Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format

Improvement of in-gel digestion efficiency is highly desirable for one- or two-dimensional gel electrophoretic separation and mass spectrometric (MS) analysis in proteomics, because the resultant increases in sequence coverage and MS signal intensity lead to higher confidence in protein identification. Here an optimized in-gel digestion system, in combination with thin-gel separation and negative staining in a high-throughput format using 96-well plates, is described. The combination of negative staining and protein separation on a 0.9 mm thick gel showed a clear improvement in in-gel digestion efficiency in comparison with the more typical protocols such as the combination of silver staining and a 1.0 mm gel. In addition, the use of 96-well plates to increase throughput did not decrease the efficiency of this strategy when the stirring of the gel pieces in processes such as destaining, washing, gel-shrinking and peptide extraction was performed by sonication instead of shaking the plates. This procedure was optimized and applied to identify proteins of the postsynaptic density fraction; 105 proteins were identified after SDS-PAGE separation.     

Deuterium substitution effect on proton relaxation times as a direct means for elucidating molecular interaction in solution. An application to 2′,3′-isopropylideneadenosine

Proton T₁ measurement with the Fourier transform method combined with quenching of dipolar coupling through selective deuterium substitution is shown to be a useful method for elucidating intra- and intermolecular interactions in solution, with 2′,3′-isopropylideneadenosine as an example. Average distances between H-8 and ribose protons are determine in combination with carbon-13 T₁ measurement. The method is compared with the nuclear Overhauser effect.     

Identification of Shiga toxins in Shiga toxin-producing Escherichia coli using immunoprecipitation and high-performance liquid chromatography-electrospray ionization mass spectrometry

We developed a rapid and reliable identification method for Shiga toxins in Shiga toxin-producing Escherichia coli (STEC) using immunoprecipitation and high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS). Polyclonal antisera specific for Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2) were raised in rabbits so as to be used for the immunoprecipitation. The immunoprecipitaion was carried out by mixing sample solutions with 50 microl each of the antisera to Stx1 and Stx2 followed by allowing the mixed solutions to stand for 30 min. The quantity required to obtain the immunoprecipitate was more than 0.5 microg of Shiga toxins. HPLC-ESI-MS analysis of the resulting immunoprecipitates provided accurate molecular weight information on Shiga toxins, leading to direct evidence for the presence of these toxins. It requires at most two days to perform our procedure from toxin extraction to measurement of HPLC-ESI-MS whereas the previous method using isolation procedures required about two weeks to complete. The usefulness of the present method has been demonstrated by identifying Stx1, Stx2 and a variant of Stx2 (Stx2e) in the immunoprecipitates prepared from STEC strains.     

Palladium-catalyzed aminoallylation of activated olefins with allylic halides and phthalimide

The three-component aminoallylation reaction of the activated olefins 2 with the phthalimide 1a and allyl chloride proceeded very smoothly in the presence of Pd(2)dba(3).CHCl(3) (5 mol %)/P(4-FC(6)H(4))(3) (40 mol %) and Cs(2)CO(3) (3 equiv against 2) in dichloromethane at room temperature to give the corresponding aminoallylated products, N-pent-4-enylphthalimides 3, in 58-99% yields. The reaction of oxazolidinone 1b also proceeded very smoothly to give N-(2,2-dicyano-1-phenylpent-4-enyl)oxazolidinone in a quantitative yield; however, the Tsuji-Trost-type allylation products 4 were obtained in the case of dibenzylamine, N-tosylaniline, and pyrrolidin-2-one. Further, 2 underwent cycloaddition with N-tosylvinylaziridine 9a in the presence of Pd(2)dba(3).CHCl(3) (5 mol %)/P(4-FC(6)H(4))(3) (40 mol %) in THF at room temperature, giving the corresponding pyrrolidines 11 in 69-99% yields.     

Dynamic stability of carbonyl ylides

The non- and fluorine-substituted singlet carbonyl ylides are studied by using ab initio MCSCF calculations. The thermodynamic stability of the carbonyl ylides and the intramolecular stability to isomerization or fragmentation reaction coordinates is demonstrated in terms of the topological structure of the ab initio potential energy surfaces. The allylic resonance is found to be dynamically unstable, considering out-of-plane vibrational mode. The instability is studied by the symmetries of the low-lying excitations out of the MCSCF wave function.     

Electrophoretic mobility of a charged cylindrical colloidal particle covered with an ion-penetrable uncharged polymer layer

Expressions are derived for the electrophoretic mobility of a cylindrical charged colloidal particle carrying a low zeta potential covered with an ion-penetrable uncharged polymer layer in an electrolyte solution. These expressions involve numerical integration of modified Bessel functions but are easily calculable with Mathematica. The obtained mobility expressions are a modification of Henry's mobility formula for a cylindrical particle taking into account the presence of the uncharged polymer layer.