Small-scale fractionation of proteins and nucleic acids by isoelectric focusing in polyacrylamide gels

Selection of pH ranges in 2DE

This chapter describes the technical improvements of the two-dimensional electrophoresis pattern resulting of an optimized pH range in the first dimension. Various types of pH gradients are available. Different strategies can be applied in order to select the pH ranges for the exploration of a proteome. The resulting gels are analysed for their background, resolution, sensitivity in relation with the sample complexity. As the complete dynamic range of protein expression cannot be visualized, the high loading capacity of immobilized narrow pH gradients can be used. The limitations and possible enhancements are discussed.

Isolation and purification of enterocin E-760 with broad antimicrobial activity against gram-positive and gram-negative bacteria

Strain NRRL B-30745, isolated from chicken ceca and identified as Enterococcus durans, Enterococcus faecium, or Enterococcus hirae, was initially identified as antagonistic to Campylobacter jejuni. The isolate produced a 5,362-Da bacteriocin (enterocin) that inhibits the growth of Salmonella enterica serovar Enteritidis, S. enterica serovar Choleraesuis, S. enterica serovar Typhimurium, S. enterica serovar Gallinarum, Escherichia coli O157:H7, Yersinia enterocolitica, Citrobacter freundii, Klebsiella pneumoniae, Shigella dysenteriae, Pseudomonas aeruginosa, Proteus mirabilis, Morganella morganii, Staphylococcus aureus, Staphylococcus epidermidis, Listeria monocytogenes, Campylobacter jejuni, and 20 other Campylobacter species isolates. The enterocin, E-760, was isolated and purified by cation-exchange and hydrophobic-interaction chromatographies. The proteinaceous nature of purified enterocin E-760 was demonstrated upon treatment with various proteolytic enzymes. Specifically, the antimicrobial peptide was found to be sensitive to beta-chymotrypsin, proteinase K, and papain, while it was resistant to lysozyme and lipase. The enterocin demonstrated thermostability by retaining activity after 5 min at 100 degrees C and was stable at pH values between 5.0 and 8.7. However, activity was lost below pH 3.0 and above pH 9.5. Administration of enterocin E-760-treated feed significantly (P < 0.05) reduced the colonization of young broiler chicks experimentally challenged and colonized with two strains of C. jejuni by more than 8 log(10) CFU. Enterocin E-760 also significantly (P < 0.05) reduced the colonization of naturally acquired Campylobacter species in market age broiler chickens when administered in treated feed 4 days prior to analysis.

Mass distribution, polydispersity and focusing properties of carrier ampholytes for IEF II: pH 4–6 intervals

For studying the M(r) distribution and number of species in narrow-range (2 pH-unit wide, in the nominal pI 4-6 interval) carrier ampholytes from four commercial sources (Bio-Lyte, Servalyt, Ampholine and Pharmalyte), a 2-D technique was adopted consisting of a focusing step in a liquid phase (Rotofor, yielding 20 fractions) followed by orthogonal CE in both, acidic and basic buffers. As a final step, every other fraction was analyzed by CE-MS. The findings: Ampholine contains 80 different M(r) compounds, in the M(r) interval 203 to 893 Da, for a total of 325 isoforms. Bio-Lyte consists of 66 different M(r) species, in the M(r) range 388 to 835 Da, for a total of 436 isoforms. Servalyt is made of 199 different M(r) compounds, in the M(r) interval 204 to 907 Da, for a total of 1302 isoforms. Pharmalyte pH 4-6.5, comprises 217 amphoteres, in the M(r) range 150 to 1179 Da, for a total of 812 isoforms. Pharmalyte appears to be the best brand, with the vast majority of species focusing sharply at their pI position and <5% "poor" species, distributed along the entire pH gradient, denoting an extremely shallow pH/mobility curve across the pI value.

