Western blots using stained protein gels.

A general method is described for the electrophoretic transfer of proteins from stained gels to membranes and subsequent Western detection of specific proteins on the stained membranes. Proteins are separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, and the gels are stained using either of two different methods followed by electrophoretic transfer to nitrocellulose or Immobilon-P membranes. The transferred proteins remain stained during immunodetection, providing a set of background markers for protein location and size determination.     

Basic nuclear proteins in the aquatic fungus Achlya ambisexualis.

The complement of basic chromosomal proteins in the aquatic fungus Achlya ambisexualis has been characterized. Achlya nuclei contain proteins with electrophoretic mobilities on acetic acid/urea and dodecyl sulphate polyacrylamide gels which are comparable to rabbit kidney histones H3, H4 and H2A. In contrast, the behavior of putative H2B and H1 proteins from Achlya showed greater analogy on acid/urea gels to higher plant histones. A closely related water fungus Saprolegnia ferax contained basic nuclear proteins which were very similar to those of Achlya.     

Analysis of supra-nucleosome particles from unfertilized eggs of sea urchins

Two discrete supranucleosomal particles that differ in their electrophoretic migration on 1% agarose gels were isolated from unfertilized sea urchin eggs. Both particles contain the same complement of cleavage stage (CS) chromosomal proteins, which is identical to the complete set of basic proteins isolated directly from chromatin by extraction with 0.25 N HCl. DNA fragments between 210 and 1500 bp were found in both particles, and the basic unit of DNA repeat length determined by micrococcal nuclease digestion was 126 +/- 3 bp. The isolated nucleoparticles are electrophoretically stable over a wide range of DNA sizes (126-1500 bp) indicating that their structure is maintained by internal interactions among the CS chromosomal proteins, previously designated CS A through CS G. Based on these results we conclude that the CS chromosomal proteins are functionally equivalent to classical histones in their ability to direct higher ordered structures of chromatin.     

Isolation and characterization of histones and other acid-soluble chromosomal proteins from Physarum polycephalum

Chromosomal basic proteins were isolated from amoebal and plasmodial stages of the acellular slime mold Physarum polycephalum. Polyacrylamide electrophoresis on high resolution acid-urea gels separated the five histone fractions in the sequence H1, H2A, H2B, H3, and H4. Under these electrophoretic conditions Physarum histones migrated more like plant (rye) than animal (calf) histones. Furthermore, Physarum histones H1, H2A, and H2B have higher molecular weights on sodium dodecyl sulfate (SDS) gels than the corresponding calf fractions. No differences were detected between amoebal and plasmodial histones on either acid-urea or SDS-polyacrylamide gel electrophoresis. Amoebal basic proteins were fractionated by exclusion chromatography. The five histone fractions plus another major acid-soluble chromosomal protein (AS) were isolated. The Physarum core histones had amino acid compositions more closely resembling those of the calf core histones than of rye, yeast, or Dictyostelium. Although generally similar in composition to the plant and animal H1 histones, the Physarum H1 had a lower lysine content. The AS protein was extracted with 5% perchloric acid or 0.5 M NaCl, migrated between histones H3 and H4 on acid-urea polyacrylamide gels, and had an apparent molecular weight of 15 900 on SDS gels. It may be related to a protein migrating near H1. Both somewhat resembled the high mobility group proteins in amino acid composition.     

Purification and characterization of proteins,including procollagen type III,in salt extracts of fetal bovine skin

The nature of high-molecular-weight proteins in salt extracts of fetal bovine skin was investigated. A series of DEAE cellulose ion-exchange columns separated the mature collagen from the high molecular weight proteins and also separated the high molecular weight proteins from each other. The following proteins were isolated: (a) a very high molecular weight protein which appears to be aggregated mature collagen; (b) two high molecular weight proteins of slightly faster mobility on SDS polyacrylamide gels, one of which is collagen-like and one of which is not; and (c) a type III procollagen, purer than those previously reported in the literature. These latter three proteins were characterized by amino acid analysis, SDS polyacrylamide gel electrophoretic mobility, collagenase sensitivity, and CNBr peptide patterns from SDS-PAGE.     

