Mechanistic study on the Knorr pyrazole synthesis-thioester generation reaction

A novel Fmoc-SPPS compatible peptide thioester generation method leveraging Knorr pyrazole synthesis was reported recently. C-terminal peptide hydrazides, pentane-2,4-dione and excess arylthiol were added in one-pot to efficiently produce peptide thioesters in acidic aqueous solution at room temperature. To elucidate the detailed mechanism of this reaction and the origin of the effect of solution acidity, a theoretical investigation on the Knorr pyrazole synthesis-thioester generation reaction was carried out. Our computational results suggest that the reaction generally proceeds through three stages: hydrazone formation, pyrazole formation and thioester formation. The rate-determining step is the CO bond cleavage step in the pyrazole formation stage. The formed pyrazole is readily converted to thioester in the presence of excess thiophenol. The effect of solution acidity originates from the need for protonation of oxygen atoms to increase the electrophilicity of carbonyl group or the leaving ability of hydroxyl group.     

Characterization of native and anodic oxide films formed on commercial pure titanium using electrochemical properties and morphology techniques

Potentiostatically anodized oxide films on the surface of commercial pure titanium (cp-Ti) formed in sulfuric (0.5 M H₂SO₄) and in phosphoric (1.4 M H₃PO₄) acid solutions under variables anodizing voltages were investigated and compared with the native oxide film. Potentiodynamic polarization and electrochemical impedance spectroscopy, EIS, were used to predicate the different in corrosion behavior of the oxide film samples. Scanning electron microscope, SEM, and electron diffraction X-ray analysis, EDX, were used to investigate the difference in the morphology between different types of oxide films. The electrochemical characteristics were examined in phosphate saline buffer solution, PSB (pH 7.4) at 25 °C. Results have been shown that the nature of the native oxide film is thin and amorphous, while the process of anodization of Ti in both acid solutions plays an important role in changing the properties of passive oxide films. Significant increase in the corrosion resistance of the anodized surface film was recorded after 3 h of electrode immersion in PSB. On the other side, the coverage (θ) of film formed on cp-Ti was differed by changing the anodized acid solution. Impedance results showed that both the native film and anodized film formed on cp-Ti consist of two layers. The resistance of the anodized film has reached to the highest value by anodization of cp-Ti in H₃PO₄ and the inner layer in the anodized film formed in both acid solutions is also porous.     

A simple light-emitted diode-induced fluorescence detector using optical fibers and a charged coupled device for direct and indirect capillary electrophoresis methods

We constructed a simple fluorescence detector for both direct and indirect CE methods using a blue light-emitted diode (470 nm) as excitation source, a bifurcated optical fiber as a waveguide, and a CCD camera as a detector. The connection of all the components is fairly easy even for nonexperts and the use of a CCD camera improves the applicability of this detector compared to the others using PMTs because it permits the recording of 2-D electropherograms or phosphorescence measurements. This detector provides a compact, low cost, and rapid system for the determination of native fluorescence compounds which have high quantum yields by CE with direct fluorescence detection, showing an LOD of 2.6 x 10(-6) M for fluorescein; the determination of fluorescence derivative compounds by CE with direct fluorescence detection, showing an LOD of 1.6 x 10(-7) M for FITC-labeled 1,6-diaminohexane; and nonfluorescence compounds by CE with indirect fluorescence detection with an LOD of 2.7 x 10(-6) M for gallic acid.     

Rapid and easy protein staining for SDS-PAGE using an intramolecular charge transfer-based fluorescent reagent

