Immobilized pH Gradients Research Articles

Characterization of acidic and basic variants of IgG1 therapeutic monoclonal antibodies based on non-denaturing IEF fractionation.

Characterization of both the acidic and basic regions of imaged capillary isoelectric focusing (icIEF) profile of an IgG1 antibody was achieved through preparative immobilized pH gradient isoelectric focusing (IPG-IEF) fractionation. Recent attempts at using this method to fractionate charge variants of monoclonal antibodies (mAbs) have shown promising results, but identification of the chemical modifications in the variants was limited to the basic species. We have optimized the method to achieve enrichment of each variant across the icIEF profile of an IgG1 mAb. The fractionation was followed by extended characterization to elucidate the composition of the acidic, main, and basic species observed in the icIEF profile. Deamidation, sialylation, glycation, and fragmentation were identified as the main modifications contributing to acidic variants of the mAb while C-terminal lysine, C-terminal proline amidation, and uncyclized N-terminal glutamine were the major species contributing to the basic variants. This characterization allows a better understanding of the modifications that contribute to the charge variants observed by icIEF, facilitating the evaluation of impacts on product safety and efficacy.

Microchip with an open tubular immobilized ph gradient for UV whole column imaging detection.

This study reports a new method for establishing an open tubular IPG in a microchip coupled with a whole column image detection (WCID) system for protein separation applications. This method allows a wider range of immobilized pH (2.6-9.5) to be established in a PDMS/quartz channel by controlling the diffusion of acidic and basic polymer solutions into the channel through well-designed channel dimensions. The developed pH gradient was experimentally validated by performing the separation of a mixture of standard pI markers. It was further validated by the separation of the hemoglobin control AFSC sample. This method is advantageous over existing IPG methods because it has a wider range of pH and maintains the open tubular feature that matches the UV WCID to improve the sensitivity.

In situ photo-immobilised pH gradient isoelectric focusing and zone electrophoresis integrated two-dimensional microfluidic chip electrophoresis for protein separation

A method is introduced for open-column photo-induced site-selective immobilization of pH gradients in a layer of PEG-methacrylate in a multi-dimensional microfluidic chip for use in electrophoresis. It has several attractive features: (a) mixtures of fluorescently labelled proteins carbonic anhydrase, catalase and myoglobin in their native state can be separated by pH-gradient isoelectric focusing (IEF) and zone electrophoresis (CZE) using integrated 2D chip electrophoresis; (b) compared to strip packing or monolithic photo-immobilization, it overcomes the shortcomings of free carrier ampholyte-based 2D chip electrophoresis in an easy way; (c) larger amount of sample can be loaded into the open column-mode electrophoresis (d) immobilized pH gradients can be re-used and the chip can be recycled; (e) a multilayer 3D pH gradient is established by a layer-by-layer assembly technique to further increase the separation capacity. In our perception, this strategy has a large potential in microfluidic chip-based separation schemes because of its simplicity, separation power, re-usability, and separation capacity.

Using 7 cm immobilized pH gradient strips to determine levels of clinically relevant proteins in wheat grain extracts.

The aim of the work was to test a relatively simple proteomics approach based on phenol extraction and two-dimensional gel electrophoresis (2-DE) with 7 cm immobilized pH gradient strips for the determination of clinically relevant proteins in wheat grain. Using this approach, 157 2-DE spots were quantified in biological triplicate, out of which 55 were identified by matrix-assisted laser desorption/ionization – time of flight tandem mass spectrometry. Clinically relevant proteins associated with celiac disease, wheat dependent exercise induced anaphylaxis, baker’s asthma, and food allergy, were detected in 24 2-DE spots. However, alcohol-soluble gliadins were not detected with this approach. The comparison with a recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for the detection and quantification of clinically relevant proteins in wheat grain.

