Evaluation of isoelectric focusing running conditions during two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis: variation of gel patterns with changing conditions and optimized isoelectric focusing conditions

Five major isoelectric focusing (IEF) parameters--volt-hours; concentrations of acrylamide, NaOH, and H3PO4; and equilibration time--were systematically varied to determine the effect of each on two-dimensional IEF/sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel patterns and to optimize IEF conditions. Alterations in each parameter affected the gel pattern, frequently causing uncertainty in the identification of spots between conditions. The results emphasize the need for internal analytical consistency, and indicate that gel pattern comparisons between laboratories can be complicated if different IEF conditions are employed. The systematic evaluation indicated that optimized patterns were obtained when increased concentrations of NaOH and H3PO4 (to 50 and 25 mM, respectively) and run durations of 10,000 V-h or longer were used.     

Gel gradient electrophoresis, isoelectric focusing and two-dimensional techniques in horizontal, ultrathin polyacrylamide layers

An ultrathin layer, horizontal polyacrylamide gel system for electrophoresis, isoelectric focusing and two-dimensional techniques is described. Gel slabs 240 micron thin for unidimensional, or 360 micron thin for two-dimensional runs are cast on cellophane foils as support. The sample is loaded in pockets pre-cast in the gel (2--3 microliter size) or in trenches for two-dimensional experiments. The second dimension is routinely performed in concave exponential gel gradients, spanning an acrylamide concentration from 4% to 22.5%. The sensitivity with the common Coomassie Blue stain is very high, well below 0.1 microgram protein/band. Zymogram detections can be developed within a few minutes, thus retaining the band sharpness of the focused zones or of the bands separated in pore gradient electrophoresis. Sample handling, staining and destaining and gel drying and storage are greatly simplified and performed in a fraction of the time needed for conventional, thick gels in the 1-2 mm thickness range.     

Detection of alginate lyases by isoelectric focusing and activity staining

A sensitive method has been developed for the rapid analysis of mutliple forms of alginate lyases in crude bacterial extracts. The technique is based on isoelectric focusing with a substrate-overlay technique for the direct measurement of enzyme activity. Isoelectric point values have been determined for the alginate lyases present in five strains of bacteria using, typically, 5.7 × 10⁻ units of activity. Multiple forms of these enzymes have been observed in three of the five bacterial strains studied. The method has also been used to compare the pI value of the -guluronate lyase from Klebsiella pneumoniae with those for the cloned gene products in strains of Escherichia coli.     

Human globin chain separation by isoelectric focusing

Human globin chain separation, a key procedure in the study of hemoglobinopathies, is routinely performed by chromatography on carboxymethylcellulose. This method, though relatively easy and highly reliable, is expensive and time consuming. A new procedure, based on isoelectric focusing, is presented which allows the simultaneous separation of globin chains from multiple samples (at least 20 per gel slab). The method is rapid, inexpensive and can be easily carried out in clinical laboratories, and its high sensitivity allows the identification of radioactive bands even with minute amounts of labelled material. A new phenomenon, called the 'Nonidet P-40 effect', which greatly enhances the separation between gamma and beta chains by binding to these two chains and shifting their pI values in opposite directions, is described.     

New polyacrylamide matrices for drift-free isoelectric focusing

The major cause for pH gradient decay and cathodic drift during isoelectric focusing in polyacrylamide gels has been found to be electroendo-osmotic flow generated by fixed charges in the gel matrix. These charges have the following causes: (a) trace impurities of acrylic acid in the co-monomers; (b) covalent incorporation of catalysts (persulphate and riboflavin 5'-phosphate) as terminal groups in polyacrylamide chains; (c) hydrolysis of amide groups to acrylic acid in the gel layer underneath the cathodic filter paper strip. The result of these fixed negative charges in the matrix is a movement of counter-ions with hydration water towards the cathode (i.e. electroendo-osmosis) with concomitant drift of pH gradient and focused protein zones in the same direction. It is impossible to cure the cathodic drift by increasing the pH of the anolyte, or decreasing the pH of the catholyte, or both, as previously suggested. One way to reduce the cathodic drift efficiently is to incorporate covalently in the matrix tertiary or quaternary groups (3-dimethylaminopropylmethacrylamide) in stoichiometric amounts as compared with the negative charges.This ‘balanced’ polyacrylamide displays zero drift for at least 5000V·h, which is considered to be an ample time for equilibrium separation of protein species in isoelectric focusing.     

High-molecular-weight carrier ampholytes for isoelectric focusing of peptides

A method is described for the synthesis of high-molecular-weight carrier ampholytes for preparative isoelectric focusing of peptides. A giant polyethylene imine ($\text{M}{}_{\mathrm{<mtext>r</mtext>}}\text{40 000–60 000}$) is mixed with a linear gradient of acrylic acid in a flow-through system and let to react at 80°C for 70 h. Giant carrier ampholytes ($\text{M}{}_{\mathrm{<mtext>r</mtext>}}\text{range}\text{50 000–90 000}$) are thus obtained. These compounds interact very strongly among themselves, probably not by hydrogen bonds or hydrophobic interactions but ionic bonds. In fact, the aggregates are split by high salt (NaCl) or by zwitterionic compounds (Gly, taurine) or at acidic or alkaline pHs. They appear to interact only weakly and reversibly with proteins and no interactions are apparent with model dipeptides (His-Ser, His-Met, His-Phe and His-Lys).     

