Designing sequence to control protein function in an EF-hand protein

The extent of conformational change that calcium binding induces in EF-hand proteins is a key biochemical property specifying Ca(2+) sensor versus signal modulator function. To understand how differences in amino acid sequence lead to differences in the response to Ca(2+) binding, comparative analyses of sequence and structures, combined with model building, were used to develop hypotheses about which amino acid residues control Ca(2+)-induced conformational changes. These results were used to generate a first design of calbindomodulin (CBM-1), a calbindin D(9k) re-engineered with 15 mutations to respond to Ca(2+) binding with a conformational change similar to that of calmodulin. The gene for CBM-1 was synthesized, and the protein was expressed and purified. Remarkably, this protein did not exhibit any non-native-like molten globule properties despite the large number of mutations and the nonconservative nature of some of them. Ca(2+)-induced changes in CD intensity and in the binding of the hydrophobic probe, ANS, implied that CBM-1 does undergo Ca(2+) sensorlike conformational changes. The X-ray crystal structure of Ca(2+)-CBM-1 determined at 1.44 A resolution reveals the anticipated increase in hydrophobic surface area relative to the wild-type protein. A nascent calmodulin-like hydrophobic docking surface was also found, though it is occluded by the inter-EF-hand loop. The results from this first calbindomodulin design are discussed in terms of progress toward understanding the relationships between amino acid sequence, protein structure, and protein function for EF-hand CaBPs, as well as the additional mutations for the next CBM design.     

Europium-Containing Organic Gels and Organic and Carbon Aerogels. Preparation and Initial Applications in Catalysis

We prepared organic gels and organic and carbon aerogels doped with europium through sol–gel processes. Eu-gels were prepared by sol–gel polymerization of the potassium salt of 2,4-dihydroxybenzoic acid with formaldehyde followed by ion-exchange with Eu(OTf)₃. Eu–organic aerogels were obtained after CO₂ supercritical drying of the gels and Eu–carbon aerogels were obtained by pyrolysing the organic aerogels. The Eu-gels containing 12% europium proved to be efficient as recoverable catalyst in Michael additions.     

Organocatalytic synthesis of dipyrromethanes by the addition of N-methylpyrrole to aldehydes

The reaction of aldehydes with N-methylpyrrole carried out in the presence of catalytic pyrrolidinium tetrafluoroborate at room temperature affords the corresponding dipyrromethanes and minor amounts of tripyrranes. This new, mild, and convenient process represents the first organocatalytic synthesis of dipyrromethanes. The products are obtained in chemical yields similar to those obtained with existing methods, which, however, require either a much larger excess of heterocycle (when aldehydes are employed as starting materials), or more drastic reaction conditions (when aldehyde equivalents are used as starting materials) than those employed here. A mechanism is proposed to explain the course of this reaction.     

Stereoselective dimerization of 3-arylisoxazoles to cage-shaped bis-β-lactams syn 2,6-diaryl-3,7-diazatricyclo[4.2.0.0]octan-4,8-diones induced by hindered lithium amides

3-Arylisoxazoles react with hindered lithium amides giving syn 2,6-diaryl-3,7-diazatricyclo[4.2.0.0^2,5]octan-4,8-diones in good to fair yields. Stereochemistry of the so-obtained cage-shaped bis-β-lactams was assigned by X-ray diffraction analysis. Concerning the mechanism of formation of such hitherto unknown molecules, dimerization of an azetinone anion intermediate stereoselectively induced by Li⁺ chelation is suggested.     

Differentially-protected steroidal triamines; scaffolds with potential for medicinal, supramolecular, and combinatorial chemistry

Cholic acid 2a has been converted into two new orthogonally-protected triamino scaffolds, 13 and 14. The synthesis proceeds via the bis-Boc-NH-substituted azide 10, for which an improved preparation is described. After removal of the Boc groups, the two axial amines are differentiated through a novel monoprotection employing 1-(2-nitrobenzenesulfonyloxy)-benzotriazole 29. Regioselectivity of > or 50 : 1 is achieved, presumably reflecting an exceptional sensitivity to steric hindrance. Protection of the remaining amino group as Boc or Alloc gives the scaffolds in approximately 40% overall yield from cholic acid. Scaffold 13 has been sequentially deprotected and derivatised with N-carbamoyl amino acids, to give a model for tripodal peptide libraries.     

