Polymerization kinetics of polyacrylamide gels containing immobilized ph gradients for isoelectric focusing

Paleoproteomics explained to youngsters: how did the wedding of two-dimensional electrophoresis and protein sequencing spark proteomics on: let there be light

Taking the opportunity of the 20th anniversary of the word "proteomics", this young adult age is a good time to remember how proteomics came from enormous progress in protein separation and protein microanalysis techniques, and from the conjugation of these advances into a high performance and streamlined working setup. However, in the history of the almost three decades that encompass the first attempts to perform large scale analysis of proteins to the current high throughput proteomics that we can enjoy now, it is also interesting to underline and to recall how difficult the first decade was. Indeed when the word was cast, the battle was already won. This recollection is mostly devoted to the almost forgotten period where proteomics was being conceived and put to birth, as this collective scientific work will never appear when searched through the keyword "proteomics".

BIOLOGICAL SIGNIFICANCE

The significance of this manuscript is to recall and review the two decades that separated the first attempts of performing large scale analysis of proteins from the solid technical corpus that existed when the word "proteomics" was coined twenty years ago. This recollection is made within the scientific historical context of this decade, which also saw the blossoming of DNA cloning and sequencing. This article is part of a Special Issue entitled: 20 years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.

Focusing of low-molecular-mass heparins in polycationic polyacrylamide matrices

A novel method for separation of low-molecular-mass heparins is reported here, on the basis of migrating the polyanionic heparins in a polycationic polyacrylamide gel, made by incorporating a gradient of positively charged monomers (the Immobilines used for creating immobilized pH gradients) into the neutral polyacrylamide backbone. Separations can be operated either in linear or nonlinear gradients of positive charges, thus modulating at whim the separation power. This allows the polydisperse heparins to reach a steady-state position along the migration path and condense (focus) in an environment inducing charge neutralization. It is shown that the separations obtained are a complex function of both size and charge distribution along the oligosaccharide chains. This novel methodology represents a marked improvement over existing techniques and appears to hold promise for applications in screening of commercial lots of heparins, also in view of possible presence of contaminants, such as those recently detected in imported heparins.

Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels

Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.

A new approach for on-line enrichment in electrophoresis of dilute protein solutions

A method is described for on-line enrichment/zone sharpening of a sample of negatively charged proteins (an analogous method for cationic proteins can be designed). The sample is applied on the top of a 5-mm thick layer of a neutral polyacrylamide gel which rests on another 5-mm thick, large-pore polyacrylamide gel which contains positively charged groups. The latter gel layer is attached to the neutral gel column, used for the electrophoretic separation of the proteins. When a voltage is applied the proteins start migrating and become electrostatically adsorbed at the top of the charged, large-pore gel layer (pH 5.4). With the upper electrode vessel filled with a buffer of a pH higher (pH 7.7) than that employed in the enrichment step and with a voltage between the electrodes, these enriched proteins are released (because the enrichment gel is non-charged at pH 7.7) with zone sharpening and migrate into the 5-cm long column (i.d. 5 mm) of a neutral, large-pore polyacrylamide gel for electrophoretic analysis. Upon the electrophoretic migration from the enrichment gel into the separation gel a second zone sharpening may occur, if the increase in pH from 5.4 to 7.7 in the separation gel is not close to momentary. By employing colored test proteins the efficiency of the enrichment step is visually illustrated by a picture. The principle of the concentration method described has been employed also in chromatographic experiments and can with appropriate modifications also be used in other electrophoretic methods, such as capillary electrophoresis.