Characterizing bisexual Artemia populations by isoelectric focusing

Isoelectric focusing (IEF) of protein extracts, -Esterase and Phosphoglucose isomerase, from groups of Artemia adults from different bisexual populations were studied. Both gave clear separation between the Old and New World species. The second was more polymorphic, allowing a discrimination among Mediterranean populations.     

Iodine stain for detection of peptides after isoelectric focusing

Iodine stain is used for the detection of peptides after isoelectric focusing has been developed. Ultrathin gels (240–360 μm) are cast and, after focusing, dried at 110°C on a filter paper sheet. The paper-pasted gel is then exposed to iodine vapors for a few seconds to a few minutes, depending on the peptide load. White peptide zones are visivle on a brown, uniform background. The reaction is fully reversible and can be used also for small-scale preparative purification of peptides. Better than 80% recoveries of peptide from the gel can be obtained by elution in 80% acetic acid.     

iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing

Immobilized pH gradient isoelectric focusing (IPG-IEF) has emerged as a highly promising alternative to strong-cation exchange fractionation as the first dimension in shot-gun proteomics. Herein is shown the compatibility of this method with iTRAQ isotope labeling for relative quantitation and validation of sequence matches from database searching.     

A modified column for sperm isoelectric focusing

A modified U-shaped column is described for efficient isoelectric focusing of spermatozoa, other cells, and protein. The washed spermatozoa of the rabbit showed a PI of 4.4. After sonication, heads and tails focused at same pH, indicating similar and equal charge.     

Effect of 2-mercaptoethanol on pH gradients in isoelectric focusing

When hydrophobic samples, or membrane proteins, are disaggregated in buffers containing detergents (e.g. Nonidet P-40), urea and 2-mercaptoethanol, and applied at the cathodic end of a gel cylinder or slab for isoelectric separation, as routinely performed for two-dimensional techniques, a severe disturbance of the alkaline region of the pH gradient ensues. This phenomenon has been attributed to high protein loads, which supposedly overcome the buffering power of isoelectric carrier ampholytes. On the contrary, in the present study it has been found that this suppression of the alkaline end of the pH gradient is due to 2-mercaptoethanol, which is a buffer with pK 9.5. This compound ionizes at the basic gel end and is driven electrophoretically along the pH gradient, sweeping away, along its path, and focused carrier ampholytes.     

Isoelectric focusing following by electrophoresis of proteins for visualizing their titration curves by zymogram and immunofixation

After isoelectric focusing followed by electrophoresis at right angles in the same gel slab, it is possible to visualize the titration curve of proteins by zymograms or immunofixation even of an unpurified sample. This information can be very useful for the selection of the proper purification strategy by charge-dependent methods, e.g. ion-exchange chromatography, zone and disc electrophoresis and isotachophoresis. The titration curve also gives information on the stability of the protein as a function of the prevailing pH of the medium, in the pH 3-10 range. A region of instability is found for most proteins in acidic conditions, below pH 4.5, while most proteins are stable in the alkaline pH region, at least up to pH 10. The best method for developing zymograms and immunoprints appears to pH 10. The best method for developing zymograms and immunoprints appears to be the 'sandwich technique', by which a thin agarose slab, cast on an hydrophilic polyester sheet, and impregnated with appropriate reagents, is left in contact with a polyacrylamide gel thin layer used to generate the titration curves.     

Detection and differentiation of microbial siderophores by isoelectric focusing and chrome azurol S overlay

Siderophores are microbial, low molecular weight iron-chelating compounds. Fluorescent Pseudomonads produce different, strain-specific fluorescent siderophores (pyoverdines) as well as non-fluorescent siderophores in response to low iron conditions. We present an isoelectric focusing method applicable to unpurified as well as to purified pyoverdine samples where the fluorescent siderophores are visualized under UV illumination. Siderophores from different Pseudomonas sp., amongst which are P. aeruginosa, P. fluorescens and P. putida, including egg yolk, rhizospheric and clinical isolates as well as some derived Tn5 mutants were separated by this technique. Different patterns could be observed for strains known to produce different siderophores. The application of the chrome azurol S assay as a gel overlay further allows immediate detection of non-fluorescent siderophores or possibly degradation products with residual siderophore activity. The method was also applied to other microbial siderophores such as deferrioxamine B.     

