Urine protein quantification in stacking gel by SDS‐PAGE

Urine total protein concentration is usually measured by the pyrogallol red‐molybdate (PRM) assay in clinical laboratories, but it is often subject to sample interference. Here, we introduce a stacking gel‐based method for accurate protein quantitation. In this method, the urine protein samples are run into the stacking gel by SDS‐PAGE where it is concentrated into a single band, and then quickly stained by 0.001% Coomassie at high temperature. High correlations were found between the BSA and urine protein standards (R² = 0.997 and 0.990, respectively). Addition of 80 ng urine protein standard into each of the ten clinical urine specimens with questionable PRM results yielded the expected increase in the results by this method. Comparison of the PRM method and with the gel quantitation approach on about 60 clinical urine samples demonstrated a general consistency between the results (R² = 0.825), but in PRM samples with lower protein concentration showed more variations. Overall, the stacking gel method might be a good alternative for clinical urine samples with suspicious protein concentration results.     

Sequential double fluorescent detections of total proteins and phosphoproteins in SDS‐PAGE

A fluorescent staining technique, using selective chelation with fluorophore and metal ion to the phosphate groups of phosphoproteins in SDS‐PAGE is described. As a fluorescent dye and a metal ion, Fura 2 pentapotassium salt and Al³⁺ were employed, respectively. The staining method, Fura 2 stain, has sensitivities of 16–32 ng of α‐casein and β‐casein, 62 ng of ovalbumin, phosvitin, and κ‐casein using an ultraviolet transilluminator. Furthermore, Fura 2 stain is able to carry out continuative double detection of total proteins and phosphoproteins on the same gel within 3.5 h. Consequently, selective phosphoprotein and total protein detections could be obtained without other poststaining. Considering the low cost, simplicity, and speed, Fura 2 staining may provide great practicalities in routine phosphoproteomics research.     

Specific glutamic acid residues in targeted proteins induce exaggerated retardations in Phos‐tag SDS‐PAGE migration

We describe two unique proteins, Escherichia coli ClpX and human histone H2A, that show extremely retarded migrations relative to their molecular weights in Phos‐tag SDS‐PAGE, despite being nonphosphorylated. Although ClpX separated into multiple migration bands in Phos‐tag gels, the separation was not due to phosphorylation. The N‐terminal 47–61 region of ClpX was responsible for producing multiple phosphorylation‐independent structural variants, even under denaturing conditions, and some of these variants were detected as highly up‐shifted bands. By systematic Ala‐scanning mutation analysis in the N‐47–61 region, we concluded that the Glu‐51 or Glu‐54 residue was responsible for the appearance of exaggerated mobility‐shifting bands. Histone H2A showed a much slower migration in Phos‐tag gels in comparison with other major histones having similar molecular weights, and we found that the Glu‐62 or Glu‐65 residue caused the retarded migration. In addition, Phos‐tag SDS‐PAGE permitted us to detect a shift in the mobility of the phosphorylated form of histone H2A from that of the nonphosphorylated one. This is the first report showing that exaggerated retardation in the migration of a certain protein in Phos‐tag SDS‐PAGE is induced by interactions between the Phos‐tag molecule and the carboxylate group of a specific Glu residue on the target.     

Combination of SDS‐PAGE and intact mass analysis for rapid determination of heterogeneities in monoclonal antibody therapeutics

mAbs are currently mainstream in biopharmaceuticals, and their market has been growing due to their high target specificity. Characterization of heterogeneities in mAbs is performed to secure their quality and safety by physicochemical analyses. However, they require time‐consuming task, which often strain the resources of drug development in pharmaceuticals. Rapid and direct method to determine the heterogeneities should be a powerful tool for pharmaceutical analysis. Considering the advantages of electrophoresis and MS, this study addresses the combination of SDS‐PAGE and intact mass analysis, which provides direct, rapid, and orthogonal determination of heterogeneities in mAb therapeutics. mAb therapeutics that migrated in SDS‐PAGE were recovered from gel by treatment with SDC‐containing buffer. Usage of SDC‐containing buffer as extraction solvent and ethanol‐based staining solution enhanced the recovery of intact IgG from SDS‐PAGE gels. Recovery of mAbs reached more than 86% with 0.2% SD. The heterogeneities, especially N ‐glycan variants in the recovered mAb therapeutics, were clearly determined by intact mass analysis. We believe that the study is important in pharmaceuticals‧ perspective since orthogonal combination of gel electrophoresis and intact mass analysis should be pivotal role for rapid and precise characterization of mAbs.     