DNA separation methodology based on charge neutralization in a polycationic gel matrix

A novel method for separation of DNA fragments is here reported, based on migrating the polyanionic DNA fragments in a polycationic polyacrylamide gel, made by incorporating positively charged monomers (the Immobilines used for creating immobilized pH gradients) into the neutral polyacrylamide backbone. Separations can be operated under two working conditions: either against a gradient of positive charges, to allow the various DNA fragments to reach a steady-state position along the migration path and condense (focus) in an environment inducing charge neutralization, or in a plateau gel (i.e., in a gel containing a constant level of positive charges from anode to cathode). In this last case, separation is still obtained due to differential charge modulation of the various DNA fragments. In the 100-1000-bp length, it is shown that separation can be obtained even for fragments differing in length by <0.5%, as shown in the splitting of a 656- and 659-bp doublet, that could not be resolved by conventional polyacrylamide gels. In the 10-100-bp range, it is shown that the present method can resolve single nucleotide polymorphisms, i.e. fragments of identical number of nucleotides but differing by one base substitution. In this last case, separations are obtained only in gradient gels containing a much steeper gradient of charges (0-20 mM Immobiline pK 10.3 and pK 12, as opposed to gradients of only 2-4 mM positive charges for larger size fragments). This novel methodology represents a marked improvement over existing techniques and appears to hold promises for applications in diverse fields, such as molecular biology, forensic medicine, and genetic screening.

Effect of residual acrylamide monomer from two-dimensional gels on matrix-assisted laser desorption/ionization peptide mass mapping experiments

Residual acrylamide can cause severe suppression of signal intensity during matrix-assisted laser desorption/ionization (MALDI) peptide mass mapping experiments. This suppression phenomenon can compromise the ability to detect low picomole and subpicomolar amounts of peptides extracted from two-dimensional gels. A rapid and simple method that exploits the use of pipette tips incorporating C18 packing materials for the enhancement of MALDI signal intensity is presented. The utility of the method is demonstrated with peptide solutions incorporating residual acrylamide and/or gel monomer components.

Assessment of the kinetics and sites of reaction of some immobiline chemicals with proteins and peptides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

A number of proteins and peptides have been incubated with some Immobiline chemicals commonly used in the production of immobilised pH gradients for isoelectric focusing. After various incubation intervals, the resulting reaction mixtures were examined by matrix-assisted laser desorption/ionisation mass spectrometry. At pH 9-10, and after 15-h incubation time, no significant interaction was observed with the two of the investigated proteins which have no Cys residues in their sequences. On the other hand, intense multiple reaction channels were observed with sequences containing a number of Cys residues. The present measurements provide useful information on the kinetics of the reaction and its sensitivity to both the pK(a) of the Immobiline chemicals and the presence of Cys in the investigated sequences. Post source decay measurements on peptides with and without Cys in their sequences provided unambiguous evidence for the involvement of this residue in the reaction conducted at pH 9-10. Possible implications of some of the present deductions for isoelectric focusing separations on immobilised pH gradients are discussed.

pH changes in Immobiline gels due to low-molecular mass ion adsorption and conditions for salt front formation during electrophoretic desorption

A simple theoretical model of low molecular mass ion adsorption on a weak exchanger is proposed. For a system containing immobilized charges in uniform concentration the pH change values connected with neutral salt addition and followed by further washing and voltage application are evaluated. The question of stability of the moving boundary, arising in the area near the electrodes, is considered for the constant current stabilization at different values of Immobiline concentration, pK values of Immoboline and salt concentration. The threshold values of ion mobility capable of providing a sharp salt front formation are also evaluated for conditions of strong adsorption. We found that, with extremely acidic Immobilines, a sharp salt front does not arise under the latter condition, even in the case of very high Immobiline concentrations.

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.

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.

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).

Towards new formulations for polyacrylamide matrices: N-acryloylaminoethoxyethanol, a novel monomer combining high hydrophilicity with extreme hydrolytic stability

Matrices for electrokinetic separations, based on a unique class of mono- and disubstituted (on the amido nitrogen) acrylamides such as e.g., N-acryloylaminoethoxyethanol (AAEE) and acrylamido-N,N-diethoxyethanol, offer the following advantages: (i) strong resistance to alkaline hydrolysis (most zone separations occurring at basic pH values), (ii) high hydrophilicity and (iii) greater porosity, due to the higher molecular weight of the monomers. When compared with conventional poly(acrylamide), a poly(AAEE) matrix, when subjected to mild alkaline hydrolysis (0.1 N NaOH, 70 degrees C) appears to be 500 times more stable. Such stability is also confirmed under strong alkaline hydrolysis (1 N NaOH, 100 degrees C) as well as under mild and strong acidic hydrolysis. Mildly hydrolyzed poly(AAEE) matrices still perform extremely well in both conventional isoelectric focusing and immobilized pH gradients, techniques which are quite sensitive to traces of acrylate in the polymer coil. Conversely, mildly hydrolyzed poly(acrylamide) matrices, when used in isoelectric focusing, generate pH gradients between pH 4 and 5, having an inflection point (pH 4.6) equivalent to the pK value of acrylic acid. This novel class of monomers shows great promise for future applications in all electrokinetic methodologies.

