Blue-stained Proteins Research Articles

Post-staining electroblotting for efficient and reliable peptide blotting.

Post-staining electroblotting has been previously described to transfer Coomassie blue-stained proteins from polyacrylamide gel onto polyvinylidene difluoride (PVDF) membranes. Actually, stained peptides can also be efficiently and reliably transferred. Because of selective staining procedures for peptides and increased retention of stained peptides on the membrane, even peptides with molecular masses less than 2 kDa such as bacitracin and granuliberin R are transferred with satisfactory results. For comparison, post-staining electroblotting is about 16-fold more sensitive than the conventional electroblotting for visualization of insulin on the membrane. Therefore, the peptide blots become practicable and more accessible to further applications, e.g., blot overlay detection or immunoblotting analysis. In addition, the efficiency of peptide transfer is favorable for N-terminal sequence analysis. With this method, peptide blotting can be normalized for further analysis such as blot overlay assay, immunoblotting, and N-terminal sequencing for identification of peptide in crude or partially purified samples.

Blotting of Coomassie Blue-Stained Proteins from PAGE Gels to Transparencies.

A simple, convenient, and inexpensive method for long-term non-photographic storage of information present in electrophoresis gel, based on protein blotting patterns, is presented here.

Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis.

We statistically analysed various factors to get accurate estimates of protein quantities from two-dimensional gels. Yeast proteins were labelled with (35)S or stained with Coomassie Brilliant Blue G-250, and spots were automatically quantified with software packages Kepler, ImageQuaNT, Melanie 3.0 and Progenesis. The different software packages proved to have very similar performances. With (35)S-labelled actin spot as a reference, we studied the staining efficiency of colloidal Coomassie blue as a function of amino acid composition of the protein, and derived an equation to estimate the number of molecules per cell from blue-stained proteins. Absolute quantification of most glycolytic enzymes was carried out in two yeast strains.

Use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Automated liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis of >100 tryptic digests carried out on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separated, Coomassie Blue-stained proteins that were prepared by >50 different laboratories demonstrates that a commercial electrospray/quadrupole ion trap mass spectrometer and the tandem mass correlation algorithm developed by Eng et al. (Am. Soc. Mass Spectrom. 1994, 5, 976-989) provide an extremely robust and facile approach to routine protein identification. By requiring a minimum of two significant matches to peptides that would be predicted to be produced by the protease that was used, low pmol levels of proteins can be identified with high confidence while minimizing the probability of identifying the protease itself and/or the ubiquitous contaminant, keratin. Hence, in only 7% of the digests analyzed was keratin identified and in only 5% of the digests analyzed was the protease itself identified. In contrast, 58% of the analyzed samples were identified and, in many instances, multiple proteins were identified in the same sample. Although the median amount of digest analyzed was 6.1 pmol, the limit of sensitivity (as the instrument is configured with a flow rate of 4 microL/min) appears to be at the 500 fmol level. Since one of the primary reasons for not identifying a sample is that its sequence is not yet in the database searched, the utility of an LC MS/MS approach to protein identification will certainly increase in the future as the sequences of more genomes are completed.

Stoichiometry of the subunits of flavocytochrome b558 of the NADPH oxidase of phagocytes.

Flavocytochrome b558, the membrane-spanning component of the NADPH oxidase system of phagocytic cells, is composed of two subunits, p22phox and gp91phox (where phox stands for phagocyte oxidase). The stoichiometry of the subunits has been determined for purified flavocytochrome b556 by: (1) densitometry of Coomassie Blue-stained proteins separated by SDS/PAGE, (2) aromatic absorbance at 280 mm by the subunits after separation by gel filtration under denaturing conditions, (3) crosslinking studies with bis[sulphosuccinimidyl]suberate, where the molecular mass of the cross-linked complex was determined by Western blotting, and (4) radiolabelling of pure flavocytochrome b556 on lysine residues with 125I-labelled Bolton-Hunter reagent (N-succinimidyl-3-(4-hydroxy-5-[125I]iodophenyl)propionate), followed by SDS/PAGE and determination of the radioactivity on each subunit. The ratio of p22phox to gp91phox in the purified flavocytochrome b556 was related back to that in the neutrophil membrane by quantitative Western and dot-blotting to ensure that the stoichiometry was maintained during purification. These measurements showed that the two subunits were present in neutrophil membranes in a molar ratio of 1:1.

