Dye ligand chromatography and two-dimensional electrophoresis of complex protein extracts from mouse tissue

Reducing the complexity of the Escherichia coli proteome by chromatography on reactive dye columns

High-resolution 2-dimensional gel electrophoresis (2DGE) is a key technology in the analysis of cellular proteomes particularly in the field of microbiology. However, the restricted resolution of 2DGE and the limited dynamic range of established staining methods limit its usefulness for characterising low abundance proteins. Consequently, methods have been developed to either enrich for low abundance proteins directly or to deplete the highly abundant proteins present in complex samples. We present a protocol for affinity chromatography on reactive dye resins for the analysis of the Escherichia coli proteome. Using a range of commercially available reactive dye resins in a traditional chromatography system we were able to enrich low abundance proteins to levels suitable for their reliable detection and, most importantly, their identification using standard peptide mass mapping and MALDI-TOF MS methods. Under the chromatography conditions employed up to 4.42% of the proteins present in the total nonfractionated E. coli cell lysates bound to the reactive dye column and were subsequently eluted by 1.5 M NaCl. Of the bound proteins approximately 50% were considered to be enriched compared to the nonfractionated cell lysate. The ability to detect low abundance proteins was due to a combination of the specific enrichment of the proteins themselves as well as the depletion of highly abundant cellular proteins, which otherwise obscured the low abundance proteins. There was evidence of some selectivity between the different reactive dye resins for particular proteins. However, the selection of suitable dye resins to selectively enrich for particular classes of proteins remains largely empirical at this time.

Applications of affinity chromatography in proteomics

Affinity chromatography is a powerful protein separation method that is based on the specific interaction between immobilized ligands and target proteins. Peptides can also be separated effectively by affinity chromatography through the use of peptide-specific ligands. Both two-dimensional electrophoresis (2-DE)- and non-2-DE-based proteomic approaches benefit from the application of affinity chromatography. Before protein separation by 2-DE, affinity separation is used primarily for preconcentration and pretreatment of samples. Those applications entail the removal of one protein or a class of proteins that might interfere with 2-DE resolution, the concentration of low-abundance proteins to enable them to be visualized in the gel, and the classification of total protein into two or more groups for further separation by gel electrophoresis. Non-2-DE-based approaches have extensively employed affinity chromatography to reduce the complexity of protein and peptide mixtures. Prior to mass spectrometry (MS), preconcentration and capture of specific proteins or peptides to enhance sensitivity can be accomplished by using affinity adsorption. Affinity purification of protein complexes followed by identification of proteins by MS serves as a powerful tool for generating a map of protein-protein interactions and cellular locations of complexes. Affinity chromatography of peptide mixtures, coupled with mass spectrometry, provides a tool for the study of protein posttranslational modification (PTM) sites and quantitative proteomics. Quantitation of proteomes is possible via the use of isotope-coded affinity tags and isolation of proteolytic peptides by affinity chromatography. An emerging area of proteomics technology development is miniaturization. Affinity chromatography is becoming more widely used for exploring PTM and protein-protein interactions, especially with a view toward developing new general tag systems and strategies of chemical derivatization on peptides for affinity selection. More applications of affinity-based purification can be expected, including increasing the resolution in 2-DE, improving the sensitivity of MS quantification, and incorporating purification as part of multidimensional liquid chromatography experiments.

Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography

We describe an approach for fractionating complex protein samples prior to two-dimensional gel electrophoresis using reversed-phase high-performance liquid chromatography. Whole lysates of cells and tissue were prefractionated by reversed-phase chromatography and elution with a five-step gradient of increasing acetonitrile concentrations. The proteins obtained at each step were subsequently separated by high-resolution two-dimensional gel electrophoresis (2-DE). The reproducibility of this prefractionation technique proved to be optimal for comparing 2-DE gels from two different cell states. In addition, this method is suitable for enriching low-abundance proteins barely detectable by silver staining to amounts that can be detected by Coomassie blue and further analyzed by mass spectrometry.

Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation

The total protein of the mouse brain was fractionated into three fractions, supernatant, pellet extract and rest pellet suspension, by a procedure that avoids any loss of groups or classes of proteins. The supernatant proteins were resolved to a maximum by large-gel two-dimensional electrophoresis. Two-dimensional patterns from ten individual mice of the commonly used inbred strain C57BL/6 (species: Mus musculus) were prepared. The master pattern was subjected to densitometry, computer-assisted image analysis and treatment with our spot detection program. The resulting two-dimensional pattern, a standard pattern for mouse brain supernatant proteins, was divided into 40 squares, calibrated, and specified by providing each spot with a number. The complete pattern and each of the 40 squares are shown in our homepage (http://www.charite.de/ humangenetik). The standard pattern comprises 8767 protein spots. To identify the proteins known so far in the brain fraction investigated, a first set of 200 spots was analyzed by matrix-assisted laser desorption/ionization - mass spectrometry (MALDI-MS) after in-gel digestion. By screening protein databases 115 spots were identified; by extending the analysis to selected, genetically variant protein spots, 166 spots (including some spot series) were identified in total. This number was increased to 331 by adding protein spots identified indirectly by a genetic approach. By comparing the two-dimensional patterns from C57BL/6 mice with those of another mouse species (Mus spretus), more than 1000 genetically variant spots were detected. The genetic analysis allowed us to recognize spot families, i.e., protein spots that represent the same protein but that are post-translationally modified. If some members of the family were identified, the whole family was considered as being identified. Spot families were investigated in more detail, and interpreted as the result of protein modification or degradation. Genetic analysis led to the interesting finding that the size of spot families, i.e., the extent of modification or degradation of a protein, can be genetically determined. The investigation presented is a first step towards a systematic analysis of the proteome of the mouse. Proteome analysis was shown to become more efficient, and, at the same time, linked to the genome, by combining protein analytical and genetic methods.

Protein analysis on a genomic scale

Methods for protein analysis, such as chromatography, electrophoresis, enzyme tests, receptor assays and immunological tests, have always been aimed in a classical reductionistic manner at investigating single proteins isolated from the complex protein composition of biological compartments. The complexity of the protein composition in biological systems was first visualized by two-dimensional electrophoresis (2-DE). Using 2-DE like a molecular microscope, protein variations between different biological situations may be detected by subtractive 2-DE analyses. Combining 2-DE with microsequencing, amino acid analysis and mass spectrometry protein spots on 2-DE gels may be identified. The sequence information can be used to find the gene. However, by 2-DE not only single protein changes can be detected and investigated on the gene level, but also complex changes of many proteins on a genomic scale.

Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome

The two-dimensional electrophoresis (2-DE) technique developed by Klose in 1975 (Humangenetik 1975, 26, 211-234), independently of the technique developed by O'Farrell (J. Biol. Chem. 1975, 250, 4007-4021), has been revised in our laboratory and an updated protocol is presented. This protocol is the result of our experience in using this method since its introduction. Many modifications and suggestions found in the literature were also tested and then integrated into our original method if advantageous. Gel and buffer composition, size of gels, use of stacking gels or not, necessity of isoelectric focusing (IEF) gel incubation, freezing of IEF gels or immediate use, carrier ampholytes versus Immobilines, regulation of electric current, conditions for staining and drying the gels - these and other problems were the subject of our concern. Among the technical details and special equipment which constitute our 2-DE method presented here, a few features are of particular significance: (i) sample loading onto the acid side of the IEF gel with the result that both acidic and basic proteins are well resolved in the same gel; (ii) use of large (46 x 30 cm) gels to achieve high resolution, but without the need of unusually large, flat gel equipment; (iii) preparation of ready-made gel solutions which can be stored frozen, a prerequisite, among others, for high reproducibility. Using the 2-DE method described we demonstrate that protein patterns revealing more than 10 000 polypeptide spots can be obtained from mouse tissues. This is by far the highest resolution so far reported in the literature for 2-DE of complex protein mixtures. The 2-DE patterns were of high quality with regard to spot shape and background. The reproducibility of the protein patterns is demonstrated and shown to be thoroughly satisfactory. An example is given to show how effectively 2-DE of high resolution and reproducibility can be used to study the genetic variability of proteins in an interspecific mouse backcross (Mus musculus x Mus spretus) established by the European Backcross Collaborative Group for mapping the mouse genome. We outline our opinion that the structural analysis of the human genome, currently pursued most intensively on a worldwide scale, should be accompanied by a functional analysis of the genome that starts from the proteins of the organism.

