Two-dimensional Electropherograms Research Articles

Biotechnological techniques for intensification of protein extraction from the porcine pancreas

Processing of secondary products after slaughter of farm animals is in demand. The pancreas is a rich source of bioactive protein substances, effective extraction of which is a serious problem today due to their aggregation. The aim of the work was to assess the extractivity of protein substances of the porcine pancreas using sodium chloride, trehalose, arginine, and combination of glycine and proline. The protein concentration was determined in the obtained extracts by the biuret reaction and their protein composition was assessed by densitometry of two-dimensional electropherograms using software ImageMaster™ 2D Platinum powered by Melanie 8.0. The results showed a positive effect of anti-aggregation agents on the release of protein substances into a solution. The highest protein concentration (33.36±0.64 g/l) was observed when adding 1М L-arginine; however, it was conditioned mainly by an increase in the content of three major protein fractions rather than by diversity of the protein composition. In general, the use of 0.9% NaCl as an extractive agent was quite effective, but selectivity to certain protein groups was observed for anti-aggregation agents such as sodium chloride, trehalose, arginine, glycine and proline, as well as their combination. The obtained results are important for intensifying extraction of protein substances including target ones with the subsequent application in different fields.

Coupling immobilized alkaline phosphatase-based automated diagonal capillary electrophoresis to tandem mass spectrometry for phosphopeptide analysis

Automated diagonal capillary electrophoresis is a two-dimensional separation method that incorporates an immobilized enzyme reactor at the distal end of the first capillary and employs identical electrophoretic separation modes in both dimensions. Components undergo a preliminary separation in the first capillary. Fractions are parked in the reactor where some components undergo transformation. The fractions are then periodically transferred to the second capillary and replaced by the next components in the sample. Components that are not modified by the reactor will have identical mobility in both dimensions and fall on the diagonal of a reconstructed two-dimensional electropherogram, while analyte that undergoes modification will fall off the diagonal. In this study, alkaline phosphatase was immobilized in a monolithic reactor. An LTQ-Orbitrap Velos mass spectrometer was used to monitor analytes as they migrated from the second capillary. The system was used to characterize the phosphorylation status of a tryptic digest of α-casein in a background prepared from a 22-fold excess of the tryptic digest of bovine serum albumin. 120 fractions underwent automated treatment in the alkaline phosphatase reactor and separation in the second dimension capillary for over 40min; nine phosphorylated α-casein peptides that produced 20 different phosphorylation states were detected with high confidence.

Automated Enzyme-Based Diagonal Capillary Electrophoresis: Application to Phosphopeptide Characterization

Diagonal capillary electrophoresis is a form of two-dimensional capillary electrophoresis that employs identical separation modes in each dimension. The distal end of the first capillary incorporates an enzyme-based microreactor. Analytes that are not modified by the reactor will have identical migration times in the two capillaries and will generate spots that fall on the diagonal in a reconstructed two-dimensional electropherogram. Analytes that undergo enzymatic modification in the reactor will have different migration times in the second capillary and will generate spots that fall off the diagonal in the electropherogram. We demonstrate the system with immobilized alkaline phosphatase to monitor the phosphorylation status of a mixture of peptides. This enzyme-based diagonal capillary electrophoresis assay appears to be generalizable; any post-translational modification can be detected as long as an immobilized enzyme is available that reacts with the modification under electrophoretic conditions.

Proteomic analysis of Staphylococcus aureus biofilms grown in vitro on mechanical heart valve leaflets

The in vitro colonization of three commercial heart valve leaflets by Staphylococcus aureus was investigated. The leaflets, made of pyrolytic carbon alloyed with or without silicon, displayed similar surface properties (wettability, roughness) and were readily colonized by S. aureus that formed patchy biofilms on the three supports. A proteomic approach was used to assess the physiological status of biofilm populations by comparing their protein maps to those of bacteria cultured as free cells in the presence or absence of biofilm substratum. Principal component analysis (PCA) revealed, for each tested leaflet, statistical relationships between the protein maps of the biofilm and free-floating microbial populations. A spot-by-spot comparison of protein levels on two-dimensional electropherograms showed that many proteins were accumulated or underproduced by microbial populations grown in the presence of a leaflet compared with protein levels in control free populations. The number of accumulated proteins was noticeably higher than that of underproduced polypeptides. This protein overproduction was emphasized in biofilm populations. Several proteins, some of which were identified, were differentially produced by both surface-associated planktonic and biofilm-grown cell populations compared with control free-cell ones cultured in the absence of leaflet, whatever the leaflet tested. The potential of this proteomic approach for fighting against microbial adhesion and biofilm formation is discussed.

