A non-damaging method to analyze the configuration and dynamics of nitrotyrosines in proteins

Often, deregulation of protein activity and turnover by tyrosine nitration drives cells toward pathogenesis. Hence, understanding how the nitration of a protein affects both its function and stability is of outstanding interest. Nowadays, most of the in vitro analyses of nitrated proteins rely on chemical treatment of native proteins with an excess of a chemical reagent. One such reagent, peroxynitrite, stands out for its biological relevance. However, given the excess of the nitrating reagent, the resulting in vitro modification could differ from the physiological nitration. Here, we determine unequivocally the configuration of distinct nitrated-tyrosine rings in single-tyrosine mutants of cytochrome?c. We aimed to confirm the nitration position by a non-destructive method. Thus, we have resorted to (1)H-(15)N heteronuclear single quantum coherence(HSQC) spectra to identify the (3)J(N?H) correlation between a (15)N-tagged nitro group and the adjacent aromatic proton. Once the chemical shift of this proton was determined, we compared the (1)H-(13)C HSQC spectra of untreated and nitrated samples. All tyrosines were nitrated at ε positions, in agreement to previous analysis by indirect techniques. Notably, the various nitrotyrosine residues show a different dynamic behaviour that is consistent with molecular dynamics computations.     

Platinum-catalysed bisindolylation of allenes: a complementary alternative to gold catalysis

Pt versus Au: Platinum-catalysed addition of nucleophiles to allenes follows a distinctly different pathway to the process catalysed by gold(I) complexes; the platinum catalyst leads to different products with indoles involving a bisindolylation reaction, whereas gold(I) gives allyl indoles from a single addition (see scheme).     

Synthesis,crystal structure and magnetic properties of the helical oxalate-bridged copper(II) chain {[(CH3)4N]2[Cu(C2O4)2] · H2O}n

The preparation, crystal structure and magnetic properties of a new oxalate-containing copper(II) chain of formula {[(CH₃)₄N]₂[Cu(C₂O₄)₂] · H₂O}_n (1) [(CH₃)₄N⁺ = tetramethylammonium cation] are reported. The structure of 1 consists of anionic oxalate-bridged copper(II) chains, tetramethylammoniun cations and crystallization water molecules. Each copper(II) ion in 1 is surrounded by three oxalate ligands, one being bidentate and the other two exhibiting bis-bidenate coordination modes. Although all the tris-chelated copper(II) units from a given chain exhibit the same helicity, adjacent chains have opposite helicities and then an achiral structure results. Variable-temperature magnetic susceptibility measurements of 1 show the occurrence of a weak ferromagnetic interaction through the oxalate bridge [J = +1.14(1) cm⁻¹, the Hamiltonian being defined as H = –J ∑_nmS_i · S_j]. This value is analyzed and discussed in the light of available magneto-structural data for oxalate-bridged copper(II) complexes with the same out-of-plane exchange pathway.     

Preparation of Biodegradable Polylactide Microparticles via a Biocompatible Procedure

PLA MPs are prepared via a novel and toxic‐chemical‐free fabrication route using ethyl lactate, a green solvent and FDA‐approved aroma. MPs are obtained by a solution jet break‐up and solvent displacement method. Adjusting flow parameters allows the tuning of MPs size between 60 and 180 µm, with reduced polydispersity. Morphological analysis shows microporous particles with Janus‐like surface. A fluorophore is successfully loaded into the MPs during their formation step. This versatile green solvent‐based procedure is proven to be suitable for drug encapsulation and delivery applications. The method may be extended to different droplet generation techniques.

     

Specific peptides as alternative to antibody ligands for biomagnetic separation of Clostridium tyrobutyricum spores

Nowadays, the reference method for the detection of Clostridium tyrobutyricum in milk is the most-probable-number method, a very time-consuming and non-specific method. In this work, the suitability of the use of superparamagnetic beads coated with specific antibodies and peptides for bioseparation and concentration of spores of C. tyrobutyricum has been assessed. Peptide or antibody functionalized nanoparticles were able to specifically bind C. tyrobutyricum spores and concentrate them up to detectable levels. Moreover, several factors, such as particle size (200 nm and 1 μm), particle derivatization (aminated and carboxylated beads), coating method, and type of ligand have been studied in order to establish the most appropriate conditions for spore separation. Results show that concentration of spore is favored by a smaller bead size due to the wider surface of interaction in relation to particle volume. Antibody orientation, related to the binding method, is also critical in spore recovery. However, specific peptides seem to be a better ligand than antibodies, not only due to the higher recovery ratio of spores obtained but also due to the prolonged stability over time, allowing an optimal recovery of spores up to 3 weeks after bead coating. These results demonstrate that specific peptides bound to magnetic nanoparticles can be used instead of traditional antibodies to specifically bind C. tyrobutyricum spores being a potential basis for a rapid method to detect this bacterial target.     

