The Immobiline family: from "vacuum" to "plenum" chemistry

Tunable in-situ electro-polymerization of hydrogel films for microchip-based bioanalysis

Electro-polymerization phenomena have been previously investigated at the macroscale in the context of producing polymeric coatings over extended surface areas. But electrical actuation also offers exquisite local control of the polymerized films' position, morphology, and thickness, suggesting compelling advantages in microfluidic-based analysis systems. Here, we introduce a microfabricated platform incorporating arrays of individually addressable on-chip electrodes capable of generating discretely positioned electro-polymerized hydrogel films inside microchannels in timescales of ∼5 min. Sequential actuation of specific electrode pairs initiates localized propagation of anchored polyacrylamide gel films and permits directed control of their size, shape, and growth rate. In addition to precise positioning of hydrogel films, obstacles, and barriers within microchannel networks, our approach makes it possible to encapsulate macromolecules within the films during polymerization, suggesting utility in a host of areas including separations, sample purification, and immunoassays.

Concentration and fractionation by isoelectric trapping in a micropreparative-scale multicompartmental electrolyzer having orthogonal pH gradients. Part 1

A multicompartmental electrolyzer called ConFrac has been developed and tested for micropreparative-scale isoelectric trapping separations. ConFrac contains n separate, minimalistic isoelectric trapping core units, each with a separate anode compartment, anodic flow-through compartment, collection compartment, cathodic flow-through compartment and a shared cathode compartment. The collection compartments are all isolated from each other and have volumes of 100 μL each. The liquid held in the collection compartments is stagnant. The respective anodic and cathodic flow-through compartments are hydraulically serially connected to each other by flexible, minimum-length, narrow internal diameter tubes. The respective feed solutions whose volumes are larger and variable are recirculated through the serially connected flow-through compartments. Poly(vinyl alcohol)-based buffering membranes are placed between the anode compartments, anodic flow-through compartments, collection compartments, cathodic flow-through compartments and cathode compartment. The membranes establish two orthogonal pH gradients in ConFrac. The primary pH gradient is parallel with the direction of the recirculating flows and orthogonal to that of the electric field. The secondary pH gradient is parallel with the direction of the electric field and orthogonal to that of the recirculating flows. Since the recirculating liquids are kept in thermostated reservoirs and the residence times in the flow-through compartments are shorter than 2 s, ConFrac can tolerate power loads as high as 2 W without overheating the solutions. The operation and performance of ConFrac has been quantitatively characterized: four 25 μM ampholytic components were isolated from 5 mL of feed solution in 20 min and their concentration increased approximately 50-fold.

Recent advances in electrophoretic techniques for the characterization of protein biomolecules: a poker of aces

The four classical modes of electrophoresis of protein molecules (sodium dodecyl sulphate electrophoresis, SDS-PAGE, isoelectric focusing, IEF, and immobilized pH gradients, IPGs, two-dimensional maps, 2D, and capillary electrophoresis, CE) are here reviewed, with special emphasis on recent innovations. Thus, in the case of SDS-PAGE, a novel method, consisting in focusing SDS-protein micelles against a gradient of cationic charges grafted onto a polyacrylamide gel is presented. In the case of IEF, the recent decoding of the structure, polydispersity, molecular mass distribution and buffering properties of the soluble carrier ampholyte buffers are here discussed. In regard to two dimensional mapping, recent instrumentation for performing 2D maps in horizontal, large gel slabs (up to 30 cm × 40 cm) and in a radial format for the SDS dimension is here evaluated. Finally, in the case of CE, three major applications are presented: a thorough study of capillary IEF and of all experimental variables, a method of importance in screening of rDNA products; the possibility of running proteins and peptide separations in very acidic, amphoteric, isoelectric buffers in absence of any capillary coating; finally, the possibility of producing a facile, user friendly, covalent coating of the wall silanols via bonding of quaternarized piperazines endowed with an iodinated tail. In acidic, volatile buffers, such protein/peptide runs can be directly interfaced with mass spectrometry instrumentation.