Electrophoretic artifacts arising from the use of thiol-containing reagents

Thiol reagents migrate as a curtain behind the salt front when loaded with the sample solution onto disc-electrophoresis gels. In immobilized pH gradients (IPG) the same compounds are driven by electrophoresis and electroosmosis from the alkaline to the neutral and acidic regions of the gradients. In either case, a dose-dependent sideways spreading results in spurious reduction between adjacent lanes if samples with and without reducing agent are loaded side by side.

On the efficiency of methylene blue versus persulfate catalysis of polyacrylamide gels, as investigated by capillary zone electrophoresis

The efficiency of a novel method of photopolymerization, based on photoinitiating the reaction with methylene blue (MB), in presence of a redox couple (sodium toluenesulfinate and diphenyliodonium chloride), vs, the conventional persulfate--N,N,N',N'-tetramethylethylenediamine redox couple was investigated as a function of different effectors in solution. Oxygen dissolved in the gelling mixture strongly quenches persulfate catalysis, while leaving essentially unaltered the process initiated by photopolymerization. On the contrary, the presence of 8 M urea substantially accelerates a persulfate-driven reaction, boosting the conversion of monomers to near completion (> 98%) while leaving the photopolymerization process largely unaffected. Polyacrylamide polymerization has also been performed in a number of hydroorganic solvents (all in a 50:50 v/v ratio): dimethyl sulfoxide (DMSO), tetramethylurea, formamide and dimethylformamide. In all cases, the persulfate-catalyzed reaction was strongly quenched and even completely inhibited (in DMSO), whereas the photopolymerization process was essentially unaffected by any of these organic solvents. The reaction kinetics of the methylene blue-driven reaction could not be ameliorated when admixing an anionic dye (e.g., eosin Y) to the cationic MB, even when amply changing their molar ratios. Thus, it appears that photocatalysis with MB (and the redox couple sodium toluene-sulfinate and diphenyliodonium chloride) is a unique process, proceeding at optimum rate under the most adverse conditions, completely insensitive to any kind of positive and negative effectors and able to ensure at least 95% monomer conversion under the standard conditions of 1 h reaction time at room temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of haemoglobin variants using immobilized pH gradients

We present a new method for analysis of haemoglobin variants in immobilized pH gradients. The isoelectric fractionation is performed in polyacrylamide gels with copolymerized pH gradients between pH 7.0 and 8.0. The common haemoglobin variants (HbA, HbF, HbS, HbC, HbE and HbA2) are clearly resolved within this pH range. The high resolving power and reproducibility of immobilized pH gradients combined with extremely short separation times make this fractionation technique superior to all electrokinetic procedures used for haemoglobin analysis. At present, isoelectric focusing in immobilized pH gradients is a complementary tool for haemoglobin analysis when classical electrophoretic techniques do not provide sufficient resolution. We hope that in the future this technique will gain the popularity it deserves.

Preincubation with cysteine prevents modification of sulfhydryl groups in proteins by unreacted acrylamide in a gel

It has been found that the double bond of free, unreacted acrylamide in a gel can react with a free -SH group of proteins, forming a cysteinyl-S-propionamide adduct. When beta-lactoglobulin was incubated at concentration levels lower than those of free acrylamide, left after polymerizing a 5% T, 4% C gel (barely 12 mM), under anaerobic conditions in 0.1 M borate, pH 9.5, for 1 h and then the tryptic digests analyzed by high performance liquid chromatography (HPLC), two new peptides were detected. The two new peaks were recovered and sequenced by the Edman degradation procedure. They correspond to the sequence from Leu-149 to Ile-162. Residue No. 160 was found to be a cysteinyl-S-propionamide reaction product. Interestingly, only this residue, out of a total of 5 Cys residues, had reacted. No other amino acids (including -NH2 terminus and free -NH2 in Lys) reacted with free acrylamide. The addition of free acrylamide to the -SH group could be completely inhibited if: (i) the gel was extensively washed prior to sample application, or (ii) the gel was incubated for 1 h in 100 mM free Cys.

