Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma

This paper presents the recently introduced Off-Gel electrophoresis (OGE) technology as a versatile tool to reproducibly fractionate intact proteins and peptides into discrete liquid fractions. The coupling of two stages of OGE, i.e., the separation of intact proteins in a first-stage followed by fractionation of peptides derived from each protein fraction after proteolysis in a second stage, results in an array of 15 x 15 fractions that are directly amenable to additional peptide fractionation like reverse-phase liquid chromatography (RPC). The analysis of all second-stage peptide fractions from only the first-stage protein fraction representing pH 5.0 -5.15 by on-line reverse-phase LC-tandem mass spectrometry resulted in the identification of 53 proteins (337 peptides), of which 10 were on different immunoglobulin (Ig) chains, with an input of only 1.5 mg human blood plasma proteins. Increasing the protein load to approximately 12 mg increased the number of identified proteins in the same protein fraction to 73 proteins (449 peptides), of which 15 were Ig-related. Immunodepletion of six of the most abundant proteins (albumin, transferrin, haptoglobin, IgG, IgA, and alpha-1-antitrypsin) prior to first-stage OGE with an input of 1.5 mg of protein (equivalent to approximately 10 mg nondepleted plasma) resulted in the identification of 81 proteins (660 peptides), of which three were still Ig fragments. The pI-based separation of peptides appears to be nonuniform based on the theoretically determined pI values of identified peptides. This observation specifically accounts for the neutral zone (pI 5-8) and can be accounted for by the physicochemical properties of the peptides given by their amino acid composition. The power of OGE separation of proteins and peptides is discussed with a focus on the use of the knowledge about the pI of proteins and peptides that assist the validation of correct identifications together with the retention time of peptides on RPC.     

Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra

The infrared (IR) and Raman spectra of eight substitutional carbon defects in silicon are computed at the quantum mechanical level by using a periodic supercell approach based on hybrid functionals, an all electron Gaussian type basis set and the CRYSTAL code. The single substitutional C _s case and its combination with a vacancy (C _sV and C _sSiV) are considered first. The progressive saturation of the four bonds of a Si atom with C is then examined. The last set of defects consists of a chain of adjacent carbon atoms C, with i = 1–3. The simple substitutional case, C _s, is the common first member of the three sets. All these defects show important, very characteristic features in their IR spectrum. One or two C related peaks dominate the spectra: at 596 cm⁻¹ for C _s (and C _sSiV, the second neighbor vacancy is not shifting the C _s peak), at 705 and 716 cm⁻¹ for C _sV, at 537 cm⁻¹ for C and C (with additional peaks at 522, 655 and 689 for the latter only), at 607 and 624 cm⁻¹, 601 and 643 cm⁻¹, and 629 cm⁻¹ for SiC, SiC, and SiC, respectively. Comparison with experiment allows to attribute many observed peaks to one of the C substitutional defects. Observed peaks above 720 cm⁻¹ must be attributed to interstitial C or more complicated defects.     

Optimization of spiroimidazolidinone derivatives synthesis on solid phase using SynPhase™ Lanterns

We report the synthesis of 1,4,8-triazaspiro[4.5]decan-2-one derivatives from N-benzyl-4-piperidone and N-protected amino acid amides on solid support. We have translated the chemistry from solution to solid phase using a backbone amide linker (BAL) mimic. Using a parallel combinatorial approach, we performed the optimization of the synthesis on SynPhase™ Lanterns.     

Titanates de cuivre substitués à structure bixbyite: Les composés Cu1−xTi1−xFe2xO3 (0.15 ≤ x ≤ 0.33)

A new bixbyite family, Cu_1?xTi_1?xFe_2xO₃ (0.15 ≤ x ≤ 0.33) has been synthesized and characterized. The unit cell is cubic: a ～ 9.40Å. The X-ray powder diffraction study shows up an isotypism with the (Fe, Mn)₂O₃ compounds. There is a disordered distribution of Cu^II, Ti^IV, and Fe^III over the two cyrstallographic sites: P_I and P_II. P_II is highly distorted (two long MO distances) by the Jahn-Teller effect of Cu^II. The bixbyite structure is described in terms of polyhedra arrangement, as a particular case of the CM₂O₃ family. The cation packing is discussed in relation with the existence of the bixbyite structure for the Cu_1?xTi_1?xFe_2xO₃ compounds. The electrical properties (σ ～ 10^?5(Ω cm)^?1 for x = 0.286 at room temperature) show an electron conduction with probably a hopping mechanism.     

Structure of gas phase [C5H6]+˙ ions

Charge-stripping spectra have been used to differentiate ionized cyclopentadiene from its acyclic isomers. The minimum amounts of translational energy lost during the charge-stripping processes and the relative charge-stripping efficiencies, which are also structurally important parameters, have been measured for these ionic species. [C₅H₆]⁺˙ ions, formed by dissociative ionization of various precursors in the ion source are found, usually, to be a mixture of cyclic and acyclic ions. In contrast, [C₅H₆]⁺˙ ions, derived from the dissociation of metastable molecular ions from a series of organic compounds, have the cyclopentadienyl structure. This structure was confirmed by collision-induced dissociation of ions formed in the first field-free region of a triple sector mass spectrometer.     