Third generation of focusing: gel matrices with immobilized cation gradients

A novel method is reviewed here for separation of polyanions, based not on conventional zone electrophoretic means, but on a "steady-state" process by which said polyanions are driven to stationary zones along the migration path against a gradient of positive charges affixed to the neutral polyacrylamide matrix. As the total negative surface charge of such polyanions matches the surrounding charge density of the matrix, they stop migrating and remain stationary, as typical of steady-state separation techniques. This technique has been successfully applied to SDS-protein micelles, DNAs, RNAs and heparins, with remarkable separations, often much superior than those obtained in conventional techniques. Additionally, by exploiting constant plateaus of charges, rather than gradients, it is possible to amplify the separation between species having closely spaced charge densities. This technique resembles a classical IEF process, with the proviso that the polyanions cannot be applied at any position along the gel matrix, but only at the point of low (or zero) charge density. The merits and limits of the technique are assessed.

TheAlpher, Bethe andGamow of IEF, the alpha-Centaury of electrokinetic methodologies. Part II: Immobilized pH gradients

The present review (a follow up of Electrophoresis 2006, 27, 923-938 on conventional IEF) highlights the developmental steps of the IPG technology, from a nebulous start limiting the technique to just 1 pH unit intervals up to the description of extended pH gradients, encompassing as much as 8.5 pH units. Although computer algorithms had been developed for optimizing recipes so as to obtain the most precise and most linear pH gradients, it was also realized that nonlinear pH intervals, covering the pH 3-10 range, would be extremely beneficial in 2-D map analysis, since they would follow the pI distribution of proteins in living systems. The synthesis of a number of Immobiline chemicals (the acrylamido weak acids and bases meant to be incorporated into the nascent polyacrylamide chains) is also reported. The review ends with preparative aspects of IPGs, with the introduction of multicompartment electrolyzers with Immobiline membranes.

Hydrolytically stable, diaminocarboxylic acid-based membranes buffering in the pH range from 6 to 8.5 for isoelectric trapping separations

Diaminocarboxylic acid carrier ampholytes, such as L-histidine, 2,3-diaminopropionic acid, L-ornithine, and L-lysine, were reacted with glycerol-1,3-diglycidyl ether (GDGE) and poly(vinyl alcohol) (PVA) in the presence of sodium hydroxide to produce hydrolytically and mechanically stable hydrogels, supported on a PVA substrate, for use as buffering membranes in isoelectric trapping (IET) separations. The pH values of the DACAPVA membranes were determined with the help of small-molecule pI markers and proteins and were found to be in the 6 < pH < 8.5 range. The membranes were successfully used to isoelectrically trap small ampholytes, desalt ampholyte solutions in IET mode, and effect the binary separation of chicken egg white proteins.

Application of two-dimensional protein gels in biotechnology

The optimal use of biological systems for technologically developed products will not be achieved until biological systems are completely defined in biochemical terms. Two-dimensional polyacrylamide gel electrophoresis, 2-D gels, are contributing to this goal. These gels separate complex mixtures of proteins into individual polypeptide species. The ultimate use of 2-D gels is the construction of cellular 2-D gel databases which identify the proteins on the gels and catalog their responses to different environmental conditions. In addition to these global analyses, many applications for 2-D gels in basic, applied and clinical research have been shown.

Synthesis of zwitterionic acrylic acid buffers for isoelectric focusing in immobilized pH gradients

A range of zwitterionic acrylic acid derivatives, buffering in the neutral and basic pH ranges, have been synthesized by the Mannich reaction of malonic acid, formaldehyde and a secondary amine. These compounds include 2-(4-morpholinomethyl)propenoic acid pK2 7.59 +/- 0.03 (23 degrees C), 2-[bis(2-hydroxyethyl)aminomethyl]propenoic acid pK2 approximately 8.6 (20 degrees C), 2-[bis(2-hydroxypropyl) aminomethyl]propenoic acid PK2 approximately 8.7 (20 degrees C), 2-[N-(2-hydroxyethyl)-N-methylaminomethyl]propenoic acid pK2 9.22+/-0.08 (22 degrees C), 2-[N-ethyl-N-(2hydroxyethyl)aminomethyl]-propenoic acid pK2 approximately 9.6 (20 degrees C), and 2-[4-(2-carboxyprop-2-enyl)piperazinylmethyl]propenoic acid, which has a sigmoidal buffering profile over the pH range 3-10. These zwitterionic acrylic acid buffers were successfully copolymerized with acrylamide to prepare immobilized pH gradients (IPGs) in the neutral to alkaline portion of the pH range. Bovine erythrocyte carbonic anhydrase isozymes were resolved on a pH 5-8 IPG prepared using 2-[4-(2-carboxyprop-2-enyl)piperazinylmethyl]propenoic acid as the immobilized buffer, and horse heart myoglobin was focused on pH 7.1-8.1 and pH 7.5-7.7 IPGs, using 2-(4-morpholinomethyl)propenoic acid as the immobilized buffer. In both cases the pK 9.3 Immobiline compound was used as the strongly basic titrant. These new compounds, besides possessing more hydrophilic residues than the corresponding commercial basic acrylamido buffers (Immobilines), resist hydrolysis at alkaline pH values.