The induction of metachromasia and circular dichroism of coomassie brilliant blue R-250 with collagen and histone H1 is due to the low content of hydrophobic amino acid residues in these proteins.

Collagen and histone H1 are stained a pink-red color with Coomassie Brilliant Blue R-250 (Coomassie R) instead of the blue color of most proteins after SDS-PAGE. Spectrophotometrically, this metachromasia was characterized by an increase in the absorbance at 535 nm and a decrease in the absorbance at 600 nm. The ratio of the absorbance at 535 nm to that at 600 nm ranged from 1.5 to 2.5 for the pink-red-stained proteins and was about 1 for the blue stained proteins. In their amino acid composition, the pink-red-stained proteins collagen and histone H1 contained less than 11% of hydrophobic amino acid residues, whereas the five blue-stained proteins examined contained more than 25% of such residues. Collagen and histone H1 also induce circular dichroism (CD) of Coomassie R in the visible region with a different CD spectrum. In the case of native collagen, a CD (+) band at 530 nm with 10(5) molar ellipticity was observed, while the denatured collagen showed a CD(-) band at 530 nm. When the amino groups of the amino acid residues in collagen and histone H1 were converted into hydrophobic groups by fluorescamine treatment, these proteins stained bluer than pink-red and the induced CD was a lower intensity. This is the first report of the metachromatic interaction between a protein and Coomassie R that is accompanied by CD induction. This report also suggests that the induction of metachromasia and CD of Coomassie R was due to the low content of hydrophobic amino acid residues in the peptides.

Internal Sequences from Proteins Digested in Polyacrylamide Gels

A simple method for proteolytic digestion of Coomassie blue-stained proteins in a polyacrylamide matrix is presented. It consists of first reducing and alkylating the stained proteins with dithiothreitol and iodoacetamide in the presence of 0.1% sodium dodecyl sulfate and subsequent digestion with the endoproteinase LysC. The reduction and alkylation step was introduced since experiments with lysozyme and ribonuclease A showed that extremely complex peptide patterns were obtained if no precautions were taken to suppress disulfide bond formation during in-gel digestion of proteins. The advantage of this method is that no blotting step is required for generating internal sequences and that extensive proteolysis occurs which closely resembles that resulting from solution digests. The method has been successfully used to generate internal sequence data from low microgram quantities of proteins excised from 2-dimensional Coomassie blue-stained gels.

ADP-Ribosylation of Heterogeneous Ribonucleoproteins in HeLa Cells

Poly and mono(ADP-ribosyl) transferases catalyze the transfer of ADP-ribose from nicotinamide adenine dinucleotide (NAD) to acceptor proteins. Protein substrates of ADP-ribosylation reactions were investigated in human cervical carcinoma (HeLa) cells in the exponential phase of growth. Permeabilized cells were incubated with [32P]-NAD and ADP-ribosylated proteins were detected by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and autoradiography. Microsequencing of two coomassie blue-stained proteins corresponding to 32P-labeled proteins on autoradiographs revealed sequence identity with heterogeneous ribonucleoproteins (hnRNPs) A1 and A2/B1, consistent with the isoelectric points, molecular sizes, and 2D-PAGE map locations of these proteins. ADP-ribosylation of hnRNPs may thus serve to modulate the activity of these proteins in the nucleus.