Ultraviolet imaging densitometry of unstained gels for two-dimensional electrophoresis

A system suitable for ultraviolet imaging densitometry of two-dimensional electrophoretic gels that are unstained is described, together with its applications. A flying-spot densitometer linked with a personal computer was used for data acquisition, generation of mapping data, and image processing. Randomly distributed zones of proteins on two-dimensional gels were detected at 280 nm without being stained by two-dimensional scanning, and the densitometric value of each pixel (0.2 x 0.2 mm) was memorized by the computer, which generated a mapping pattern with density contours. The amount and densitometric value of cytochrome c had a linear relationship in the range of 2-200 micrograms. Zone locations of bovine liver proteins separated on two-dimensional gels were indicated on a map expressed in X-Y coordinates, and the pIs and molecular weights could be calculated from the map by use of pI and molecular weight markers on the same gel.     

Gel electrophoresis in studies of protein conformation and folding

Electrophoresis through polyacrylamide gels is a useful method for distinguishing conformational states of proteins and analyzing the thermodynamic and kinetic properties of transitions between conformations. Although the relationship between protein conformation and electrophoretic mobility is quite complex, relative mobilities provide qualitative estimates of compactness. Conformational states which interconvert slowly on the time scale of the electrophoretic separation can often be resolved, and the rates of interconversion can be estimated. If the transitions are more rapid, then the electrophoretic mobility represents the equilibrium distribution of conformations. Protein unfolding transitions induced by urea are readily studied using slab gels containing a gradient of urea concentration perpendicular to the direction of electrophoresis. Protein applied across the top of such a gel migrates in the presence of continuously varying urea concentrations, and a profile of the unfolding transition is generated directly. Transitions induced by other agents could be studied using analogous gradient gels. Electrophoretic methods are especially suited for studying small quantities of protein, and complex mixtures, since the different components can be separated during the electrophoresis.     

Protein metabolism of Drosophila melanogaster male accessory glands—I: Characterization of secretory proteins

The electrophoretic properties of male accessory gland proteins of Drosophila melanogaster were studied in both the native and the denatured state. The molecular weights and the isoelectric points were determined. In addition, the relative abundance of individual fractions was measured. More than 40 protein bands were observed on one-dimensional dissociative gels, approx. 85 proteins were separated on two-dimensional gels. Secretions and epithelia of both the accessory gland and the ductus ejaculatorius each contain a distinct complement of proteins. The majority of accessory secretion proteins are basic. In the native state they are only soluble with difficulty. In the presence of urea, however, 21 fractions can be separated by one-dimensional electrophoresis with a low-pH buffer system. For two-dimensional separation non-equilibrium pH gel electrophoresis gave best results. All but one of the proteins of the ductus ejaculatorius secretion are acidic. The epithelial proteins were found to be acidic.     

Comparative studies on the electrophoretic patterns of acid-soluble chromosomal proteins duringZea mays early stages of embryo germination and root cell differentiation

Acid-soluble chromosomal proteins were extracted from purified nuclei, isolated from 3 – 4 h, 12 –14 h and 24 –26 h maize embryos, as well as from nuclei isolated from meris-tematic, elongating and differentiated cells, from 2 and 3-day-oldZea mays seedlings primary roots. Using polyacrylamide gel electrophoresis (urea-acetic acid in the cylindrical gels and slab-SDS-electrophoresis), it was established that germination and root cell differentiation induced changes in some nuclear acid-soluble chromosomal proteins, especially in histone H1. The results of proteins belonging to the high-mobility group proteins (HMG) and some other acid-soluble proteins with unknown nature for the plants, based on the electrophoretic mobility, were discussed.     

Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form.

A discontinuous electrophoretic system for the isolation of membrane proteins from acrylamide gels has been developed using equipment for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Coomassie dyes were introduced to induce a charge shift on the proteins and aminocaproic acid served to improve solubilization of membrane proteins. Solubilized mitochondria or extracts of heart muscle tissue, lymphoblasts, yeast, and bacteria were applied to the gels. From cells containing mitochondria, all the multiprotein complexes of the oxidative phosphorylation system were separated within one gel. The complexes were resolved into the individual polypeptides by second-dimension Tricine-SDS-PAGE or extracted without SDS for functional studies. The recovery of all respiratory chain complexes was almost quantitative. The percentage recovery of functional activity depended on the respective protein complex studied and was zero for some complexes, but almost quantitative for others. The system is especially useful for small scale purposes, e.g., separation of radioactively labeled membrane proteins, N-terminal protein sequencing, preparation of proteins for immunization, and diagnostic studies of inborn neuromuscular diseases.     