Resolution of fibronectin and other uncharacterized proteins by two-dimensional polyacrylamide electrophoresis with thiourea

Several proteins, which are recognized components of serum, are not resolved by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) under standard conditions. One major example is fibronectin, which is detected in fairly high concentration (milligram range) by immunoassays, while undetectable in 2D-PAGE gels. Following several experiments with a combination of zwitterionic and chaotropic substances we obtained a good resolution of the protein in gels containing 0.5 M thiourea plus 8 M urea. By this technique, fibronectin was, for the first time, found to be microheterogeneous between pl values of 5.3 and 5.6. Besides fibronectin we detected three other families of uncharacterized proteins with Mr of 130000, 110000 and 34000 respectively, whose identity and function are currently under investigation.

Proteomic 'contigs' of Ochrobactrum anthropi, application of extensive pH gradients

The most extensive linear pH gradients yet employed in combination with two-dimensional gel electrophoresis are described, along with their application in proteome analysis. A significant proportion of the protein compliment of bacterial species is believed to be accessible using an extended linear pH gradient of 2.3 to 11.0. Protein standards with predicted isoelectric points (pI) ranging from 3.24 to 9.56 were used to confirm focusing positions with respect to the immobilised pH gradients (IPG) prior to mapping studies of Ochrobactrum anthropi. Multiple gel images were used to construct contiguous windows of protein expression ('proteomic contigs') within 18 cm pH gradients 2.3-5, 4-7, and 6-11 in conjunction with 15% T and 7.5% T acrylamide gels, the latter being used to resolve higher molecular weight (M(r)) proteins. Each IPG had a 5 cm region of similar pH gradient overlap at pH 4-5 and pH 6-7 that was used to construct an image of protein expression characteristic of whole cell lysates. This is reminiscent of genomic sequencing initiatives whereby portions are combined to form a contiguous picture of the whole. The protein maps obtained demonstrated a means of resolving the many tens of thousands of cellular proteins likely to occur in eukaryotic systems, but also highlighted the need to further optimise protein extraction, equilibration buffers, and separation conditions of higher M(r) proteins occurring at extreme pI. Theoretical 2-D protein maps were constructed for five organisms for which the total DNA sequence is now available. In all cases, higher M(r) acidic and basic proteins were shown to be common.

Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients

Membrane and nuclear proteins of poor solubility have been separated by high resolution two-dimensional (2-D) gel electrophoresis. Isoelectric focusing with immobilized pH gradients leads to severe quantitative losses of proteins in the resulting 2-D map, although the resolution is usually high. Protein solubility could be improved by using denaturing solutions containing various detergents and chaotropes. Best results were obtained with a denaturing solution containing urea, thiourea, and detergents (both nonionic and zwitterionic). The usefulness of thiourea-containing denaturing mixtures is shown for microsomal and nuclear proteins as well as for tubulin, a protein highly prone to aggregation.

Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients

Membrane proteins were separated by high resolution two-dimensional (2-D) electrophoresis. On isoelectric focusing (IEF) with immobilized pH gradients severe protein losses in the resulting 2-D map were observed when compared with carrier ampholyte-based IEF. This has been noticed for two different biological systems, namely the chloroplast envelope of spinach and the endocytic vesicles from Dictyostelium discoideum. The possible mechanisms of these losses on immobilized pH gradients are discussed.

