Second-generation mimics of ganglioside GM1 oligosaccharide: a three-dimensional view of their interactions with bacterial enterotoxins by NMR and computational methods

As a step to delineate a strategy of ligand design for cholera toxin (CT), NMR studies were performed on several mimics of the GM1 ganglioside oligosaccharide. The conformation of these analogues was investigated first in solution and then upon binding to cholera toxin by transferred nuclear Overhauser effect (TR-NOE) measurements. It was demonstrated that CT selects a conformation similar to the global minima of the free saccharides from the ensemble of presented conformations. No evidence of major conformational distortions was obtained, but one or two of the available conformers of the hydroxyacid side chain appear to be selected in the bound state. The NMR data were interpreted with the aid of computer models, generated and analyzed by using a combination of different approaches (MacroModels' MC/EM and MC/SD, Autodock, and GRID). Analysis of the NMR data supported by computational studies allowed us to interpret the experimental observations and to derive workable models of the ligand:toxin complexes. These models suggest that the higher affinity of the (R)-lactic acid derivative 3 may stem from lipophilic interactions with a hydrophobic area in the toxin binding site located in the vicinity of the sialic acid side chain binding region of the CT:GM1 complex, and formed by the side chain of Ile-58 and Lys-34. Thus, the models obtained have allowed us to make useful design suggestions for the improvement of ligand affinity.     

Characterization of low-energy chlorophylls in the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. A site-selective fluorescence study

Almost all photosystem I (PSI) complexes from oxygenic photosynthetic organisms contain chlorophylls that absorb at longer wavelength than that of the primary electron donor P700. We demonstrate here that the low-energy pool of chlorophylls in the PSI-LHCI complex from the green alga Chlamydomonas reinhardtii, containing five to six pigments, is significantly blue-shifted (A(max) at 700 nm at 4 K) compared to that in the PSI core preparations from several species of cyanobacteria and in PSI-LHCI particles from higher plants. This makes them almost isoenergetic with the primary donor. However, they keep the other characteristic features of "red" chlorophylls: clear spectral separation from the bulk chlorophylls, big Stokes shift revealing pronounced electron-phonon coupling, and large homogeneous and inhomogeneous broadening of approximately 170 and approximately 310 cm(-1), respectively.     

X-ray diffraction and solid-state NMR studies of a germanium binuclear complex

A compound formulated as (C4H12N2)[Ge2(pmida)2(OH)2] x 4 H2O (where pmida(4-) = N-(phosphonomethyl)iminodiacetate and C4H12N2(2+) = piperazinedium cation), containing the anionic [Ge2(pmida)2(OH)2]2- complex, has been synthesised by the hydrothermal approach and its structure determined by single-crystal X-ray diffraction analysis. Several high-resolution solid-state magic-angle spinning (MAS) NMR techniques, in particular two-dimensional 1H-X(13C,31P) heteronuclear correlation (HETCOR) and 1H-1H homonuclear correlation (HOMCOR) experiments incorporating a frequency-switched Lee-Goldburg (FS-LG) decoupling scheme, have been employed for the first time in such a material. Using these tools in tandem affords an excellent general approach to study the structure of other inorganic-organic hybrids. We assigned the NMR resonances with the help of C...H and P...H internuclear distances obtained through systematic statistical analyses of the crystallographic data. The compound was further characterised by powder X-ray diffraction techniques, IR and Raman spectroscopy, and by elemental and thermal analyses (thermogravimetric analysis and differential scanning calorimetry).     

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.     

Bioavailability, bioaccumulation and tolerance of chromium: consequences in the food chain of freshwater ecosystems

Many abiotic and biotic factors can influence the partitioning equilibrium of heavy metals, thus influencing metal impact on aquatic environments. Unicellular algal species release soluble organic substances able to complex metals. In our laboratory a Cr-tolerant strain was selected and isolated from a wild type strain of Scenedesmus acutus. The exudates released by the two strains counteracted the growth inhibition caused by Cr(VI) and the exudates of the Cr-tolerant strain were more effective. On the contrary, the exudates did not reduce chromium toxicity to the cladoceran Daphnia magna. The reduction of chromium effect on algae seems the consequence of an algae-specific interaction among Cr(VI), exudates and algal cells. Chromium uptake resulted to be energy-dependent since bioaccumulation rate in subdued light condition was lower than at high light intensity. The effect of Cr(VI) on algae changed depending on metabolism of the cells and in particular it seemed to be related to the bioaccumulation rate. Tolerance in the selected strain could not be ascribed to a lower uptake of chromium. The difference in sensitivity to chromium between the two strains was exploited to evaluate if tolerance acquired by algae could have consequences for Daphnia. After treatment with Cr(VI), the two strains of S. acutus were used as food source for D. magna. The results indicate that chromium is accumulated by algae in a form not available for daphnids and that Cr tolerance acquired by the algae can be of some advantage to the consumer organism.     

Gallium metal mediated allylation of carbonyl compounds and imines under solvent-free conditions

Gallium metal is effective in mediating the allylation of various carbonyl compounds and imines under solvent-free conditions, with the application of sonic energy, affording the corresponding homoallylic alcohols and amines. The imines themselves were also prepared under solventless conditions in high yield, thereby establishing a two-step solvent-free synthesis of homoallylic amines. In comparison, indium metal produced a mixture of the desired homoallylic secondary amine and the bis-allylated species via an iminium ion intermediate.     

Solvent and temperature effects on the fluorescence and competitive photoreactions of cis-9-styrylanthracene

A fluorimetric and photochemical study of cis-9-styrylanthracene as a function of temperature has been carried out in different solvents with the aim of answering some open questions about the behavior of its first excited singlet state, S₁. In non-polar solvents, a parallel photoreactive pathway, leading to a cyclization adduct, was found to compete with fluorescence and isomerization already at 200 K, its contribution increasing markedly with temperature. The cis » trans photoisomerization occurs prevalently by a triplet mechanism, a detectable contribution of diabatic and adiabatic isomerization in S₁ being operative in these solvents from room temperature upwards. In polar solvents, the main deactivation pathway competitive with fluorescence is isomerization to trans, which occurs prevalently through a mixed singlet mechanism with a major diabatic and a minor adiabatic components.     

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.     

Effect of the rhenium additive to VOx/TiO2 and MoOx/TiO2 catalysts on their properties in oxidative dehydrogenation of propane

VO_x/TiO₂ and MoO_x/TiO₂ catalysts with the addition of Re (Re/V or Mo = 0.5) were synthetized and tested in oxidative dehydrogenation of propane and in reduction by propane. XPS measurements showed depletion of the surface in Re. The Re additive does not affect the total conversion of propane, but increases the selectivity to propene. The effect is more pronounced for the MoO_x/TiO₂ catalyst. The increase in the selectivity to propene is accompanied with the increase in the reducibility of the catalysts.