Role of aromatic residues in stabilization of the [Fe4S4] cluster in high-potential iron proteins (HiPIPs): physical characterization and stability studies of Tyr-19 mutants of Chromatium vinosum HiPIP.

The functional role of residue Tyr-19 of Chromatium vinosum HiPIP has been evaluated by site-directed mutagenesis experiments. The stability of the [Fe4S4] cluster prosthetic center is sensitive to side-chain replacements. Polar residues result in significant instability, while nonpolar residues (especially with aromatic side chains) maintain cluster stability. Two-dimensional NMR data of native and mutant HiPIPs are consistent with a model where Tyr-19 serves to preserve the structural rigidity of the polypeptide backbone, thereby maintaining a hydrophobic barrier for exclusion of water from the cluster cavity. Solvent accessibility results in more facile oxidation of the cluster by atmospheric oxygen, with subsequent rapid hydrolysis of the [Fe4S4]3+ core.

Molecular and biochemical characterization of dNOS: a Drosophila Ca2+/calmodulin-dependent nitric oxide synthase.

Nitric oxide (NO) is an intercellular messenger involved with various aspects of mammalian physiology ranging from vasodilation and macrophage cytotoxicity to neuronal transmission. NO is synthesized from L-arginine by NO synthase (NOS). Here, we report the cloning of a Drosophila NOS gene, dNOS, located at cytological position 32B. The dNOS cDNA encodes a protein of 152 kDa, with 43% amino acid sequence identity to rat neuronal NOS. Like mammalian NOSs, DNOS protein contains putative binding sites for calmodulin, FMN, FAD, and NADPH. DNOS activity is Ca2+/calmodulin dependent when expressed in cell culture. An alternative RNA splicing pattern also exists for dNOS, which is identical to that for vertebrate neuronal NOS. These structural and functional observations demonstrate remarkable conservation of NOS between vertebrates and invertebrates.

Molecular characterization of a second melatonin receptor expressed in human retina and brain: the Mel1b melatonin receptor.

A G protein-coupled receptor for the pineal hormone melatonin was recently cloned from mammals and designated the Mel1a melatonin receptor. We now report the cloning of a second G protein-coupled melatonin receptor from humans and designate it the Mel1b melatonin receptor. The Mel1b receptor cDNA encodes a protein of 362 amino acids that is 60% identical at the amino acid level to the human Mel1a receptor. Transient expression of the Mel1b receptor in COS-1 cells results in high-affinity 2-[125I]iodomelatonin binding (Kd = 160 +/- 30 pM). In addition, the rank order of inhibition of specific 2-[125I]iodomelatonin binding by eight ligands is similar to that exhibited by the Mel1a melatonin receptor. Functional studies of NIH 3T3 cells stably expressing the Mel1b melatonin receptor indicate that it is coupled to inhibition of adenylyl cyclase. Comparative reverse transcription PCR shows that the Mel1b melatonin receptor is expressed in retina and, to a lesser extent, brain. PCR analysis of human-rodent somatic cell hybrids maps the Mel1b receptor gene (MTNR1B) to human chromosome 11q21-22. The Mel1b melatonin receptor may mediate the reported actions of melatonin in retina and participate in some of the neurobiological effects of melatonin in mammals.

The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif.

Ran/TC4 is an essential, nuclear GTPase implicated in the initiation of DNA replication, entry into and exit from mitosis, and in nuclear RNA and protein transport through the nuclear pore complex. This diversity of functions suggests that Ran interacts with a large number of down-stream targets. Using an overlay assay, we detected a family of putative target proteins that associate with GTP-bound Ran. The sequence of only one such protein, HTF9a/RanBP1, is known. We have now cloned two additional Ran-binding proteins, allowing identification of a distinctive, highly conserved sequence motif of approximately 150 residues. This motif represents a minimal Ran-binding domain that stabilizes the GTP-bound state of Ran. The isolated domain also functions as a coactivator of Ran-GTPase-activating protein. Mutation of a conserved residue within the Ran-binding domain of HTF9a protein drastically reduced Ran binding. Ran-binding proteins coimmunoprecipitated with epitope-tagged Ran from cell lysates, suggesting that these proteins may associate in vivo. A previously uncharacterized Caenorhabditis elegans gene could encode a protein (96 kDa) possessing two Ran-binding domains. This open reading frame also contains similarities to nucleoporins, suggesting a functional link between Ran and nuclear pore complexes.