Micropreparative immobilized pH gradient two-dimensional electrophoresis in combination with protein microsequencing for the analysis of human liver proteins

Simplified methodology has been developed for the direct N-terminal amino acid microsequencing of human liver and hepatoma derived polypeptides, following micropreparative two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Utilization of immobilized pH gradient (IPG) gel strips in the first dimension permitted protein loading of 0.5-2.0 mg with negligible diminution of polypeptide resolution. Following 2-D separation and electrotransfer to polyvinylidene difluoride (PVDF) membranes nearly 100 well resolved Ponceau S stained polypeptides were readily visualized, from which, 32 adult liver S-9 and 72 HepG2 nuclear cytosolic polypeptides were subjected to N-terminal microsequencing. Twenty normal adult liver and 54 HepG2 polypeptides yielded N-terminal sequence information, of which 17 and 19 polypeptides, respectively, exhibited high sequence homology to previously identified proteins. The initial yields of the proteins sequenced ranged from 2-14 pmols and yielded sequences of 14-26 amino acid residues. Many of the adult liver and HepG2 proteins contained inferred leader sequences since the first sequenced residue was several (20-30) residues from the methionine initiation site predicted by the cDNA of the adult liver. Quantitative comparison of 60 well characterized hepatic proteins between normal adult liver and two nontransformed, Chang and WRL-68, and four human hepatoma derived cell lines, HepG2, Huh-7, FOCUS, and SK-Hep, revealed a high homogeneity of protein expression both qualitatively and quantitatively in both whole cell lysate and purified nuclear preparations. Most notable differences include the previously characterized polypeptides: carbamoyl phosphate synthase, MER5 homologous protein, cytidylate kinase, phosphatidylethanolamine-binding protein and mitochondrial enoyl-CoA hydratase as well as three N-terminally blocked polypeptides: 11 (63 kDa/pI 7.00), 56 (26/6.45) and 59 (22/6.00) all of which were expressed at similar levels in normal adult liver tissue and each of the nontransformed, Chang and WRL-68, cell lines but not expressed or expressed at greatly decreased levels in each of tumor derived liver cell lines. Pyruvate carboxylase, superoxide dismutase, serotransferrin, liver fatty acid binding protein, 1-hydroxyprostaglandin dehydrogenase, NADH dehydrogenase (ubiquinone) as well as three N-terminally blocked polypeptides: 9 (57/6.00), 53 (24/4.90) and 63 (16/4.70) were detected only in whole adult liver tissue and not in any of the cultured cell lines. Two additional polypeptides: U35, (27/6.05) and 58 (22/5.70) yielded N-terminal partial amino acid sequences but were not identified in established protein databases. We have shown that micropreparative IPG 2-D PAGE In combination with protein microsequencing provides a convenient one step procedure to rapidly obtain partial amino acid sequence information for nearly 100 individual polypeptides directly from a single 2-D PAGE gel with numerous applications to a wide variety of biological model systems.

Programmed cell death in sympathetic neurons: a study by two-dimensional polyacrylamide gel electrophoresis using computer image analysis

The technique of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) coupled with computer image analysis was used in this study to examine changes in protein expression occurring during the onset of programmed cell death (PCD) in rat sympathetic neurons following withdrawal of nerve growth factor (NGF). Sympathetic neurons from superior cervical ganglia of postnatal day-one Wistar rats were cultured in the presence of NGF for 24 h and then either maintained in the presence of NGF or deprived of NGF for a period of 8 h. To label the proteins being synthesised, neurons were cultured in the presence of L-[35S]methionine for a further 2 h under the same conditions but with 3% of the normal methionine concentration. Neuronal proteins were then analysed by 2-D PAGE using immobilised pH gradient (IPG) gel strips in the first dimension. For the second dimension a custom-built electrophoresis system capable of running multiple sodium dodecyl sulfate (SDS)-PAGE slab gels in a vertical configuration, with good temperature control (+/- 0.7 degrees C) was used and is described in this paper. Proteins resolved on the dried gels were visualised using storage phosphor technology and the digitised images subjected to rigorous analysis using the QUEST II software system. Seventeen proteins whose relative synthesis decreased and four proteins that increased upon NGF withdrawal were located and are documented.

