Focusing of alkaline proteases (subtilisins) in pH 10-12 immobilized gradients

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.

Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing

We have investigated the use of a variety of different techniques to identify as many proteins as possible in a yeast lysate, with the aim of investigating the overlap and complementarity of data from different approaches. A standard lysate was prepared from log phase yeast (Saccharomyces cerevisiae). This was then subjected to analysis via five different approaches aimed at identifying as many proteins as possible using an ion trap mass spectrometer. The total number of non-redundant protein identifications from each experiment was: 524 proteins by 2-D (SCX/C18) nanoflow liquid chromatography-liquid chromatography tandem mass spectrometry (nanoLC-LC MS/MS (MudPIT)); 381 proteins by nanoLC-MS/MS with gas phase fractionation by mass range selection; 390 proteins by nanoLC-MS/MS with gas phase fractionation by ion abundance selection; 898 proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation of proteins, in-gel digestion, and nanoLC-MS/MS of gel slices; and 422 proteins by isoelectric focusing of proteins, in-gel digestion and nanoLC-MS/MS of gel slices. The total number of non-redundant protein identifications in the five experiments was 1204. Combining only the two best experiments, the SDS-PAGE gel slices and the Mudpit, produces 1024 proteins identified, more than 85% of the total. Clearly, combining a Mudpit analysis with an SDS-PAGE gel slice experiment gives the greatest amount of protein identification information from a limited amount of sample.

Alkaline proteins of Bacillus subtilis: first steps towards a two-dimensional alkaline master gel

The genomic sequence of Bacillus subtilis, which is the best studied Gram-positive bacterium, enabled us to obtain a theoretical two-dimensional (2-D) map, demonstrating that about one-third of this proteome has a theoretical alkaline isoelectric point (pI). This represents an important part of the entire proteome, which is not detectable in conventional 2-D gels (pH range 4-7). Sequence analysis revealed that 91% of the ribosomal proteins and a high amount of theoretical membrane proteins should be localized in the alkaline pH range requiring different protein extraction procedures. In order to find the pH range which gives the best resolution results for the alkaline proteins of B. subtilis, immobilized pH gradients (IPGs) with different pH ranges (pH 6-10, 6-11, 4-12, 9-12, and 3-10) were tested and optimized for IPG 4-12. Here we present a version of a first alkaline master 2-D gel for B. subtilis, which is a further complement of the already existing master gel (pH 4-7) in the Sub2D database. Almost 150 spots could be detected and 41 proteins have already been identified.

Proteome mapping by two-dimensional polyacrylamide gel electrophoresis in combination with mass spectrometric protein sequence analysis

The high resolving power of two-dimensional polyacrylamide gel electrophoresis 2D-PAGE and its full analytical and preparative potential have been described with special emphasis on reproducibility and standardization of protein spot patterns, enhanced protein detection sensitivity, and computer analysis database development. New methodologies for peptide mass fingerprinting, peptide, sequence, and fragmentation tagging have been highlighted. Major challenges associated with 2D-PAGE/mass spectrometric protein sequencing were outlined which need to be addressed in the future, including sample enrichment, use of alternative gel matrices, improvements in separation systems interfaced directly to the mass spectrometer, and design of high-sensitivity instruments with very high mass ranges. It is hoped that comparative studies to identify, quantitate, and characterize proteins differentially expressed in normal versus diseased cells would give insight into mechanisms of pathogenesis and allow the development of a way to control both the etiology and the course of diseases.

Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: current status

There is currently much interest, as we enter the postgenome era, in studying gene expression at the protein level. Two-dimensional electrophoresis (2-DE) using immobilized pH gradients (IPG), coupled with mass spectrometry (MS), is currently the most widely utilized approach for the analysis of whole tissue proteins. The methodology for IPG-based 2-DE, since the introduction of the technique in the 1980s, is reviewed. In its present form the IPG methodology is mostly useful as a research tool. In general, high reproducibility and high resolution have been achieved. However, the lack of substantial automation and the limited sensitivity of the current overall methodology continue to represent drawbacks for biomedical applications. Further developments to increase throughput and to reduce sample requirement would substantially benefit the application of IPG-based 2-DE to biomedicine and would enhance the prospects for introducing the methodology into the clinical laboratory.

