Simultaneous electrophoretic analysis of proteins of very high and low molecular mass using Tris‐acetate polyacrylamide gels

To separate and analyze giant and small proteins in the same electrophoresis gel, we have used a 3–15% polyacrylamide gradient gel containing 2.6% of the crosslinker bisacrylamide and 0.2 M of Tris‐acetate buffer (pH 7.0). Samples were prepared in a sample buffer containing lithium dodecyl sulphate and were run in the gel described above using Tris‐Tricine‐SDS‐sodium bisulfite buffer, pH 8.2, as electrophoresis buffer. Here, we show that this system can be successfully used for general applications of SDS‐PAGE such as CBB staining and immunoblot. Thus, by using Tris‐acetate 3–15% polyacrylamide gels, it is possible to simultaneously analyze proteins, in the mass range of 10–500 kDa, such as HERC1 (532 kDa), HERC2 (528 kDa), mTOR (289 kDa), Clathrin heavy chain (192 kDa), RSK (90 kDa), S6K (70 kDa), β‐actin (42 kDa), Ran (24 kDa) and LC3 (18 kDa). This system is highly sensitive since it allows detection from as low as 10 μg of total protein per lane. Moreover, it has a good resolution, low cost, high reproducibility and allows for analysis of proteins in a wide range of weights within a short period of time. All these features together with the use of a standard electrophoresis apparatus make the Tris‐acetate‐PAGE system a very helpful tool for protein analysis.     

Chromatographic and electrophoretic methods used for analysis of milk proteins.

Current knowledge of milk proteins and their behavior in dairy foods is based on early applications of chromatography and electrophoresis. Electrophoretic identification of the number and genetic variety of milk proteins inaugurated a research effort in which chromatographic techniques were successfully applied to the isolation of each milk protein, thus facilitating the characterization and further study of milk and dairy products. This review focuses on recent applications of chromatography for separations and analysis and on analytical applications of electrophoresis.     

Two-dimensional electrophoretic analysis of human milk proteins

Identification of human milk proteins and formulation of a two-dimensional map is a first step in a project which intends to survey human milk proteins by two-dimensional electrophoresis. Thirty-four proteins have been identified using the Iso-Dalt method of separation and Western blot with immunoprobes. Identification confirms that milk is species-specific, and, therefore, breast feeding confers a decided advantage for the infant. Using antisera for identification has revealed relationships between molecules which have not been previously noted. The antibody recognizes a common epitope between the IgA alpha chain and lactoferrin, and between the IgD d chain and beta casein. Milk protein concentrations vary longitudinally, diurnally, and individually. Identification of the proteins contributes meaning to the varying patterns. Knowledge of human milk proteins will help to elucidate human nutrition and health needs.     

Time-based analysis of silver-stained proteins in acrylamide gels

Silver staining of proteins after PAGE often remains the method of choice in many laboratories. Nevertheless, it is known that quantification of protein levels is keenly restricted to a small range of protein concentrations leading to an over- or underestimation of protein amounts. To overcome this, a time-based analysis method was developed to avoid the saturation effect of the silver-staining reaction, thus resulting in an improved dynamic range of the gel image produced and therefore better quantification of proteins. Instead of the well-known end-point image analysis, gray intensities of time series images of a developing gel are determined and times until a threshold gray value is reached are calculated. These times are used to calculate a new grayscale image which can be analyzed using commercial image processing software.     

Two-dimensional electrophoretic analysis of nuclear proteins from human tumors

During the last decade several strategies have been developed to identify proteins which could serve as markers in tumor biology. One avenue of great promise to detect such proteins seems to be the separation of prefractionated organelles from tumor cells by high resolution two-dimensional electrophoresis. Using detergent-lysed nuclei from several human tumor cell lines, especially from brain tumors, and two-dimensional electrophoresis, we analyzed the nuclear protein pattern obtained after sequential salt extraction of tumor cell nuclei. In addition to proteins occurring in all tumor cell lines, the pattern of different tumor cell lines exhibits considerable differences when proteins were visualized by silver staining, thus emphasizing the specificity of nuclear proteins with respect to the cell type. Even quantitative variations of the nuclear phosphoproteins 23/4 were detectable, indicating a potential correlation between their synthesis/phosphorylation and the proliferation behavior of tumor cells. The data indicate that nuclear proteins with their distinct heterogeneity and tissue specificity may represent a powerful source in determining tumor-specific proteins. The extent of chromosomal protein heterogeneity may be additionally increased by their covalent modification by nuclear kinases; therefore, tumor-specific nuclear proteins may occur as quantitative and qualitative variations.     