Direct spectrophotometric analysis of hemoglobin in isoelectric focusing tube gels

Methods are described for the direct spectrophotometric analysis of human oxyhemoglobin, deoxyhemoglobin, and methemoglobin focused in polyacrylamide tube gels. Visible absorption spectra (350-650 nm) of electrofocused hemoglobin bands were recorded using a diode array rapid-scan spectrophotometer. Direct optical sampling of gels allowed the identification of focused hemoglobin valency hybrids which contain two oxidized monomers per tetramer.     

Thin-layer isoelectric focusing of multiple forms of tomato pectinesterase

Commercial tomato pectinesterase has been separated into at least eight multiple forms by thin-layer isoelectric focusing. The enzyme components were basic proteins in the range pH 7–9.3, the predominant form having an isoelectric point of 8.6. The enzyme was detected with a staining procedure, employing the reaction of hydroxylamine with the ester groups of pectin. The MW's of the multiple forms of pectinesterase were in the range of 27000 ± 5000.     

Characterization of phospholipid-protein interactions by capillary isoelectric focusing with whole-column imaging detection

The integration of functional proteins in the phospholipid bilayer is one of the most crucial features of biological membrane architecture. Phospholipid-protein interactions play an important role in the functions of bounded proteins in the phospholipid membrane. When the phospholipid-protein interactions occur, the protein structure tends to alter, which can result in a change in the isoelectric points (pI) of protein. Capillary isoelectric focusing (cIEF) with whole-column imaging detection (WCID) is an attractive technique that has the features of simple operation, high resolution, and fast separation without focused band mobility for detection of amphoteric biomolecules. In this study, a cIEF-WCID method was developed to characterize the phospholipids-protein interactions by monitoring the protein cIEF profiles. Seven proteins with different pI and molecular mass , and a zwitterionic phosphatidylcholine (PC) with zwitterionic properties, were used to evaluate the feasibility of the cIEF-WCID approach in the study of phospholipid-protein interactions. The cIEF profiles changed in response to the changes in protein conformation, clearly exhibiting interactions between the PC vesicles and the targeted proteins. The formation of PC-protein complex was observed in the cIEF electropherograms. It was demonstrated that seven proteins displayed distinct interactions with the PC vesicles due to their different chemical and physical properties. The influences of the PC concentration, incubation time, and incubation temperature on the phospholipids-protein interactions were investigated. This study validated a novel analytical approach for the characterization of phospholipid-protein interactions.     

Horse haemoglobin phenotyping by agarose gel isoelectric focusing comparison of Thoroughbreds with other Equidae*

By using isoelectric focusing in thin agarose slab gels 1049 Thoroughbred, 82 Nooit-gedachter, 45 Percheron and 244 horses of other breeds were examined. The numbers of other Equidae tested were 107 donkeys, 50 mules, 4 common zebras (Equus burchelli boehmi) and 8 mountain zebras (Equus zebra hartmannae). Phenotypic data are presented for all tested animals and gene frequencies are calculated for the horses.     

Biochemical characterisation of Australian strains of Echinococcus granulosus by isoelectric focusing of soluble proteins

The existence of three distinct strains of E. granulosus in Australia has been previously demonstrated on the basis of several criteria. In the present study, numerous isolates of E. granulosus from domestic and wild animal populations in different geographical areas of Australia were subjected to detailed biochemical analysis using isoelectric focusing of soluble proteins. Three different populations were recognised which corresponded to the three strains described previously, thus confirming their genetic distinction. One strain is common to all domestic intermediate hosts on the Australian mainland. Evidence is presented that humans and macropod marsupials are also susceptible to infection with this strain and that it is similar to E. granulosus occurring in sheep in New Zealand and the United Kingdom. The other two strains are confined to macropod marsupials on the Australian mainland and sheep in Tasmania respectively.     

Preparative isoelectric focusing in immobilized pH gradients. I. General principles and methodology

A new method for preparative protein purification is described, based on the use of Immobiline matrices. After electrofocusing, the protein zone of interest is recovered by electrophoretic transfer to a hydroxyapatite gel, from which it is eluted with 0.2 M phosphate buffer, pH 6.8, with yields for the proteins studied in the range 76-98%. For six different proteins, the focusing step gives a common upper limit of approximately 45 mg protein/ml gel as mean concentration in a focused protein zone. It is demonstrated that in practical preparative work, components with a pI difference of 0.007 pH units can be completely resolved, and that on a 5-mm-thick gel of dimensions 240 X 110 mm, samples containing as much as 400 mg of the major protein component can be applied. Focusing of large amounts of a salt-containing sample is demonstrated with the aid of human serum. A theoretical expression is given relating the concentration distribution and maximum protein concentration within a focused zone to the applied voltage, the pH slope used and the zone width. Based on this expression and the finding of an upper concentration limit for a protein we shown how to optimize the parameters in preparative work with immobilized pH gradients in relation to the separation power needed. Finally, it is shown that, in comparison with conventional preparative electrofocusing in polyacrylamide gels, immobilized pH gradients allow a ten-fold increase in load, whilst still giving a resolution comparable to that of analytical isoelectric focusing.