Electrophoresis gel media: the state of the art

Some unique events have occurred in the last few years which might revolutionize the field of polyacrylamide gel electrophoresis. While it was widely recognized that such matrices could normally be cast with a small pore size distribution, typically of the order of a few nanometers diameter (for protein sieving), recent developments suggest that "macroporous" gels could also be produced in the domain of polyacrylamides. If constraints to chain motion are imposed during gel polymerization, large-pore structures can be grown. Such constraints can originate either from low temperatures or from the presence of preformed polymers in the gelling solution; in both cases, the growing chains are forced to "laterally aggregate" via inter-chain hydrogen bond formation. Upon consumption of pendant double bonds, such bundles are frozen in the three-dimensional space by permanent cross-links. As an additional development, a novel photopolymerization system is described, comprising a cationic dye (methylene blue) and a redox couple (sodium toluene sulfinate, a reducer, and diphenyliodonium chloride, a mild oxidizer). Methylene blue catalysis is characterized by a unique efficiency, ensuring >96% conversion of monomers, even in hydro-organic solvents and in the presence of surfactants, which normally quench or completely inhibit the persulphate-driven reaction. In addition, methylene blue-sustained photopolymerization can be operated in the entire pH 3-10 interval, where most other systems fail. Perhaps the most striking novelty in the field is the appearance of a novel monomer (N-acryloylaminopropanol, AAP) coupling a high hydrophilicity with a unique resistance to alkaline hydrolysis. Given the fact that a poly(AAP) matrix is 500 times more stable than a poly(acrylamide) gel, while being twice as hydrophilic, it is anticipated that this novel chemistry will have no difficulties in replacing the old electrophoretic anticonvective media. The review ends with a glimpse at novel sieving media in capillary zone electrophoresis: polymer networks. Such media, by providing an almost infinite range of pore sizes, due to the absence of a rigid support, allow sieving mechanisms to be operative over a wide interval of particle sizes, even up to genomic DNA. Viscous solutions of polymer networks, made with the novel poly(AAP) chemistry, allow repeated use of the same separation column, well above 50 injections. Silica-bound poly(AAP) chains provide effective quenching of electroosmosis and >200 analyses by isoelectric focusing.

Isoelectric focusing in immobilized pH gradients: an update

The latest trends on isoelectric focusing (IEF) in immobilized pH gradients (IPG) are here reviewed. The major advances on IPG technologies have been made when interfacing this technique with sodium dodecyl sulfate-polyacrylamide gel electrophoresis to produce two-dimensional (2-D) maps. Previous 2-D maps were routinely performed using conventional IEF as a first dimension, which typically resulted in poor reproducibility of spot position. With IPGs, correlation between experimental and calculated protein pI values is as good as +0.01 to 0.02 pH units. A new software has also been released, permitting easy calculation and optimization of linear, concave and convex exponential gradients, even in very complex recipes utilizing all ten Immobiline chemicals. It has also been proven that IPGs can be interfaced with mass spectrometry, thus obtaining a novel 2-D map with the best of pI measurements in the first dimension coupled with the best of mass determination in the second dimension. Recently, it has been shown that IPGs can be exploited to charter forbidden grounds, with the creation of non-linear pH gradients covering the extreme alkaline pH 10-12 gradient. In such basic regions, excellent steady-state patterns of histones and subtilisin mutants have been reported. Different families of histones could be mapped not only in this pH 10-12 interval, but also in 2-D maps exploiting this very alkaline gradient in the first dimension. Although the IPG technique is now a trouble-free, user-friendly technique, some annoying artefacts, producing severe protein smears and precipitation, were very recently reported, but found to be linked to some commercial Immobiline preparations containing up to 5% oligomers. Better quality control on the part of the company producing such chemicals should eliminate even this last source of troubles.

Very alkaline immobilized pH gradients for two-dimensional electrophoresis of ribosomal and nuclear proteins

Basic proteins normally lost by the cathodic drift of carrier ampholyte focusing, or separated by NEPHGE with limited reproducibility, could be well separated by two-dimensional (2-D) electrophoresis under equilibrium conditions using immobilized pH gradients (IPGs) 4-10 and 6-10 using a previously published protocol (Görg et al., Electrophoresis 1988, 9, 531-546). In the present study we have extended the pH gradient to pH 12 with IPGs 8-12, 9-12 and 10-12 for the analysis of very basic proteins. Different optimization steps with respect to pH engineering, gel composition and running conditions, such as substitution of acrylamide by dimethylacrylamide and addition of isopropanol with and without methylcellulose to the IPG rehydration solution (in order to suppress the reverse electroosmotic flow) were necessary to obtain highly reproducible 2-D patterns of ribosomal proteins from HeLa cells and mouse liver. Histones from chicken erythrocyte nuclei as well as total cell extracts of erythrocytes were also successfully separated under steady-state conditions. Due to the selectivity of isoelectric focusing in IPG 9-12, where the more acidic proteins abandon the gel, the tedious procedure of nuclei preparation prior to histone extraction can be omitted.