Presenilin-1 regulates the constitutive turnover of the fibronectin matrix in endothelial cells

Background

Presenilin-1 (PS1) is a transmembrane protein first discovered because of its association with familial Alzheimer’s disease. Mice with null mutations in PS1 die shortly after birth exhibiting multiple CNS and non-CNS abnormalities. One of the most prominent features in the brains of PS1?/? embryos is a vascular dysgenesis that leads to multiple intracerebral hemorrhages. The molecular and cellular basis for the vascular dysgenesis in PS1?/? mice remains incompletely understood. Because the extracellular matrix plays key roles in vascular development we hypothesized that an abnormal extracellular matrix might be present in endothelial cells lacking PS1 and examined whether the lack of PS1 affects expression of fibronectin a component of the extracellular matrix known to be essential for vascular development.

Results

We report that primary as well as continuously passaged PS1?/? endothelial cells contain more fibronectin than wild type cells and that the excess fibronectin in PS1?/? endothelial cells is incorporated into a fibrillar network. Supporting the in vivo relevance of this observation fibronectin expression was increased in microvascular preparations isolated from E14.5 to E18.5 PS1?/? embryonic brain. Reintroduction of PS1 into PS1?/? endothelial cells led to a progressive decrease in fibronectin levels showing that the increased fibronectin in PS1?/? endothelial cells was due to loss of PS1. Increases in fibronectin protein in PS1?/? endothelial cells could not be explained by increased levels of fibronectin RNA nor based on metabolic labeling studies by increased protein synthesis. Rather we show based on the rate of turnover of exogenously added biotinylated fibronectin that increased fibronectin in PS1?/? endothelial cells results from a slower degradation of the fibronectin fibrillar matrix on the cell surface.

Conclusions

These studies show that PS1 regulates the constitutive turnover of the fibronectin matrix in endothelial cells. These studies provide molecular clues that may help to explain the origin of the vascular dysgenesis that develops in PS1?/? embryonic mice.

     

Molybdenum- and tungsten(II) monometallic 3-(2-pyridyl)pyrazole and bimetallic 3-(2-pyridyl)pyrazolate complexes

Molybdenum and tungsten complexes containing the pypzH (3-(2-pyridyl)pyrazole) ligand as a chelating bidentate are prepared: [Mo(CO)(4)(pypzH)], cis-[MoBr(η(3)-allyl)(CO)(2)(pypzH)], cis-[MoCl(η(3)-methallyl)(CO)(2)(pypzH)], [MI(2)(CO)(3)(pypzH)] (M = Mo, W) from [Mo(CO)(4)(NBD)] or the adequate bis(acetonitrile) complexes. The deprotonation of the molybdenum allyl or methallyl complexes affords the bimetallic complexes [cis-{Mo(η(3)-allyl)(CO)(2)(μ(2)-pypz)}](2) or [cis-{Mo(η(3)-methallyl)(CO)(2)(μ(2)-pypz)}](2) (μ(2)-pypz = μ(2)-3-(2-pyridyl-κ(1)N)pyrazolate-2κ(1)N). The allyl complex was subjected to an electrochemical study, which shows a marked connection between both metallic centres through the bridging pyridylpyrazolates.     

Quantitative analysis of structure and bandgap changes in graphene oxide nanoribbons during thermal annealing

Graphene oxide nanoribbons (GONRs) are wide bandgap semiconductors that can be reduced to metallic graphene nanoribbons. The transformation of GONRs from their semiconductive to the metallic state by annealing has attracted significant interest due to its simplicity. However, the detailed process by which GONRs transform from wide-bandgap semiconductors to semimetals with a near zero bandgap is unclear. As a result, precise control of the bandgap between these two states is not currently achievable. Here, we quantitatively examine the removal of oxygen-containing groups and changes in the bandgap during thermal annealing of GONRs. X-ray photoelectron spectroscopy measurements show the progressive removal of oxygen-containing functional groups. Aberration-corrected scanning transmission electron microscopy reveals that initially small graphene regions in GONRs become large stacked graphitic layers during thermal annealing. These structural and chemical changes are correlated with progressive changes in the electrochemical bandgap, monitored by cyclic voltammetry. These results show that small changes in the thermal annealing temperature result in significant changes to the bandgap and chemical composition of GONRs and provide a straightforward method for tuning the bandgap in oxidized graphene structures.     

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.