Protein composition of the human heart: the construction of a myocardial two-dimensional electrophoresis database

Molecular changes occurring in myocardial diseases are not well understood. Proteins, as regulatory molecules, should play an important role in the etiology of these diseases. The method of two-dimensional electrophoresis (2-DE) allows the analysis of some thousand proteins with one experiment. An important prerequisite for this kind of investigation is the possibility of identifying the proteins separated by 2-DE. We resolve 3239 proteins of the human myocardium and tried to identify 33 proteins by amino acid analysis and microsequencing. Twenty proteins were identified by search for the protein-chemical data obtained in the Martinsried Institute Protein Sequence Database. Comparisons of 2-DE patterns of different size, which were obtained in different laboratories, were performed with the result that proteins identified on a 2-DE map of one laboratory can be assigned to spots of 2-DE maps produced by another laboratory. Our results show the usefulness of a myocardial 2-DE database; they can be used in different laboratories and make it possible to generate a collection of important human myocardial proteins in a 2-DE database for comparative studies worldwide.

Classification of mouse liver proteins by immobilized metal affinity chromatography and two-dimensional electrophoresis

Mouse liver proteins were classified into metal-binding and non-binding proteins by combining immobilized metal ion affinity chromatography (IMAC) and two-dimensional electrophoresis (2-DE). The proteins were fractionated by three metal ions, Zn2+, Ni2+ and Cu2+, immobilized on iminodiacetic acid and then separated by 2-DE. The total number of protein spots resolved by 2-DE increased approximately twofold when the proteins were prefractionated by IMAC. By establishing 2-DE standard patterns, 371 proteins were selected and then characterized according to their specificity in binding the three different metal ions. Only 48 proteins did not bind to any of the three metal ions investigated. Cu2+ was the most efficient ion in binding different proteins (310) compared to the other metals. Cu2+ bound to 42 proteins specifically and to 268 proteins unspecifically. Both Zn2+ and Ni2+ showed specific affinity only to four proteins.

Protein purification by dye-ligand chromatography

Dye-ligand chromatography has developed into an important method for large-scale purification of proteins. The utility of the reactive dyes as affinity ligands results from their unique chemistry, which confers both the ability to interact with a large number of proteins as well as easy immobilization on typical adsorbent matrices. Reactive dyes can bind proteins either by specific interactions at the protein's active site or by a range of non-specific interactions. Divalent metals participate in yet another type of protein-reactive dye interactions which involve the formation of a ternary complex. All of these types of interactions have been exploited in schemes for protein purification. Many factors contribute to the successful operation of a dye-ligand chromatography process. These include adsorbent properties, such as matrix type and ligand concentration, the buffer conditions employed in the adsorption and elution stages, and contacting parameters like flowrate and column geometry. Dye-ligand chromatography has been demonstrated to be suitable for large-scale protein purification due to their high selectivity, stability, and economy. Also, the issue of dye leakage and process validation of large-scale dye-ligand chromatography has been discussed. Reactive dyes have also been applied in high performance liquid affinity chromatographic techniques for protein purification, as well as non-chromatographic techniques including affinity partition, affinity membrane separations, affinity cross-flow filtration, and affinity precipitation.