SDS‐PAGE procedure: Application for characterization of new entirely uncharged nucleic acids analogs

SDS‐PAGE is considered to be a universal method for size‐based separation and analysis of proteins. In this study, we applied the principle of SDS‐PAGE to the analysis of new entirely uncharged nucleic acid (NA) analogues, – phosphoryl guanidine oligonucleotides (PGOs). The procedure was also shown to be suitable for morpholino oligonucleotides (PMOs) and peptide nucleic acids (PNAs). It was demonstrated that SDS can establish hydrophobic interactions with these types of synthetic NAs, giving them a net negative charge and thus making these molecules mobile in polyacrylamide slab gels under the influence of an electric field.     

Improved disc SDS‐PAGE for extraction of low molecular weight proteins from serum

The low molecular weight proteins can provide a lot of valuable information of biomarkers. To study these proteins, the high abundance and high molecular weight proteins must be removed prior to analysis. In this work, a simple and inexpensive disc SDS‐PAGE to extract low molecular weight proteins from human serum and cutoff proteins larger than 30 kDa was developed. Some experimental conditions were examined. The experimental results obtained by plate SDS‐PAGE and MALDI‐TOF MS showed that the molecular weight of extracted proteins was about in the range from 0.3 to 28 kDa. Some experiments, including precipitation of proteins in organic solvents, SPE and cytochrome C test, were carried out and the experimental results demonstrated successful recovery of proteins/peptides with molecular weight from several hundreds of dalton to about 30 kDa. The experimental results obtained by plate SDS‐PAGE indicated the repeatability was satisfactory.     

Sensitive phosphoprotein detection in SDS‐PAGE via Anthracene Chrome Red A stain

Protein phosphorylation, one of the most important post‐translational modifications, plays critical roles in many biological processes. Thus, it is necessary to precisely detect, identify and understand the phosphoproteins from protein mixture for the study of cell biology. We introduce a sensitive and specific detection method for phosphoproteins in sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE). Anthracene Chrome Red A (ACRA) combined with the trivalent metal ion (Al³⁺) is converted to fluorescent complex and the fluorescence is sharply increased by a change of pH environment. Phosphoproteins and non‐phosphoproteins can be easily distinguished by the fluorescence quenching due to the structural change of ACRA‐Al³⁺‐phosphoprotein complex, unlike non‐phosphoprotein complex. The method using ACRA is a negative staining based on the fluorescence quenching and has a high sensitivity comparable to Pro‐Q Diamond stain. ACRA stain can detect 1–2 ng of α‐casein and β‐casein, 8–16 ng of ovalbumin (OVA) and κ‐casein within 130 min. Moreover, the ACRA stain showed similar linear dynamic ranges and RSD to Pro‐Q stain. The linear dynamic ranges of ACRA and the values of correlation coefficient were for OVA (8–500 ng, correlation coefficient r = 0.999), α‐casein (4–500 ng, r  = 0.992), β‐casein (4–500 ng, r  = 0.996), and κ‐casein (8–500 ng, 0.998), respectively. On the other hand, the values of the relative standard deviations (RSD) ranged from 2.33 to 3.56% for ACRA. The method is sensitive, specific, simple, rapid and compatible with total protein stain such as SYPRO Ruby stain. Therefore, ACRA stain can be an advanced method for phosphoprotein detection in gels.     

Alternative visualization of SDS‐PAGE separated phosphoproteins by alizarin red S‐aluminum (III)‐appended complex

A novel fluorescence detection system using a chemosensor for phosphoprotein in gel electrophoretic analysis has been developed. The system employed the alizarin red S‐aluminum (III)‐appended complex as a fluorescent staining dye to perform the convenient and selective detection of phosphorylated proteins and total proteins in SDS‐PAGE, respectively. Therefore, a full and selective map of proteins can be achieved in the same process without resorting to other compatible detection methods. As low as 62.5 ng of α‐ (seven or eight phosphates) and β‐casein (five phosphates), 125 ng of ovalbumin (two phosphates), and κ‐casein (one phosphate) can be detected in approximately 135 min, with the linear responses of rigorous quantitation of changes over a 125–4000 ng range. As a result, alizarin red S‐aluminum (III) stain may provide a new choice for selective, economic, and convenient visualization of phosphoproteins.     