Tuning the functional properties of Silicon Carbide Thin Film and Nanowires

The present thesis has been devoted to the synthesis and investigation of functional properties of silicon carbide thin films and nanowires. The work took profit from the experience of the research group in the synthesis of 3C-SiC from vapour phase. 3C-SiC thin films Thin films heteroepitaxy on silicon substrates was carried out in a vapour phase epitaxy reactor. The initial efforts were committed to the process development in order to enhance the crystal quality of the epi-layer. The carbonization process and a buffer layer procedure were optimized in order to obtain good quality monocrystalline 3C-SiC layers. The films characterization was used not only to improve the entire process, but also to assess the crystalline quality and to identify the defects. Methyltrichlorosilane (MTS) was introduced during the synthesis to increase the growth rate and enhance crystalline quality. The effect of synthesis parameters such as MTS flow and process temperature was studied in order to promote defect density reduction and the release of the strain due to lattice mismatch between 3C-SiC and silicon substrate. In-growth n-type doping was implemented using a nitrogen gas line and the effect of different synthesis parameters on doping level was studied. Raman measurements allowed a contactless characterization and evaluation of electrically active dopant. The effect of MTS on nitrogen incorporation was investigated and a promotion of dopant concentration together with a higher growth rate were demonstrated. This result allows to obtain higher doping concentrations without deteriorating crystal quality in 3C-SiC and, to the best of our knowledge, it has never been demonstrated before. 3C-SiC nanowires Core-shell SiC-SiO2 nanowires were synthesized using a chemical vapour deposition technique in an open tube configuration reactor on silicon substrates. Metal catalyst were used to promote a uniaxial growth and a dense bundle of nanowires 100 µm long and 60 nm thick was obtained. Substrate preparation was found to be fundamental in order to obtain a uniform nanowire density. Morphological characterization was carried out using scanning electron microscopy and the analysis of structural, compositional, optical properties is reported.

Textural Characterization of Micro- and Mesoporous Carbons Using Combined Gas Adsorption and n-Nonane Preadsorption

Porous carbon and carbide materials with different structures were characterized using adsorption of nitrogen at 77.4 K before and after preadsorption of n-nonane. The selective blocking of the microporosity with n-nonane shows that ordered mesoporous silicon carbide material (OM-SiC) is almost exclusively mesoporous whereas the ordered mesoporous carbon CMK-3 contains a significant amount of micropores (25%). The insertion of micropores into OM-SiC using selective extraction of silicon by hot chlorine gas leads to the formation of ordered mesoporous carbide-derived carbon (OM-CDC) with a hierarchical pore structure and significantly higher micropore volume as compared to CMK-3, whereas a CDC material from a nonporous precursor is exclusively microporous. Volumes of narrow micropores, calculated by adsorption of carbon dioxide at 273 K, are in linear correlation with the volumes blocked by n-nonane. Argon adsorption measurements at 87.3 K allow for precise and reliable calculation of the pore size distribution of the materials using density functional theory (DFT) methods.