Current two-dimensional electrophoresis technology for proteomics

Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the workhorse for proteomics. In spite of promising alternative or complementary technologies (e.g. multidimensional protein identification technology, stable isotope labelling, protein or antibody arrays) that have emerged recently, 2-DE is currently the only technique that can be routinely applied for parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. 2-DE enables the separation of complex mixtures of proteins according to isoelectric point (pI), molecular mass (Mr), solubility, and relative abundance. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms or post-translational modifications. This is in contrast to liquid chromatography-tandem mass spectrometry based methods, which perform analysis on peptides, where Mr and pI information is lost, and where stable isotope labelling is required for quantitative analysis. Today's 2-DE technology with IPGs (Görg et al., Electrophoresis 2000, 21, 1037-1053), has overcome the former limitations of carrier ampholyte based 2-DE (O'Farrell, J. Biol. Chem. 1975, 250, 4007-4021) with respect to reproducibility, handling, resolution, and separation of very acidic and/or basic proteins. The development of IPGs between pH 2.5-12 has enabled the analysis of very alkaline proteins and the construction of the corresponding databases. Narrow-overlapping IPGs provide increased resolution (delta pI = 0.001) and, in combination with prefractionation methods, the detection of low abundance proteins. Depending on the gel size and pH gradient used, 2-DE can resolve more than 5000 proteins simultaneously (approximately 2000 proteins routinely), and detect and quantify < 1 ng of protein per spot. In this article we describe the current 2-DE/MS workflow including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 2-DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two-dimensional protein databases.

From genomics to proteomics: new directions in molecular neuropsychiatry

Neuropsychiatry, like many other biomedical sciences, has been revolutionized by the advances in genomic technologies over the years. The advent of PCR (polymerase chain reaction) and the sequencing of the human genome have provided invaluable insights into the molecular genetics of the various psychiatric disorders through the study of candidate genes and linkage analyses. However, biological phenotype is dictated by protein expression, which has been shown to stray from the genetic blueprint designated by the genome. Consequently, the field of proteomics has recently emerged as a powerful means of exploring protein structure, function, and expression patterns. The ability to study disease at the gene and protein levels presents a tremendous opportunity for neuropsychiatric research, particularly in terms of the potential for developing therapeutic agents for novel protein targets.

Dynamics of gel isoelectric focusing with ampholytic dyes monitored by camera in real-time

The dynamics of gel isoelectric focusing were studied by using amphoteric low-molecular-mass colored substances (isoelectric point markers). The polyacrylamide gel in slab format was in direct contact with the electrodes. In addition to isoelectric focusing with a pH gradient composed of synthetic carrier ampholytes, pH gradients created by simple buffers of acetic acid, 2-(N-morpholino)ethanesulfonic acid, histidine and N,N,N',N'-tetramethylethylenediamine were applied. The progress of the electrofocusing process was monitored by a charge-coupled device camera and video recording. The gradient profile and dynamics were approximated from the positions of isoelectric point markers, which were focused both on boundaries between individual zones of simple buffers and within the zones themselves. The obtained animated records enabled the observation of the entire real focusing run within fractions of a minute, which is useful both for the understanding and optimization of the focusing.

Theory and practice of isoelectric focusing of interacting systems

The theory of mass transport coupled to reversible protein interactions forms the basis for computer simulation of the isoelectric focusing behavior of several model systems. These include pH-dependent conformational transition, carrier ampholyte-induced interactions and protein-ligand interactions. The computational results compare favorably with experimental observations. In addition, a method is formulated for an isoelectric focusing procedure which enables determination of intrinsic ligand-binding constants for statistical binding of a charged ligand, binding to heterogeneous sites, and cooperative binding.