Isoelectric focusing in immobilized pH gradient of melon (Cucumis melo L.) seed protein: methodical and genetic aspects, and application in breeding

Genetic variability of melon seed proteins was studied by separation of seed protein by isoelectric focusing in immobilized pH gradient (IEF-IPG) under denaturing conditions. A routine procedure was developed for IEF-IPG of hundreds of individual melon seeds per day. A group of 74 accessions from 19 morphologically distinct groups and from different geographic origin were studied by IEF-IPG using pH gradients of 4-10, 4-7 and 6-10. The electrophoretic analysis of the 74 accessions showed 270 reproducible seed protein bands of which 70 were variable. Genetic evaluation led to the conclusion that at least 20 loci govern the variation found. The phylogenetic trees constructed using the protein data on one hand and the morphological data on the other hand were compared and their use was evaluated. A number of commercial Cantaloup F1 hybrid descendants derived from the F1 hybrids by diplohaploidization or single plot descent were studied by IEF-IPG using pH gradients of 4-7 and 6-10. Among the F1 hybrids and their descendants 265 reproducible protein bands could be identified of which 72 were variable as to presence versus absence. The genetic interpretation of the protein pattern as found by IEF-IPG and the use of IEF-IPG in plant breeding was discussed. It was concluded that IEP-IPG of melon seed proteins is a valuable tool in breeding.

Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension

We describe a modification in the sample application mode for isoelectric focusing with immobilized pH gradients. Instead of being applied at the surface of the gel in a sample cup, the sample is introduced into the gel during the immobilized pH gradient strip rehydration step. This modification implies the use of low percentage gels (below 3.5% T) and specially designed, but simple, rehydration chambers. The main advantages are a uniform resolution without side effects and the possibility of handling large sample volumes (500 microL for a standard 3 x 160 x 0.5 mm strip), allowing micropreparative work (milligram samples) with a simple experimental design.

Immobilized pH gradients: new pK values of acrylamido buffers in poly(N-acryloylaminoethoxyethanol) matrices

A novel matrix consisting of N-acryloylaminoethoxyethanol, a hydrophilic monomer extremely resistant to hydrolysis, was recently reported by Chiari et al. (Electrophoresis, 1994, 15, 177-186). When using it as a matrix for grafting immobilized pH gradients for isoelectric focusing, a shift in protein spot position was noticed. This was attributed to a shift in pK values of the Immobiline buffers when changing from the standard poly(acrylamide) to a poly(N-acryloylaminoethoxyethanol) matrix. A series of 1 pH unit gradients was constructed, where a single buffering Immobiline was used and titrated with a counterion having a pK removed by at least 3 pH units from the nearest extreme of the generated pH interval. It was noted that all compounds became weaker acids and bases, with a delta pK ranging from -0.02 to -0.06 for the acids (pK 3.6, 4.4, and 4.6) and a delta pK ranging from -0.12 tp -0.20 for the bases. The new pK values for the seven commercially available buffers are thus pK 3.6-->pK 3.58, pK 4.4-->pK 4.36, pK 4.51-->4.45, pK 6.21-->6.09, pK 7.06-->6.94, pK 8.50-->pK 8.37, and pK 9.59-->pK 9.39. These values refer to 10 degrees C in the gel phase, the first value in poly(acrylamide) and the second in poly(N-acryloylaminoethoxyethanol).

Immobilized buffers for isoelectric focusing: from gradient gels to membranes

Some major improvements to a pH gradient simulator for isoelectric focusing in immobilized buffers are here described. They allow creation of graphs (giving the profiles of pH gradient, deviation from ideal shape, buffering power and ionic strength) with up to 200 increments (which, in a 1 pH unit span means mapping of pH intervals at barely 0.005 pH increments per step). In addition, for preparative purification protocols, utilizing multicompartment electrolyzers with isoelectric, buffering membranes, this modified program allows easy calculation of the precise pI value at any point along the pH gradient used for the analytical assessment of the pI values of the proteins to be purified. At the desired pH value, reached by moving the cursor along the pH gradient, a simple clicking of the mouse button allows the display of the instant Immobiline composition responsible for that pH value. The molarity ratio of the various Immobilines present at this precise point of the pH scale in fact gives the composition (with the accompanying value of buffering power and ionic strength) of the membrane to be utilized as a pH-stat in the preparative scale run. This is the only method that allows reproducible and valid scaling up from the analytical to the preparative scale.