Characterization of soluble and bound EPS obtained from 2 submerged membrane bioreactors by 3D-EEM and HPSEC

This research study deals with the quantification and characterization of the EPS obtained from two 25 L bench scale membrane bioreactors (MBRs) with micro-(MF-MBR) and ultrafiltration (UF-MBR) submerged membranes. Both reactors were fed with synthetic water and operated for 168 days without sludge extraction, increasing their mixed liquor suspended solid (MLSS) concentration during the experimentation time. The characterization of soluble EPS (EPSs) was achieved by the centrifugation of mixed liquor and bound EPS (EPSb) by extraction using a cationic resin exchange (CER). EPS characterization was carried out by applying the 3-dimensional excitation–emission matrix fluorescence spectroscopy (3D-EEM) and high-performance size exclusion chromatography (HPSEC) with the aim of obtaining structural and functional information thereof. With regard to the 3D-EEM analysis, fluorescence spectra of EPSb and EPSs showed 2 peaks in both MBRs at all the MLSS concentrations studied. The peaks obtained for EPSb were associated to soluble microbial by-product-like (predominantly protein-derived compounds) and to aromatic protein. For EPSs, the peaks were associated with humic and fulvic acids. In both MBRs, the fluorescence intensity (FI) of the peaks increased as MLSS and protein concentrations increased. The FI of the EPSs peaks was much lower than for EPSb. It was verified that the evolution of the FI clearly depends on the concentration of protein and humic acids for EPSb and EPSs, respectively. Chromatographic analysis showed that the intensity of the EPSb peak increased while the concentrations of MLSS did. Additionally, the mean MW calculated was always higher the higher the MLSS concentrations in the reactors. MW was higher for the MF-MBR than for the UF-MBR for the same MLSS concentrations demonstrating that the filtration carried out with a UF membrane lead to retentions of lower MW particles.

Synthesis and Characterization of Lactic Acid Oligomers: Evaluation of Performance as Poly(Lactic Acid) Plasticizers

The use of fully bio-based and biodegradable materials for massive applications, such as food packaging, is an emerging tendency in polymer research. But the formulations proposed in this way should preserve or even increase the functional properties of conventional polymers, such as transparency, homogeneity, mechanical properties and low migration of their components to foodstuff. This is not always trivial, in particular when brittle biopolymers, such as poly(lactic acid) (PLA), are considered. In this work the formulation of innovative materials based on PLA modified with highly compatible plasticizers, i.e. oligomers of lactic acid (OLAs) is proposed. Three different synthesis conditions for OLAs were tested and the resulting additives were further blended with commercial PLA obtaining transparent and ductile materials, able for films manufacturing. These materials were tested in their structural, thermal and tensile properties and the best formulation among the three materials was selected. OLA with molar mass (Mn) around 1,000 Da is proposed as an innovative and fully compatible and biodegradable plasticizer for PLA, able to replace conventional plasticizers (phthalates, adipates or citrates) currently used for films manufacturing in food packaging applications.

Generation of nitrogen functionalities on activated carbons by amidation reactions and Hofmann rearrangement: Chemical and electrochemical characterization

Nitrogen functionalization of a highly microporous activated carbon (BET surface area higher than 3000 m2/g) has been achieved using the following sequence of treatments: (i) chemical oxidation using concentrated nitric acid, (ii) amidation by acyl chloride substitution with NH4NO3 and (iii) amination by Hoffman rearrangement. This reaction pathway yielded amide and amine functional groups, and a total nitrogen content higher than 3 at.%. It is achieved producing only a small decrease (20%) of the starting microporosity, being most of it related to the initial wet oxidation of the activated carbon. Remarkably, nitrogen aromatic rings were also formed as a consequence of secondary cyclation reactions. The controlled step-by-step modification of the surface chemistry allowed to assess the influence of individual nitrogen surface groups in the electrochemical performance in 1 M H2SO4 of the carbon materials. The largest gravimetric capacitance was registered for the pristine activated carbon due to its largest apparent surface area. The nitrogen-containing activated carbons showed the highest surface capacitances. Interestingly, the amidated activated carbon showed the superior capacitance retention due to the presence of functional groups (such as lactams, imides and pyrroles) that enhance electrical conductivity through their electron-donating properties, showing a capacitance of 83 F/g at 50 A/g.

