Characterization of rhinovirus subviral A particles via capillary electrophoresis, electron microscopy and gas-phase electrophoretic mobility molecular analysis: Part I

During infection, enteroviruses, such as human rhinoviruses (HRVs), convert from the native, infective form with a sedimentation coefficient of 150S to empty subviral particles sedimenting at 80S (B particles). B particles lack viral capsid protein 4 (VP4) and the single-stranded RNA genome. On the way to this end stage, a metastable intermediate particle is observed in the cell early after infection. This subviral A particle still contains the RNA but lacks VP4 and sediments at 135S. Native (150S) HRV serotype 2 (HRV2) as well as its empty (80S) capsid have been well characterized by capillary electrophoresis. In the present paper, we demonstrate separation of at least two forms of subviral A particles on the midway between native virions and empty 80S capsids by CE. For one of these intermediates, we established a reproducible way for its preparation and characterized this particle in terms of its electrophoretic mobility and its appearance in transmission electron microscopy (TEM). Furthermore, the conversion of this intermediate to 80S particles was investigated. Gas-phase electrophoretic mobility molecular analysis (GEMMA) yielded additional insights into sample composition. More data on particle characterization including its protein composition and RNA content (for unambiguous identification of the detected intermediate as subviral A particle) will be presented in the second part of the publication.     

The initial step of silicate versus aluminosilicate formation in zeolite synthesis: a reaction mechanism in water with a tetrapropylammonium template

The initial step for silicate and aluminosilicate condensation is studied in water in the presence of a realistic tetrapropylammonium template under basic conditions. The model corresponds to the synthesis conditions of ZSM5. The free energy profile for the dimer formation ((OH)(3)Si-O-Si-(OH)(2)O(-) or [(OH)(3)Al-O-Si-(OH)(3)](-)) is calculated with ab initio molecular dynamics and thermodynamic integration. The Si-O-Si dimer formation occurs in a two-step manner with an overall free energy barrier of 75 kJ mol(-1). The first step is associated with the Si-O bond formation and results in an intermediate with a five-coordinated Si, and the second one concerns the removal of the water molecule. The template is displaced away from the Si centres upon dimer formation, and a shell of water molecules is inserted between the silicate and the template. The main effect of the template is to slow down the backward hydrolysis reaction with respect to the condensation one. The Al-O-Si dimer formation first requires the formation of a metastable precursor state by proton transfer from Si(OH)(4) to Al(OH)(4)(-) mediated by a solvent molecule. It then proceeds through a single step with an overall barrier of 70 kJ mol(-1). The model with water molecules explicitly included is then compared to a simple calculation using an implicit continuum model for the solvent. The results underline the importance of an explicit and dynamical treatment of the water solvent, which plays a key role in assisting the reaction.     

Nature and structure of aluminum surface sites grafted on silica from a combination of high-field aluminum-27 solid-state NMR spectroscopy and first-principles calculations

The determination of the nature and structure of surface sites after chemical modification of large surface area oxides such as silica is a key point for many applications and challenging from a spectroscopic point of view. This has been, for instance, a long-standing problem for silica reacted with alkylaluminum compounds, a system typically studied as a model for a supported methylaluminoxane and aluminum cocatalyst. While (27)Al solid-state NMR spectroscopy would be a method of choice, it has been difficult to apply this technique because of large quadrupolar broadenings. Here, from a combined use of the highest stable field NMR instruments (17.6, 20.0, and 23.5 T) and ultrafast magic angle spinning (>60 kHz), high-quality spectra were obtained, allowing isotropic chemical shifts, quadrupolar couplings, and asymmetric parameters to be extracted. Combined with first-principles calculations, these NMR signatures were then assigned to actual structures of surface aluminum sites. For silica (here SBA-15) reacted with triethylaluminum, the surface sites are in fact mainly dinuclear Al species, grafted on the silica surface via either two terminal or two bridging siloxy ligands. Tetrahedral sites, resulting from the incorporation of Al inside the silica matrix, are also seen as minor species. No evidence for putative tri-coordinated Al atoms has been found.     