Isoelectric focusing in immobilized pH gradients: recent analytical and preparative developments

Isoelectric focusing in immobilized pH gradients (IPG), covering both analytical and preparative aspects, is here reviewed. An extensive introduction covers the development of the technique from its inception in 1982 to present day methodology, with particular emphasis on the development of computer programs able to calculate and optimize linear and nonlinear pH gradients, spanning as much as 9 pH units, from a mixture of as many as 10 different buffering ions and titrants. The unique resolving power of IPGs is illustrated with the resolution of fetal globin chains differing by an Ala/Gly substitution in residue 75, this bringing about a minute difference in pI value of only 0.001 pH units. IPG runs, performed under denaturing conditions, allow an excellent correlation between experimental and theoretical protein pIs, to the extent that outliers were found to be polypeptide chains which had undergone post-synthetic modifications. The IPG methodology allows easy interfacing with mass spectrometry, due to the fact that proteins eluted from an IPG gel are isoionic as well as isoelectric, and thus are not contaminated by any buffer ion. The review ends with an excursus on preparative aspects of IPGs: a novel apparatus, based on the principle of isoelectric, buffering membranes, allows pilot-scale purification of r-DNA proteins to extreme purity, with recovery in a liquid vein. Isoelectric membranes have a selectivity based on a continuous titration process, and thus act as isoelectric traps for individual protein species. This same preparative apparatus can be used as a novel immobilized enzyme reactor, with superior performance compared to conventional types of reactors.

Isoelectric focusing as a tool for the investigation of post-translational processing and chemical modifications of proteins

It has been demonstrated that good agreement may be observed between computed and experimental isoelectric point (pI) values when proteins of known sequence are focused under denaturing conditions on immobilized pH gradient IPG slabs, at least in the pH range 4-7.5. Hence, discrepancies between expected and found in this experimental set-up may be reliably ascribed to some kind of post-transcriptional processing, or chemical modification, having taken place in the sample. This evaluation is made easier when the comparison is set between the pI of a parent molecule and that (or those) of one to several of its derivatives as resolved in a single experiment (for instance, as a spot row in two-dimensional maps); no previous knowledge is required in these cases about the amino acid composition of the primary structure. The effects on protein surface charge are discussed in this review mainly for two biologically relevant processes, glycosylation and phosphorylation. Then, the pI shifts are analysed for some protein modifications that may occur naturally but can also be artefactually elicited, such as NH2 terminus blocking, deamidation and thiol redox reactions. Finally, carboxymethylation and carbamylation are used to exemplify chemical treatments often applied in connection with electrophoretic techniques and involving charged residues. Procedures to be applied in order to verify whether a given modification has occurred, and often relying on the focusing of a treated specimen, are detailed in each section. Numerical examples on model proteins are also discussed. As an important field of application of the above concepts may be genetic engineering, an exhaustive bibliographic list dealing with pI evaluation and structural assessment on recombinant proteins is included.

Two-dimensional polyacrylamide gel electrophoresis of membrane proteins

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is one of the most powerful separation techniques for complex protein solutions. The proteins are first separated according to their isoelectric point, driven by an electric field across a pH gradient. The pH gradient necessary for the separation according to isoelectric point (pL) is usually established by electrophoresing carrier ampholytes prior to and/or concomitantly with the sample. The second dimension is usually a separation according to molecular size. Mostly this separation is performed after complete denaturation of the proteins by sodium dodecyl sulfate and 2-mercaptoethanol (SDS-PAGE). This standard method has considerable disadvantages when relatively hydrophobic membrane proteins are to be separated: cathodic drift, resulting in nonreproducible separation, and the denaturation of the proteins, mostly making it impossible to detect native properties of the proteins after separation (e.g., enzymatic activity, antigenicity, intact multimers, and so on). The protocols presented here take care of most of these obstacles. However, there is probably no universal procedure that can guarantee success at first try for any mixture of membrane proteins; some experimentation will be necessary for optimization. Two procedures are each presented: a denaturing (with urea) and a nondenaturing method for IEF in immobilized pH gradient gels using Immobilines, and a denaturing (with SDS and 2-mercaptoethanol) and a nondenaturing technique (with CHAPS) for the second dimension. Essential tips and tricks are presented to keep frustrations of the newcomer at a low level.

