Enhancement of resolution in two-dimensional gel electrophoresis and simultaneous resolution of acidic and basic proteins

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.

Analysis of the proteins of aging Caenorhabditis elegans by high resolution two-dimensional gel electrophoresis

The metabolic rate decreases dramatically as a function of age in the nematode worm Caenorhabditis elegans. Superoxide anion production, which is tightly linked to oxygen consumption, and thus to metabolic rate, drops to a 20-fold lower level in 10-day-old, senescent worms, as compared to 4-day-old young adults. In a long-lived mutant strain of the same species metabolic activity is much better preserved. High resolution two-dimensional gel electrophoresis was employed to study alterations in the protein profile, correlating with changes of metabolic activity. Surprisingly, few proteins show age- or age- and strain-specific variations of spot intensity. The abundance of the huge majority of proteins displayed on these gels remains unaltered, irrespective of age and strain differences. These results imply that there are no major age-related alterations of proteins due to faulty protein synthesis or free radical attack, and that age-related changes in the rate of protein synthesis and breakdown must be strictly coordinated throughout the aging process.

Sponge-like electrophoresis media: mechanically strong materials compatible with organic solvents, polymer solutions and two-dimensional electrophoresis

A new range of sponge-like media, called "electrophoresis sponges", is presented. They differ from electrophoresis gels primarily in that they are mechanically stronger, providing a permanent structure of directly measurable pore size dimensions. The new media are similar to capillary electrophoresis in terms of pore size range, they are mechanically strong with directly definable walls, and are compatible with polymer solutions. The sponges differ from capillary electrophoresis in that they provide large numbers of channels, with a corresponding high load capacity for simultaneous runs in multiple channels and they are compatible directly with multi-dimensional separations, such as high resolution two-dimensional electrophoresis. Furthermore, they can be molded (or cut) to any shape and retain that shape, they can be handled more easily than gels, they can be reused if necessary, they can be distributed in the same format between labs easily, and they can be stored indefinitely. Chemically, they can be hydrophilic or hydrophobic, with capability ranging from inert to reactive surfaces. Pore sizes can range from the sub-nanometer to 100 micron scale. Results with various hydrophobic sponges are reported for the carrier ampholyte-based isoelectric focusing of proteins. Broad and narrow pH gradients are established in the sponges that are more linear than those achieved with polyacrylamide gels. One- and two-dimensional electrophoresis of proteins has been achieved, for example with high resolution of the charge isomers of the haptoglobin beta chain, using sponge-based isoelectric focusing. Isoelectric focusing is about threefold faster in the tested sponges than in equivalent polyacrylamide gels. This improved speed is probably related to the larger sponge pores.(ABSTRACT TRUNCATED AT 250 WORDS)

Two-dimensional electrophoresis of basic proteins with equilibrium isoelectric focusing in carrier ampholyte-pH gradients

A modified procedure for the two-dimensional electrophoretic analysis of basic polypeptides is described. This method uses isoelectric focusing with carrier ampholytes in the first dimension, and sodium dodecyl sulfate-electrophoresis in the second dimension. Counteraction of the cathodic drift is achieved by glass tube treatment (silanization), electrolyte modification (use of weak bases and acids), protection of the catholyte from carbon dioxide, and the addition of glycerol to the gel mix. Better resolution and reproducibility are obtained than with nonequilibrium pH gradient electrophoresis, since quasi equilibrium focusing can be obtained.

Biomedical relevance of two-dimensional protein mapping

State-of-the-art and future perspectives are discussed for the application of two-dimensional protein maps to basic medical research and routine clinical chemistry problems. Despite the technical advances that allow effective processing of a large number of samples and the refinement of devices and procedures for image analysis, at present two-dimensional maps are mostly confined to research purposes, i.e. to the inventory of normal constituents of body fluids and tissues on the one hand, and to qualitative-quantitative alterations of some protein spots in a number of instances (genetic, degenerative, infectious or xenobiotic diseases) on the other. It is hoped that in some instances a single primarily affected component will be able to be identified and then specifically tested (for instance by immunological means) as a diagnostic marker, but complex pathological patterns would still require the analysis of a large number of peptides at the resolution level only afforded by two dimensions. Further simplification of the protocols, for example with ready-made gels, and data reduction systems might then allow the application of the technique to be extended to general clinical laboratories.

Image analysis techniques for automatic evaluation of two-dimensional electrophoresis

Techniques for automatic analysis of two-dimensional electrophoresis gels by computer-aided image analysis are described. Original gels or photographic films are scanned using a laser scanner and the files are transferred to a microcomputer. The program package first performs a compression and preevaluation of the files. Spot identification and quantification is performed by the chain code algorithm after appropriate zooming and cutting. Labeling facilitates spot identification and quantification in numerical and graphical (pseudocolor) representation on peripheral devices for camera ready output. Interpolation between measured basepoints is performed by cubic spline algorithms which are automatically switched on and off, depending on the need by the program. High speed analysis and graphic representation is achieved using fast Assembler language routines rather than high level languages. One-dimensional gels can be analyzed using the same software. Spot matching between parallel two-dimensional gels has not yet been implemented.