Monosaccharide and oligosaccharide analysis of proteins transferred to polyvinylidene fluoride membranes after sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

We have developed an intermediate method toward the complete carbohydrate analysis of proteins, which should be universally applicable to all proteins and independent of sample matrix. Using only Coomassie Blue-stained proteins which have been electroblotted onto polyvinylidene fluoride membranes, we report a strategy for: (i) determining unequivocally whether a protein is glycosylated; (ii) obtaining a complete monosaccharide composition; (iii) oligosaccharide mapping which separates most forms according to size, charge and isomerity; and (iv) sequentially releasing and analyzing specific classes of oligosaccharides with endoglycosidases. The method was shown to be applicable to a variety of well characterized soluble glycoproteins and to the membrane-bound protein, the gastric H+, K(+)-ATPase. The monosaccharide composition of the H+,K(+)-ATPase revealed the absence of N-acetylneuraminic or N-glycolylneuraminic acids and a monosaccharide composition which indicated O-linked sugar chains. Oligomannosidic/hybrid and biantennary oligosaccharides were sequentially released and analyzed from one electroblotted band of recombinant tissue plasminogen activator using endo-beta-N-acetylglucosaminidase H and endo-beta-N-acetylglucosaminidase F2, respectively. Sialylated polylactosamine structures were identified and quantified by analyzing high performance liquid chromatography profiles of oligosaccharides first released by peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase and then treated with endo-beta-galactosidase, using a single, stained band of recombinant erythropoietin. This recombinant erythropoietin was found to contain eight times more tetrasialylated oligosaccharides than previously reported (Sasaki, H., Bothner, B., Dell, A., and Fukuda, M. (1987) J. Biol. Chem. 262, 12059-12076); 47% of released oligosaccharides were identified as polylactosamine structures.

Immunodetection after complete destaining of Coomassie blue-stained proteins on immobilon-PVDF

A technique that simplifies the localization of an immunodetectable protein in relation to the other electrophoresed proteins is described. Proteins are transblotted onto a polyvinylidene difluoride (PVDF) membrane and visualized by staining with Coomassie brilliant blue R-250, and a photograph of the protein pattern is taken. The Coomassie blue-stained PVDF membrane is then completely destained using a 25% acetic acid/50% methanol solution that allows subsequent immunostaining on the same membrane. The technique uses common laboratory reagents, is rapid, and has been shown to be applicable for a variety of proteins using both monoclonal and polyclonal antibodies and a variety of transblots.

Nuclear matrins: identification of the major nuclear matrix proteins.

A preparative two-dimensional polyacrylamide gel system was used to separate and purify the major Coomassie blue-stained proteins from the isolated rat liver nuclear matrix. Approximately 12 major proteins were consistently found. Of these, 5 proteins represented identified proteins, including nuclear lamins A, B, and C, the nucleolar protein B-23, and residual components of core heterogeneous nuclear ribonucleoproteins. The remaining eight major proteins termed the nuclear matrins consisted of matrin 3 (125 kDa, slightly acidic), matrin 4 (105 kDa, basic), matrins D-G (60-75 kDa, basic), and matrins 12 and 13 (42-48 kDa, acidic). Peptide mapping and two-dimensional immunoblot studies indicate that matrins D-G compose two pairs of related proteins (matrins D/E and F/G) and that none of the matrins resemble the nuclear lamins or any of the other major proteins detected on our two-dimensional gels. Subfractionation immunoblot experiments demonstrated the nearly exclusive localization of matrins F/G and other matrins to the nuclear matrix fraction of the cell. These results were further supported by indirect immunofluorescence microscopy that showed a strictly interior nuclear localization of the matrins in intact cells in contrast to the peripherally located nuclear lamins. We conclude that the nuclear matrins are a major class of proteins of the nuclear matrix interior and are distinct from the nuclear lamins.