PTH-092 Discovery and quantitation of novel liver fibrosis biomarkers using proteomics

Introduction Liver biopsy is the reference standard for assessing liver fibrosis and serum biomarkers can be used as a less invasive approach. Various antibody-based assays for serum biomarkers are currently in use to help diagnose fibrosis stage. However, these immunoassays have potential disadvantages such as the inability to detect degraded proteins and often these assays are time consuming. We have developed an antibody-free method to detect and quantify novel liver fibrosis biomarkers in human plasma/serum which overcomes these disadvantages. Method Novel liver fibrosis biomarkers were identified by analysing proteins in plasma/serum samples from controls and patients with varying stages of liver fibrosis using a proteomics technique: two dimensional gel electrophoresis (2DE). For the most promising liver fibrosis biomarkers, an antibody-free assay (parallel reaction monitoring using mass spectrometry) was used which detects tryptic peptides of the biomarkers and their fragments. A calibration curve, established from known amounts of synthetic isotopically labelled peptides, was used to determine the concentrations of our biomarkers in serum/plasma samples from patients with varying stages of liver fibrosis. Results Several candidate biomarkers for hepatic fibrosis were identified using 2DE. Our best biomarkers were promising when compared by Western blotting to the proteins used in existing serum biomarker tests for liver fibrosis. Using parallel reaction monitoring, antibody-free assays were developed for our most promising biomarkers which were able to successfully discriminate between neighbouring stages of liver fibrosis. Conclusion We have developed a fast, sensitive and robust antibody-free method to detect and quantify novel liver fibrosis biomarkers in human plasma/serum. Unlike immunoassays which are restricted on the number of biomarkers due to antibody cost, our method can successfully detect and quantify more than 50 biomarkers in a single 30 min run. This novel assay may help clinicians to assess hepatic fibrosis and reduce the need for invasive liver biopsies. Disclosure of interest None Declared. References Bevin Gangadharan et al . Discovery of novel biomarker candidates for liver fibrosis in hepatitis C patients. PLoS One 2012;7:e39603 Bevin Gangadharan et al . Two dimensional gel electrophoresis using pH3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers. Nature Protocol Exchange , 2011:doi:10.1038/protex.2011.261 Bevin Gangadharan et al . New approaches for biomarker discovery: The search for liver fibrosis markers in hepatitis C patients. J Proteome Res 2011;10:2643 Bevin Gangadharan et al . Novel serum biomarker candidates for liver fibrosis in hepatitis C patients. Clin Chem 2007;53:1792

Proteome Approach as a Tool for the Efficient Separation of Seed Storage Proteins from Buckwheat

Two-dimensional electrophoresis (2-DE) was executed to separate the seed storage proteins from the buckwheat. The proteins extracted from the whole seed proteins were better separated and observed in the use of lysis buffer. Using this method, the highly reproducible isoelectric focusing (IEF) can be obtained from polyacrylamide gels, and IEF from the polyacrylamide gel at all the possible pH range (5.0-8.0) was more easily separated than IPG (immobilized pH gradient) gels. The polyacrylamide gels in the first dimension in 2-DE was used to separate and identify a number of whole seed proteins in the proteome analysis. In this new apparatus using 2-DE, 27cm in length of plate coated with polyacrylamide gel was used and the experiment was further investigated under the various conditions.

The exoproteomes of clonally related Staphylococcus aureus strains are diverse

Several studies have shown that protein expression patterns vary in unrelated bacterial strains due to genomic plasticity and gene regulation, resulting in enhanced heterogeneity in the infection potential. However, exoprotein expression patterns of closely related clonal strains have not been well characterized. Here, we used medium-range (pH 4–7) immobilized pH gradient–two-dimensional gel electrophoresis to investigate the exoproteome from closely related Staphylococcus aureus clonal isolates. Interestingly, we found that, under identical in vitro experimental conditions, a number of protein spots were uniquely present in samples from each clonal isolate irregardless of the similarity of the genotype and the same virulence gene profile. Only a few abundant invariant proteins were found among identical genotypic isolates. Our results clearly shown that heterogeneity in the exoproteome was present even among clonally related strains. We suggest that this heterogeneity may contribute to the degree of virulence even within one clonal genotype. The heterogeneity in the exoproteome of closely related S. aureus strains observed in the current study postulates that pre-existing antibodies are not very protective during recurrent infection with the same strain. Therefore, our findings underscore the importance of taking all clonally related strains into account during proteome analyses.