Immobilized pH gradient focusing of alkaline proteins: analysis of the isoform composition of purified human non-secretory ribonucleases from kidney, liver and spleen

Previous studies on the isoform composition of human ribonucleases (RNAases) have resulted in confusing and inconsistent results, presumably due to methodological problems in electrofocusing of alkaline proteins. In the present study, immobilized pH gradient (IPG) carrier ampholyte (CA) isoelectric focusing (IEF) and conventional CA-IEF have been evaluated for the analysis of the isoforms of human non-secretory RNAases purified from kidney, liver and spleen. CA-IEF proved unsuitable since the alkaline RNAase isoforms migrated into the cathode. IPG-CA-IEF, however, resolved the RNAase isoforms and marker proteins in the basic region of the gel matrix. The three RNAases had comparable isoform profiles, each with two protein bands with approximate pI values of 10.3 and 10.4. Western blotting showed that the two protein bands of each RNAase were immunoreactive (with polyclonal antibodies that recognize RNAase), indicating that the protein bands are RNAase isoforms. The present results provide reliable pI data on human RNAase isoforms and suggest that IPG-CA-IEF should be a suitable technique for analysing the isoforms of other alkaline proteins.

The separation and detection of alkaline oligoclonal IgG bands in cerebrospinal fluid using immobilised pH gradients

A method is described for the separation and detection of highly alkaline IgG bands in unconcentrated cerebrospinal fluid (CSF). These bands are frequently found in the cerebrospinal fluid of patients with inflammatory diseases of the central nervous system, particularly in the case of multiple sclerosis, and their detection is an important aid in clinical diagnosis. An isoelectric focusing technique using an immobilised pH gradient in polyacrylamide gel has been developed over the pH range 7-10, producing a linear and stable pH gradient with excellent resolution. After electrofocusing, the protein patterns were blotted onto polyvinylidene difluoride membranes and visualised using anti-human IgG followed by an enzyme-labelled second antibody. Blotting could be carried out by capillary diffusion for up to 16 h duration without any loss in resolution. Using this method, highly alkaline intrathecal IgG bands were found in the cerebrospinal fluid of all of the 14 multiple sclerosis patients. There were also 2 patients with alkaline IgG bands in their cerebrospinal fluid who were not diagnosed as multiple sclerosis. By contrast, no alkaline IgG bands with an isoelectric point (pI) greater than 8.6 were found in any of the serum samples studied (n = 50) from patients with various neurological disorders including multiple sclerosis.

Two-dimensional electrophoresis with immobilized pH gradients of leaf proteins from barley (Hordeum vulgare): method, reproducibility and genetic aspects

Leaf proteins from 14 barley cultivars (Hordeum vulgare) were analyzed by two-dimensional electrophoresis with immobilized pH gradients (IPG 4-7 and IPG 6-10) in the first dimension. Highly reproducible two-dimensional patterns were obtained, owing to constant spot positions along the isoelectric focusing axis. A number of variety-specific protein spots were detected, allowing us to discriminate barley cultivars not only into main groups but into individual cultivars.

Properties of acid beta-galactosidase from fowl spermatozoa

1. Two forms, I and II, of beta-galactosidase [EC 3.2.1.23] from fowl spermatozoa were separated by Blue-Sepharose CL-6B chromatography. 2. The two forms of the enzyme yielded different pI values (4.1 and 4.7 for form I and 5.3 for form II). 3. Their gel filtration patterns were also different: form I resolved into two peaks with Mr about 65,000 and 80,000, whereas form II resolved into a single peak with an Mr of about 65,000. 4. Both forms had similar optimum pH, pH stability, thermal stability and Km values. 5. Differences between the characteristics of beta-galactosidase forms from spermatozoa and from seminal plasma suggest that the beta-galactosidases investigated in this study are spermatozoa-specific.

