerogels exhibit smaller-sized mass-fractal domains with larger mass-fractal dimension accounting for some porosity elimination on drying. The pore volume of the aerogels increases significantly with the P123 amount and it is even larger in the APD aerogels than in the SCD aerogels. © 2013 Elsevier B.V. All rights reserved.

Small-angle X-ray scattering and structural modeling of full-length: Cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations. © 2013 Springer Science+Business Media Dordrecht.

Dielectric and structural characterization of Pb1-xAxZr0.40Ti0.60O3 (A = Sr, Ca) ferroelectric ceramics

This paper reports the influence of Sr- and Ca-substitution on the structural and ferroelectric properties of Pb1-xSrxZr0.40Ti0.60O3 (PSZT) and Pb1-xCaxZr0.40Ti0.60O3 (PCZT) ceramic systems. The dielectric measurements show that these substitutions cause a diffuse behavior in the dielectric permittivity curves for all samples. According to the X-ray absorption near-edge structure (XANES) spectra collected at Ti K- and LIII-edge, when Pb was replaced by Sr or Ca, a decrease in the local distortion around Ti atoms in the TiO6 octahedron could be observed. The O K-edge XANES spectra also revealed that the hybridization between O 2p and Pb 6sp states decreased as the amount of Sr or Ca atoms increased. Based on these results, it was possible to ascertain that the ferroelectric behavior in PSZT and PCZT samples bears a close correlation to the hybridization weakening between O 2p and Pb 6 sp states. © 2013 by American Scientific Publishers.

Structural transition of ZnO thin films produced by RF magnetron sputtering at low temperatures

Zinc oxide (ZnO) thin films were prepared using reactive radio-frequency magnetron sputtering of a pure metallic zinc target onto glass substrates. The evolution of the surface morphology and the optical properties of the films were studied as a function of the substrate temperature, which was varied from 50 to 250 C. The surface topography of the samples was examined using atomic force microscopy (AFM), and their optical properties were studied via transmittance measurements in the UV-Vis-NIR region. DRX and AFM analyses showed that the surface morphology undergoes a structural transition at substrate temperatures of around 150 C. Actually, at 50 C the formation of small grains was observed while at 250 C the grains observed were larger and had more irregular shapes. The optical gap remained constant at ∼3.3 eV for all films. In the visible region, the average optical transmittance was 80 %. From these results, one can conclude that the morphological properties of the ZnO thin films were more greatly affected by the substrate temperature, due to mis-orientation of polycrystalline grains, than were the optical properties. © 2013 Springer Science+Business Media New York.