A tunable isoelectric focusing via moving reaction boundary for two-dimensional gel electrophoresis and proteomics

Routine native immobilized pH gradient isoelectric focusing (IPG-IEF) and two-dimensional gel electrophoresis (2DE) are still suffering from unfortunate reproducibility, poor resolution (caused by protein precipitation) and instability in characterization of intact protein isoforms and posttranslational modifications. Based on the concept of moving reaction boundary (MRB), we firstly proposed a tunable non-IPG-IEF system to address these issues. By choosing proper pairs of catholyte and anolyte, we could achieve desired cathodic and anodic migrating pH gradients in non-IPG-IEF system, effectively eliminating protein precipitation and uncertainty of quantitation existing in routine IEF and 2DE, and enhancing the resolution and sensitivity of IEF. Then, an adjustable 2DE system was developed by combining non-IPG-IEF with polyacrylamide gel electrophoresis (PAGE). The improved 2DE was evaluated by testing model proteins and colon cancer cell lysates. The experiments revealed that (i) a tunable pH gradient could be designed via MRB; (ii) up to 1.65 fold improvement of resolution was achieved via non-IPG-IEF; (iii) the sensitivity of developed techniques was increased up to 2.7 folds; and (iv) up to about 16.4% more protein spots could be observed via the adjustable 2DE as compared with routine one. The developed techniques might contribute to complex proteome research, especially for screening of biological marker and analysis of extreme acidic/alkaline proteins.

Time to dig deep into the plant proteome: a hunt for low-abundance proteins.

Two-dimensional gel electrophoresis (2-DGE) has come a long way since its introduction around 40 years by the pioneering work of these three researchers (Klose, 1975; O'Farrell, 1975; Scheele, 1975). 2-DGE was one of the major breakthroughs in proteomics, enabling researchers to detect, analyze and identify the whole set of proteins of a cell or tissue, simultaneously. With the advancement in technology, some modifications to this technique like development of immobilized pH gradient (IPG) strips were introduced, which undoubtedly, made this technique more simple, rapid and autonomous (Bjellqvist et al., 1982). After its introduction to the present, 2-DGE has been the method of choice for analyzing the complex proteomes of plants. 2-DGE has been used extensively to investigate the effects of biotic and abiotic stress, role of hormones, and developmental changes of plants, among others (Agrawal and Rakwal, 2008). However, it was slowly realized that identification of the plant proteins led to the repeated detection of high-abundance proteins (HAPs) including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and other housekeeping proteins, which are present at 106-105 order of magnitude (Gygi et al., 2000; Patterson and Aebersold, 2003; Gorg et al., 2004). Signaling and other regulatory proteins are generally present 100 molecules per cells. Subsequently, these proteins are difficult to identify by either gel-based or gel-free proteomic approaches, even with access to the latest mass spectrometers. RuBisCO comprises of a large percentage in the total proteins and thus hinders the absorption of low-abundance proteins (LAPs) on the IPG strips, which subsequently results in the poor detection and identification of LAPs on 2D gels and by mass spectrometry (MS), respectively. Therefore, the time has come for all plant proteomers to realize the need to hunt for the LAPs, moving one step ahead from the present. As RuBisCO is the major HAP in plant leaves, here we recommend the incorporation of a RuBisCO depletion/removal method in every plant protein extraction step to look deeper into the plant proteome. RuBisCO depletion will definitely improve the proteome coverage and will lead to the detection of novel unidentified LAPs.