Mass spectrometric characterization of the zein protein composition in maize flour extracts upon protein separation by SDS‐PAGE and 2D gel electrophoresis

Highly homogenous α zein protein was isolated from maize kernels in an environment‐friendly process using 95% ethanol as solvent. Due to the polyploidy and genetic polymorphism of the plant source, the application of high resolution separation methods in conjunction with precise analytical methods, such as MALDI‐TOF‐MS, is required to accurately estimate homogeneity of products that contain natural zein protein. The α zein protein product revealed two main bands in SDS‐PAGE analysis, one at 25 kDa and other at 20 kDa apparent molecular mass. Yet, high resolution 2DE revealed approximately five protein spot groups in each row, the first at ca. 25 kDa and the second at ca. 20 kDa. Peptide mass fingerprinting data of the proteins in the two dominant SDS‐PAGE bands matched to 30 amino acid sequence entries out of 102 non‐redundant data base entries. MALDI‐TOF‐MS peptide mapping of the proteins from all spots indicated the presence of only α zein proteins. The most prominent ion signals in the MALDI mass spectra of the protein mixture of the 25 kDa SDS gel band after in‐gel digestion were found at m/z 1272.6 and m/z 2009.1, and the most prominent ion signals of the protein mixture of the 20 kDa band after in‐gel digestion were recorded at m/z 1083.5 and m/z 1691.8. These ion signals have been found typical for α zein proteins and may serve as marker ion signals which upon chymotryptic digestion reliably indicate the presence of α zein protein in two hybrid corn products.     

Blue native/SDS‐PAGE combined with iTRAQ analysis reveals advanced glycation end‐product‐induced changes of synaptosome proteins in C57 BL/6 mice

Evidence shows that administration of high‐level D ‐galactose induces the production of advanced glycation end‐products (AGEs) that have been implicated in the development of diabetic complications such as neuropathy. The deterioration of learning and memory during neuropathy might be associated with the altered expression of proteins in synapse. To evaluate AGE‐induced protein network alterations in synapse, blue native/SDS‐PAGE and iTRAQ proteomic methods were used to screen for differentially expressed synaptic proteins of cerebral cortex in D ‐galactose‐induced C57 BL/6 mice. In total, the expression level of 84 proteins is changed during AGE accumulation. The significantly differentially expressed proteins mainly participate in neurotransmission, energy metabolism and signal transduction pathway, suggesting that energy metabolism is damaged and neurotransmission is attenuated in synapse. The results of in vivo activities of malondialdehyde and superoxide dismutase suggested that AGE accumulation in the brain leads to the generation of reactive oxygen species. Therefore, elucidating the differentially expressed proteins underlying the AGE accumulation will open a new window to the mechanism of learning and memory impairments in neuropathy.     

Quantitative assessment of multi‐laboratory reproducibility of SDS‐PAGE assays: Digestion pattern of β‐casein and β‐lactoglobulin under simulated conditions

A digestion protocol was applied in triplicate by ten laboratories, simulating in vivo gastric and duodenal conditions. The intra‐ and inter‐laboratory variability in the kinetics of protein degradation was quantified, focussing on the digestion of β‐casein under gastric conditions, and of β‐lactoglobulin (β‐Lg) under duodenal conditions. The addition of surfactants such as phosphatidylcholine (PC) in the digestion mix was also evaluated. Identification and quantification of peptide bands on SDS‐PAGE gels formed the basis for analysis. An average intensity loss of 69% (SD=13.5) at 5 min (89% at 10 min, with SD=5.5) was observed for β‐casein, whereas the β‐Lg duodenal digestion showed an 82% loss at 30 min (SD=14.2). Constant rates of first‐order reactions showed that for fast reactions, inaccuracies in the time of first sampling contributed to the variability, which were also affected by image quality, saturation, and the splitting of time courses across gels. Breakdown products for β‐casein included ten other polypeptides, with four detected in all and two in most gels, and for β‐Lg ten polypeptides, with five detected in most, and two in two‐third of the cases. Addition of PC in the gastric phase led to β‐Lg intensity loss only a quarter as large as without PC and altered β‐Lg proteolysis in the duodenal compartment.     

