IEF Separation Research Articles

Steady-state protein focusing in carrier ampholyte based isoelectric focusing: Part I-Analytical solution.

The determination of an analytical solution to find the steady-state protein concentration distribution in IEF is very challenging due to the nonlinear coupling between mass and charge conservation equations. In this study, approximate analytical solutions are obtained for steady-state protein distribution in carrier ampholyte based IEF. Similar to the work of Svensson, the final concentration profile for proteins is assumed to be Gaussian, but appropriate expressions are presented in order to obtain the effective electric field and pH gradient in the focused protein band region. Analytical results are found from iterative solutions of a system of coupled algebraic equations using only several iterations for IEF separation of three plasma proteins: albumin, cardiac troponin I, and hemoglobin. The analytical results are compared with numerically predicted results for IEF, showing excellent agreement. Analytically obtained electric field and ionic conductivity distributions show significant deviation from their nominal values, which is essential in finding the protein focusing behavior at isoelectric points. These analytical solutions can be used to determine steady-state protein concentration distribution for experiment design of IEF considering any number of proteins and ampholytes. Moreover, the model presented herein can be used to find the conductivity, electric field, and pH field.

Combining TBP-based rOFFGEL-IEF with FASP and nLC–ESI-LTQ-MS/MS for the analysis of cisplatin-binding proteins in rat kidney

In this work, a methodology based on a reducing IEF separation in combination with a FASP tryptic digestion able to maintain the integrity of cisplatin-protein complexes has been developed. The method is based on OFFGEL-IEF under conditions provided by the thiol-free reducing agent TBP, which allowed the separation of cisplatin-binding proteins in liquid fractions. The FASP procedure is applied as an intermediate stage between the IEF separation and MS analysis where the proteins are retained and concentrated in a commercially available ultrafiltration device. The filter unit acts as a proteomic reactor for detergent removal, buffer exchange, chemical modification (reduction and alkylation) and protein digestion. Finally, purified peptides are recovered by centrifugation. This procedure provides efficiencies comparable to standard in-solution digestion and the risk of platinum-complexes loss is minimized due to the fact that reagents employed along the process are subsequently eliminated before the following step. The stability of platinum-protein complexes under the FASP tryptic digestion, either using TBP or DTT as reducing agents, was maintained, allowing the identification of several platinum-containing peptides from cisplatin-HSA. This methodology was applied to the separation of platinum-enriched protein fractions obtained by SEC-ICP-MS in a kidney tissue extract from a rat treated with cisplatin, followed by further identification by nLC-ESI-LTQ-MS/MS after FASP tryptic digestion of selected platinum-containing liquid fractions.

Selective Carbonylation Of The Skeletal Muscle Mitochondrial Proteome In Aging Mice: The Role Of Lifelong Physical Activity

Skeletal muscle presents clear age associated deterioration in structure and function. The underlying mechanisms are usually related with enhanced oxidative stress being muscle mitochondria a key organelle in the aging process. PURPOSE: To better understand the mitochondrial functional alterations of aging skeletal muscle and how they are affected by lifestyle, we performed a global search of the potential mitochondrial protein targets for carbonylation. METHODS: C57BL/6 mice mitochondria from young (2 months) and old (25 months) mice, aged with or without access to running wheels, were isolated from skeletal muscle. Histochemical staining of BN-PAGE respiratory complexes was used to evaluate functionality differences between experimental groups. To assess the mitochondrial proteome differential susceptibility to carbonylation, we have performed 2 DE oxyblots by derivatizing IPG strips with DNPH between IEF and molecular weight separation, followed by electrotransfer to nitrocellulose membrane and immune detection of carbonyl derivatives. Coupling this with Maldi TOF/TOF protein identification, we have identified the preferential targets of protein oxidation. RESULTS: It was found that aging induces mitochondria proteome changes, with an increased susceptibility of specific proteins to oxidative damage. Nevertheless, lifestyle modulates mitochondria functionality being clear that lifelong physical activity contributes to the maintenance of mitochondrial homeostasis, while sedentariness promotes mechanistic adaptations leading to organelle dysfunction. Though some proteins were found carbonylated in the three groups (young, old-active and old-sedentary mice), other proteins, such as Complex III iron sulphur subunit, MnSOD, aspartate aminotransferase and malate dehydrogenase were only specifically found carbonylated in aged mice. Furthermore, ATP synthase D chain, Complex I MLRQ subunit, cytochrome c and cytochrome c1 were only found carbonylated on aged sedentary mice. CONCLUSION: The preferential targeting of electron transport chain subunits to sedentariness-related carbonylation might explain the observed differences in muscle functionality. Supported by FCT grant PTDC/DES/70757/2006