Two dimensional gel electrophoresis using narrow pH 3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers in plasma or serum

Two dimensional gel electrophoresis using narrow pH 3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers in plasma or serum

In-gel peptide IEF sample preparation for LC/MS analysis.

The technique of proteolytically digesting a sample and identifying its protein components by liquid chromatography followed by mass spectrometry (LC-MS) is a widely used analytical tool. Prior fractionation by isoelectric focusing (IEF) may be performed to increase the depth of proteome coverage. Here, we describe a method for in-gel IEF separation of a proteolytic digest that utilizes commercially available immobilized pH gradient (IPG) strips and a widely used IEF instrument.

Blotting from Immobilized pH Gradient Gels: Application to Total Cell Lysates.

Isoelectric focusing as used in the first dimension of two-dimensional gel electrophoresis separates protein isoforms such as those due to phosphorylation and acetylation. The immunoblotting method described here reveals this diversity by a one-dimensional separation. Using commercially available immobilized pH gradient plates or strips, the resolved proteins are transferred to PVDF membranes by diffusion and are probed with protein-specific antibody. The system is useful for monitoring changes of banding patterns and permits parallel processing of samples. Since the effect of posttranslational modifications on the isoelectric point can be predicted, inferring the number and extent of modifications is possible.

Protein profiling and phosphoprotein analysis by isoelectric focusing.

Protein profiling enables the qualitative characterization of a proteome of interest. Phosphorylation is a post-translational modification with regulatory functions in a plethora of cell processes. We present an experimental workflow for simultaneous analysis of the proteome and phosphoproteome with no additional enrichment for phosphoproteins/phosphopeptides. Our approach is based on isoelectric focusing (IEF) which allows the separation of peptide mixtures on an immobilized pH gradient (IPG) according to their isoelectric point. Due to the negative charge of the phosphogroup, most of the phosphopeptides migrate toward acidic pH values. Peptides and phosphopeptides are then identified by mass spectrometry (MS) and phosphopeptide spectra are manually checked for the assignment of phosphorylation sites. Here, we apply this methodology to investigate synaptosome extracts from whole mouse brain. IEF-based peptide separation is an efficient method for peptide and phosphopeptide identification.

Proteins purified from Mycobacterium tuberculosis MDR and Susceptible clinical isolates: Identification by proteomics approach