Two-dimensional electrophoretic analysis of Corynebacterium glutamicum membrane fraction and surface proteins

An improved protocol for the two-dimensional analysis of proteins of the Corynebacterium glutamicum cytoplasmic membrane fraction is described. By use of increased 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) concentrations (2-4%) and an optimized electrophoresis protocol, horizontal streaking of proteins of the cytoplasmic membrane fraction was almost completely avoided. More important, in contrast to a previously published method, both a sample tray and IPG-phor isoelectric focusing unit can be used for the in-gel application of proteins. The described protocol was also found to be suitable for hydrophilic cytoplasmic proteins. Additionally, the preparation and analysis of C. glutamicum cell surface proteins is described. Proteins were extracted with lauroyl sarcosinate and 100-120 spots were separated on two-dimensional (2-D) gels in comparison to 18-20 spots observed previously by standard sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). C. glutamicum proteins can now be separated into three distinct fractions resembling different functional units of the bacterial cell.     

Two-dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays

Two-dimensional electrophoresis (2-DE) is known as the most effective as well as one of the simplest methods for separating proteins. However, a few hundred plant leaf proteins out of thousands visualized on a 2-DE gel can be identified by chemical analysis due to the presence of ribulose bisphosphate carboxylase/oxygenase (Rubisco) that limits protein loading. We describe the extraction and fractionation technique with polyethylene glycol (PEG) to analyze rice leaf proteins. Rice proteins were extracted with Mg/NP-40 extraction buffer. The Mg/Nonidet P-40 (NP-40) buffer extract was further fractionated with PEG into three fractions: 10% PEG and 10-20% PEG precipitants and the final supernatant fraction that was precipitated with acetone. Rubisco, the most abundant rice leaf protein, was enriched in the 20% PEG precipitant. This fractionation technique analyzed at least 2,600 well-separated protein spots and exhibited less than 1.2% of noticeable overlapping spots. An immunological approach was used to verify the efficiency whether PEG fractionation technique can detect or enrich signal transduction components such as Galpha, ADP ribosylation factor, small GTP binding protein and 14-3-3. The ADP ribosylation factor (ARF) and Galpha were only detected in the PEG supernatant fraction not in the total protein fraction. The small GTP binding protein (Rab 7) was identified in the 10% PEG fraction and only faintly in the total protein fraction. The 14-3-3 protein was detected in all fractions but was especially prevalent in the 20% PEG fraction.     

Capillary electrophoretic behaviour of humic substances in physical gels

We investigated the principles of the capillary electrophoretic behaviour of humic substances (HSs) in physical gels. Long chain (Mr 4000, 6000 and 20,000) polyethylene glycols (PEGs) at concentrations above their entanglement threshold caused the separation of HS fractions according to molecular size differences. Close linear relationships between effective mobilities and mean apparent molecular masses were observed at PEG concentrations between 2.5 and 15%. The efficiency of the separation does not increase in gels of increasing polymer concentrations. The possibility of interactions between HSs and gel-forming polymers was also investigated. Short chain (Mr 400) PEGs, added to the buffer at concentrations from 2.5 to 12.5%, increased the migration times of all HS fractions, but no separation was obtained even at large polymer concentrations, showing that gel formation was essential for the separation. In 2.5% polyvinyl alcohol (PVA) 49 000 all fractions show two unresolved, but well defined peaks. This separation is probably artefactual and depends on the relative concentration of HSs and PVA, as the relative abundance of the peaks changes with the sample concentration.     

Utilizing the pH hysteresis effect for versatile and simple electrophoretic analysis of proteins in bare fused-silica capillaries

The analysis of peptides and proteins by CE is often desirable due to low sample consumption and possibilities for nondenaturing yet highly effective separations. However, adsorption to the inner surfaces of fused-silica capillaries often is detrimental to such analyses. This phenomenon is especially pronounced in the analysis of basic proteins and proteins containing exposed positively charged patches. To avoid wall interactions numerous buffer additives and static and dynamic wall coating principles have been devised. We previously showed (J. Chromatogr. A 2004, 1059, 215-222) that CE of the basic protein beta2-glycoprotein was rendered possible by an acidic pretreatment step, and we attributed this observation to the so-called pH hysteresis effect that influences the time for pH equilibration of the capillary wall and thus the effective wall charge and the electroosmotic mobility. We here investigate the effects of different pretreatment techniques on EOF values and on the rate of the deprotonation of silanol groups when performing the electrophoresis at neutral pH. We show the utility of this simple approach for the CE analysis of a number of basic proteins in plain silica capillaries at physiological pH.     

Hydrocolloid gels of polysaccharides and proteins

Recent developments from 1997 to 2000 in hydrocolloid gels which consist of dispersed phase (polysaccharide or protein) and dispersing medium (water) are reviewed in the present paper. Gels and gelling processes of polysaccharides such as gellan gum, methylcellulose, xyloglucan, curdlan, konjac glucomannan and starch are described. Fluid gels and galactomannan gels prepared by freeze-thaw cycling are also described. Effects of pH and ionic strength on the gelation of proteins such as casein and β-lactoglobulin are described. Fractal treatment is introduced to study the structure–property relationship for globular protein gels. Gels formed by different hydrocolloids are also described briefly.     