Protein expression in Escherichia coli S17-1 biofilms: impact of indole

Bacteria undergo significant changes during adherence to surfaces and biofilm development. Cell-to-cell signalling molecules are known to be involved in these phenotypic adaptations to the sessile mode of life. We demonstrated previously that indole can act as an extracellular signal to regulate biofilm formation in E. coli. To identify proteins over- or under-expressed in response to E. coli biofilm formation and indole signalling, we compared the proteomes of the E. coli S17-1 wild-type and 3714 (S17-1 tnaA::Tn5) tryptophanase-negative mutant cells (which don't produce indole) grown as suspensions or biofilms in the presence or absence of exogenous indole. From computer-assisted image analysis, 407 spots were discriminated on two-dimensional electropherograms. Principal component analysis (PCA) of the electropherograms did not discriminate between the proteomes of the wild-type and mutant cells grown as suspensions indicating that indole has a limited impact onto protein expression of planktonic cells. The first principal component extracted by PCA, after standardization of the observations, opposed planktonic and biofilm cells confirming the existence of changes in protein expression during E. coli biofilm formation. Among proteins over- or under-expressed by both sessile wild-type and mutant cells, we identified metabolic enzymes, transporters, proteins involved in the translation and transcription machinery, stress response and regulation, and signalling proteins. The wild-type and mutant strains grown as biofilms in the presence of indole were discriminated by the second component. The role of some proteins whose expression was altered in biofilm bacteria compared to suspended counterparts is discussed.

Protein profile changes in the human breast cancer cell line MCF‐7 in response to SEL1L gene induction

The ectopic expression of the gene SEL1L in the human breast carcinoma cell line MCF-7 resulted in a reduction of the aggressive behaviour of these cells in vitro. In addition, in vivo analysis on a series of primary breast carcinomas revealed an association between the SEL1L protein levels and the patient's overall survival. We aimed to find those proteins, associated with SEL1L, which may be involved in modulating the aggressive or invasive behaviour of breast cancer cells. For this purpose, we used both the proteomic and microarray approaches. Image analysis of two-dimensional electropherograms revealed the presence of 27 qualitative and 35 quantitative variations between the MCF7-SEL1L expressing cells compared to control. Mass spectrometry identified 32 changing proteins mostly involved in cytoskeletal and metabolic activities, stress response and protein folding, selenoprotein synthesis and cellular proliferation. Five of these also showed changes in transcript levels, as assessed by Affymetrix microarray analysis. Interestingly, seven proteins: carbonic anhydrase (CA) II, ovarian/breast septin, S100A16 calcium binding protein, 14-3-3 protein sigma, proteasome subunit beta type 6, Hsp60 and protein disulphide-isomerase A3 merit particular attention since they are known to be involved in cancer, in response to cellular stress and in protein folding.

High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry

It is expected that the composition of the serum proteome can provide valuable information about the state of the human body in health and disease and that this information can be extracted via quantitative proteomic measurements. Suitable proteomic techniques need to be sensitive, reproducible, and robust to detect potential biomarkers below the level of highly expressed proteins, generate data sets that are comparable between experiments and laboratories, and have high throughput to support statistical studies. Here we report a method for high throughput quantitative analysis of serum proteins. It consists of the selective isolation of peptides that are N-linked glycosylated in the intact protein, the analysis of these now deglycosylated peptides by liquid chromatography electrospray ionization mass spectrometry, and the comparative analysis of the resulting patterns. By focusing selectively on a few formerly N-linked glycopeptides per serum protein, the complexity of the analyte sample is significantly reduced and the sensitivity and throughput of serum proteome analysis are increased compared with the analysis of total tryptic peptides from unfractionated samples. We provide data that document the performance of the method and show that sera from untreated normal mice and genetically identical mice with carcinogen-induced skin cancer can be unambiguously discriminated using unsupervised clustering of the resulting peptide patterns. We further identify, by tandem mass spectrometry, some of the peptides that were consistently elevated in cancer mice compared with their control littermates.

Fully Automated Two-dimensional Capillary Electrophoresis for High Sensitivity Protein Analysis

We report a system for automated protein analysis. In the system, proteins are labeled with the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde, which reacts with lysine residues and creates a highly fluorescent product. These labeled proteins are analyzed by submicellar capillary electrophoresis at pH 7.5 to perform a first dimension separation. Once the first components migrate from the capillary, a fraction is transferred to a second dimension capillary, where electrophoresis is performed at pH 11.1 to further separate the proteins. Laser-induced fluorescence is used as an ultrasensitive detector of the separated proteins. Successive fractions are transferred from the first dimension capillary to the second dimension capillary for further separation to generate, in serial fashion, a two-dimensional electropherogram. The transfer of fractions is computer-controlled; there is no operator intervention once the sample has been injected. Zeptomoles of labeled proteins are detected, providing exquisite sensitivity.

Point pattern matching in the analysis of two-dimensional gel electropherograms.