Systematic analysis of the total proteins of a mammalian organism: principles, problems and implications for sequencing the human genome

High-resolution two-dimensional electrophoresis (2-DE) has reached a technological level that allows us to resolve most of the numerous unknown protein species of a mammalian organism if appropriate strategies are used. We will discuss the problems of classification and characterization of proteins and propose a systematic approach to the analysis of the total protein complex. Both a comprehensive as well as a pragmatic approach towards systematic analysis have been considered. A "complex protein database" is suggested and considered with regard to various uses. A systematic analysis of the mouse proteins has been started and some of the preliminary results are summarized here. In particular, genetic properties of the proteins were investigated and are presented in order to demonstrate the significance of a systematic analysis of proteins for research and practical application (e.g. mutagenicity testing). A concept is presented for sequencing the coding DNA of mouse and man, starting with a systematic analysis of mouse proteins and then using two recently developed methods - microsequencing of proteins from spots of 2-DE protein patterns, and utilization of the relatively short N-terminal sequences obtained - to produce the corresponding cDNA's of these proteins.

The use of ultrathin-layer polyacrylamide gel isoelectric focusing in two-dimensional analysis of plant and fungal proteins

Although use of ultrathin polyacrylamide gel isoelectric focusing in the first dimension of two-dimensional analysis bestows a number of advantages, it has been little used by the plant science community. Nonstandardization along with problems unique to the format have probably delayed wider adoption. Relevant parameters were therefore tested in order to optimize resolution, reproducibility, economy and ease of use. Ultrathin-layer gels (200 microns in this study) used in the first dimension require a semirigid backing for support. Widely available matte-finished thin polyester film without chemical pretreatment was found to bind the gel adequately. The gel adheres to the film through all processing steps, yet, if desired, can be easily transferred to Whatman 3MM paper for special applications such as Western blotting. The ultrathin first-dimensional gels can be quickly dried on the polyester backing for convenient handling and long term storage. Strips cut from the dried gel for use in the second dimension are more easily manipulated than their tube format counterparts. The difficulty of disrupting and recovering microsamples of labeled leaf and root tissue prompted the invention of an efficient and simple communition device. An economical and efficient silver stain process is also described. This analytical technique was applied in an attempt to detect resistance gene products in different genetic backgrounds of maize. Although the ultrathin flatbed format provides as good as or better resolution than the tube gel system, the level of sensitivity was still inadequate to reveal the apparently rare resistance gene product.

Dual-label autoradiographic analysis of human skin fibroblast and myoblast proteins by two-dimensional polyacrylamide gel electrophoresis using immobilised pH gradients in the first dimension

Horizontal two-dimensional polyacrylamide gel electrophoresis with immobilised pH gradients in the first dimension has been applied to the analysis of human skin fibroblast and muscle myoblast total cell proteins. Excellent two-dimensional separations of skin fibroblast proteins were obtained using pH 4-10 immobilised pH gradient gels with a long interelectrode distance (16 cm), but resolution was degraded, particularly of the more acidic proteins, by the use of shorter (10 cm) gels. Improved resolution of acidic and basic proteins was obtained using separate pH 4-7 and pH 7-10 immobilised pH gradient gels respectively in the first dimension. Two-dimensional protein maps of skin fibroblast proteins were visualised both by silver staining and by autoradiography of samples labelled synthetically with [35S]methionine. Horizontal two-dimensional electrophoresis, using pH 4-7 and pH 7-10 immobilised pH gradient gels in the first dimension, was applied to the analysis of protein samples from skin fibroblasts and muscle myoblasts dual-labelled synthetically with [35S]methionine and [75Se]selenomethionine in an attempt to identify sets of proteins specific to each cell type. In addition, two-dimensional maps or protein samples derived from normal individuals and patients with Duchenne muscular dystrophy were compared to search for protein changes associated with the disease state. Although sets of qualitative protein spot differences were observed by visual inspection of the two-dimensional gels, more rigorous qualitative and quantitative analysis of the patterns using a computerised analysis system will be required to obtain the maximum amount of information from these data.

A comparative study of protein synthesis by keratinocytes and fibroblasts in vitro using two-dimensional gel electrophoresis and dual isotope autoradiography

A procedure is described for the detection of keratinocyte specific proteins. Fibroblasts and keratinocytes were isolated from human skin and radiolabelled in vitro. Samples were separated by two-dimensional polyacrylamide gel electrophoresis to compare the proteins synthesised by the different types of cultured skin cells. Dual label autoradiography of samples radiolabelled with [35S]methionine and [75Se]selenomethionine was used to identify keratinocyte specific proteins. We report 45 keratinocyte-specific components and identify some of these proteins. The differential expression of these proteins and their relevance to epidermal differentiation are discussed.