High-performance staining for 1-D and 2-D SDS-PAGE was carried out using a novel protein-binding fluorophore (Dye 1), which noncovalently interacts with proteins and provides a fluorescence emission response to proteins by intramolecular charge transfer. In order to achieve the high-throughput analysis of proteins for SDS-PAGE, the general protocols for in-gel protein staining (SDS-PAGE, fixation, staining, washing, and detection) were simplified to produce an easy and rapid protocol (SDS-PAGE together with staining, washing, and detection). This method was performed by preparation of an electrophoresis buffer containing Dye 1 under optimum conditions, and by the binding of Dye 1 to proteins in the gel during the SDS-PAGE. As a result, this study required only 15 min for protein staining as a minimum time. On the other hand, it takes several hours for the general protein staining method, such as SYPRO Ruby staining (18 h) and CBB staining (105 min). Moreover, the protein-to-protein variation was low, and the detection limit was 7.0 ng/band of BSA (S/N = 3.0) in this method, which was as sensitive as the short-protocol silver staining methods. On the basis of these results, this rapid and easy protocol for SDS-PAGE using Dye 1 may be widely applicable and convenient for users in the various scientific and medical fields.     

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of proteins in dry-cured hams: data registration and multivariate analysis across multiple gels

This study investigates whether dry-cured hams from two European countries can be distinguished using SDS-PAGE. Thirty-seven commercial hams (19 Spanish, 18 French) were used in the study. Four protein fractions were extracted from each sample, with sufficient material prepared to allow each fraction to be analysed in triplicate lanes. The complete extraction process was carried out in duplicate. The 24 specimens originating from each ham sample were randomly allocated to different lane positions and gels, as were at least two reference lanes (for reference proteins). In total, 118 gels were prepared. Mathematical routines were developed using a matrix language to process the gel image files. Procedures were written to carry out 'within-gel' image correction, lane extraction and normalization, 'between-gel' data registration and linear discriminant analysis (LDA) of each fraction's data to establish whether the provenance could be systematically distinguished. The between-gel registration was carried out using a genetic algorithm (GA). Feature selection was also performed using a GA, to pass subsets of features to the LDA routine. Cross-validated classification success rates were 84, 91, 81 and 85%, respectively, for the four fractions. We conclude that SDS-PAGE can be conducted in a sufficiently quantitative manner and can potentially verify the provenance of regional speciality dry-cured hams.     

Discontinuous native protein gel electrophoresis

Analysis of the oligomeric state of a native protein usually requires analytical ultracentrifugation or repeated gel filtration to calculate the protein's size. We have developed a discontinuous native protein gel electrophoresis system that allows the separation of even basic proteins according to their size, oligomeric state, and shape. This gel system combines the addition of negative charges to the proteins by Serva Blue G with a discontinuous buffer system and gradient gels. As in SDS-PAGE, chloride constitutes the high mobility anion in the gel and anode buffer. However, for sample focusing this system employs histidine instead of glycine as the slow dipolar ion following from the cathode buffer to improve migration of basic proteins. In addition, proteins run into gel pores corresponding to their size and shape in the gradient gel. Using this gel system, we show that the polypyrimidine tract-binding protein (PTB) is a monomer.     

Simultaneous electrophoretic analysis of proteins of very high and low molecular mass using Tris‐acetate polyacrylamide gels

To separate and analyze giant and small proteins in the same electrophoresis gel, we have used a 3–15% polyacrylamide gradient gel containing 2.6% of the crosslinker bisacrylamide and 0.2 M of Tris‐acetate buffer (pH 7.0). Samples were prepared in a sample buffer containing lithium dodecyl sulphate and were run in the gel described above using Tris‐Tricine‐SDS‐sodium bisulfite buffer, pH 8.2, as electrophoresis buffer. Here, we show that this system can be successfully used for general applications of SDS‐PAGE such as CBB staining and immunoblot. Thus, by using Tris‐acetate 3–15% polyacrylamide gels, it is possible to simultaneously analyze proteins, in the mass range of 10–500 kDa, such as HERC1 (532 kDa), HERC2 (528 kDa), mTOR (289 kDa), Clathrin heavy chain (192 kDa), RSK (90 kDa), S6K (70 kDa), β‐actin (42 kDa), Ran (24 kDa) and LC3 (18 kDa). This system is highly sensitive since it allows detection from as low as 10 μg of total protein per lane. Moreover, it has a good resolution, low cost, high reproducibility and allows for analysis of proteins in a wide range of weights within a short period of time. All these features together with the use of a standard electrophoresis apparatus make the Tris‐acetate‐PAGE system a very helpful tool for protein analysis.