Capillary electrophoresis of macromolecules in 'syrupy' solutions: facts and misfacts

'Syrupy' solutions of liquid linear polyacrylamide (> or = 10%T, 0%C) appear to be excellent for fractionation of oligonucleotides and, potentially, for DNA sequencing. For such analyses, the silica wall must be coated by covalently bound strings of polyacrylamide; otherwise, the electroosmotic flow will slowly pump out the viscous electrolyte solution. Due to the enormous viscosity (100 Pa s for an 8% T solution) the polymer strings must be prepared in situ, by filling the capillary with the appropriate monomer solution. The reaction, however, cannot be driven to better than 80-85% conversion: in 10%T, the concentration of unreacted monomers will thus be 200-300 mM. This will give a substantial background absorbance (even at 254 nm) and leave a huge amount of potentially harmful reacting species in the background electrolyte. A chemical scavenging method is proposed here: after polymerization, a 100 mM solution of cysteine is driven in from the cathode and allowed to react for up to 10 h. At the end of the reaction period, the excess cysteine and its acrylamido adduct are driven out electrophoretically and the column is reconstituted with its normal background electrolyte. Columns thus preconditioned have been found to perform extremely well and to last as long as the inner coating (and the linear polymer filling) will last. No 'carry over' from run to run was experienced.

Characterization of immobiline membranes for application in a multicompartment electrolyzer for protein purification

The efficient use of preparative protein purification in a multicompartment electrolyzer with Immobiline membranes depends on the knowledge of membrane characteristics. For that purpose, an experimental investigation of the effects of ionic charges on the membrane characteristics has been carried out through the measurements of membrane swelling and conductance. We also investigated the effects on the electrolyzer behaviour of operating parameters such as the Immobiline concentration and the presence of ion-exchange membranes. Data show that polyacrylamide gel degree of swelling is strongly dependent upon the pH and the ionic strength of the bathing solution as well as on the type and molarity of charges incorporated in the gel. The conductance of supported Immobiline gels in contact with uni-univalent chloride solutions has been measured by means of a mercury cell. The membrane conductance is also influenced by the ionic strength of the equilibrium solution and the presence of weak ionizable groups in the gel matrix. This study has demonstrated the close link between electrochemical and electromechanical properties of Immobiline membranes.

New developments in protein isolation, purification, and characterization

The most significant advancements in techniques and methods for protein purification and analysis have been made in liquid chromatography and in electrophoresis. In the area of chromatography, adsorbents based on new affinity principles have been prepared. New packing materials have facilitated the rapid progress of high-performance techniques. A great many new techniques in the field of electrophoresis have emerged. On an analytical scale, electrophoretic methods in two dimensions or in capillaries are unsurpassed in resolution power. Development of techniques for protein transfer between different media is a prerequisite for a full exploitation of the new methods. Modern techniques for analysis of submicrogram quantities facilitate the separation, detection, and characterization of complex protein mixtures.

Physico-chemical properties of amphoteric, isoelectric, macroreticulate buffers

We report here the properties of a new family of resins possessing an amphoteric character and able to strongly buffer at their pI values. They have been adopted as carriers for growth of cells in tissue culture and for hydroponics (Righetti et al. 1991; J. Biotechnol. 17, 169-176) but it is to be expected that such resins could have interesting chromatographic applications. It has been found that such beads [made by incorporating a pK 6.2 weak acrylamido base and a pK 4.6 weak acrylamido acid in a 2:1 ratio (thus with a pI of 6.2) into a neutral polyacrylamide backbone], independently from their initial conditioning (acid- or base-washed), spontaneously seek their equilibrium position (pI value) upon washing off excess titrant. Thus, upon potentiometric titration, they are seen to buffer in both directions of the pH scale (contrary to the behaviour of a pure carboxyl or a pure amino surface, which will exhibit only unidirectional buffering power). From the behaviour of these amphoteric beads when polymerized in the absence or in the presence of salts (0.2 M NaCl), it is hypothesized that, for exerting buffering power, both the buffering ion and its counterion must be incorporated non-randomly in the chain, but as a couple or in close proximity. Upon random incorporation of the two ions, buffering power is lost.