Unveiling the relevance of the redox character of nitroaromatic and nitroheteroaromatic compounds as potential medicines

This review discusses the state of the art, challenges, and perspectives in recent applications of nitroaromatics and nitroheteroaromatics, which are redox-bio-activated drugs or leads, in Medicinal Chemistry. It deals mainly with the electrochemical approach toward the electron transfer-based molecular mechanisms of drug action, drug design, estimation and measurement of redox potentials, correlation of physicochemical and pharmacological data, and electrochemical studies of the main representatives of nitro-containing prodrugs, along with approaches to combat their toxicity issues, aiming at a better therapeutic profile. Electrochemical investigation plays essential roles, being strategic in the design and discovery of potential medicines.     

Direct, two-step synthetic pathway to novel dibenzo[a,c]phenanthridines

Novel dibenzo[a,c]phenanthridines are prepared regioselectively by the application of a straightforward synthetic pathway, starting from new 3,4-diaryl- and 3,4-dihydro-3,4-diarylisoquinolines prepared via Ritter-type heterocyclization and the more classical two-step reductive amination/Bischler-Napieralski cyclization of triarylethanones, respectively. A comparative study of nonphenolic oxidative coupling methodologies provides a highly efficient procedure, based on the hypervalent iodine reagent phenyliodine(III) bis(trifluoroacetate) (PIFA), to accomplish the final coupling step.     

N-Glycosidase treatment with 18O labeling and de novo sequencing argues for flagellin FliC glycopolymorphism in Pseudomonas aeruginosa

In prokaryote organisms, N-glycosylation of proteins is often correlated to cell–cell recognition and extracellular events. Those glycoproteins are potential targets for infection control. To date, many surface-glycosylated proteins from bacterial pathogens have been described. However, N-linked Pseudomonas surface-associated glycoproteins remain underexplored. We report a combined enrichment and labeling strategy to identify major glycoproteins on the outside of microorganisms. More precisely, bacteria were exposed to a mix of biotinylated lectins able to bind with glycoproteins. The latter were then recovered by avidin beads, digested with trypsin, and submitted to mass spectrometry. The targeted mixture of glycoproteins was additionally deglycosylated in the presence of H₂ ¹⁸O to incorporate ¹⁸O during PNGase F treatment and were also analyzed using mass spectrometry. This approach allowed us to identify a few tens of potential N-glycoproteins, among which flagellin FliC was the most abundant. To detect the possible sites of FliC modifications, a de novo sequencing step was also performed to discriminate between spontaneous deamidation and N-glycan loss. This approach led to the proposal of three potential N-glycosylated sites on the primary sequence of FliC: N26, N69, and N439, with two of these three asparagines belonging to an N-X-(S/T) consensus sequence. These observations suggest that flagellin FliC is a heterogeneous protein mixture containing both O- and N-glycoforms.

QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface

We present a new software to easily perform QM:MM and QM:QM' calculations called QMX. It follows the subtraction scheme and it is implemented in the Atomic Simulation Environment (ASE). Special attention is paid to couple molecular calculations with periodic boundaries approaches. QMX inherits the flexibility and versatility of the ASE package: any combination of methods namely force field, semiempirical, first principle, and ab initio, can be used as hybrid potential energy surface (PES). Its ease of use is demonstrated by considering the adsorption of Al₂Cl₃Me₃ on silica surface and by combining different levels of theory (from standard DFT to MP2 calculations) for the so‐called High Level cluster with standard PW91 density functional theory calculations for the Low Level environment. It is shown that the High Level cluster must contain the silanol group close to the aluminum atoms. The bridging adsorption is favored by 58 kJ mol^?1 at the MP2:PW91 level with respect to the terminal position. Using large clusters at the MP2:PW91 level, it is shown that PW91 calculations are sufficient for structure optimization but that embedded methods are required for accurate energy profiles. © 2013 Wiley Periodicals, Inc.