In the automation of proteome analysis, matching of two-dimensional (2-D) electropherograms represents a bottleneck in the process. Here we present a point pattern recognition approach to the matching of spots in 2-D electropherograms. The algorithm is based on a comparison of spot neighborhoods, converted to point patterns between reference and compared gels. The neighborhood was characterized by a syntactic descriptor which minimized the influence of spot displacements. A combined criterion utilizing the similarity of point patterns and a metric definition of position similarity was derived. The efficiency and accuracy of the algorithm was tested on a set of 69 gels with different levels of similarity. For a typical gel the accuracy of matching was higher than 98% and the number of correctly identified spots was higher than 95%.

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis.

The allocation of proteins to stimulons and regulons is an essential step towards the understanding of the global regulation of the expression of entire genomes. The computer-aided evaluation and matching of two-dimensional protein gels loaded with radioactively labeled proteins from exponentially growing or stressed cells is a useful but time-consuming procedure for the description of stimulons and regulons. This paper describes the dual-channel image analysis that offers the opportunity to visualize the content and synthesis rate of a whole set of bacterial proteins on a single electropherogram. By pulse-labeling with L-[35S]methionine, the protein synthesis pattern (red color) can be directly compared with the protein level pattern (green color). Because matching of other gels can be avoided, this new technique is useful for the rapid search for proteins that belong to different stimulons or regulons. This approach was tested for the identification of proteins of heat stress or oxidative stress stimulons. Proteins that were induced by heat or oxidative stress colored red while proteins whose synthesis was switched off by the stress factor colored green. Proteins that were continuously synthesized before and after the imposition of stress retained their yellow color. The advantages and possible pitfalls of the technique are discussed.

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis

In situ evaluation of esterase stereoselectivity in two-dimensional electropherograms and tissue sections

Staining with both enantiomers of an α-naphthyl ester plus a diazonium salt and comparing the color intensities given by the two enantiomers is a convenient method to evaluate the esterase stereoselectivity for that ester in two-dimensional electropherograms and tissue sections. Application of this method for rat liver has shown that (1) several esterases, e.g., one of p I 6.4 and M r 118 kDa, are moderately stereoselective against α-naphthyl ( R)- N-acetylalaninate and ( R)- N-methoxycarbonylalaninate but strictly stereoselective against α-naphthyl ( S)- N-methoxycarbonylvalinate, implying that esterase stereoselectivity may be inverted by changing the ester structure; and (2) these esterases are mainly contained in the hepatocytes around central veins.

Determination of the amino acid neurotransmitters in the dorsal root ganglion of the rat by capillary electrophoresis with a laser-induced fluorescence-charge coupled device

A sensitive, rapid and accurate analysis of the amino acid neurotransmitters in dorsal root ganglion (DRG) of rat was accomplished by capillary electrophoresis with a laser-induced fluorescence-charged coupled device (LIF-CCD) and fluorescein isothiocyanate (FITC) derivatization. Since the CCD is an image detector with a matrix array of photoelements, the photogenerated charge generated from single photoelements was summed up by on-chip charge binning, and used to improve the detection sensitivity. A self-compiled data processing program was used to calculate digitally the summation of the multiwavelength data and transform three-dimensional electropherograms into two-dimensional electropherograms. Use of this program improved the detection sensitivity, the extraction of useful statistical data and the performance of the quantitative analysis. Owing to its excellent detectability and the unique characteristic of its two-dimensional format, which allows to perform analog and digital summation, high detection sensitivity with detection limits ranging from 1.2 to 17.2 n M was obtained for the amino acid neurotransmitters by LIF-CCD. This method was demonstrated to be a powerful tool for analyzing the complex biological samples through quantitative determination of the six amino acid neurotransmitters in the DRG of rat.

Purification and compartmentation of α-mannosidase isoenzymes of barley leaves

Apoplastic and vacuolar forms of α-mannosidase from barley leaves were purified (the latter ca 1000-fold). Isoenzymes were separated during purification. They consisted of four subunits with an apparent M r of 53, 46,40 and 24 × 10 3 in varying proportions. In two-dimensional electropherograms, the M r 46 and 40 × 103 polypeptides were separated into two isomeric forms of different isoelectric point. The native proteins focused in a pH gradient at different isoelectric points. Their M r s ranged between 290 and 270 × 103 as judged from size exclusion chromatography and electrophoretic mobility. The compartmentation of the isoenzymes revealed tissue- and age-specificity.

Evaluation of two-dimensional electropherograms of proteins from the spleen cells induced by experimental infection using the 2D-Analyst II software

High resolution 2D gel electrophoresis was used for the evaluation of protein synthesis during in vivo infection with intracellular bacterial parasites. The analysis of gels was performed using Model 620 Video densitometer, combined with the 2D-Analyst II data analysis system. The newly synthetized cellular proteins from 5th, 7th and 10th day after infection and the proteins specific for individual intervals were characterized. The computer-analyzed electropherograms were exploited for the construction of database of protein information from mouse spleen cells.