Aims and objectivesTuberculosis (TB) remains a major global health problem. The incidence of multidrug-resistant tuberculosis (MDR-TB) has increased in recent years. To combat the disease, novel intervention strategies effective against drug-resistant and susceptible subpopulations of Mycobacterium tuberculosis are urgently required as adducts in present treatment regimen. This study has employed a proteomic approach, which is a direct method, to identify proteins from resistant M. tuberculosis isolates compared with sensitive isolates. MethodsThe clinical isolates M.tuberculosis strains were provided by the TB bank of Pasteur Institute of Iran. The bacilli were cultured on 7H9 broth with ADC enrichment at 37°C for 3–4weeks (late log phase). Cells were washed with PBS, suspended in sonication buffer (10mM DTT, 1μg/ml DNAse, 100mM Glycerol, 10mM Triton X100, 20mM EDTA, 50mM Tris-Hcl, 1mM PMSF, 0.02% sodium azide, pH 7.4) and then were subjected to sonication for 1h at 50Hz, in ice, and subsequently centrifuged at 5000rpm for 45min at −4°C. Proteins were precipitated by adding refrigerated ethanol or saturated ammonium sulfate to the supernatant. Pellet resuspended in PBS and then dialyzed for 24h against PBS pH 7.4. IEF was carried out using the Ettan IPGphor 3 isoelecteric focusing system. Immobilized pH gradient IPG strips of pH 4–7 and length 11cm were rehydrated overnight at 20°C with 500μg protein which was mixed with rehydration buffer. Proteins were separated in second dimension on 12% SDS-PAGE in a vertical electrophoretic dual gel. 2D gels were analyzed using Image Master, Melanie 7.0 software. Mass spectrometry was performed using Autoflex II TOF/TOF. Protein sequences were retrieved from Tuberculist server hosted by Pasteur Institute, Paris. ResultsMass spectrometry and bioinformatic characterization of both drug-resistant and sensitive isolates of M. tuberculosis showed that the majority of commonly expressed/upregulated proteins belonged to the cellular metabolism and respiration category (Rv0866, Rv3057c, Rv3248c, Rv1133c, Rv0462, and Rv1876). One hypothetical protein (Rv2744c) and two membrane and cell wall fraction proteins (Rv0379, Rv1886c) were identified. Protein spot 1 was 60kDa chaperonin-2/GroEl-2 (Rv0440). This essential gene prevents misfolding and promotes the refolding and proper assembly of unfolded/misfolded polypeptides generated under stress conditions. Further, another spot Rv2013c (HSP16.3/HSPX) has been shown to be induced under oxygen-deficient conditions. Its role in maintenance of long-term viability during latent, asymptomatic infections and in replication during initial infection has also been proposed. ConclusionSuch information could be helpful for the development of newer therapeutic agents or of diagnostic markers for better treatment or diagnosis of TB. This study extends the list of the potential determinants of differences in virulence between the two isolates (MDR and susceptible TB) and adds to the current understanding of MTB pathogenesis.

OFFGEL fractionation of peptides: Where really is your sample?

Shotgun proteomics of complex samples is generally coupled with at least one peptide fractionation step and, to this effect, peptide isoelectric focusing (IEF) in immobilized pH gradient (IPG) is one of the most used techniques. Fractionation with the OFFGEL 3100 Agilent Technologies apparatus allows the easy recovery of peptides that, after focusing, diffuse into the liquid phase above the gel strip. In this work we investigate the efficiency of peptide diffusion during OFFGEL fractionation and demonstrate that a recovery based only on the spontaneous diffusion process is far from being optimal. We show that a simple additional extraction step with acetonitrile increases of about 40% the amount of material that can be recovered after the focusing. Moreover, we show that the two populations of peptides obtained from the passive elution and from the extraction process are also qualitatively different and only partially overlapping.

Immunoproteomics of Brucella abortus RB51 as candidate antigens in serological diagnosis of brucellosis

The current brucellosis serodiagnostic assays are chiefly based on detecting anti-LPS (lipopolysaccharide) antibodies. However, cross-reaction with some gram-negative bacteria can occasionally induce due to similar O-polysaccharide (OPS) structure. Therefore, the aim of the present study was to identify new candidate antigens from Brucella abortus RB51, a mutant strain lacking the LPS portion, which might be valuable in brucellosis diagnosis. To detect potential antigens, immobilized pH gradients (IPG) strips with three ranges (pH 3–5.6, 4–7 and 6–11) were applied. After separating the insoluble proteins of B. abortus RB51 using two-dimensional electrophoresis (2-DE), their immunogenicity was evaluated by western blotting using four types of antisera – B. abortus, Yersinia enterocolitica O:9 and Escherichia coli O157:H7-positive, and B. abortus-negative bovine sera. Among the several immunogenic spots, the spots showing specific reactivity with only the B. abortus-positive antisera, were considered as candidate antigens. Overall, eleven immuno-reactive proteins were identified, as follows: Cu/Zn superoxide dismutase, histidinol dehydrogenase, chaperonin DnaK, chaperonin GroES, beta-ketoadipyl CoA thiolase, two-component response regulator, the cell-division protein FtsZ, aldehyde dehydrogenase, 50s ribosomal protein L10 and invasion protein B. These selected highly immunogenic protein spots might be useful as alternative antigens for brucellosis and helpful in reducing the cross-reactivity.