Synthesis of thiomorpholino buffers for isoelectric focusing in immobilized pH gradients

The two commercially available Immobilines having a pK of 6.2 (2-morpholino ethyl acrylamide) and 7.0 (3-morpholinopropylacrylamide) have been modified and two new buffers have been synthesized: 2-thiomorpholinoethylacrylamide, pK 6.6, and 3-thiomorpholinopropyl acrylamide, pK 7.4. The replacement of an oxygen with a sulfur atom in the morpholino ring is thus seen to shift the pK values of these two bases by +0.4 pH units. In formulations in which the two new bases replaced the standard morpholino derivatives, identical pH profiles and protein patterns were obtained. The reason for this work was to try to close the gap between the pK 7.0 and 8.5 species and to provide the users of immobilized pH gradients with more buffers in the neutral pH region. The two new thiomorpholino derivatives are an important step in this direction.

Synthesis of an hydrophilic, pK 8.05 buffer for isoelectric focusing in immobilized pH gradients

The synthesis of a new, pK 8.05 acrylamido weak base for isoelectric focusing in immobilized pH gradients (IPG) is here reported. This compound N,N-bis(2-hydroxyethyl)-N'-acryloyl-1,3-diaminopropane is strongly hydrophilic, and thus inhibits any potential hydrophobic interaction among proteins and the grafted basic groups in an IPG matrix. In addition, this novel buffer represents a step ahead towards the goal of closing the 'gap' between the commercially available Immobilines, pK 7.0 and 8.5. Owing to the large distance between these two neighboring pK values, it is difficult to arrange for linear narrow pH gradients in this region. IPG compositions obtained with this new buffer give highly linear pH gradients and protein profiles identical to those obtained with commercial Immobilines.

Human skeletal muscle myosin light chains analyzed by immobilized pH gradients during ontogenesis: identification of new phosphorylatable isoforms of light chain 2

Previous studies using two-dimensional gel electrophoresis have described adult and fetal isoforms of skeletal muscle myosin light chains (MLC). They have also revealed an embryo-specific light chain (LC1emb), apparently absent in most adult skeletal muscles. In order to characterize more thoroughly the MLC family, we have analyzed the MLCs from human skeletal muscle at different developmental stages using a two-dimensional electrophoresis technique with an immobilized pH gradient in the first dimension. The high resolution of this novel technique, resolving components which in isoelectric points are less than or equal to 0.01 pH, combined with sensitive silver staining, has allowed us to identify four phosphorylatable isoforms of MLC2: two slow-myosin light chains (MLC2Sa and b), two fast myosin light chains (MLC2Fa and b), and their phosphorylated counterparts: MLC2SaP and bP, MLC2FaP and bP. The following major modifications during development were observed: (i) The embryonic LC (LC1emb) persists up to at least 26 weeks of fetal life. (ii) The polymorphism of LC2 is already evident at 10 weeks of development but only the nonphosphorylated forms of LC2S and LC2F seem to be present. The LC2Fa form is predominant. As early as 26 weeks of fetal life, the 4 phosphorylated forms are detected. In the adult, LC2Fb is a minor component. (iii) LC3F (fast) is already expressed at an early embryonic stage (10 weeks).