Preparative electrofocusing for industrial applications

This paper presents a case study of using a multicompartment isoelectric focusing apparatus to determine the isoelectric points and focus preparative quantities of brain derived neurotrophic factor (BDNF) and neurotrophic factor 3 (NT3). A separation of PEGylated from unPEGylated forms of granulocyte colony stimulating factor (G-CSF) is described as well. Both BDNF and NT3 have substantially higher pI values in this system than is predicted from sequenced based modeling. Although PEGylated forms of G-CSF can be separated from the unPEGylated forms, separation of protein with differing degrees of PEGylation was not achieved. The paper additionally demonstrates that this technique can be used simultaneously as an analytical and preparative tool, eliminating the need for analytical IEF gels.

Purification of glycopeptide antibiotics by isoelectric focusing in multicompartment electrolyzers with immobiline membranes

The purification of small glycopeptides (a Hepta-Tyr of the teicoplanin family, exhibiting broad activity against highly glycopeptide-resistant enterococci) by isoelectric focusing in multicompartment electrolyzers with buffering, isoelectric membranes, is described. The main obstacle to such a preparative technique, in common with all focusing methodologies, is the poor solubility of the analyte at the pI value with resultant precipitation and coprecipitation of all impurities with the main fraction. A good solubilizing power was obtained in hydro-organic solvents, particularly a mixture of 6 M urea and 20-25% trifluoroethanol. Best results, however, were obtained with mixtures of 8 M urea and zwitterionic detergents, notably the 3-[(3-cholamidopropyl)dimethylammonia]-1-propanesulfonate (CHAPS) family. A unique behavior of the peptide was found in concentration gradients of CHAPS: solubility increases up to 3.5% CHAPS, but the curve shows a maximum and then solubility decreases again at 5% CHAPS. In mixtures of 8 M urea and 3.5% CHAPS, sample loads of 500 up to 1000 mg Hepta-Tyr could be purified in a single run, with recoveries > 90% and purity in excess of 99%. The main glycopeptide fraction (pI 8.56) was collected into an isoelectric trap delimited by pI 8.46 and pI 8.65 membranes. Attempts at purifying the glycopeptide by most known reversed phase-high performance liquid chromatography (RP-HPLC) techniques failed completely.

Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: I. Synthetic route and product characterization

The novel acrylamido monomer reported by our group (N-acryloylaminoethoxyethanol, AAEE; Chiari et al., Electrophoresis 1994, 15, 177-186), found to combine high hydrophilicity with extraordinary resistance to alkaline hydrolysis, has come under closer scrutiny due to unexpected and random autopolymerization while stored as a 1/1 v/v water solution at 4 degrees C (possibly due to a greater oxidability of the ether group). We have additionally found a unique degradation pathway of the monomer, called "1-6 H-transfer", by which the C1 (on the double bond site), by constantly ramming against the C6, next to the ether oxygen (O7, which in fact favors the transfer of the hydrogen atom by C1), produces radicals which more efficiently add to the monomer favoring autopolymerization and cross-linking. A number of novel monomers is proposed while maintaining the other unique characteristics of AAEE. One of them, N-acryloylaminopropanol, offers all the unique, special qualities of AAEE, without the noxious aspects of autopolymerization. Additionally, a synthetic route was optimized, yielding an essentially pure product in a single reaction step, with a yield > 99% and an equivalent purity (> 99%). The synthesis consists in reacting acryloyl chloride at -40 degrees C in presence of a twofold molar excess of aminopropanol and in ethanol (instead of methanol) as solvent. Other solvents, as well as the use of triethylamine for neutralizing the HCl produced, were found to give a variety of undesired byproducts.

Steady-state two-dimensional maps of very alkaline proteins in an immobilized pH 10-12 gradient, as exemplified by histone types

Two-dimensional steady-state patterns of histones are here reported for the first time. The first dimension run consists in nonlinear immobilized pH gradients, spanning the pH 10-12 range. The second dimension run is a standard SDS-PAGE in a constant concentration (15% T) gel slab, in presence of a 6% T stacking gel. All the histone fractions analysed (II-AS, VI-S, VII-S and VIII-S) exhibit pI values between pH 11 and 12. The M(r) values range from 13 to 32 kDa, with the heaviest distribution around 18 kDa. When running all different histone fractions in a single mixture, and analysing the 2-D gel by computerized image data acquisition, a total of 35 individual spots is detected.