Equipment for rapid homogenization of high numbers of plant tissue for electrophoretic analysis of proteins.

A homogenizing system was developed to process multiple samples of various plant tissues. The equipment consists of a motor-driven stainless steel homogenizer that fits perfectly into a hole of a disposable plate. Hard plant material like melon or squash seeds (maximal length of 1.4 cm) could be homogenized within 10 s by forcing the homogenizer towards the bottom of a 24- or 48-well tissue culture plate. Smaller seeds could be homogenized within 10 s in a similar way using a 96-well tissue culture plate. Leaf tissue, or other types of soft plant tissue, could be homogenized with the same equipment. For homogenization of small samples, e.g. pistils of small flowers, a 60-well Terasaki plate was used. For homogenization of several hundreds of leaf tissue samples, an apparatus was developed that contains 12 homogenizers driven simultaneously by an electromotor. A tissue culture plate containing 96 leaf samples could be handled in this way in less than 10 min. The performance of the equipment was evaluated by analyzing homogenates of several types of plant tissue by different electrophoretic techniques.     

Capillary electrophoretic analysis of wild type and mutant Proteus penneri outer membrane proteins

In this study the virulence factors, outer membrane proteins (OMP), lipopolysaccharides (LPS), hemolysin, and the in vivo and in vitro virulence of wild-type Proteus penneri 357 and its two isogenic mutant variants--a transposon and a spontaneous mutant--were examined. The OMPs of these variants were analyzed by a new and fast technique, "dynamic sieving" capillary electrophoresis (CE). The OMP profiles were dominated by two peaks (39 and 43 kDa). In the P. penneri clone examined, both the transposon and the spontaneous mutations induced significant changes in the OMP patterns (in the relative percentage of the dominant proteins). CE was suitable for the comparative analysis of bacterial protein patterns in the genetic variants of this strain, and provided valuable results in connection with the bacteriological virulence. The LPS composition of the genetic variants also showed alterations. The wild type of P. penneri 357 showed a typical ladder pattern, an "S" form, and the mutants possessed "R" LPS patterns (only few bands) in the gels. In the bacteriological virulence tests the wild type of P. penneri 357 was virulent in the in vivo, and toxic in the in vitro assays, while both mutants showed neither toxicity nor pathogenicity.     

Atomic-force-controlled capillary electrophoretic nanoprinting of proteins

The general nanoprinting and nanoinjection of proteins on non-conducting or conducting substrates with a high degree of control both in terms of positional and timing accuracy is an important goal that could impact diverse fields from biotechnology (protein chips) to molecular electronics and from fundamental studies in cell biology to nanophotonics. In this paper, we combine capillary electrophoresis (CE), a separation method with considerable control of protein movement, with the unparalleled positional accuracy of an atomic force microscope (AFM). This combination provides the ability to electrophoretically or electroosmotically correlate the timing of protein migration with AFM control of the protein deposition at a high concentration in defined locations and highly confined volumes estimated to be 2 al. Electrical control of bovine serum albumin printing on standard protein-spotting glass substrates is demonstrated. For this advance, fountain pen nanolithography (FPN) that uses cantilevered glass-tapered capillaries is amended with the placement of electrodes on the nanopipette itself. This results in imposed voltages that are three orders of magnitude less than what is normally used in capillary electrophoresis. The development of atomic-force-controlled capillary electrophoretic printing (ACCEP) has the potential for electrophoretic separation, with high resolution, both in time and in space. The large voltage drop at the tip of the tapered nanopipettes allows for significant increases in concentration of protein in the small printed volumes. All of these attributes combine to suggest that this methodology should have a significant impact in science and technology.      

Evaluation of the arsenic binding capacity of plant proteins under conditions of protein extraction for gel electrophoretic analysis

As prerequisite for the investigation of arsenic-binding proteins in plants, the general influence of different extraction parameters on the binding behaviour of arsenic to the plant protein pool was investigated. The concentration of the extraction buffer affected the extraction yield both for proteins and for arsenic revealing an optimal buffer concentration of 5 mM Tris/HCl, pH 8. The addition of 1 or 2% (w/v) SDS to the extraction buffer produced a two- to threefold enhancement of the total protein extraction yield but strongly suppressed the simultaneous extraction of arsenic from 80 ± 8% extraction yield obtained without SDS to 48 ± 2% in presence of 2% (w/v) SDS. The arsenic binding capacity of the protein fraction obtained after extraction with Tris buffer and protein precipitation by trichloroacetic acid in acetone was estimated to be 1.4 ± 0.6% independently on the original spiking concentration of arsenic provided in the form of monomethylarsonate to the extracts. Due to the low total protein concentrations of the plant extracts that varied in the range from 75 to 412 μg mL⁻¹ depending on the extraction parameters, high arsenic concentrations of 263-1001 mg (kg protein mass)⁻¹ resulted for spiking concentrations of 10 mg As L⁻¹. The optimized protein isolation procedure was applied to plants grown under arsenic exposure and revealed a similar arsenic binding capacity as for the spiked protein extracts.     