Casting immobilized pH gradients into cylindrical polyacrylamide gels

A novel method is described for casting immobilized pH gradients in polyacrylamide gel rods of small diameter (2 mm), based on the principle of rotational centrifugation. The tubes are filled vertically with equal volumes of dense and light solution (250 microliter each) titrated to the extremes of the desired pH gradient, and then tilted at 2.5 degrees to the level. After 5 min at rest, to allow for sliding of the two menisci to equilibrium position, the glass tubes are rotated for 3 min at 180 rpm, followed by an additional 3 min at 180 rpm by reversing the sense of rotation. A homogeneous linear gradient is thus produced. The rotating platform is then raised to 90 degrees and the gels allowed to polymerize under standard conditions. Formation of linear and reproducible pH gradients is ensured by using stabilizing density gradients of low viscosity (0-5% glycerol, having a maximal ratio viscosity/density of 1.1).

Isoelectric protein purification by orthogonally coupled hydraulic and electric transports in a segmented immobilized pH gradient

A new method is described for preparative protein purification, based on isoelectric focusing on immobilized pH gradients. The principle is entirely new, as it is based on keeping the protein of interest isoelectric, in a flow-chamber, and focusing the impurities in the Immobiline gel. For this, a hydraulic flow is coupled orthogonally to an electric flow, sweeping away the non-isoelectric impurities from the recycling chamber. The sample flow-chamber is built in the centre of the apparatus, and is coupled to an upper and lower segment of an immobilized pH gradient. The protein to be purified is kept isoelectric in the flow-chamber and prevented from leaving it by arranging for the extremities of the immobilized pH gradient, forming the ceiling and the floor of this chamber, to have isoelectric points just higher (e.g. +0.05 pH units, on the cathodic side) and just lower (e.g. -0.05 pH units, on the anodic side) than the known pI of the species of interest. Macromolecules and small ions leave the flow chamber at a rate corresponding to a first order reaction kinetics (the plot of log C vs. time being linear). In general, for macromolecules, 12 h of recycling under current allow removal of 95% impurities. After 24 h of recycling, the protein of interest is more than 99.5% pure. The recoveries are very high (approaching 100%) as the sample under purification never enters the Immobiline gel and thus does not have to be extracted from a hydrophilic matrix, as typical of preparative gel electrophoresis.

Estimation of glycated fetal hemoglobin in normal cord blood by isoelectric focusing. Correlation with maternal glycated hemoglobin and birth weight

Glycated fractions of hemoglobin F and A (F1, A1c) were measured simultaneously in cord and maternal blood, respectively, in 109 normal women at delivery using an isoelectric focusing, method in polyacrylamide gel plates. Cord blood hemoglobin F1 values (mean +/- SD) were 5.92 +/- 1.09% and maternal blood hemoglobin A1c values were 6.51 +/- 0.92%. The difference was statistically highly significant (p less than 0.001) and their values were also significantly correlated (p less than 0.001). Moreover, both values were also well correlated with those of maternal blood glucose (p less than 0.01), actual birth weight (p less than 0.01) and birth weight ratio (p less than 0.01). It is concluded that hemoglobin F1 can be successfully separated and measured by isoelectric focusing. However HbF1 estimation seems to have no obvious advantages against the maternal HbA1c measurement as an index of fetal exposure to glucose during the last weeks of pregnancy.

Theoretical and experimental study of high-performance electrophoretic mobilization of isoelectrically focused protein zones

In an earlier paper we showed that it is possible to mobilize a train of isoelectrically focused proteins and thus detect them on-tube or off-tube. The mobilization was performed in different ways, for instance electrophoretically by exchanging the anolyte for the catholyte or vice versa. In this paper we treat the electrophoretic mobilization theoretically, originating from the conditions of electroneutrality. The information thus gained was used to design anolytes and catholytes of appropriate compositions for mobilization of focused proteins. The usefulness of these electrode solutions is illustrated by focusing-mobilization experiments performed in free solution in a glass tube of length 110 mm. Since the inside diameter of the tube and its wall thickness were only 0.05 mm, the Joule heat was efficiently removed, which allowed the use of high field strengths (270 V/cm). The focusing time was therefore as short as 6 min. The time required for mobilization was about 15 min (360 V/cm). The mobilized protein zones were detected on-tube by absorbance measurements at 280 nm. The glass tube was treated with non-cross-linked polyacrylamide to eliminate electroendosmosis and adsorption of proteins onto the tube wall. The following conclusions drawn from the theoretical studies were experimentally verified: mobilization toward the anode (cathode) can be accomplished by selecting an anolyte (catholyte) containing a cation (anion) other than the proton (hydroxyl ion); the cation (anion) will then electrophoretically migrate into the separation tube and continuously increase (decrease) the pH from the anodic (cathodic) end of the tube. The pH of the electrode solution toward which the mobilization takes place is critical for off-tube, but not for on-tube detection. With the aid of the electroneutrality condition that applies in isoelectric focusing, one can easily explain the generation of the so-called plateau phenomenon.