Comparative Analysis of Rapidly Transported Axonal Proteins in Sensory Neurons of the Frog and Rat

³⁵S-labeled proteins carried by fast axonal transport in sciatic sensory axons of bullfrog and rat were separated electrophoretically on discontinuous polyacrylamide gradient slab gels. In contrast to the previously reported similarity in the electrophoretic profiles of rapidly transported proteins from functionally different neurons, we have found that there is very little correspondence in the profiles of these proteins in functionally similar neurons from two widely studied species. We also found very little correspondence between the two species in the profiles of locally synthesized sciatic nerve protein. The results demonstrate the difficulty inherent in comparing the electrophoretic profiles obtained using these two model systems for the study of rapidly transported axonal proteins. In particular, relationships between the major rapidly transported proteins in the two species could_not be analyzed with this technique.     

Detection of cellulose-binding proteins in electrophoresis gels by filter paper affinity blotting

Proteins separated in electrophoresis gels were tested for the ability to bind cellulose by a simple blotting procedure. Proteins were blotted onto Whatman No. 1 filter paper by diffusion or by electrophoretic transfer and detected by Coomassie blue staining. Certain proteins released into culture supernatant by Bacteroides succinogenes NR9 (ATCC 43854) adhered strongly to cellulose, but were not found to have carboxymethylcellulose activity. Boiling of samples prior to electrophoresis eliminated the ability of proteins to bind to cellulose. Proteins that did not adhere to filter paper cellulose were detected on a nitrocellulose membrane placed behind the filter paper during electrophoretic transfer. The technique, referred to as filter paper affinity blotting, detects cellulose-binding proteins with great sensitivity.     

Proteins induced in Escherichia coli by benzoic acid.

Proteins induced by benzoic acid in Escherichia coli were observed on two-dimensional electrophoretic gels (2-D gels). Cultures were grown in glucose-rich medium in the presence or absence of 20 mM benzoate at an external pH of 6.5, where the pH gradient (deltapH) is large and benzoate accumulates, and at an external pH of 8.0, where deltapH is inverted and little benzoate is taken up. Radiolabeled proteins were separated on 2-D gels and were identified on the basis of the index of VanBogelen and Neidhardt. In the absence of benzoic acid, little difference was seen between pH 6.5 and pH 8.0; this confirms that the mechanisms of protein homeostasis in this range are constitutive, including the transition between positive and inverted deltapH. Addition of benzoate at pH 6.5 increased the expression of 33 proteins. Twelve of the benzoate-induced proteins were induced at pH 8.0 as well, and nine of these matched proteins induced by the uncoupler dinitrophenol. Eighteen proteins were induced by benzoate only at pH 6.5, not at pH 8.0, and were not induced by dinitrophenol. One may be the iron and pH regulator Fur, which regulates acid tolerance in Salmonella spp. The other 13 proteins had not been identified previously. The proteins induced by benzoate only at a low pH may reflect responses to internal acidification or to accumulation of benzoate.     

Sarcoplasmic reticulum. X. The protein composition of sarcoplasmic reticulum membranes

The proteins of Sarcoplasmic reticulum membranes were resolved by polyacrylamide gel electrophoresis into several fractions ranging in mol wt from 300,000 to about 30,000. The ATPase enzyme involved in Ca²⁺ transport is associated with a major protein fraction and its molecular weight based on its electrophoretic mobility on polyacrylamide gels in the presence of sodium dodecylsulfate is about 106,000. Reducing agents (β-mercaptoethanol or dithiothreitol) cause the dissociation of membrane proteins into subunits of 20,000–60,000 mol wt, which can be separated by electrophoresis or Sephadex G-150 chromatography.     

Extended N-terminal sequencing of proteins of archaebacterial ribosomes blotted from two-dimensional gels onto glass fiber and poly(vinylidene difluoride) membrane

Previously uncharacterized proteins from intact ribosomes and ribosomal subunits of the extreme halophile Halobacterium marismortui (Haloarcula marismortui) were isolated and separated by high-resolution two-dimensional electrophoresis (2DE). N-Terminal amino acid sequences of 14 of these acidic large-subunit proteins were obtained by direct blotting of the separated proteins from two-dimensional electrophoresis gels to sequencer-stable supports followed by excision of the protein spots and sequencing. Furthermore, long internal sequences were obtained by in situ enzymatic cleavage of halobacterial proteins in gel pieces obtained from two-dimensional gels followed by electrophoretic separation of the fragments, blotting, and sequencing. Precautions are outlined for avoidance of N-terminal blockage of proteins, and the preparation and selection of suitable supports for obtaining extended N-terminal sequences are described. The results suggest that when prior fractionation is carried out to enrich for cell organelles, subcellular components of cells, or cell membranes, it is routinely possible to obtain numerous N-terminal sequences from one or a few 2DE gels of such fractions. Our results also indicate that, with appropriate precautions, proteins are routinely obtainable from 2DE gels in a form suitable for both N-terminal and internal sequence determination and show no detectable evidence for N-terminal blockage or destruction or modification of labile amino acid residues.     