Peptide mapping and internal sequencing of proteins electroblotted from two-dimensional gels onto polyvinylidene difluoride membranes : A chromatographic procedure for separating proteins from detergents

Direct sequence analysis of proteins electroblotted from two-dimensional polyacrylamide gels onto immobilizing matrices provides an efficient technique for obtaining N-terminal sequence data for proteins not amenable to purification by reversed-phase high-performance liquid chromatography (RP-HPLC). We present in this paper a procedure for obtaining peptide fragments from electroblotted proteins for internal amino acid sequence analysis. First, Coomassie Blue-stained proteins are extracted from polydivinylidene difluoride membranes, using a detergent mixture of sodium dodecylsulfate and Triton X-100. Proteins are then separated from the detergent mixture by a chromatographic procedure which relies on the ability of proteins to interact with certain reversed-phase sorbents at high organic solvent concentrations. Under these conditions, detergents and Coomassie Blue are not retained and pass through the column. Proteins are recovered by simultaneously: (i) introducing trifluoroacetic acid into the mobile phase and (ii) decreasing the organic solvent concentration. After proteolytic fragmentation, peptides are purified by microbore-column (1–2 mm I.D.) RP-HPLC for microsequence analysis.

Multiple phosphorylated variants of the high molecular mass subunit of neurofilaments in axons of retinal cell neurons: characterization and evidence for their differential association with stationary and moving neurofilaments.

The 200-kD subunit of neurofilaments (NF-H) functions as a cross-bridge between neurofilaments and the neuronal cytoskeleton. In this study, four phosphorylated NF-H variants were identified as major constituents of axons from a single neuron type, the retinal ganglion cell, and were shown to have characteristics with different functional implications. We resolved four major Coomassie Blue-stained proteins with apparent molecular masses of 197, 200, 205, and 210 kD on high resolution one-dimensional SDS-polyacrylamide gels of mouse optic axons (optic nerve and optic tract). Proteins with the same electrophoretic mobilities were radiolabeled within retinal ganglion cells in vivo after injecting mice intravitreally with [35S]methionine or [3H]proline. Extraction of the radiolabeled protein fraction with 1% Triton X-100 distinguished four insoluble polypeptides (P197, P200, P205, P210) with expected characteristics of NF-H from two soluble neuronal polypeptides (S197, S200) with few properties of neurofilament proteins. The four Triton-insoluble polypeptides displayed greater than 90% structural homology by two-dimensional alpha-chymotryptic iodopeptide map analysis and cross-reacted with four different monoclonal and polyclonal antibodies to NF-H by immunoblot analysis. Each of these four polypeptides advanced along axons primarily in the Group V (SCa) phase of axoplasmic transport. By contrast, the two Triton-soluble polypeptides displayed only a minor degree of alpha-chymotryptic peptide homology with the Triton-insoluble NF-H forms, did not cross-react with NF-H antibodies, and moved primarily in the Group IV (SCb) wave of axoplasmic transport. The four NF-H variants were generated by phosphorylation of a single polypeptide. Each of these polypeptides incorporated 32P when retinal ganglion cells were radiolabeled in vivo with [32P]orthophosphate and each cross-reacted with monoclonal antibodies specifically directed against phosphorylated epitopes on NF-H. When dephosphorylated in vitro with alkaline phosphatase, the four variants disappeared, giving rise to a single polypeptide with the same apparent molecular mass (160 kD) as newly synthesized, unmodified NF-H. The NF-H variants distributed differently along optic axons. P197 predominated at proximal axonal levels; P200 displayed a relatively uniform distribution; and P205 and P210 became increasingly prominent at more distal axonal levels, paralleling the distribution of the stationary neurofilament network.(ABSTRACT TRUNCATED AT 400 WORDS)

A protein associated with axon growth, GAP-43, is widely distributed and developmentally regulated in rat CNS