Purification and properties of beta-galactosidase from chicken seminal plasma

1. beta-Galactosidase (EC 3.2.1.23) from chicken seminal plasma was purified approx. 111-fold to homogeneity. 2. pH optimum of the enzyme ranged from 3.6 to 4.0 and its Km was 0.65 mM with p-nitrophenyl-beta-D-galactoside as substrate. 3. The enzyme was unstable at its optimal activity pH and was activated by Cl- ions. 4. The enzyme had pI value of 4.0. 5. The active enzyme had Mr approx. 100,000 by Sephacryl S-300 chromatography. SDS electrophoresis in the presence of beta-mercaptoethanol showed four bands corresponding to Mr of approx. 90,000, 75,000, 65,000 and 13,000.

Direct recovery of proteins into a free-liquid phase after preparative isoelectric focusing in immobilized pH gradients

A new method for electrophoretic retrieval of protein zones from Immobiline matrices is described, based on elution directly in a free liquid phase, rather than in ion-exchange beads or molecular sieves, as previously described. The chopped Immobiline gel is loaded on top of a 5% T stacking gel, 6-10 mm in height, and forced to transverse it and collect into a chamber, filled with 20% sucrose solution, closed on its anodic side by a dialysis sac. The transfer is practically quantitative, for most proteins, after 30-60 min of zone electrophoresis at 10 W (300 V potential differential). Recovery of protein mass is in general better than 90%, while for enzyme activity is in the range of 60-80%. For preserving enzyme integrity, the following precautions are recommended: short electrophoretic times; avoidance of anodic oxidation; chilling of the buffer in the anodic chamber; and use of low levels (2-5 mM) of the specific enzyme substrate throughout the entire electrophoretic system (cathode, anode and gel plug).

Differential effects of pH on calcium activation of myofilaments of adult and perinatal dog hearts. Evidence for developmental differences in thin filament regulation

Our results show that calcium activation of myofilament preparations of dog heart in the perinatal period is unaffected by a reduction in pH from 7.0 to 6.5, which, in adult heart myofilaments, induces a 0.4 pCa unit (-log molar free calcium concentration) rightward shift in the relation between pCa and myofibrillar adenosine triphosphatase activity. Acidic pH also had no effect on calcium binding to myofibrillar troponin C of perinatal hearts. The stoichiometry of troponin C bound calcium at full myofilament activation (about 3 mol calcium/mol troponin C) was the same for adult and perinatal heart myofibrils, as was their myofibrillar troponin C content. Moreover, there were no differences in isoelectric pH of troponin C from adult and perinatal hearts. We tested whether variants of myofilament proteins other than troponin C could account for the differential effects of acidic pH. In adult and perinatal dog heart preparations, myosin heavy chain isoenzymes appeared the same as measured, using native pyrophosphate gel electrophoresis. No evidence for thick filament-related calcium regulation in the perinatal heart myofilaments was obtained, when tested in studies in which native thin filaments were displaced with a 10-fold molar excess of pure actin. In preparations in which native thick filaments were displaced with a 10-fold molar excess of pure skeletal muscle myosin, the effects of acidic pH on calcium activation were the same as in native adult and perinatal preparations. Our major conclusion from these results in that the perinatal heart myofilaments are likely to possess variations in thin filament activity and structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Determination of glycosylated haemoglobin by isoelectric focusing in non-linear pH gradients