Functionalized PEG‐b‐PAGE‐b‐PLGA triblock terpolymers as materials for nanoparticle preparation

A series of poly(ethylene glycol)‐block‐poly(allyl glycidyl ether) (PEG‐b‐PAGE) macroinitiators are prepared using the living anionic ring‐opening polymerization (AROP) technique, and applied for further copolymerization studies. To overcome the low reactivity of the secondary hydroxyl end‐group of the PAGE block, a primary hydroxyl group is introduced into the macroinitiators via trityl and tert‐butyl‐dimethylsilane protective groups. The modified macroinitiators are used for copolymerization by applying different amounts of PEG‐b‐PAGE (5, 10, and 15%) and different PLGA lengths. To study their properties, nanoparticles from selected polymers are prepared and characterized by dynamic light scattering and scanning electron microscopy showing spherical particles with diameters around 200 nm and low PDI_particle values of 0.03–0.1. An advantage of the obtained polymers is the presence of double bonds in the side chain, which enables the modification via, for example, thiol‐ene reactions. For this purpose tertiary 2‐(dimethylamino)ethanethiol), acetylated thiogalactose and thiomannose are attached onto the double bonds of the PAGE‐blocks. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2163–2174     

Native PAGE eliminates the problem of PEG-SDS interaction in SDS-PAGE and provides an alternative to HPLC in characterization of protein PEGylation

PEGylation of proteins has become an increasingly important technology in recent years. However, determination and characterization of the PEGylation products are problematic especially for the reaction mixture containing various modified proteins, unreacted PEG, and unmodified protein. A comparative study was carried out with two HPLC methods and two electrophoresis methods for characterization of the reaction mixture in PEGylation of HSA with PEG 5000, 10000, and 20000. RP-HPLC fails to give the correct information about the reaction of PEG 20000. Size-exclusion HPLC (SE-HPLC) produced very poor resolution on the PEG 5000 reaction. SDS-PAGE can run multiple samples of all PEGylation but the bands were smeared or broadened probably due to the interaction between PEG and SDS. On the other hand, native PAGE eliminates the problem of PEG-SDS interaction and provides better resolutions for all samples. Various PEGylated products and unmodified protein migrate differentially in native PAGE under nondenatured conditions. The results demonstrated that native PAGE could be a good alternative to HPLC and SDS-PAGE for the analysis of PEG-protein conjugates especially for characterization of the PEGylation mixture.     

Synthesis,characterization, and curing kinetics of novel ladder‐like polysilsesquioxanes containing side‐chain maleimide groups

Two ladder‐like polysilsesquioxanes (LPS) containing side‐chain maleimide groups have been synthesized successfully by reacting N‐(4‐hydroxyphenyl)maleimide (HPM) with LPS containing 100 mol % of chloropropyl groups (Ladder A ) and 50 mol % of each methyl and chloropropyl group (Ladder B ). HPM was synthesized by reacting maleic anhydride with 4‐aminophenol, and the resulting amic acid was imidized using p‐toluenesulfonic acid as a catalyst (Scheme 1 ). The LPSs were characterized by Fourier transform infrared (FTIR), ¹H nuclear magnetic resonance (NMR), proton‐decoupled ¹³C NMR, ²⁹Si NMR, wide‐angle X‐ray diffraction (WAXD), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). Characterization indicated that these polymers had ordered ladder‐like structures with possible defects. These polymers were soluble in common solvents at ambient temperature, which suggested that they were not crosslinked. Both the polymers and the HPM were cured, and their kinetics were followed by dynamic DSC. The Ozawa and Kissinger methods were used to calculate activation energies for curing. Curing increased the temperature at which both 5% weight loss and maximum rate of weight loss were observed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4036–4046, 2004     

Differences in electrophoretic behavior between linear and branched PEG‐conjugated proteins

The objective of this study was to characterize the differences in electrophoretic behavior between linear and branched PEG‐conjugated proteins. Human growth hormone and alpha‐lactalbumin modified by linear or branched PEGs with molecular weight of 10 kDa were analyzed by SEC, MALDI‐TOF MS, SDS‐PAGE, and microchip CGE (MCGE). Chromatographic and mass spectrometric differences between the linear and branched PEG‐proteins on SEC and MALDI‐TOF MS were small, but their electrophoretic behaviors on SDS‐PAGE and MCGE were significantly different. In particular, MCGE showed significant differences in the peak width and the migration times of linear and branched PEG‐proteins, in which the branched PEG‐proteins exhibited a narrower peak and longer migration time than the linear PEG‐proteins. This phenomenon may explain the longer circulation half‐life for the branched PEG‐proteins observed in previously reported in vivo studies. Consequently, this study indicates that MCGE may be a valuable tool for differentiating linear and branched PEG‐proteins.     