Radical amination with sulfonyl azides: a powerful method for the formation of C-N bonds

A novel reaction for the introduction of an azide moiety by means of a mild radical process is currently under development. Sulfonyl azides are suitable azidating agents for nucleophilic radicals, such as secondary and tertiary alkyl radicals. More electrophilic radicals, such as enolate radicals, do not react with sulfonyl azides. This feature allowed the development of efficient intra- and intermolecular carboazidations of olefins. Due to the versatility of the azido group, this reaction has an important synthetic potential, as already demonstrated by the preparation of the core of several alkaloids, particularly those containing an amino-substituted quaternary carbon center, such as FR901483.     

Long term stability of organic selenium species in aqueous solutions

Long term stability of organic selenium compounds (selenocystine, selenomethionine, trimethylselenonium ion) has been studied over a one year period for 2 analyte concentrations: 25 and 150 μg/L Se, at pH 4.5 in the dark, under different storage conditions: temperature of –20°C, 4°C, 20°C, 40°C; in Pyrex, Teflon, or polyethylene containers; in an aqueous matrix or in the presence of a chromatographic counter ion (pentyl sulfonate at 10^–4 mol/L concentration). Light effects have also been tested. The stability of the selenium species was monitored by HPLC-ICP/MS. Storage conditions can drastically alter the stability of organic selenium species. Organoselenium compounds were shown to be stable in the dark over a one year period in an aqueous matrix at pH 4.5 in Pyrex containers at both 4°C and 20°C. Pyrex vials exposed to natural sunlight at room temperature resulted in a steady decrease of the selenoamino acid concentration. Teflon containers caused losses of less than 25% at both 4° C and 20° C in the dark. However, polyethylene vials presented, at all temperatures tested, a rapid decrease of the TMSe⁺ concentration. The stability of the Se species studied did not show significant differences between 4° C and 20° C in any container material used. Storage of solutions at 40° C led to slight differences between the Pyrex and Teflon containers. However, polyethylene presented a drastic decrease of the three species over time at this higher temperature. Solutions frozen at –20° C in polyethylene vials did not stabilize the TMSe⁺ signal. Finally, concentrations and matrices of the samples did not significantly affect the stability of the species. Received: 15 July 1996 / Revised: 14 July 1997 / Accepted: 18 July 1997     

硅表面嫁接有机单分子膜的研究近况

由于在微电子、化学 /生物化学传感器、纳米技术及太阳能等领域具有潜在的应用价值 ,通过 Si— C键在硅表面上直接嫁接有机单分子膜 ,已成为近几年新开展的研究热点 .对这一研究领域进行了概要综述     

Chemo- and Stereoselective Coordination of 5,6-Dimethylidene-7-oxabicyclo[2.2.1]hept-2-ene by d8- and d6-Metal Carbonyls. Diels-Alder reactivity of Dienes Perturbed by Remote Olefin Complexation

The endocyclic double bond C(2), C(3) in 5,6-dimethylidene-7-oxabicyclo[2.2.1]-hept-2-ene ( 1 ) can he coordinated selectively on its exo-face before complexation of the exocyclic s-cis-butadiene moiety. Irradiation of Ru₃(CO)₁₂ or Os₃(CO)₁₂ in the presence of 1 gave tetracarbonyl [(1R,2R, 3S,4S)-2,3-η-(5,6-dimethylidene-7-oxabicyclo[2.2.1]-hept-2-ene)]ruthenium ( 6 ) or -osmium ( 8 ). Similarly, irradiation of Cr(CO)₆ or W(CO)₆ in the presence of 1 gave pentacarbonyl[(1R, 2R, 3S,4S)-2,3-η-(5,6-dimethylidene-7-oxabicyclo[2.2.1]hept-2-ene)]chromium (10) or -tungsten (11) . Irradiation of complexes 6 and 11 in the presence of 1 led to further CO substitution giving bed-tricarbonyl-ae-bis[(1R,2R,3S,4S)-2,3-η-(5,6-dimethylidene-7-oxabicyclo[2.2.1]hept-2-ene)]ruthenium ( 7 ) and trans-tetracarbonyl[(1R,2R,3S,4S)-2,3-η-(5,6-dimethylidene-7-oxabicyclo-[2.2.1]hept-2-ene)]tungsten (12) , respectively. The diosmacyclobutane derivative cis-m?-[(1R,3R,3S,4S)-(5,6-dimethylidene-7-oxabicyclo[2.2.1]hepta-2,3-diyl)]bis(tetracarbonyl-osmium) (Os-Os) (9) wa also obtained. The Diels-Alder reactivity of the exocyclic s-cis-butadiene moiety in complexs 7 and 8 was found to be significantly higher than that of the free triene 1 .     

Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.