Development of non-denaturing off-gel isoelectric focusing for the separation of uranium–protein complexes in fish

An off-gel non-denaturing isoelectric focusing (IEF) method was developed to separate uranium-biomolecule complexes from biological samples as a first step in a multidimensional metalloproteomic approach. Analysis of a synthetic uranium-bovine serum albumin complex demonstrated the focusing ability of the liquid-phase IEF method and the preservation of most of the uranium-protein interactions. The developed method was applied to gill cytosol prepared from zebrafish (Danio rerio) exposed to depleted uranium. The results were compared in terms of resolution, recovery, and protein identities with those obtained by in-gel IEF using an immobilized pH gradient gel strip.

Identification and Characterization of an Oocyte Factor Required for Porcine Nuclear Reprogramming

Nuclear reprogramming of somatic cells can be induced by oocyte factors. Despite numerous attempts, the factors responsible for successful nuclear reprogramming remain elusive. In the present study, we found that porcine oocytes with the first polar body collected at 42 h of in vitro maturation had a stronger ability to support early development of cloned embryos than porcine oocytes with the first polar body collected at 33 h of in vitro maturation. To explore the key reprogramming factors responsible for the difference, we compared proteome signatures of the two groups of oocytes. 18 differentially expressed proteins between these two groups of oocytes were discovered by mass spectrometry (MS). Among these proteins, we especially focused on vimentin (VIM). A certain amount of VIM protein was stored in oocytes and accumulated during oocyte maturation, and maternal VIM was specifically incorporated into transferred somatic nuclei during nuclear reprogramming. When maternal VIM function was inhibited by anti-VIM antibody, the rate of cloned embryos developing to blastocysts was significantly lower than that of IgG antibody-injected embryos and non-injected embryos (12.24 versus 22.57 and 21.10%; p < 0.05), but the development of in vitro fertilization and parthenogenetic activation embryos was not affected. Furthermore, we found that DNA double strand breaks dramatically increased and that the p53 pathway was activated in cloned embryos when VIM function was inhibited. This study demonstrates that maternal VIM, as a genomic protector, is crucial for nuclear reprogramming in porcine cloned embryos.

Analysis of Rat Liver Proteins by Peptide Immobilized pH Gradient Isoelectric Focusing Combined with Liquid Chromatography-Tandem Mass Spectrometry

Abstract Due to the complexity of the biological sample, it is important to develop an effective pre-separation method for the liquid chromatography-mass spectrometer (LC-MS) analysis of biological samples. In this experiment, enzymatic hydrolysate of rat liver protein was pre-separated by peptide immobilized pH gradient isoelectric focusing (IPG-IEF) method, and the pre-separated components were further separated by reversed physe liquid chromatography (RPLC) and then identified by LTQ-Orbitrap MS. A total of 2039 kinds of proteins were identified, including 18 kinds of acetylated proteins, 4 kinds of proteins which were never reported before. Next, bioinformatic analysis was carried out for these proteins. The results showed that peptide IPG-IEF coupled with LC-MS/MS is an effective technique for proteomics analysis and this method is suitable for large-scale protein identification.

Proteomic analysis.

Proteome provides highly valuable information on the amount, modifications, and subcellular localization of polypeptides. Accordingly, geneticists, molecular biologists, and biochemists have logically applied these new tools to respond to different lines of biological questions (inventory of proteins, impact of a mutation, dynamics of protein regulation under a given exposure, …). However, even if the results obtained are very informative, this approach needs an excellent experimental design which ensures robustness and thus yields reproducibility. The present chapter gives appropriate methods for assessing the proteome of Pseudomonas aeruginosa by using a two-dimensional gel electrophoresis approach. Protocols for crude protein extraction, protein separation by using immobilized pH gradients, and protein identification by Liquid Chromatography coupled with tandem Mass Spectrometry (LC-MS/MS) are given.