Understanding anomalous mobility of proteins on SDS‐PAGE with special reference to the highly acidic extracellular domains of human E‐ and N‐cadherins

During SDS‐PAGE experiments, proteins generally display electrophoretic mobility in keeping with their molecular weights; however, some proteins display anomalies in mobility. Here, we focus attention on the anomalies displayed by the highly acidic ～110 residues‐long, sequence‐homologous, structurally‐analogous, extracellular domains of human E‐ and N‐cadherin. We report that there is a strong correlation between the acidity of each domain and the degree of the anomaly that it displays. The anomaly is only seen if the ratio of the numbers of negatively‐charged and positively‐charged residues is equal to or greater than the value of 1.50. The degree of the anomaly rises in proportion with this NC:PC ratio. Greater‐than‐expected anomalies are observed for domains containing dense clusters of negatively charged residues. A simple explanation for these observations is that highly acidic domains electrostatically repel SDS. This results in insufficient SDS binding, insufficient electromotive incentive and (consequently) lowered electrophoretic mobility. This explanation is in consonance with the current view that initial stages of SDS‐protein engagement tend to be dominated by electrostatics. We discuss the current anomalies within the broader context of all conceivable explanations for such anomalies.     

Polymerization of n‐phenyl maleimide by lanthanide complexes

N‐Phenyl maleimide (N‐PMI) was successfully polymerized by divalent rare‐earth complexes (ArO)₂Sm(THF)₄ (ArO = 2,6‐di‐tert‐butyl‐4‐methyl phenoxo‐; THF = tetrahydrofuran) and (Ar′O)₂Ln(THF)₃ (Ar′O = 2,6‐di‐tert‐butyl phenoxo‐; Ln = Sm, Yb, or Eu). The central metals greatly affected the reactivity, and the reactivity order was Sm(II) > Yb(II) > Eu(II). The activity of (Ar′O)₂Sm(THF)₃ was higher than that of (ArO)₂Sm(THF)₄. The polymerization yields were higher in THF than in other solvents, and the maximum yields were obtained around 25 °C. A proposed mechanism is discussed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3966–3972, 2005     

Efficient Copper(I)‐Catalyzed S‐Arylation of KSCN with Aryl Halides in PEG‐400

A simple and efficient protocol for CuI‐catalyzed C? S bond formation of aryl halides with KSCN to symmetrical diaryl sulfides was reported in PEG‐400 without any other additives. A variety of aryl halides were converted to the corresponding diaryl sulfides in good to excellent yields. The present procedure tolerated a variety of functional groups and the steric hindrance of ortho‐substituents on aryl halides did not affect the outcome.     

Development of an SDS‐gel electrophoresis method on SU‐8 microchips for protein separation with LIF detection: Application to the analysis of whey proteins

This work describes the development of an SDS‐gel electrophoresis method for the analysis of major whey proteins (α‐lactalbumin, β‐lactoglobulin, and BSA) carried out in SU‐8 microchips. The method uses a low‐viscosity solution of dextran as a sieving polymer. A commercial coating agent (EOTrol LN) was added to the separation buffer to control the EOF of the chips. The potential of this coating agent to prevent protein adsorption on the walls of the SU‐8 channels was also evaluated. Additionally, the fluorescence background of the SU‐8 material was studied to improve the sensitivity of the method. By selecting an excitation wavelength of 532 nm at which the background fluorescence remains low and by replacing the mercury arc lamp by a laser in the detection system, an LOD in the nanomolar range was achieved for proteins derivatized with the fluorogenic reagent Chromeo P540. Finally, the method was applied to the analysis of milk samples, demonstrating the potential of SU‐8 microchips for the analysis of proteins in complex food samples.