Efficient transfer of proteins from acetic acid-urea and isoelectric-focusing gels to nitrocellulose membrane filters with retention of protein antigenicity

A method which facilitates the rapid and quantitative electrophoretic transfer of proteins from gels not containing sodium dodecyl sulfate (SDS) to nitrocellulose membranes is described. The equilibration of non-SDS-polyacrylamide gel electrophoretic gels in a buffer containing SDS confers a net negative charge to the proteins present, presumably as a result of the formation of SDS-protein complexes. Proteins from gels equilibrated in the SDS buffer and then electroblotted in a Tris-glycine buffer at pH 8.3 are transferred with much greater efficiency than are proteins from untreated gels. The method has been shown to significantly enhance the electrophoretic transfer of polyoma viral proteins resolved in either acetic acid-urea or isoelectric-focusing gels to nitrocellulose membranes, and it is suggested that the method should have universal applicability to all gel electrophoresis systems currently employed. The proteins from isoelectric-focusing gels treated with SDS and transferred to nitrocellulose membranes were found to retain antigenicity to antisera prepared against either denatured or native viral proteins.     

Proteins of Friend leukemia cells. Comparison of hemoglobin-synthesizing and noninduced populations.

Proteins of Friend leukemia cells induced to form large amounts of hemoglobin by dimethylsulfoxide treatment were compared with proteins from noninduced cells by high resolution two-dimensional polyacrylamide gel electrophoresis. Approximately 98% of more than 500 proteins separated by this technique were qualitatively and quantitatively the same in both cell populations. Changes representing more than 50% of the control cell amount were detected in six non-histone chromosomal proteins, two nucleoplasmic proteins, and three cytoplasmic proteins. It is concluded that dimethylsulfoxide induces an extremely specific pattern of erythroid differentiation in these cells, which should be susceptible to detailed analysis. Comparison of protein patterns from Friend leukemia cells and HeLa cells revealed electrophoretic identity of approximately 20% of cytoplasmic proteins and 50% of non-histone chromosomal proteins.     

Specific aspects of detection of peroxidase isozymes and their genetic control in barley

Identical specimens were separated by electrophoresis in two gels to detect and fix peroxidase isozymes. Both gels were stained by Coomassie brilliant blue for detecting proteins. One gel was previously incubated for detecting peroxidase activity. The differences in electrophoretic patterns between the gels indicate the zones of peroxidase activity. It has been shown that locus Prx 6H, controlling a low-mobility grain peroxidase (PRX 6H), is localized to barley chromosome 6. Two loci, Alb 4H and Alb 7H, controlling the biosyntheses of water-soluble proteins of barley endosperm, were localized to chromosomes 4 and 7. It has been demonstrated that barley species is polymorphic at multiple molecular forms of peroxidase.     

Organization of the Chorion Genes of BOMBYX MORI, a Multigene Family. I. Evidence for Linkage to Chromosome 2

The chorion genes of silkmoths comprise a multigene family that codes for 50 or more highly specialized structural proteins found in the eggshell. A detailed study of the chromosomal organization of these genes was initiated, using inbred stocks of Bombyx mori as a source of electrophoretic variants for genetic markers. Chorion protein patterns were screened on thin-slab polyacrylamide isoelectric focusing gels. A wide range of polymorphism was observed between stocks. However, isoelectric focusing patterns obtained within a stock were nearly homogeneous, indicating that inbreeding has produced a high degree of homozygosis. Testcrosses were carried out to examine the linkage relationships between electrophoretic markers in four inbred stocks. One race (C108) was selected as a standard against which to compare the inheritance of the variants found in the other three stocks. Chorion markers behaved like codominant Mendelian traits in F₁ crosses. A total of 15 out of 16 C108 markers cosegregated in subsequent testcrosses, indicating that they are linked. These genes were mapped to the second chromosome, using markers Gr and Y.