Alexander P. Boichenko

Glycopeptide enrichment and separation for protein glycosylation analysis

Protein glycosylation plays key roles in many biological processes. In addition, alterations in protein glycosylation have been related to different diseases, as well as may affect the properties of recombinant proteins used as human therapeutics. For this reason, protein glycosylation analysis is of main interest in biomedical and biopharmaceutical research. Although recent advances in LC-MS analysis have made possible glycoprotein glycosylation site identification, characterization of glycoprotein glycan structures, as well as glycoprotein identification and quantification, protein glycosylation analysis in complex samples still remains a difficult task. This is due to low proportions of glycopeptides in comparison to peptides obtained after glycoprotein digestion, the suppression of the glycopeptide MS signals in the presence of peptides, and the high heterogeneity of glycopeptides. Thus, in the recent years, continuous efforts have been devoted to the development of glycopeptide enrichment and separation strategies to facilitate and improve glycoprotein glycosylation analysis in complex samples. This review summarizes the different methodologies that can be employed for glycopeptide enrichment/separation from complex samples including methods based on lectin affinity enrichment, covalent interactions, or chromatographic separations and solid-phase extraction.

Multidimensional separation of tryptic peptides from human serum proteins using reversed-phase, strong cation exchange, weak anion exchange, and fused-core fluorinated stationary phases

Proteome profiling of crude serum is a challenging task due to the wide dynamic range of protein concentrations and the presence of high-abundance proteins, which cover >90% of the total protein mass in serum. Peptide fractionation on strong cation exchange, weak anion exchange in the electrostatic repulsion hydrophilic interaction chromatography (ERLIC) mode, RP C18 at pH 2.5 (low pH), fused-core fluorinated at pH 2.5, and RP C18 at pH 9.7 (high pH) stationary phases resulted in two to three times more identified proteins and three to four times more identified peptides in comparison with 1D nanoChip-LC-MS/MS quadrupole TOF analysis (45 proteins, 185 peptides). The largest number of peptides and proteins was identified after prefractionation in the ERLIC mode due to the more uniform distribution of peptides among the collected fractions and on the RP column at high pH due to the high efficiency of RP separations and the complementary selectivity of both techniques to low-pH RP chromatography. A 3D separation scheme combining ERLIC, high-pH RP, and low-pH nanoChip-LC-MS/MS for crude serum proteome profiling resulted in the identification of 208 proteins and 1088 peptides with the lowest reported concentration of 11 ng/mL for heat shock protein 74.

The histone acetyltransferase p300 inhibitor C646 reduces pro-inflammatory gene expression and inhibits histone deacetylases

Lysine acetylations are reversible posttranslational modifications of histone and non-histone proteins that play important regulatory roles in signal transduction cascades and gene expression. Lysine acetylations are regulated by histone acetyltransferases as writers and histone deacetylases as erasers. Because of their role in signal transduction cascades, these enzymes are important players in inflammation. Therefore, histone acetyltransferase inhibitors could reduce inflammatory responses. Among the few histone acetyltransferase inhibitors described, C646 is one of the most potent (Ki of 0.4μM for histone acetyltransferase p300). C646 was described to affect the NF-κB pathway; an important pathway in inflammatory responses, which is regulated by acetylation. This pathway has been implicated in asthma and COPD. Therefore, we hypothesized that via regulation of the NF-κB signaling pathway, C646 can inhibit pro-inflammatory gene expression, and have potential for the treatment of inflammatory lung diseases. In line with this, we demonstrate here that C646 reduces pro-inflammatory gene expression in RAW264.7 murine macrophages and murine precision-cut lung slices. To unravel its effects on cellular substrates we applied mass spectrometry and found, counterintuitively, a slight increase in acetylation of histone H3. Based on this finding, and structural features of C646, we presumed inhibitory activity of C646 on histone deacetylases, and indeed found inhibition of histone deacetylases from 7μM and higher concentrations. This indicates that C646 has potential for further development towards applications in the treatment of inflammation, however, its newly discovered lack of selectivity at higher concentrations needs to be taken into account.

Thin-layer chromatographic plates with monolithic layer of silica: Production, physical–chemical characteristics, separation capabilities

The technique for production of thin-layer chromatographic plates with fixed monolithic layer of sorbent was developed on the basis of investigation of factors affecting sorption capacity, sorption kinetics and mechanical stability of monoliths. The optimal reaction mixture for sol-gel synthesis of monoliths consisted of tetraethoxysilane, buffer solution with pH 7.4, N,N-dimethylformamide, ethanol, polyethyleneglycol with molecular weight 1000 and cetylpyridinium chloride in molar ratio 1.0:4.6:1.4:7.6:0.26:8×10(-3). On the basis of analysis of sorption kinetics of malachite green on the monoliths it was concluded that mechanism of sorption includes chemisorption. The optimized conditions for fixing the monolithic layer on the carrier and its drying allow obtaining undisturbed monolithic layer, which was used for test mixtures separation. The increase of monolithic layer thickness in comparison with ultrathin-layer chromatographic plates allows detecting visually at reasonable concentrations and loaded sample volumes the spots of food and synthetic dyes.

The Mobile Phase Motion in Ascending Micellar Thin-Layer Chromatography with Normal-Phase Plates

The physical-chemical characteristics (surface tension and viscosity) of micellar mobile phases based on the cationic surfactant cetylpiridinium chloride and additives of alcohols (ethanol, 1-propanol, 1-butanol, 1-pentanol) have been obtained in this work. The effect of mobile phase properties on the motion of mobile phase in the ascending mode of thin-layer chromatography (TLC) was investigated. The applicability of a quadratic relationship between the time of mobile phase motion and the distance from the solvent entry position of mobile phase and front of the mobile phase was validated for micellar TLC. It was observed that the retardation factors of hydrophilic test compounds change significantly only at low contents of the modifier in micellar mobile phase.

Comparison of Targeted Mass Spectrometry Techniques With an Immunoassay: A Case Study For HSP90α

The objective of this study is to better understand factors governing the variability and sensitivity in SRM and PRM, compared to immunoassay.