Wheat straw conversion by enzymatic system of Ganoderma lucidum

The purpose of this study was to resolve the question of whether various nitrogen sources and concentrations affect characteristics of selected G. lucidum ligninolytic enzymes participating in wheat straw fermentation. This is the first study reporting the presence of versatile peroxidase activity in crude extract of G. lucidum culture, as well as isoforms profile of Mn-oxidizing peroxidases. NH4NO3 was the optimum nitrogen source for laccase and Mn-dependent peroxidase activity, while peptone was the optimum one for versatile peroxidase activity. with laccase activity were obtained by native PAGE and IEF separations from medium enriched with inorganic nitrogen source, and only two bands from medium containing organic source. Medium composition was not shown to affect isoenzyme patterns of Mn-oxidizing peroxidases. Four isoforms of Mn-dependent peroxidase and three of versatile peroxidase were obtained on native PAGE. By IEF separation, five isoforms of Mn-dependent peroxidase and only two of versatile peroxidase were observed. The results demonstrated that G. lucidum has potential for mineralization and transformation of various agricultural residues and should take more significant participation in large-scale biotechnological processes.

Separation and characterization of aggregated species of amyloid-beta peptides

We have investigated the use of isoelectric focusing and immunodetection for the separation of low molecular weight species of amyloid-beta (Abeta) peptides from their aggregates. From solutions of Abeta(1-40) or Abeta(1-42) monomeric peptides, low molecular weight material appeared at a pI value of ca. 5, while the presence of aggregates was detected as bands, observed at a pI of 6-6.5. The formation of Abeta aggregates (protofibrils) was verified by a sandwich ELISA, employing the protofibril conformation-selective antibody mAb158. In order to study the aggregation behavior when using a mixture of the monomers, we utilized the IEF separation combined with Western blot using two polyclonal antisera, selective for Abeta(1-40) and Abeta(1-42), respectively. We conclude that both monomers were incorporated in the aggregates. In a further study of the mixed aggregates, we used the protofibril conformation-selective antibody mAb158 for immunoprecipitation, followed by nanoelectrospray mass spectrometry (IP-MS). This showed that the Abeta(1-42) peptide is incorporated in the aggregate in a significantly larger proportion than its relative presence in the original monomer composition. IP-MS with mAb158 was also performed, and compared to IP-MS with the Abeta-selective antibody mAb1C3, where a monomeric Abeta(1-16) peptide was added to the protofibril preparation. Abeta(1-16) is known for its poor aggregation propensity, and acted therefore as a selectivity marker. The results obtained confirmed the protofibril conformation selectivity of mAb158.

Evaluation of microchip material and surface treatment options for IEF of allergenic milk proteins on microchips

The use of glass and PDMS microchips has been investigated to perform rapid and efficient separation of allergenic whey proteins by IEF. To decrease EOF and to limit protein adsorption, two coating procedures have been compared. The first one consists in immobilizing hydroxypropyl cellulose (HPC) and the second one poly(dimethylacrylamide-co-allyl glycidyl ether) (PDMA-AGE). EOF limitation has been evaluated using frontal electrophoresis of a fluorescent marker of known effective mobility. EOF velocity was decreased by a factor about 100 and 30, respectively. pH gradient formation has been evaluated for each microchip using fluorescent pI markers. It was demonstrated that as expected a coating was essential to avoid pH gradient drift. Both coatings were efficient on glass microchips, but only PDMA-AGE allowed satisfying focusing of pI markers on PDMS microchips. Fluorescent covalent and noncovalent labelings of milk proteins have been compared by IEF on slab-gels. IEF separation of three major allergenic whey proteins [beta-lactoglobulin A (pI 5.25) and B (pI 5.35) and alpha-lactalbumin (pI 4.2-4.5)] was performed in both microchips. Milk proteins were separated with better resolution and shorter analysis time than by classical CIEF. Finally, better resolutions for milk allergens separation were obtained on glass microchips.

