Effect of CyDye minimum labeling in differential gel electrophoresis on the reliability of protein identification

Differential 2-DE (DIGE) is a widely applied tool for the quantitative analysis of differentially represented proteins. The method involves covalent minimal labeling of proteins prior to their electrophoretic separation using CyDye DIGE Fluor minimal dyes. This methodology creates two different species per protein, the labeled (approx. 1-2%) and unlabeled (approx. 98-99%) ones, which differ in their molecular masses by 434-464 Da, depending on the attached dye. DIGE followed by automated spot picking according to the CyDye coordinates misses in many instances the exact positions where the maximum amounts of the considered proteins are located. This fact leads to a loss in sensitivity of the subsequent MALDI-MS analyses and results in a reduced reliability of protein identification and sequence coverage. In this paper, the migration differences of labeled and unlabeled species are quantified together with the impact of this effect on the certainty of protein identification and sequence coverage investigating proteins up to 90 kDa.     

Carbohydrate chain of ganglioside GM1 as a ligand: identification of the binding strategies of three 15 mer peptides and their divergence from the binding modes of growth-regulatory galectin-1 and cholera toxin

The branched pentasaccharide chain of ganglioside GM1 is a prominent cell surface ligand, for example, for cholera toxin or tumor growth-regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N-terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross-linking capacity of the natural lectins by peptide attachment to a suitable scaffold.     

Direct Catalytic Asymmetric Aldol Reaction of an α‐Azido Amide

A direct aldol reaction of an α‐azido 7‐azaindolinylamide, promoted by a Cu‐based cooperative catalyst, is documented. Aromatic aldehydes bearing an ortho substituent exhibited diastereodivergency depending on the nature of the chiral ligands used. Smooth reactions with ynals highlighted the broad substrate scope. A vicinal azido alcohol unit in the product allowed direct access to the corresponding aziridine and facile hydrolysis of the 7‐azaindolinylamide moiety furnished enantioenriched β‐hydroxy‐α‐azido carboxylic acid derivatives.     

Novel fluoro-substituted benzo- and benzothieno fused pyrano[2,3-c]pyrazol-4(1H)-ones

A straightforward, two-step synthesis of fluoro substituted chromeno[2,3-c]pyrazol- and [1]benzothieno[2′,3′:5,6]pyrano[2,3-c]pyrazol-4(1H)-ones, respectively, is presented. Hence, treatment of 1-substituted or 1,3-disubstituted 2-pyrazolin-5-ones with fluoro substituted 2-fluorobenzoyl chlorides or 3-chloro-6-fluoro-1-benzothiophene-2-carbonyl chloride using calcium hydroxide in refluxing 1,4-dioxane gave the corresponding 4-aroylpyrazol-5-ols, which were cyclized into the fused ring systems. 5-Fluorochromeno[2,3-c]pyrazol-4(1H)-one was obtained upon treatment of the 1-(4-methoxybenzyl) protected congener with trifluoroacetic acid. Treatment of 5-fluorochromeno[2,3-c]pyrazol-4(1H)-ones with methylhydrazine afforded novel tetracyclic ring systems such as 2-methyl-7-phenyl-2,7-dihydropyrazolo[4′,3′:5,6]pyrano[4,3,2-cd]indazole. Detailed NMR spectroscopic investigations (¹H, ¹³C, ¹⁵N, ¹⁹F) with the obtained compounds were undertaken.     

Studies on Immobilization and Partial Characterization of Lipases from Wheat Seeds (<Emphasis Type="Italic">Triticum aestivum</Emphasis>)

The objective of this study was to provide some features on immobilization and partial characterization of lipases from wheat seeds. The optimum pH and temperature were found to be 5.5 and 32–37 °C, respectively. The stability of the concentrated enzymatic extract to high temperatures (25, 35, 45, and 55 °C) showed that the incubation of the extract at 55 °C led to its complete inactivation. The concentrated enzymatic extract kept 90% of its hydrolytic and esterification activities until 70 and 40 days of storage at 4 °C, respectively. The extract presented higher hydrolytic specificity to substrates of medium and long chains and higher esterification affinity to fatty acids of short and medium chains and alcohols with two and three carbon atoms. After the immobilization process using activated coal and sodium alginate as supports, an enhancement of about threefold in lipase activity was observed. The development of the present work permitted us to point out some characteristics of lipases from wheat seeds necessary for the proposition of new future industrial applications for this important biocatalyst.     

