Monitoring folding transitions of synthetic,branched-chain polypeptides by capillary zone electrophoresis

The coil/helix transition of a synthetic, branched-chain polymeric polypeptide (poly (Lys(Glu(1)-DL-Ala(3))EAK), 50-Lys residues long in the backbone, as a function of increasing molarities of methanol in solution, is here studied by both, circular dichroism (CD) and capillary zone electrophoresis. CD spectra showed that, at 75% v/v methanol, the transition from random coil to fully helical structure was obtained, in a pH 1.1 HCI solution in the presence of 20 mM NaCI. CZE studies, run in parallel, exhibited the classical unfolding to folding sigmoidal transition, with mid-point at 60% v/v methanol concentration, plateauing at ca. 80% v/v organic solvent. Surprisingly, though, such unfolding to folding transition was accompanied by an expansion, rather than a contraction, of the resulting ordered polypeptide. As the charge of the polypeptide (a pure polycation at a pH of 2.1 in CZE) was kept rigorously constant, a plot of the radius of the polymer along the sigmoidal transition clearly showed that the radius of gyration of the helical, structured polypeptide was in fact larger than that of the random coil. Such results were confirmed by molecular dynamics simulations, which indicated that the dimensions of such polypeptide, in alpha-helix configuration, were 8.5 nm (in length) and 3.2 nm (in diameter), whereas those of the corresponding random coil were 7.2 nm (in length) and 5.1 nm (length of shorter axis). It would thus appear that the randomized structure assumes the shape of a more compact object, roughly resembling a "rugby ball".     

Matrix removal for the ion chromatographic determination of some trace elements in milk

An ion chromatographic method has been developed for the determination of some microelements in different types of milk. It involves oxidative photodegradation of the organic matrix with H₂O₂ in a UV digester, equipped with a high-pressure mercury lamp. The temperature of the sample is maintained at 85±5 °C by a combined air/water cooling system. This procedure provides an efficient alternative to traditional dry ashing and wet digestion methods. Milk degrades in less than 2 h, while inorganic constituents, except for iodide, nitrate, nitrite, sulfite and manganese (II), are unaffected by UV radiation. Depending upon the type of milk (whole, skimmed, powdered, evaporated, etc.) to be analysed, the amount of sample and the UV photolysis time can be adjusted as per requirements. The clear solution resulting from the UV digestion is diluted, filtered and injected onto an ion chromatograph equipped with both conductivity and variable-wavelength UV-Vis detectors. The method has been tested with standards and real milk samples and has been found to be satisfactory for the determination of total chloride, bromide, phosphorus (as phosphate) and sulfur (as sulfate), and of copper, nickel, zinc, cobalt, iron and lead.     

Complex formation equilibria between Ag(I) and thioureas in n-propanol

Complex formation equilibria between Ag(I) and thiourea or N-alkyl-substituted thioureas have been investigated in n-propanol by potentiometry at 10 °C intervals from 5 to 50 °C. Stepwise formation of tris-coordinated AgL_n (n = 1-3) complexes has been found for the majority of the ligands. ΔH and ΔS values for the complex formation reactions have been evaluated from the dependence of ln β_n on temperature. The alkyl-substituents affect the ligand affinities in different ways in relation with the coordination level n.The reactions are exothermic with few exceptions. Enthalpy favoured complex formation with negative dependence of ΔG on temperature (ΔS > 0) have been found.The enthalpy and entropy changes for the stepwise complex formation equilibria are correlated by two linear compensative relationships with the same isoequilibrium temperature 50-51 °C.     

Environmental effects on a prion's helix II domain: copper(II) and membrane interactions with PrP180-193 and its analogues

An abnormal interaction between copper and the prion protein is believed to play a pivotal role in the pathogenesis of prion diseases. Copper binding has been mainly attributed to the N-terminal domain of the prion protein, but this hypothesis has recently been challenged in some papers which suggest that the C-terminal domain might also compete for metal anchoring. In particular, the segment corresponding to the helix II region of the prion protein, namely PrP180-193, has been shown both to bind copper and to exhibit a copper-enhanced cytotoxicity, as well as to interact with artificial membranes. The present work is aimed at extending these results by choosing the most representative model of this domain and by determining its copper affinity. With this aim, the different role played by the electrostatic properties of the C- and N-termini of PrP180-193 (VNITIKQHTVTTTT) in determining its conformational behaviour, copper coordination and ability to perturb model membranes was investigated. Owing to the low solubility of PrP180-193, its copper affinity was evaluated by using the shorter PrPAc184-188NH2 (IKQHT) analogue as a model. ESI-MS, ESR, UV/Vis, and CD measurements were carried out on the copper(II)/PrPAc184-188NH2 and copper(II)/PrP180-193NH2 systems, and showed that PrPAc184-188NH2 is a reliable model for the metal interaction with the helix II domain. The affinity of copper(II) for the helix II fragment is higher than that for the octarepeat and PrP106-126 peptides. Finally, the different ability of PrP180-193 analogues to perturb the DPPC model membrane was assessed by DSC measurements. The possible biological consequences of these findings are also discussed briefly.     

Fluorinated heterocyclic compounds. An effective strategy for the synthesis of fluorinated Z-oximes of 3-perfluoroalkyl-6-phenyl-2h-1,2,4-triazin-5-ones via a ring-enlargement reaction of 3-benzoyl-5-perfluoroalkyl-1,2,4-oxadiazoles and hydrazine

The reaction of 3-benzoyl-5-perfluoroalkyl-1,2,4-oxadiazoles with hydrazine has been investigated, evidencing the possibility of competitive reaction paths. Nucleophilic addition of the hydrazine to the electrophilic C(5) of the 1,2,4-oxadiazole ring, followed by ring opening and ring closure with enlargement, leads with high yield and in very mild experimental conditions to the formation of Z-oximes of 3-perfluoroalkyl-6-phenyl-2H-1,2,4-triazin-5-ones (11a-c) as major products of the reaction. In turn, the hydrazine can attack the electrophilic carbonyl carbon giving 4-perfluoroacylamino-5-phenyl-2H-1,2,3-triazoles (13a-c) through the well-known Boulton-Katritzky rearrangement of the intermediate hydrazones.     