Development or regeneration of axons in several systems is accompanied by 20-100-fold increases in the synthesis of an acidic, axonally transported membrane protein with an apparent molecular weight of 43-50,000 (Benowitz and Lewis, 1983; Skene and Willard, 1981a, b), which we designate GAP-43. We have proposed that some step(s) in axon growth require production of GAP-43, and perhaps a small number of other "growth-associated proteins," at rates much higher than those typical of mature neurons. This hypothesis predicts that virtually all neurons synthesize GAP-43 at elevated levels during normal CNS development. Here we show that a protein similar to GAP-43 from regenerating toad nerves is prominent among the newly synthesized (35S-methionine-labeled) and total (Coomassie blue-stained) proteins in neonatal rat cerebral cortex and cerebellum, suggesting that synthesis of GAP-43 is indeed a common feature of many developing neurons. Synthesis and accumulation of the protein decline an order of magnitude as animals mature. Antibodies raised against the rat cortex GAP-43 also recognize electrophoretically similar proteins from regenerating toad optic nerves and from developing hamster sensorimotor cortex, indicating that structural features of GAP-43 are conserved in evolution. Cell-free translation of polyadenylated RNA from neonatal and adult cortex suggests that developmental regulation of GAP-43 synthesis is mediated largely through changes in mRNA abundance. These observations together suggest that developmental regulation of GAP-43 gene expression may be common to most vertebrate CNS neurons. GAP-43 remains detectable at a low level in adult rat cortex, and it co-migrates on two-dimensional gels with B-50, a synaptic membrane protein which is a preferred substrate for protein kinase C in adult brains. Phosphorylation of the protein by endogenous kinase(s) in vitro is 4-7-fold greater in growth cone membranes than in mature synaptic membranes, which raises the possibility that local modification of the protein in axon terminals may be synergistic with regulation of GAP-43 synthesis in the cell body.

A method to quantitate Coomassie blue-stained proteins in cylindrical polyacrylamide gels

A method for the quantitation of Coomassie blue-stained proteins in cylindrical polyacrylamide gels is described. It involves an elution of the dye with an 80% methanol solution in a sealed Pyrex tube at 100°C for 3 h and a measurement of its concentration at 585 nm. Using a 6.5% polyacrylamide gel and bovine serum albumin as a protein standard, the curve of absorbance of the dye solution as a function of the amount of protein was observed to be linear up to 30–40 μg of protein and as little as 0.8–1.0 μg of protein could be measured. The validity of the method was indicated by the values obtained for the relative proportions of the human erythrocyte membrane proteins. Using this method, the color yields of several proteins varying widely with respect to their size, amino acid composition, and carbohydrate content were determined in a 6.5% polyacrylamide gel. The results showed that they were generally the same except for proteins having a high carbohydrate content which were significantly lower.

The distribution of acidic coomassie blue-stained proteins from uninvolved human liver, hepatoma, normal colon, primary colon cancer, and colon metastases to the liver, determined by two-dimensional protein electrophoresis.

The distribution of Coomassie blue-stained proteins from uninvolved regions of 4 human livers, from 1 hepatocellular carcinoma, and from 4 samples each of uninvolved colon, primary adenocarcinoma of the colon, and colon cancer metastatic to the liver was analyzed by two-dimensional protein electrophoresis. From a comparison of acidic proteins between pI 3.5 and 6.5, we conclude (1) that the majority (66 of 82) of denoted acidic proteins from 4 normal liver samples were represented in the hepatocellular carcinoma. Fifty-one of 58 proteins denoted in the 4 colon samples were detected in each of the 4 primary colon cancers; (2) that the "normograms" of proteins from normal colon and normal liver differed in many details, and their dissimilar patterns identified the source of the sample; (3) that hepatoma and primary adenocarcinoma of the colon were easily distinguished by their distribution of proteins; (4) that colon cancer metastatic to the liver contained a majority (50/58) of acidic proteins enumerated in primary colon cancer. These results indicate that uninvolved liver and colon and their primary or secondary cancers can be identified by their distribution of electrophoresed acidic proteins.

Switching of beta- to alpha-tubulin phosphorylation in uterine smooth muscle of parturient rats.