Determination of important odor-active aldehydes of wine through gas chromatography-mass spectrometry of their O-(2,3,4,5,6-pentafluorobenzyl)oximes formed directly in the solid phase extraction cartridge used for selective isolation

A method for the quantitative determination of octanal, nonanal, decanal, (E)-2-nonenal and (E, Z)-2,6-nonadienal in wine has been developed. In the proposed method, 200 ml of wine percolate through a solid phase extraction (SPE) cartridge packed with 200 mg of LiChrolut EN resins. The interferences are eluted with 60 ml of an aqueous solution containing 40% of methanol and 1% of NaHCO3. In the same SPE cartridge, the corresponding O-(2,3,4,5,6-pentafluorobenzyl)oximes are formed by letting percolate 2 ml of the reagent solution (5 mg ml(-1)). At room temperature the derivatization goes to completion in 15 min. The derivatives are eluted with 2 ml of dichloromethane, and the extract is concentrated and then analyzed by gas chromatography-mass spectrometry (GC-MS). The percentage of recovery in the isolation process is better than 90% in all cases with the exception of octanal, and is independent of the wine studied. In the cases of octanal, nonanal and decanal, the detection limits of the method are determined by the contamination levels of the reagent itself, and vary between 160 and 380 ng l(-1). For (E)-2-nonenal and (E, Z)-2,6-nonadienal, the detection limits were 12 and 20 and ng l(-1), respectively. The linearity of the method upheld until 10 microg l(-1) and was satisfactory in all cases. The reproducibility of the method is independent of the concentration and ranges from 30 to 190 ng (l(-1). The method has been applied to the analysis of these components in several wine samples. With the exception of (E, Z)-2,6-nonadienal, all the components can reach concentrations above their corresponding odor threshold values.     

Effect of the systemic versus inhalatory administration of synthetic glucocorticoids on the urinary steroid profile as studied by gas chromatography-mass spectrometry

This paper presents a gas chromatography-mass spectrometry (GC-MS) study carried out on human urine to verify whether the administration of glucocorticoids can affect the urinary steroid profile, and especially the levels of endogenous glucocorticoids, androgens and their main metabolites.Betamethasone and beclomethasone, administered either systemically (per os or i.m.) or locally (by inhalation) have been studied. The determination of the urinary levels of endogenous glucocorticoids and androgens was carried out by GC-MS in electron impact ionization mode. Data were evaluated taking into account the baseline individual variability, and compared with values obtained on a control group.Detectable differences were recorded in the steroids metabolites excretion profiles between men and women. The circadian variability of the steroid profile was the same for both sexes, showing a maximum during the morning hours. After systemic treatment with synthetic glucocorticoids, the relative urinary concentrations of corticosteroids, androgens and of their metabolites were significantly altered, recording a transient decrease of the concentration of cortisol and tetrahydrocortisol and a parallel, although less pronounced, increase of the concentration of testosterone, epitestosterone and related androgenic steroids; while no effects were recorded if the administration was by inhalation.     

Electrochemical measurement of mercury concentration profiles in the pore-waters of sediments of the Venice Lagoon by ion-exchange voltammetry at polymer modified electrodes

Glassy carbon electrodes modified with coatings of poly-[1-methyl-3-(pyrrol-1-ylmethyl)pyridinium], poly-MPP, were employed for preconcentrating and detecting the anionic complex HgCl4(2-), which is the prevailing inorganic Hg(II) species in salt waters such as the pore-waters of sediments here examined. The application of ion-exchange voltammetry at poly-MPP coated electrodes in combination with an in situ pore-water sampler allowed the measurement of concentration vs. depth profiles for mercury dissolved in the pore-waters of a salt-marsh and of a mud-flat located in a polluted area of the Venice Lagoon. The trends of the mercury profiles are discussed in comparison with the trends measured from the same location for other trace metals (Zn, Cd, Cu and Pb) and reduced species such as S(-II) and Fe(II).     

Semi-empirical study of a reduced rubredoxin analogue

Molecular orbitals were determined for an analogue of reduced rubredoxin in an iterative extended Hückel (self-consistent charge) calculation. Zero field splittings and Mössbauer spectral parameters were then computed. The results are compared with available experimental data.     

Development and characterization of a solvent extraction-gas chromatographic/mass spectrometric method for the analysis of perfluorooctanesulfonamide compounds in solid matrices

A method utilizing solvent extraction and analysis by gas chromatography-positive chemical ionization mass spectrometry (SE-GC-PCIMS) was developed for the analysis of three neutral hydrophobic perfluorooctanesulfonamide compounds [perfluorooctanesulfonamide (PFOSA), N-ethyl perfluorooctanesulfonamide (N-EtPFOSA), and N,N-diethyl perfluorooctanesulfonamide (N,N-Et2PFOSA)]. These compounds are suspected metabolic precursors of perfluorooctane sulfonate. The SE-GC-PCI-MS method was used to analyze all three perfluorooctanesulfonamides in fast food, fish, and Arctic marine mammal liver samples. The SE-GC-PCI-MS method produced relatively higher recoveries of the analytes (averaging 83 +/- 6%, 84 +/- 9%, and 89 +/- 19% for N,N-Et2PFOSA, N-EtPFOSA, and PFOSA, respectively) with lower coefficients of variation, and less susceptibility to matrix effects, than ion pair extraction-liquid chromatography-tandem mass spectrometric methods. Method detection limits (MDLs) were 100, 120, and 250 pg/g for N,N-Et2PFOSA, N-EtPFOSA, and PFOSA, respectively. The three compounds were found at concentrations ranging from below the MDL to 22 ng/g wet weight in fast food, fish, and Arctic marine mammal liver samples.