Preparative purification of human monoclonal antibody isoforms in a multi-compartment electrolyser with immobiline membranes

The performance of a multi-compartment electrolyser with isoelectric Immobiline membranes for large-scale protein purification is evaluated. Owing to the presence of isoelectric membranes possessing a high buffering capacity and ionic strength, isoelectric protein precipitation inside the membranes, one of the major drawbacks of present membrane uses, is fully avoided. In addition, owing to this novel membrane technology, pH gradient decay, typical of isoelectric focusing in carrier ampholytes, is fully eliminated and pH and conductivity constancy is guaranteed in all flow chambers for running periods of more than 11 days (160,000 V h). The membranes described possess a unique selectivity, in that they act by modulating the surface charge (i.e., the mobility) of macroions crossing or tangential to them. The concept of isoelectric Immobiline membranes acting like a pH-stat unit is introduced. Protein homogeneity in each chamber of the electrolyser can be achieved even when purifying human monoclonal antibodies against HIV-1, which possess high pI values (9.0-9.6), are large molecules (Mr 150,000) and are fractionated in the presence of large micelles of neutral detergents.

Formulations for immobilized pH gradients including pH extremes

Formulations are given both for narrow (less than 2 pH units) and for wide range (up to 8 pH units) immobilized pH gradients, spanning between pH 2.5 and pH 11. The contribution from water to the buffering power (beta) at these pH extremes requires the recipes to be optimized (in terms of gradient linearity) for each desired level of beta av.

HydroLink gel electrophoresis (HLGE). I. Matrix characterization

A new gelatinous matrix is reported, having intermediate properties between those of polyacrylamide and agarose gels. The matrix has the unique property of being amphiphilic, i.e. of swelling in both plain water and polar organic solvents, and seems particularly well suited for electrophoresis of DNA. The compatibility with organic solvents includes 50% dimethyl sulphoxide, 50% tetramethyl urea, 50% acetonitrile and 50% tetrahydrofuran, the latter having a dielectric constant of 20. The matrix is hypothesized to consist of brush-like pillars, having a hydrophobic core and a hydrophilic coating. The latter is formed by short chains protruding in the surrounding liquid and able to coordinate large amounts of water.

Charge heterogeneity of recombinant pro-urokinase and urinary urokinase, as revealed by isoelectric focusing in immobilized pH gradients

When analysing homogeneous preparations of recombinant pro-urokinase and urinary urokinase by isoelectric focusing (IEF) in immobilized pH gradients, an extreme charge heterogeneity was detected (at least ten major and ten minor bands in the pH range 7-10). This extensive polydispersity was not caused by different degrees of glycosylation, or by IEF artefacts, such as binding to carrier ampholytes or carbamylation by urea. A great part of this heterogeneity could be traced back to the existence of a multitude of protein molecules containing Cys residues at different oxidation levels (-SH, -S-S-, even cysteic acid). Owing to the very large number of Cys residues in pro-urokinase (24 out of a total of 411 amino acids) and to the relatively high pI of its native forms (pI 9.5-9.8; the native form is believed to contain all Cys residues as -S-S- bridges), the presence of SH or cysteic acid residues would increase the negative surface charge, as even SH groups would be extensively ionized. In pro-urokinase, part of the heterogeneity was also due to spontaneous degradation to urokinase and possibly also to cleavage into lower-molecular-mass fragments. When all these causes of heterogeneity were removed, the pI spectrum was reduced to only four, about equally intense bands. The cause of this residual heterogeneity is unknown.

Use of physiological substrates for zymograms of disaccharidases after separation in immobilized pH gradients

A new technique is described for in situ visualization of the activity of intestinal disaccharidases after isoelectric focusing in immobilized pH gradients using their physiological substrates. The reaction principle is based on the oxidation of D-glucose, liberated by the disaccharidases, into D-gluconolactone and the production of NADH by glucose dehydrogenase. At the sites of enzymatic activity, tetrazolium salts present in the reaction mixture are reduced to relatively water-insoluble formazans by NADH. The rate of formazan production is increased by the presence of phenazine methosulfate. An additional modification of the technique involves the use of polyvinyl alcohol in the substrate solution. Due to the increase in the viscosity of the substrate solution, leakage of the enzyme from the IPG gels is minimized. Incubation times can thus be prolonged without loss of resolution and band-blurring.

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).