Simulations of IEF in microchannel with variable cross‐sectional area

This study develops a 1-D mass transport model to describe the electrophoresis transport behavior within a microchannel with a variable cross-sectional area. Utilizing three different numerical schemes, simulations are performed to investigate the IEF of proteins in ampholyte-based pH gradients within both a planar microchannel and a contraction-expansion microchannel, respectively. The simulation results obtained using the modified 1-D mass transport model and the finite-volume method (FVM) for the IEF separation of a single protein sample in a ten-ampholyte-based pH gradient within a planar microchannel are consistent with those presented by Shim et al. [Electrophoresis 2007, 28, 572-586] using a 2-D FVM scheme. In addition, the Courant-Friedrichs-Lewy number insensitive conservation element and solution element (CNI-CESE) method is found to be both more robust and more computationally efficient than the conventional CESE scheme when modeling IEF phenomena within a contraction-expansion microchannel. In modeling the IEF separation of four sample ampholytes in a 20-ampholtye-based pH gradient within a contraction-expansion microchannel, the results obtained using the CNI-CESE scheme are in good agreement with those published in literature. Moreover, the simulations can be performed significantly faster with the new 1-D model and the CNI-CESE scheme. Finally, the results obtained using the modified 1-D mass transport model and the CNI-CESE scheme demonstrate that the concentration of the focused test sample and the resolution of the pH gradient within the microchannel increase as the number of ampholytes used to accomplish the IEF separation process is increased.

An update on the mouse liver proteome

BackgroundDecoding of the liver proteome is subject of intense research, but hampered by methodological constraints. We recently developed an improved protocol for studying rat liver proteins based on 2-DE-MALDI-TOF-MS peptide mass finger printing.This methodology was now applied to develop a mouse liver protein database.ResultsLiver proteins were extracted by two different lysis buffers in sequence followed by a liquid-phase IEF pre-fractionation and separation of proteins by 2 DE at two different pH ranges, notably 5-8 and 7-10. Based on 9600 in gel digests a total of 643 mouse liver proteins with high sequence coverage (> 20 peptides per protein) could be identified by MALDI-TOF-MS peptide mass finger printing. Notably, 255 proteins are novel and have not been reported so far by conventional two-dimensional electrophoresis proteome mapping. Additionally, the results of the present findings for mouse liver were compared to published data of the rat proteome to compile as many proteins as possible in a rodent liver database.ConclusionBased on 2-DE MALDI-TOF-MS a significantly improved proteome map of mouse liver was obtained. We discuss some prominent members of newly identified proteins for a better understanding of liver biology.

Isoelectric focusing in an ordered micropillar array

An original micropillar array dedicated to electrophoretic separations has been developed. It consists of a rectangular zone of PDMS micropillars protruding on a PDMS block. This area has been chosen to mimic a diluted gel structure and remains uncovered to keep the ability to perform an immunoblot after the protein separation for further applications in the field of allergy diagnosis. The micropillar array geometry has been optimized by evaluating the influence of pillar shape, pillar size and interpillar distance on evaporation and IEF separation. The separation conditions namely electrolyte composition, temperature and sample loading have been studied. Finally a protein mixture with pI ranging from 4.7 to 10.6 has been successfully separated within this microdevice by IEF without decreasing the resolving power obtained with conventional minigel. The micropillar array developed for electrophoretic separations leads to much shorter analysis times and can be reused several times while gels are disposable.

Microchip Isoelectric Focusing Applications

This review summarizes all available publications on isoelectric focusing carried out on planar microfabricated devices. Characteristic features of microchip isoelectric focusing (MC-IEF), such as resolution independence of separation length and compression of pH gradient, are discussed. An overview of materials used for microchip fabrication and developed detection strategies is given. Accomplishments in on-chip coupling of MC-IEF with other electrophoretic separation techniques or with mass spectrometry are briefly described. The review ends with alternative approaches to MC-IEF separation in terms of unusual sample introduction, kinds of support used for IEF separation, and in manner in which the pH gradient is generated.

Improved Method for Proteome Mapping of the Liver by 2-DE MALDI-TOF MS

Identifying the liver proteome has been the subject of intensified research. Notably, due to their strong heterogeneity in size, charge, solubility, and relative abundance, different strategies of pre-fractionation must be employed to increase the number of identifiable proteins. In our efforts, we used two different lysis buffers in sequence, a liquid-phase IEF pre-fractionation and separation of protein mixtures at three different pH ranges (3-10, 5-8, and 7-10). Then, >15 000 gel digested proteins were investigated. We report an identification of 590 different gene products, including some isoforms. More than 150 proteins have not been reported so far by two-dimensional electrophoresis (2-DE) proteome mapping. We further studied the transcript expression of more than 33 000 genes in rat liver to explore correlations between transcript and protein expression. Overall, we report a method for the separation of rat liver proteins and their identification by mass spectrometry. The newly identified proteins will enable an improved understanding of liver biology.