A new isoelectric focusing technique for the separation and quantitation of glycosylated haemoglobin (HbA1c) is described. By using an equimolar mixture of two separators (0.2 M beta-alanine + 0.2 M 6-aminocaproic acid) a 2-pH unit Ampholine range (pH 6-8) is transformed in a shallow, 0.6-pH unit span (pH 6.7-7.3). This brings about an increment of resolution between HbA and HbA1c by a factor of about three, thus allowing proper densitometric evaluation of the trichloroacetic acid-fixed MetHb bands by conventional gel scanners. Excellent agreement is found among microchromatography, isoelectric focusing followed by densitometry in situ, and isoelectric focusing followed by band excision, elution and spectrophotometric determination. The present method also allows full resolution between HbA1c and fetal haemoglobins (F and Fac bands).

High-resolution two-dimensional electrophoresis with isoelectric focusing in immobilized pH gradients

Due to the high reproducibility of pH gradient slope and width, immobilized pH gradients (IPG) have been used as the first dimension of two-dimensional techniques in order to generate maps of constant spot position in the pI/Mr plane. However, when coupling IPG to SDS (sodium dodecyl sulphate) gels two problems were encountered: vertical streaking, due to incomplete zone solubilization in SDS, and horizontal streaking, due to spot fusion along the pH axis caused by the electroendosmosis of the charged Immobiline gels. Two methodical modifications are herewith described to overcome these drawbacks: (a) the SDS equilibration time of the first-dimension gel has been prolonged to at least 30 min; (b) the SDS electrophoresis gel has been cast together with a starting gel, containing 2.5 mM of each Immobiline species used in the first dimension, which serves as a transition from the charged to the uncharged gel.

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.

Preparative isoelectric focusing in immobilized pH gradients. II. A case report

The preparative aspects of isoelectric focusing (IEF) in immobilized pH gradients (IPG) have been investigated as a function of the following parameters: environmental ionic strength (I), gel geometry and shape of pH gradient. As model proteins, hemoglobin (Hb) A and a minor, glycosylated component (HbA1c), with a delta pI = 0.04 pH units, have been selected. The load capacity increases almost linearly, as a function of progressively higher I values, from 0.5 X up to 2 X molarity of buffering Immobiline (pK 7.0) to abruptly reach a plateau at 3 X concentration of buffering ion. The load capacity also increases almost linearly as a function of gel thickness from 1 to 5 mm, without apparently levelling off. When decreasing the pH interval from 1 pH unit (pH 6.8-7.8) to 1/2 pH unit (pH 7.05-7.55) the amount of protein loaded in the HbA zone could be increased by 40%. In 5 mm thick gels, at 2 X pK 7.0 Immobiline concentration, over a 1/2 pH unit span, up to 350 mg HbA (in a 12.5 X 11 cm gel) could be loaded in a single zone, the load limit of the system being around 45 mg protein/ml gel volume.

Isoelectric focusing in immobilized pH gradients: generation and optimization of wide pH intervals with two-chamber mixers

A new technique for generating extended pH gradients (5 pH units) in Immobiline gels is reported. The previously described (J. Biochem. Biophys. Methods 7, 1983, 123-142) five-chamber gradient mixer has been replaced by a two-vessel device. A single mixture of the available Immobilines (pK 3.6, 4.6, 6.2, 7.0, 8.5 and 9.3) is made, with relative concentrations adjusted so as to produce the most uniform buffering power throughout the desired pH interval. This mixture is then divided into two portions, which are titrated to the extremes of the required pH span with an acidic titrant (Immobiline pK approximately 1) and a basic species (Immobiline pK 9.95). Highly reproducible pH gradients (pH 4-9) are thus generated, which appear extremely useful for the first dimensioned of 2-dimensional techniques. Our previously reported computer program has been implemented with an optimization algorithm which, given any cocktail of Immobilines, automatically adjusts the relative initial concentrations until the smoothest possible beta power is found. For the first time it is possible to perform IEF under controlled physico-chemical parameters: pH span and linearity, beta power, ionic strength and molarity of the buffering species.