Focusing of pepsin in strongly acidic immobilized pH gradients

A new acrylamido buffer has been synthesized, for use in isoelectric focusing in immobilized pH gradients. This compound (2-acrylamido glycolic acid) has a pK = 3.1 (at 25 degrees C, 20 mM concentration during titration) and is used, by titration with the pK 9.3 Immobiline, to produce a linear pH gradient in the pH 2.5-3.5 interval. Pepsin (from pig stomach) focused in this acidic pH gradient is resolved into four components, two major (with pI values 2.76 and 2.78) and two minor (having pI values 2.89 and 2.90). This is the first time that such strongly acidic proteins could be focused in an immobilized pH gradient. Even in conventional isoelectric focusing in amphoteric buffers it has been impossible to focus reproducibly very-low-pI macromolecules.

A horizontal apparatus for isoelectric protein purification in a segmented immobilized pH gradient

A modification of the previously described apparatus (Faupel et al. (1987) J. Biochem. Biophys. Methods 15, 147-162), for recycling isoelectric focusing in a segmented immobilized pH gradient, is here reported. The most important improvements are: (1) a horizontal, vs. the previously vertical assembly; (2) a reduction of the thickness of the central flow chamber to 6 mm, vs. the previous 3 cm length and (3) the introduction, at both gel extremities of each Immobiline segment, of polypropylene filters, thus efficiently blocking the gel in situ. The advantages are: (i) the spontaneous removal of air bubbles, which in the vertical apparatus tend to accumulate in the ceiling of the flow chamber and to obstruct the flow of electric current; (ii) a more efficient hydraulic flow with a reduced chance of heating the liquid stream in the flow chamber, due to its reduced length along the separation path and (iii) a reduced risk of gel detachment from the tube walls, due to osmotic swelling caused by focused protein zones in the gel phase and by the fixed Immobiline charges in the polyacrylamide matrix.

Isoelectric protein purification in segmented immobilized pH gradients. Effect of salts on rate of contaminants' removal

A method is described for keeping a constant salt background during protein purification in a segmented immobilized pH gradient. It is based on an external hydraulic flow replenishing the salt loss due to combined electric and diffusional mass transport (similar to the concept of Ribes' steady-state rheoelectrolysis). Such a minimum of ionic strength might be needed for proteins which tend to precipitate and aggregate at or in vicinity of the isoelectric point. However, it is found that any salt level in the sample feed (already at 1 mM concentration) deteriorates transport of non-isoelectric proteins, because of the much larger current fraction carried by the ions themselves as opposed to proteins. In addition, high salt levels in the sample reservoir might form cathodic and anodic ion boundaries, alkaline and acidic, respectively, which might hamper protein migration and even induce denaturation. Thus, when high salt backgrounds are needed in the sample feed, external pH control should be exerted, e.g. with a pH-stat. Three parameters influence protein transport in the segmented IPG chamber: (a) cross-sectional area of the Immobiline membranes; (b) delta pI between the isoelectric protein and the contaminants and (c) salt molarity in the sample reservoir. The first 2 show a positive, the last a negative correlation.

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.

Protein desalting by isoelectric focusing in a segmented immobilized pH gradient

We have recently described an apparatus for protein purification based on a segmented Immobiline gel, having one or more liquid interlayers in between. 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 an Immobiline gel. For this, a hydraulic flow is coupled orthogonally to an electric flow, sweeping away the non-isoelectric impurities from the recycling chamber. We now demonstrate that the present apparatus can be efficiently used for protein desalting. Hemoglobin A samples, containing 50 mM NaCl or 50 mM ammonium acetate, could be efficiently desalted in 2 h of recycling, after which the total salt content had decreased to less than 0.005 mM (a salt decrement of more than 10,000 fold the initial input). However, with polyprotic buffers (sulphate, citrate, phosphate, oligoamines) the desalting process was much slower, typically of the order of 20 h, possibly due to interaction of these species with the surrounding Immobiline matrix. In this last case, outside pH control (e.g. with a pH-stat) is necessary during protein purification, as, due to the faster removal of the monovalent counterion, the solution in the recycling chamber can become rather acidic or alkaline. It is demonstrated that the 2 extremities of the Immobiline segments facing the sample recycling chamber act indeed as isoelectric membranes, having a good buffering capacity, preventing the protein macroion from leaving the chamber by continuously titrating it to its isoelectric point.