Combined cup loading, bis(2‐hydroxyethyl) disulfide, and protein precipitation protocols to improve the alkaline proteome of Lactobacillus hilgardii

Despite the large number of papers dealing with bacterial proteomes, very few include information about proteins with alkaline pI's, because of the limits inherent in 2-DE technology. Nonetheless, analyses of in silico proteomes of many prokaryotes show a bimodal distribution of their proteins based on their pI's; the most crowded areas lying between pI 4-7 and 9-11. The aim of the present research was to set up a general, simple, and standardizable 2-DE protocol suitable for studying the alkaline proteome of Lactobacillus hilgardii, a Gram-positive bacillus isolated from wine. The method has also been tested on a Gram-negative bacterium able to degrade aromatic pollutants, Acinetobacter radioresistens S13. Optimization of the method was mainly focused on improving protein extraction and IEF (pI 6-11) separation protocols. Concerning IEF, different methods for sample loading (in-gel rehydration and cup loading), and different reducing agents (DTT and bis(2-hydroxyethyl) disulfide (HED)) were tested and compared. The proposed protocol was found to resolve efficiently alkaline proteins from both of our Lactobacillus and Acinetobacter strains, in spite of their different external layers, thus, enabling a more comprehensive study of their proteomes.

A Dataset of Human Fetal Liver Proteome Identified by Subcellular Fractionation and Multiple Protein Separation and Identification Technology

A high throughput process including subcellular fractionation and multiple protein separation and identification technology allowed us to establish the protein expression profile of human fetal liver, which was composed of at least 2,495 distinct proteins and 568 non-isoform groups identified from 64,960 peptides and 24,454 distinct peptides. In addition to the basic protein identification mentioned above, the MS data were used for complementary identification and novel protein mining. By doing the analysis with integrated protein, expressed sequence tag, and genome datasets, 223 proteins and 15 peptides were complementarily identified with high quality MS/MS data.

Effects of separation length and voltage on isoelectric focusing in a plastic microfluidic device

This paper describes the investigation on the effects of separation length and voltage on IEF in a plastic microfluidic device. A LIF, whole-channel imaging detection (WCID) system was developed to monitor proteins while they were moving under an electric field. IEF was carried out in a separation medium consisting of carrier ampholytes and a mixture of linear polymers (hydroxyethylcellulose and hydroxypropylcellulose). We found that the IEF separation resolution is essentially independent of separation length when the same voltage is applied, which agrees with the theory. This result supports the notion that IEF in a microfabricated device leads to more rapid analysis without sacrificing the resolving power. A higher separation voltage also brought about more rapid analysis and superior separation resolution. IEF of two proteins (green fluorescence protein and R-phycoerythrin) was achieved in 1.5 min when 500 V was applied across a 1.9-cm channel. We found that a linear relationship exists between the focusing time and the inverse of the electrical field strength. In addition, we confirmed the phenomenon in which the pH gradient was compressed to the middle of a channel, and we found that the relative amount of the gradient compression decreased with the channel length.

Active Kinase Proteome Screening Reveals Novel Signal Complexity in Cardiomyopathy

Recent advances in the characterization of the phosphoproteome have been limited to measuring phosphorylation statuses, which imply but do not measure protein kinase activity directly. As such, the ability to screen, compare, and define multiple protein enzymatic activities across divergent samples remains a daunting challenge in proteomics. Here, we describe a gel-based kinase assay coupled to MS identification as an approach to map global kinase activity and assign pathway architecture to specified biologic contexts. We demonstrate the utility of this method as a platform for the comparison of proteomes based on differences in both kinase activities and for use in the de novo substrate identification for individual kinases. This approach allowed us to map the signal perturbations in the post-natal heart that were associated with activation of a myopathic cascade as mediated by the mitogen-activated protein kinase MKK6 and established the novel observation that MKK6 promotes the development of cardiomyopathy through multiple substrate interactions.

Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins.