Endogenous growth of the population of reverse micelles

The coupling reaction between cetylbromide (CB) and trimethylamine (TMA) to yield the surfactant cetyltrimethylammonium bromide (CTAB) is studied in the system chloroform/isooctane (2/1,v/v)/water in which CTAB forms reverse micelles. This system affords an endogenous micelle population growth, i.e., an increase of the concentration of the micelles due to appearance of the surfactant in situ. The reaction is studied in the presence of preexisting CTAB reverse micelles. The rate of CTAB formation is measured by NMR spectroscopy, and the endogenous micelle population growth is directly monitored by time-resolved fluorescence quenching analysis. Under our experimental conditions, a 100% yield of the chemical reaction brings about a fourfold increase in the population of the reverse micelles. Since the water concentration is constant during chemical reaction, the newly formed water pools are formed at the expense of the initial ones, which brings about a decrease of the average water pool radius during micellar growth. The implication of the endogenous micelle population growth as a model for biological systems is briefly discussed.     

Mononuclear heterocyclic rearrangements. Part 4 Synthesis and characterization of the E-isomer phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole

3-Benzoyl-5-phenyl-1,2,4-oxadiazole (I) with phenylhydrazine in acetic acid gives the two geometrical isomers, phenylhydrazones II-Z and II-E, which have been characterized by uv-visible, ir, and nmr spectra. The possible II-E ? II-Z isomerization as well as the rearrangement of II-Z and of II-E into 2,5-diphenyl-4-benzoylamino-1,2,3-triazole (III) has been pointed out.     

Spot overlapping in two-dimensional polyacrylamide gel electrophoresis separations: a statistical study of complex protein maps

A statistical approach able to extract the information contained in a two-dimenisional polyacrylamide gel electrophoresis (2-D PAGE) separation is here reported. The method is based on the quantitative theory of peak overlapping, a procedure previously developed by the authors and here extended to 2-D separations. The whole map is divided into many strips in order to obtain 1-D separations on which the statistic procedure is applied: the developed algorithms, on the basis of spot experimental data (intensity and spatial coordinates) permit to estimate the intrinsic number of components and to single out the specific order present in spot positions. The procedure was validated on computer-simulated maps. Its applicability to real samples was tested on maps obtained from literature sources. The following important information on protein mixtures can be extracted: (i) the number of proteins can be accurately estimated, on the basis of the spatial coordinates and intensities of spots detected in the 2-D PAGE map; (ii) the model describing distribution of interdistance between adjacent spots can be identified in both the separation dimensions; (iii) the presence of repeated interdistances in spot positions in the maps can be easily singled out: these regularities suggest specific protein modifications.     

The ring-opening reaction of chromenes: a photochemical mode-dependent transformation

The efficiency of the photochemical ring-opening of chromenes (or benzopyrans) depends on the vibronic transition selected by the chosen excitation wavelength. In the present work, ab initio CASPT2//CASSCF calculations are used to determine the excited-state ring-opening reaction coordinate for 2H-chromene (C) and 2,2-diethyl-2H-chromene (DEC) and provide an explanation for such an unusual mode-dependent behavior. It is shown that excited-state relaxation and decay occur via a multimodal and barrierless (or nearly barrierless) reaction coordinate. In particular, the relaxation out of the Franck-Condon involves a combination of in-plane skeletal stretching and out-of-plane modes, while the second part of the reaction coordinate is dominated exclusively by a different out-of-plane mode. Population of this last mode is shown to be preparatory with respect to both C-O bond breaking and decay via an S(1)/S(0) conical intersection. The observed mode-dependent ring-opening efficiency is explained by showing that the vibrational mode corresponding to the most efficient vibronic transition has the largest projection onto the out-of-plane mode of the reaction coordinate. To support the computationally derived mechanism, we provide experimental evidence that the photochemical ring-opening reaction of 2,2-dimethyl-7,8-benzo(2H)chromene, that similarly to DEC exhibits a mode-dependent photoreaction, has a low ( approximately 1 kcal mol(-1)) activation energy barrier.     

Solid State NMR and TG/MS Study on the Transformation of Methyl Groups During Pyrolysis of Preceramic Precursors to SiOC Glasses

The sol-gel method was used to prepare two different starting gels containing SiCH₃-groups for the preparation of SiOC ceramics. To understand the role of Si—H bonds in the incorporation of carbon into the SiOC network, gels prepared from a 1:2 mixture of triethoxysilane and methyldiethoxysilane (T^HD^H2) and solely methyltriethoxysilane (T^Me) were investigated. Thermogravimetric analysis coupled with mass spectroscopy (TG-MS) in inert atmosphere was performed to attain an insight into the decomposition reactions involved during gel-glass transformation. Samples calcined at different temperatures up to 1000°C were characterized by ²⁹Si and ¹³C magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. The presence of SiH groups in the starting gel allows an efficient conversion of Si—CH₃ groups into CSi₄ sites at lower temperatures. As a result, despite a much lower amount of carbon in the starting T^HD^H2 gel (C/Si = 0.33) compared to the T^Me gel (C/Si = 1), the amount of carbon inserted into the SiOC network of both glasses is equivalent, but the T^Me sample contains the 10 fold amount of free carbon.