Two-dimensional gel electrophoresis of proteins

The high-resolution capacity of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) makes it an excellent tool for the analysis and characterisation of complex protein mixtures. The evolution of two-dimensional electrophoresis is briefly described. The various steps involved in 2-D PAGE, the identification and characterization of proteins separated by 2-D PAGE and the quantitative and qualitative analysis of 2-D patterns are discussed in detail and some new approaches are described. In the final section a brief outline of some of the biomedical applications of 2-D PAGE to screening of body fluids, genetic diseases, inborn errors of metabolism, cancer and neoplastic transformation are discussed.

Amphoteric, isoelectric immobiline membranes for preparative isoelectric focusing

Amphoteric, isoelectric agarose membranes, as devised by Martin and Hampson [Martin, A.J.P. and Hampson, F. (1978) J. Chromatogr. 159, 101-110], are found unsuitable for blocking electroendosmosis in multi-compartment electrolysers during preparative isoelectric focusing, due to the poor and highly unpredictable incorporation of carboxyls and amino groups on the polysaccharide moiety. New, polyacrylamide-based membranes are described, containing as buffers and titrants the Immobiline chemicals used to produce immobilized pH gradients. These new membranes are supported on both faces by a non-woven polypropylene cloth, a material exhibiting minimal adsorption properties for proteins. Due to the extensively developed Immobiline technology, membranes with highly predictable isoelectric points, well-defined buffering capacity and conductivity can be synthesized at any pH value along the pH 3-10 scale. They are effective in blocking electroendosmosis even when the delta pH on either side of the membrane is as high as 1.5 pH unit.

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).

pH measurements in ultranarrow immobilized pH gradients

It is possible to measure pH values in immobilized pH gradients (IPG) when the polyacrylamide matrix is made to contain an additional, carrier ampholyte-generated pH gradient. After an IPG run, 5 mm gel segments, along the separation axis, are cut and eluted in 300 microliter of 10 mM KCl and the pH read with a standard pH meter. When using ultranarrow pH gradients, larger gel segments (ca. 265 microliter) are eluted in 900 microliter of 100 mM KCl and the pH assessed with a differential pH meter. In the latter case, either internal or external standards are used as a reference, or starting point, to convert delta pH values into an actual pH curve. The reproducibility of the system is better than +/- 0.05 pH units, with a ca. 15% error over a 0.3 pH unit span. In ultranarrow pH gradients, it is imperative to use mixtures of all commercially available carrier ampholytes, so as to smoothen conductivity and buffering capacity gaps. By the present method, it is also possible to convert a wide (2-3 pH unit) carrier ampholyte interval into a narrow (0.2-0.3 pH unit) one.

Antenatal diagnosis of beta-thalassemia by isoelectric focusing in immobilized ph gradients

A new method for antenatal diagnosis of thalassemias is reported based on the analysis of the major Hb components of fetal cord blood, sampled at week 18 of pregnancy under ultrasonic guidance, by isoelectric focusing in immobilized pH gradients (IPG). In an IPG gel encompassing a pH 6.7-7.6 span, HbA and HbFac are separated by a distance nine times greater than in a conventional carrier ampholyte pH 6-8 gel and three times greater than in an ampholine gel with separators (an equimolar mixture of beta-alanine and 6-amino caproic acid). Band evenness (in terms of uniform protein concentration within a zone) and straightness (in terms of parallel alignment of the bands to the electrodes), because of insensitivity of IPG gels to salt distortions, allows for accurate and reproducible quantitation of HbF, -A, and -Fac levels. The possibility of greatly overloading IPG matrices in total Hbs increases the sensitivity of the technique to the detection of only 0.5% HbA in the total Hb mixture, the lower limit of conventional IEF being only 2.5% HbA. Of 15 fetuses from couples at risk analyzed in the region of Ozieri, three were found to be homozygous beta-thalassemic, eight heterozygous, and four normal with no false-positives or -negatives.