Refined method of potential enhancement in the equilibria characterization of activated carbon. Comparison with GCMC and DFT

In this paper, we present a technique for equilibria characterization of activated carbon having slit-shaped pores. This method was first developed by Do (Do, D. D. A new method for the characterisation of micro-mesoporous materials. Presented at the International Symposium on New Trends in Colloid and Interface Science, September 24-26, 1998 Chiba, Japan) and applied by his group and other groups for characterization of pore size distribution (PSD) as well as adsorption equilibria determination of a wide range of hydrocarbons. It is refined in this paper and compared with the grand canonical Monte Carlo (GCMG) simulation and density functional theory (DFT). The refined theory results in a good agreement between the pore filling pressure versus pore width and those obtained by GCMG and DFT. Furthermore, our local isotherms are qualitatively in good agreement with those obtained by the GCMC simulations. The main advantage of this method is that it is about 4 orders of magnitude faster than the GCMC simulations, making it suitable for optimization studies and design purposes. Finally, we apply our method and the GCMG in the derivation of the PSD of a commercial activated carbon. It was found that the PSD derived from our method is comparable to that derived from the GCMG simulations.

Pore characterization of carbonaceous materials by DFT and GCMC simulations: A review

A review is given of the pore characterization of carbonaceous materials, including activated carbon, carbon fibres, carbon nanotubes, etc., using adsorption techniques. Since the pores of carbon media are mostly of molecular dimensions, the appropriate modem tools for the analysis of adsorption isotherms are grand canonical Monte Carlo (GCMC) simulations and density functional theory (DFT). These techniques are presented and applications of such tools in the derivation of pore-size distribution highlighted.

Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome

Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by cysteines and histidines. The zinc finger domain defines one of the largest protein superfamilies in mammalian genomes; 46 different conserved zinc finger domains are listed in InterPro (http://www.ebi.ac.uk/InterPro). Zinc finger proteins can bind to DNA, RNA, other proteins, or lipids as a modular domain in combination with other conserved structures. Owing to this combinatorial diversity, different members of zinc finger superfamilies contribute to many distinct cellular processes, including transcriptional regulation, mRNA stability and processing, and protein turnover. Accordingly, mutations of zinc finger genes lead to aberrations in a broad spectrum of biological processes such as development, differentiation, apoptosis, and immunological responses. This study provides the first comprehensive classification of zinc finger proteins in a mammalian transcriptome. Specific detailed analysis of the SP/Kruppel-like factors and the E3 ubiquitin-ligase RING-H2 families illustrates the importance of such an analysis for a more comprehensive functional classification of large protein families. We describe the characterization of a new family of C2H2 zinc-finger-containing proteins and a new conserved domain characteristic of this family, the identification and characterization of Sp8, a new member of the Sp family of transcriptional regulators, and the identification of five new RING-H2 proteins.

Functional serotonin 5-HT4 receptors in porcine and human ventricular myocardium with increased 5-HT4 mRNA in heart failure