Proteins from pregnant rat uterine myometrium, previously incubated in the presence of (32P)orthophosphate, were analyzed by one- and two-dimensional polyacrylamide gel electrophoresis and subsequent autoradiography. Electrophoretic patterns of Coomassie blue-stained proteins in preterm and labor myometria were indistinguishable. However, radioactivity incorporated into tubulin in preterm myometrium was predominantly associated with the beta-subunit, whereas in labor, the alpha-subunit was labeled. Endogenous phosphorylated alpha- and beta-tubulins were clearly identified on two-dimensional gel electrophoretograms by apparent molecular weights, isoelectric points, co-migration with marker brain tubulin, and reactivity to specific antitubulin antibodies. The antibodies were incubated with nitrocellulose sheets onto which the myometrial proteins were electrophoretically transferred from the two-dimensional gels. The switching in phosphorylation of beta- to alpha-tubulin in the labor myometrium appears to be a manifestation of estrogen action. The labor-specific phosphorylation changes occurred in parallel with changes in serum estradiol/progesterone ratios. Indeed, estrogen administered to ovariectomized rats caused the appearance of phosphorylated alpha-tubulin, and this effect was inhibited by progesterone. Although the significance of tubulin phosphorylation is not currently understood, the switching in phosphorylation from beta- to alpha-tubulin under estrogen domination may help clarify the role of microtubule phosphorylation.

In vitro phosphorylation of murine leukemia virus proteins: Specific phosphorylation of Pr65 gag, the precursor to the internal core antigen

In vitro phosphorylation of Nonidet P-40 disrupted murine leukemia virus with [γ- 32P]ATP showed that Pr65 gag, which is present as a relatively minor component (14% of total Coomassie blue-stained virus proteins), was the major (80% labeling) phosphorylated species. A small amount of 32P label (i.e., 3–9%) was associated with proteins whose mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis was the same as Pr40 gag, Pr27 gag, p12, and p10. In contrast, long-term (20 hr) in vivo phosphorylation with [ 32P]orthophosphate showed that p12 was the most highly phosphorylated viral protein species. In neither case did we find any label associated with the major virion proteins, p30, p15, or gp70. These results suggest that phosphorylation is specific for certain viral proteins and, further, that if Pr65 gag is packaged as an uncleaved polyprotein into virions it remains relatively unphosphorylated. We have also found that the kinase activity which phosphorylates Pr65 gag in vitro is tightly associated with immature core subparticles and can phosphorylate the exogenous substrate phosvitin. The same or an additional kinase activity can also be detected in the soluble fraction of detergent-disrupted virus using endogenous viral proteins or phosvitin as substrate. Based on an analysis of the tryptic peptide patterns of pPr65 gag phosphorylated in vitro and in vivo, it appears that the in vitro phosphorylation of Pr65 gag occurs at serine residues which are identical to or similar to those found for pPr65 gag in vivo, i.e., on pp12, as well as at another site. This other site is also probably on p12 since in vitro phosphorylated pPr65 gag when cleaved in vitro by the murine Pr65 gag proteolytic factor, produces as its initial product a phosphorylated vand that has the molecular weight of pPr27 gag and the antigenic determinants of p15 and p12.

On the relationship of CSF pleocytosis to immunoglobulin levels as estimated by different techniques

One might expect a positive correlation between the number of CSF lymphocytes and the relative amount of CSF IgG, especially in cases of local synthesis of IgG within the CNS. However, previous attempts at correlating the number of CSF lymphocytes with IgG levels have yielded varying results. Since it is known that the estimation of CSF IgG levels can vary according to the method of immunoglobulin determination used, we decided to perform the analyses by three separate methods: (1) the commonly used, immunoprecipitation technique of radial immunodiffusion; (2) physico-chemical separation on the basis of hydrated size/charge using alkaline electrophoresis through the molecular sieving effects of polyacrylamide gels, followed by densitometry of the γ region of Coomassie Blue-stained proteins; (3) separation into constituent Ig heavy chains and light chains on the basis of unfolded chain lengths by molecular sieving using sodium dodecyl sulphate (SDS), followed by densitometry of heavy chains of immunoglobulins having been labelled with the fluorescent dye dansyl chloride. Our results show a correlation of white count with the latter two techniques but not the former. Possible reasons for discrepancies in the literature are discussed with regard to the peculiar physical properties of the selected CSF IgG molecules.