Biomimetic membrane arrays on cast hydrogel supports

Lipid bilayers are intrinsically fragile and require mechanical support in technical applications based on biomimetic membranes. Tethering the lipid bilayer membranes to solid substrates, either directly through covalent or ionic substrate-lipid links or indirectly on substrate-supported cushions, provides mechanical support but at the cost of small molecule transport through the membrane-support sandwich. To stabilize biomimetic membranes while allowing transport through a membrane-support sandwich, we have investigated the feasibility of using an ethylene tetrafluoroethylene (ETFE)/hydrogel sandwich as the support. The sandwich is realized as a perforated surface-treated ETFE film onto which a hydrogel composite support structure is cast. We report a simple method to prepare arrays of lipid bilayer membranes with low intrinsic electrical conductance on the highly permeable, self-supporting ETFE/hydrogel sandwiches. We demonstrate how the ETFE/hydrogel sandwich support promotes rapid self-thinning of lipid bilayers suitable for hosting membrane-spanning proteins.     

Effect of the amine type on thermal stability of modified mesoporous silica used for CO2 adsorption

In this study, the preparation by grafting of amino-functionalized SBA-15 molecular sieves was carried out. Amino-functionalized molecular sieves were synthesized using a silane coupling agent and different types of amination reagents which react with modified SBA-15. These composites were characterized by FT-IR spectroscopy, X-ray diffraction at low angles, nitrogen physisorption at 77 K, and evaluated by the adsorption of CO₂ and its temperature-programmed desorption—TPD. Thermal stability was investigated by TGA and DTA methods. In the view of a possible use of these amino-functionalized molecular sieves as sorbents for CO₂ removal, their adsorption–desorption properties towards CO₂ were also investigated by the TPD method. The mass loss of amino-functionalized molecular sieves above 215 °C was due to the oxidation and decomposition of amino propyl functional groups. This means that these composites could be used for adsorption of CO₂ at temperatures below 215 °C. The adsorption of CO₂ and its temperature programmed desorption using thermogravimetry were studied for amino-functionalized molecular sieves at 60 °C. The evolved gases during the adsorption–desorption of CO₂ on amino-functionalized molecular sieves were identified by online mass spectrometry coupled with thermogravimetry. CO₂ adsorption isotherms of functionalized samples at 60 °C showed that both the adsorption capacity (mg CO₂/g adsorbent) and the efficiency of amino groups (mol CO₂/mol NH₂) depend on the type of amination reagents and the amount of organic compound used.

     

Dissolvable disulphide-polyacrylamide gels for the electrophoretic analysis of chromosomal proteins and for affino-electrophoresis of thiol-proteins

A discontinous gel system is described that is composed of the dissolvable, disulphide-containing acrylamide gel developed by Hansen and the acetic acid-urea gel as introduced by Panyim and Chalkley. A cleavable SDS gel is used for the identification and an initial separation of proteins according to molecular weight; it is then solubilized by tris-mercaptoethanol and layered on the acidic gel, where it functions as a stacking gel with a pronounced concentrating capacity. The final resolution obtained by this technique permits the identification of single protein species according to the degree of enzymatic modification (acetylation and phosphorylation). Side reactions of the disulphide gel matrix with thiol proteins are discussed and other possible application are considered.     

On-column polymer-imbedded graphite inlet electrode for capillary electrophoresis coupled on-line with flow injection analysis in a poly(dimethylsiloxane) interface

A method for coupling an electrophoretic driven separation to a liquid flow, using conventional fused-silica capillaries and a soft polymeric interface is presented. A novel design of the electrode providing high voltage to the electrophoretic separation was also developed. The electrode consisted of a conductive polyimide/graphite imbedded coating immobilized onto the capillary electrophoresis (CE) column inlet. This integrated electrode gave the same separation performance as a commonly used platinum electrode. The on-column electrode also showed good electrochemical stability in chronoamperometric experiments. In addition, with this electrode design, the electrode position relative to the inlet end of the CE column will always be constant and well defined. The on-line flow injection analysis (FIA)-CE system was used with electrospray ionization (ESI)-time of flight (TOF)-mass spectrometry detection. The preparation of the PDMS (poly(dimethylsiloxane)) interface for FIA-CE is described in detail and used for initial tests of the on-column polymer-imbedded graphite inlet electrode. In this interface, a pressure-driven liquid flow, a make up CE electrolyte and a CE column inlet meet in a two-level cross (95 microm ID) in the PDMS structure, enabling independent flow characterization.