Hydrophobic proteins are difficult to analyze by two-dimensional electrophoresis (2-DE) because of their intrinsic tendency to self-aggregate during the first dimension (isoelectric focusing, IEF) or the equilibration steps. This aggregation renders their redissolution for the second dimension uncertain and results in the reduction of the number and intensity of protein spots, and in undesirable vertical and horizontal streaks across gels. Trifluoroethanol (TFE) is traditionally used at high concentration to solubilize peptides and proteins for NMR studies. Depending upon its concentration, TFE strongly affects the three-dimensional structure of proteins. We report here a phase separation system based on TFE/CHCl(3), which is able to extract a number of intrinsic membrane proteins. The addition of TFE in the in-gel sample rehydration buffer to improve membrane protein IEF separation is also presented. The procedure using urea, thiourea, and sulfobetaine as chaotropic agents was modified by the addition of TFE and removing of sulfobetaine at an optimized concentration in the solubilization medium used for the first dimension. When using membrane fractions isolated from Escherichia coli, the intensity and the number of spots detected from 2-DE gels that used TFE in the solubilization medium were significantly increased. The majority of the proteins identified using peptide mass fingerprinting and tandem mass spectrometry (MS/MS) were intrinsic membrane proteins, proteins of beta barrel structure or transmembrane proteins.

Purification and characterization of the raffinose oligosaccharide chain elongation enzyme, galactan : galactan galactosyltransferase (GGT), from Ajuga reptans leaves.

Galactan: galactan galactosyltransferase (GGT), an enzyme involved in the biosynthesis of the long-chain raffinose family of oligosaccharides (RFOs) in Ajuga reptans, catalyses the transfer of an alpha-galactosyl residue from one molecule of RFO to another one resulting in the next higher RFO oligomer. This novel galactinol (alpha-galactosyl-myo-inositol)-independent alpha-galactosyltransferase is responsible for the accumulation of long-chain RFOs in vivo. Warm treatment (20 degrees C) of excised leaves resulted in a 34-fold increase of RFO concentration and a 200-fold increase of GGT activity after 28 days. Cold treatment (10 degrees C/3 degrees C day/night) resulted in a 26- and 130-fold increase, respectively. These data support the role of GGT as a key enzyme in the synthesis and accumulation of long-chain RFOs. GGT was purified from leaves in a 4-step procedure which involved fractionated precipitation with ammonium sulphate as well as lectin affinity, anion exchange, and size-exclusion chromatography and resulted in a 200-fold purification. Purified GGT had an isoelectric point of 4.7, a pH optimum around 5, and its transferase reaction displayed saturable concentration dependence for both raffinose (Km = 42 mM) and stachyose (Km = 58 mM). GGT is a glycoprotein with a 10% glycan portion. The native molecular mass was 212 kDa as determined by size-exclusion chromatography. Purified GGT showed one single active band after native PAGE or IEF separation, respectively, which separated into three bands on SDS-PAGE at 48 kDa, 66 kDa, and 60 kDa. The amino acid sequence of four tryptic peptides obtained from the major 48-kDa band showed a high homology to plant alpha-galactosidase (EC 3.2.1.22) sequences. GGT differed, however, in its substrate specificity from alpha-galactosidases; it neither hydrolysed nor transferred alpha-galactosyl-groups from melibiose, galactinol, UDP-galactose, manninotriose, and manninotetrose. Galactinol, sucrose, and galactose inhibited the GGT reaction considerably at 10-50 mM.

High sensitivity mass spectrometric methods for obtaining intact molecular weights from gel-separated proteins.

The molecular weight measurement of intact Escherichia coli proteins separated by isoelectric focusing-immobilized pH gradient (IEF-IPG) gels and analyzed by mass spectrometry is presented. Two methods are discussed: (i) electrospray ionization (ESI) mass spectrometry (MS) of extracted proteins, and (ii) matrix-assisted laser desorption/ionization (MALDI)-MS analysis directly from IEF-IPG gels. Both ESI and MALDI methods yield sub-picomole sensitivity and good mass measurement accuracy. The use of an array detector for ESI-MS was essential to discriminate against contaminating background ions and to selectively detect high mass protein ions. MALDI-MS offers high-throughput analysis of one- and potentially two-dimensional (2-D) gels. The "virtual 2-D" gel method with first-dimensional IEF separation and the second dimension as molecular mass determination by MS, is a particularly promising method for protein analysis due to its ultra high sensitivity and correspondence to classical 2-D gels. Further sensitivity enhancements for the MALDI-MS method are provided by post acceleration detection optimized for high mass time-of-flight analysis.

A reliable method for the analysis of human MHC class II α and β chains by Western blotting of IEF gels

The solubility and ensuing transfer problems associated with IEF separation and blotting of membrane proteins have been eliminated by confining NP40 to the sample region of the gel and replacing it with octylglycoside in the separating gel. This permitted excellent separation of both the α and β chains of the human MHC antigens and their subsequent detection by Western blotting.