Serotonin (5-hydroxytryptamine, 5-HT) increases contractile force and elicits arrhythmias through 5-HT4 receptors in porcine and human atrium, but its ventricular effects are unknown. We now report functional 5-HT4 receptors in porcine and human ventricle. 5-HT4 mRNA levels were determined in porcine and human ventricles and contractility studied in ventricular trabeculae. Cyclic AMP-dependent protein kinase (PKA) activity was measured in porcine ventricle. Porcine and human ventricles expressed 5-HT4 receptor mRNA. Ventricular 5-HT4(b) mRNA was increased by four times in 20 failing human hearts compared with five donor hearts. 5-HT increased contractile force maximally by 16% (EC50=890 nM) and PKA activity by 20% of the effects of (-)-isoproterenol (200 muM) in ventricular trabeculae from new-born piglets in the presence of the phosphodiesterase-inhibitor 3-isobutyl-1-methylxanthine. In ventricular trabeculae from adult pigs (3-isobutyl-1-methylxanthine present) 5-HT increased force by 32% (EC50=60 nM) and PKA activity by 39% of (-)-iso-proterenol. In right and left ventricular trabeculae from failing hearts, exposed to modified Krebs solution, 5-HT produced variable increases in contractile force in right ventricular trabeculae from 4 out of 6 hearts and in left ventricular trabeculae from 3 out of 3 hearts- range 1-39% of (-)-isoproterenol, average 8%. In 11 left ventricular trabeculae from the failing hearts of four beta-blocker-treated patients, pre-exposed to a relaxant solution with 0.5 mM Ca2+ and 1.2 mM Mg2+ followed by a switch to 2.5 mM Ca2+ and 1 mM Mg2+, 5-HT (1-100 muM, 3-isobutyl-1-melhylxanthine present) consistently increased contractile force and hastened relaxation by 46% and 25% of (-)-isoproterenol respectively. 5-HT caused arrhythmias in three trabeculae from 3 out of I I patients. In the absence of phosphodiesterase inhibitor, 5-HT increased force in two trabeculae, but not in another six trabeculae from 4 patients. All 5-HT responses were blocked by 5-HT4 receptor antagonists. We conclude that phosphodiesterase inhibition uncovers functional ventricular 5-HT4 receptors, coupled to a PKA pathway, through which 5-HT enhances contractility, hastens relaxation and can potentially cause arrhythmias.

Enzymatic characterization and homology model of a catalytically active recombinant West Nile virus NS3 protease

West Nile Virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection causes severe neurological disease and fatalities in both human and animal hosts. The West Nile viral protease (NS2B-NS3) is essential for post-translational processing in host-infected cells of a viral polypeptide precursor into structural and functional viral proteins, and its inhibition could represent a potential treatment for viral infections. This article describes the design, expression, and enzymatic characterization of a catalytically active recombinant WNV protease, consisting of a 40-residue component of cofactor NS2B tethered via a noncleavable nonapeptide (G(4)SG(4)) to the N-terminal 184 residues of NS3. A chromogenic assay using synthetic para-nitroanilide (pNA) hexapeptide substrates was used to identify optimal enzyme-processing conditions (pH 9.5, I < 0.1 M, 30% glycerol, 1 mM CHAPS), preferred substrate cleavage sites, and the first competitive inhibitor (Ac-FASGKR- H, IC50 &SIM; 1 μM). A putative three-dimensional structure of WNV protease, created through homology modeling based on the crystal structures of Dengue-2 and Hepatitis C NS3 viral proteases, provides some valuable insights for structure-based design of potent and selective inhibitors of WNV protease.

Non-additivity of attractive potentials in modeling of N-2 and Ar adsorption isotherms on graphitized carbon black and porous carbon by means of density functional theory

We present a new approach accounting for the nonadditivity of attractive parts of solid-fluid and fluidfluid potentials to improve the quality of the description of nitrogen and argon adsorption isotherms on graphitized carbon black in the framework of non-local density functional theory. We show that the strong solid-fluid interaction in the first monolayer decreases the fluid-fluid interaction, which prevents the twodimensional phase transition to occur. This results in smoother isotherm, which agrees much better with experimental data. In the region of multi-layer coverage the conventional non-local density functional theory and grand canonical Monte Carlo simulations are known to over-predict the amount adsorbed against experimental isotherms. Accounting for the non-additivity factor decreases the solid-fluid interaction with the increase of intermolecular interactions in the dense adsorbed fluid, preventing the over-prediction of loading in the region of multi-layer adsorption. Such an improvement of the non-local density functional theory allows us to describe experimental nitrogen and argon isotherms on carbon black quite accurately with mean error of 2.5 to 5.8% instead of 17 to 26% in the conventional technique. With this approach, the local isotherms of model pores can be derived, and consequently a more reliab * le pore size distribution can be obtained. We illustrate this by applying our theory against nitrogen and argon isotherms on a number of activated carbons. The fitting between our model and the data is much better than the conventional NLDFT, suggesting the more reliable PSD obtained with our approach.