Association of RNA with thymidylate synthase from methotrexate-resistant Streptococcus faecium

Thymidylate synthase (5,10-methylenetetrahydrofolate:dUMP C-methyltransferase, EC 2.1.1.45) from methotrexate-resistant Streptococcus faecium has a UV absorbance peak at 259 nm and stains with acridine orange because of the presence of RNA on the protein. Material having an absorbance peak at 254 nm, obtained from the enzyme by phenol extraction, is degraded by treatment with pancreatic RNase, T1 RNase, and alkali but is stable to DNase. Dowex-1 chromatography of the pure enzyme yields two polynucleotide fragments in addition to the apoenzyme. As estimated from their absorbance, these fragments contain 4 and 11 mononucleotide residues per mole of enzyme, respectively. In crude extracts, thymidylate synthase is associated with rapidly sedimenting material that is sensitive to RNase. Treatment of crude extracts with RNase, as is done routinely during thymidylate synthase purification, most likely results in the formation of the small polynucleotides found on the enzyme. The RNA is not required for enzyme activity.

Computer applications in analysis, mapping and cataloging of proteins separated by two dimensional electrophoresis

Two dimensional electrophoretic separation of complex mixtures of proteins can only be exploited to its fullest potential using sophisticated computerized spot detection, quantification, pattern recognition, pattern normalization, data reduction and data storage. We present a discussion of some of the technical problems and of the options available which will ultimately lead toward full computerization of the data.

Streptokinase-dependent delayed activation of horse plasminogen

Complete activation of purified horse plasminogen to plasmin was obtained with a 1:10 molar ratio of streptokinase to plasminogen after 5 min of incubation at 37 degrees C. At a 1:1 molar ratio, maximal activity did not appear until 15-30 min, while at a ratio of 6:1 complete activation was delayed for 120-180 min. Gel filtration studies of isotopically labeled streptokinase and horse plasminogen suggest that the delay was due to impaired formation of a streptokinase-plasminogen complex. The predominant streptokinase moiety within the streptokinase-plasmin complex which forms from the streptokinase-plasminogen complex had a molecular weight of about 25000. The streptokinase-horse plasmin complex activated bovine plasminogen and was relatively stable. Native streptokinase was rapidly modified by horse plasmin predominantly to a fragment with a molecular weight comparable to that of the streptokinase moiety within the horse streptokinase-plasmin complex, about 25000 daltons. Partial characterization of horse plasminogen revealed no striking differences from human plasminogen in terms of molecular weight, N-terminal analysis and amino acid composition. However, horse plasminogen did not react with antibodies to human plasminogen, and its isoenzymes were more acidic than those of the human. Further characterization of horse plasminogen will be required to ascertain whether activation by streptokinase can serve as a model for the altered kinetics which have recently been described for the activation of aberrant types of human plasminogen.

Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications

A new technique for generating pH gradients in isoelectric focusing is described, based on the principle that the buffering groups are covalently linked to the matrix used as anticonvective medium. For the generation of this type of pH gradient in polyacrylamide gels, a set of buffering monomers, called Immobiline (in analogy with Ampholine), is used. The pH gradient gels are cast in the same way as pore gradient gels, but instead of varying the acrylamide content, the light and heavy solutions are adjusted to different pH values with the aid of the Immobiline buffers. Available Immobiline species make it possible to generate any narrow linear pH gradient between pH 3 and 10. The behaviour of these types of gradients in isoelectric focusing is described. Immobilized pH gradients show a number of advantages compared with carrier ampholyte generated pH gradients. The most important are: (1) the cathodic drift is completely abolished; (2) they give higher resolution and higher loading capacity; (3) they have uniform conductivity and buffering capacity; (4) they represent a milieu of known and controlled ionic strength.