Recombinant autofluorescent landmarks for standardization of electrophoretic migration of proteins

Unequivocal identification of unknown protein spot patterns in two-dimensional (2-D) electrophoresis still represents a major problem when performing comparative studies of different 2-D electrophoresis gels. Inhomogeneity of gels due to variations in the gel casting procedure, electroendoosmosis and heterogeneity of proteins are major contributions to variations in migration patterns. By fusing green fluorescent protein to a number of well-defined selected proteins (human lysozyme, initiation factor 5a (EIF5a), rapamycin-selective 25 kDa immunophilin (FKBP25), and heat shock protein 90 beta (hsp90)), the isoelectric points and the molecular mass were designed. Proteins were additionally tagged with the FLAG tag enabling rapid purification by immunoaffinity chromatography. The fusion proteins were expressed intracellularly in yeast to avoid heterogeneity caused by post-translational modifications. The quality and applicability was tested in 1-D and 2-D electrophoresis. Sharp bands or symmetric spots were obtained. The proteins are considered as a new generation of reference proteins for electrokinetic separation methods.     

Distortion of the electrophoretic titration curves of some proteins

The electrophoretic titration curves of complex mixtures of vitamin K-dependent human blood proteins and proteins of Bothrops asper venom were investigated. In both protein mixtures some curves exhibited marked distortions such as additional maxima and minima when Pharmalyte 3-10 carrier ampholytes were used for isoelectric focusing in agarose gels. The distortions result from an unspecific interactions between some carrier ampholyte constituents with particular proteins. The interacting carrier ampholyte components could be completely removed by binding to albumin and ultrafiltration through a UM-2 Amicon membrane with resultant regular titration curves. The interacting carrier ampholyte species were only partially removed by ultrafiltration through a UM-2 membrane without incubation with albumin.     

Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two-dimensional gels and using one-dimensional gels for insoluble and large proteins.

The number of unique protein species in proteomes from a single mammalian cell type is not well defined but is likely to be at least 10000-20000. Since standard-size two-dimensional gels typically resolve only about 1500 to 3000 spots, they merely analyze a small portion of these proteomes. In addition, all insoluble proteins and typically proteins > 100 kDa are seldom resolved on two-dimensional (2-D) gels. The current study demonstrates the feasibility of an overall strategy for more comprehensive quantitative comparisons of complex proteomes derived from physiological fluids or mammalian cell extracts. A key feature of this approach is to prefractionate samples into a few well-resolved fractions based on the proteins' isoelectric points (pIs) using microscale solution isoelectric focusing. These fractions are then separated on narrow pH range two-dimensional gels approximately +/- 0.1 pH unit wider than the prefractionated pool. When this prefractionation approach is applied to complex mammalian proteomes, it improves resolution and spot recovery at high protein loads compared with use of parallel narrow pH range gels without prefractionation. The minimal cross-contamination between fractions allows quantitative comparisons in contrast to most alternative prefractionation methods. In addition, complementary data can be obtained by parallel analysis of the solubilized fraction on high-resolution large-pore-gradient one-dimensional gels followed by mass spectrometric identification to analyze proteins between 100 and approximately 500 kDa. Similarly, insoluble proteins can be analyzed using large-pore gels for large proteins and 10-12% one-dimensional sodium dodecyl sulfate (SDS) gels for smaller proteins. Together, these strategies should permit more reliable quantitative comparisons of complex mammalian proteomes where detection of at least 10000 protein spots is needed in order to analyze the majority of the unique protein species.     

Separation of chromosomal length DNA molecules: pneumatic apparatus for rotating gels during electrophoresis

The maximum length of DNA molecules that can be separated by gel electrophoresis can be increased greatly by periodically altering the direction of the electric field with respect to the gel by an angle that exceeds 90 degrees. One method involves rotating the gel by the desired angle in alternate directions periodically during electrophoresis. We describe a modification of the rotating gel electrophoresis apparatus developed by Serwer (Electrophoresis 1987, 8, 301-304) that uses a pneumatic rotary actuator instead of a stepping motor, hence reducing the cost by about 50%. Other advantages of our design are a lower center of gravity that makes the apparatus more stable and the removal of all electrical power from beneath the fluid-filled electrophoresis chamber. We present data demonstrating the separation of chromosomal length DNA molecules from Saccharomyces cerevisiae strain 334 into 14 resolved bands in parallel lanes.