Properties of thin-rod immobilized pH gradients

Immobilized pH gradient gel rods, 1.5 mm in diameter, were cast with a manifold connected to high-precision burettes. The reproducibility of gel length was ca. 1.7 mm. The average standard deviation sigma x for spot position was 2 mm after one-dimensional and 5.8 mm after two-dimensional runs. In order to bring to completion the elution of the salt fronts into the electrode compartments, carrier ampholytes had to be included in the gel formulation at concentrations of at least 0.5-1%, depending on the pH range. The presence of carrier ampholytes, however, was troublesome in two respects: the gel tended to shrink and the cathodic bands drifted with time. Ionic components in the sample were tolerated up to the following concentrations: NaCl 8 mumoles, sodium dodecyl sulfate 10 micrograms per tube. In presence of non-ionic detergents, the gels moved as a whole towards the cathode.

Additives for immobilized pH gradient two-dimensional separation of particulate material: comparison between commercial and new synthetic detergents

We describe the synthesis of two detergents, L and A15, whose performances as solubilizing agents and as additives in the first-dimension step of a two-dimensional separation are compared with those of some commercial compounds, i.e., Nonidet P-40, 3-[(3-cholamidopropyl)dimethylammonio]propanesulfonate(Chaps), and sulfobetaine, on three membrane protein preparations: rat RBC ghosts, beef kidney microvilli, and spinach thylakoids. L is 3-]3-dodecylamidoprophylcbdimethylammonio propane-1-sulfonate; owing to the substitution of a dodecylamido for the dodecyl residue of SB 3-12, the concentration of urea compatible with 2% detergent increases from 4.5 M for the parent molecule up to 7 M. With all three biological samples on which the panel of different detergents has been tested in parallel, L + urea scores as the most effective solubilization medium. On red blood cells a notable qualitative difference is observed with the selective extraction by L as well as by N-dodecyl-N,N-dimethylammonio-3-propanesulfonate of a major protein (pI = ca. 5.5, Mr = ca. 100,000). A15 is derived from a tertiary amine, with one alkylic substituent (either C11 or C13) and two poly(ethylene oxide) tails (totaling 15 ethoxy residues), which is reacted with propane sultone. Approximately 30% of the product corresponds to the N-adduct and is a truly zwitterionic detergent, while 60% is an O-derivative and still contains a titratable amino group (with a pK of 7.2). A15 can thus be used for isoelectric focusing on immobilized pH gradients, as in this work, but would not be compatible with carrier ampholyte isoelectric focusing.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Lectin blotting of human muscle. Identification of a high molecular weight glycoprotein which is absent or altered in Duchenne muscular dystrophy

Using a combination of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting, a high molecular weight Ricinus communis I (RCA I)-binding glycoprotein (approx. Mr 370000) has been identified in human muscle that is consistently altered or absent in muscle from patients with Duchenne muscular dystrophy (DMD). In addition, a Mr 54000 RCA I-binding glycoprotein was identified in 4 out and 8 DMD muscle samples that was not present in normal muscle. The possibility that the Mr 370000 glycoprotein could be a muscle membrane glycoprotein which is altered or absent in DMD is discussed.

A simple and economical method for studying protein phosphorylation in vivo in the rat brain

A simple and economical procedure, capable of routine application, is described for the labelling of cerebral phosphoproteins in vivo. [32P]Orthophosphate, in high concentration, was infused into selected brain areas of anaesthetised rats under stereotaxic control. The animals were frozen with liquid N2 and the labelled tissue punched out of frozen thick sections. [32P]Polypeptides were analysed by high-resolution two-dimensional gel electrophoresis. Several phosphoproteins on the gels were provisionally identified, including synapsin I, MAP-2 and an 82-87 kdalton substrate of protein kinase 'C'.

Changes in protein phosphorylation during the maturation of mammalian oocytes in vitro

Cumulus-enclosed sheep oocytes were cultured in gonadotrophin-containing medium for up to 9 hr and were then incubated for 3 hr in the presence of [32P]phosphate. The incorporation of 32P into TCA-insoluble material was measured, and oocyte proteins were separated by one- and two-dimensional gel electrophoresis. Incorporation of [32P]phosphate into protein increased after 3 hr culture and again after 9 hr, the time of germinal vesicle breakdown (GVBD). Qualitative and quantitative changes in the phosphorylation of proteins occurred over the 12-hr period studied. One of the most prominent changes was the appearance of a band of Mr 33,000, which was absent at 0-3 hr but appeared with increasing intensity with longer periods of culture. Two-dimensional electrophoresis revealed that the bulk of material in this band was a neutral polypeptide. No significant incorporation of [32P]phosphate was found in ribosomal extracts of oocytes.