Nuclear antigen with a molecular weight of 48,000 associated with malignant tranformation

1. 1. Analysis of immunoblots of one- and two-dimensional electropherograms of non-histone proteins from Kirkman-Robbins hepatoma, Morris hepatoma 7777, regenerating liver and normal liver demonstrated the presence of elevated level of nuclear antigen with mol. wt of 48,000 and pI of 5.4 in tumour cells. 2. 2. Small amounts only were detected in proliferating and quiescent cells suggesting that different expression of this component may reflect biochemical events related to malignant transformation rather than to general cell activation.

Mechanism of cytotoxicity of methylmercury

Mechanism of methylmercury cytotoxicity was investigated with special reference to its preferential action on microtubules and protein biosynthesis in cultured cells. The tubulin synthesis analyzed by autoradiography of two-dimensional electropherogram using 35S-methionine was inhibited by 50-70% in mouse glioma cells exposed to 5 x 10(-6) M methylmercury for 3 h, which almost completely depolymerized microtubules. Total protein synthesis monitored by incorporation of labeled methionine into acid insoluble fraction was decreased slightly but significantly and the protein bands other than tubulin on gradient urea-PAGE gel appeared to remain unchanged under the experimental condition used. These results suggest that the inhibition of protein synthesis observed on exposure to methylmercury can be ascribed, at least partly, to a possible autoregulatory depression in tubulin synthesis owing to the increase in the pool of tubulin subunits resulted from microtubule depolymerization by methylmercury.

Suppression of tropomyosin synthesis, a common biochemical feature of oncogenesis by structurally diverse retroviral oncogenes.

To identify proteins whose production may be altered as a common event in the expression of structurally diverse oncogenes, we compared two-dimensional electropherograms of newly synthesized proteins from NIH/3T3 cell lines transformed by a variety of retroviral oncogenes, from cellular revertant lines, and from a line (433.3) which expresses the v-ras oncogene in response to corticosteroids. Most alterations in the synthesis of specific proteins detected by this approach appeared to be the result of selection during prolonged cultivation and were probably unrelated to the transformation process. However, we detected seven proteins whose synthesis was strongly suppressed in cell lines transformed by each of the six retroviral oncogenes we studied and whose production was fully or partially restored in two cellular revertant lines. Suppression of two of these proteins was also correlated with the initial appearance of morphological alteration during corticosteroid-induced oncogene expression in 433.3 cells. These proteins (p37/4.78 and p41/4.75) were identified as tropomyosins, a group of at least five cytoskeletal proteins. Transformation by the papovaviruses simian virus 40 and polyomavirus caused no suppression of synthesis of these tropomyosins. This indicates that suppression of tropomyosin synthesis is not a nonspecific response by cells to being forced to grow with the transformed phenotype but is specifically associated with oncogenesis by diverse retroviral oncogenes. The results are consistent with the hypothesis that the different biochemical processes initiated by expression of structurally diverse retroviral oncogenes may converge on a limited number of common targets, one of which is the mechanism which regulates the synthesis of tropomyosins.

Suppression of tropomyosin synthesis, a common biochemical feature of oncogenesis by structurally diverse retroviral oncogenes.

To identify proteins whose production may be altered as a common event in the expression of structurally diverse oncogenes, we compared two-dimensional electropherograms of newly synthesized proteins from NIH/3T3 cell lines transformed by a variety of retroviral oncogenes, from cellular revertant lines, and from a line (433.3) which expresses the v-ras oncogene in response to corticosteroids. Most alterations in the synthesis of specific proteins detected by this approach appeared to be the result of selection during prolonged cultivation and were probably unrelated to the transformation process. However, we detected seven proteins whose synthesis was strongly suppressed in cell lines transformed by each of the six retroviral oncogenes we studied and whose production was fully or partially restored in two cellular revertant lines. Suppression of two of these proteins was also correlated with the initial appearance of morphological alteration during corticosteroid-induced oncogene expression in 433.3 cells. These proteins (p37/4.78 and p41/4.75) were identified as tropomyosins, a group of at least five cytoskeletal proteins. Transformation by the papovaviruses simian virus 40 and polyomavirus caused no suppression of synthesis of these tropomyosins. This indicates that suppression of tropomyosin synthesis is not a nonspecific response by cells to being forced to grow with the transformed phenotype but is specifically associated with oncogenesis by diverse retroviral oncogenes. The results are consistent with the hypothesis that the different biochemical processes initiated by expression of structurally diverse retroviral oncogenes may converge on a limited number of common targets, one of which is the mechanism which regulates the synthesis of tropomyosins.