A method for the quantitative determination of protein incorporated in solubilizable polyacrylamide gels

Dense and light polyacrylamide gels containing N,N′-(1,2-dihydroxyethylene)bisacrylamide (DHEBA) or N,N′-diallyltartardiamide (DATD) as the crosslinker have been tested for their solubilization properties. Both types of gel can be dissolved in 10 m periodic acid. The time and temperature required for complete dissolution of slabs of DHEBA crosslinked gels (12 h at 50°C), however, greatly exceed those required for dissolving slabs of DATD-polyacrylamide gel (0.5 h at 22°C). Bovine serum albumin kept under the respective dissolving conditions gave a lower response in the Lowry protein assay in instances where hot periodic acid had been used. Nearly independent of the type and concentration of their constituents, the different dissolved polyacrylamide gels interfere slightly with the Lowry assay by causing some “aspecific” color development. A method is outlined enabling a reliable quantitative determination of protein incorporated in DHEBA or DATD crosslinked polyacrylamide gels.     

Polyacrylamide gels with modified cross-linkages

The retention of low molecular weight proteins during electrophoresis through gradient polyacrylamide gels was improved when a gradient of N,N′,N″-triallyl citric triamide (TACT) was superimposed on the gradient of acrylamide and N,N′-methylenebisacrylamide (MBA). Gels cross-linked only with N,N′-(1,2-dihydroxyethylene)bisacrylamide (DHEBA) are soluble in dilute periodic acid or dilute aqueous solutions of bases. DHEBA cross-linked gradient gels have a smaller pore structure at high acrylamide concentrations and a more open structure at low acrylamide concentrations than gels cross-linked with MBA. Proteins labeled with tritium and carbon-14 were fractionated through DHEBA cross-linked gradient gels and the isotopes measured after solution of the gel with periodic acid. The mild solubilizing conditions enhanced isotope resolution. The characteristics of several cross-linking molecules are discussed and reasons advanced for the superiority of those with acrylamido end groups.     

Properties of SDS-polyacrylamide gels highly cross-linked with N,N'-diallyltartardiamide and the rapid isolation of macromolecules from the gel matrix.

Polyacrylamide gels cross-linked with N,N′-diallyltartardiamide (DATD) are, in contrast to gels cross-linked with N,N′-methylenebisacrylamide (Bis), readily solubilized by periodic acid (Anker, H. S., 1970, FEBS Lett.7, 293), thus permitting efficient analyses of electrophoretically separated, labeled biological material. The capacities of polyacrylamide gels, cross-linked with Bis and DATD, to serve as media for electrophoretic separation of proteins, were compared. As DATD-cross-linked gels were inferior to equimolar Bis-crosslinked gels with 5% cross-linking (C_Bis = 5%) by the criteria of more pronounced swelling, markedly softer gels and, less concentrated and bended protein zones on electrophoresis and subsequent staining, gels cross-linked with different percentage CDATD were examined. The water regain of DATD-cross-linked gels, the retardation coefficients, and free mobilities of different proteins in equimolar Bis- and DATD-cross-linked gels were determined. When the DATD concentration in gels was increased to C_DATD = 27%, gels assumed physical characteristics comparable to those cross-linked with Bis at C_Bis = 5%. We report further the rapid, facile isolation of protein bands out of the gel matrix cross-linked with DATD. However, the isolation procedure results in an irreversible loss of biological activity.     

Transfer of small DNA fragments from polyacrylamide gels to diazobenzyloxymethyl-paper and detection by hybridization with DNA probes.

A method for transferring small DNA fragments from composite polyacrylamide-agarose gels to diazobenzyloxymethyl (DBM)-paper is described. DNA fragments are separated by electrophoresis in polyacrylamide-agarose gels crosslinked with N,N′-diallyltartardiamide instead of N,N′-methylenebis-acrylamide. The crosslinks are cleaved by treating the gel with periodic acid after electrophoresis and the DNA is denatured with alkali. After neutralization, the single stranded DNA fragments are transferred to DBM-paper and detected by hybridization with labeled DNA probes. The procedure has been used to transfer and visualize unlabeled SV40 DNA fragments in the size range 28 to 1790 base pairs.     

Multiple forms of glucocorticosteroid receptors in the neural retina of chick embryo,revealed by polyacrylamide gel electrophoresis

The glucocortiocoid receptors in the cytosol of neural retina of the 15-day chick embryo were analyzed by quantitative polyacrylamide gel electrophoresis. Maintenance of the triamcinolone acetonide (TA)-receptor complexes under conditions of electrophoretic analysis is dependent on temperatures not exceeding ?2 °C and is favored by low ionic strength, but is relatively insensitive to changes in pH between 5 and 10. Polyacrylamide gel electrophoresis in highly crosslinked Resolving Gels (15% crosslinking with N,N′-diallyltartardiamide) at low wattage and under temperature control at ?2 °C, allowed for detection and partial characterization of over 80% of the specific TA-binding activity of the tissue. One form of the glucocorticoid receptor, designated as complex II, was found to have a molecular weight (M_r) of 175,000. In addition, specifically bound TA was found in a multimillion M_r aggregate which was unable to enter gels of any concentration investigated and has been designated TA-complex I. The ratio of complex I/complex II increased with increasing gel concentration, indicating physical or chemical interaction between II and I. A polyacrylamide gel electrophoresis rerun of isolated TA-complex II gave rise to two smaller TA-binding species: Component B, of M_r 108,000 and component A, a relatively fast migrating molecule which could not be characterized under the conditions used. The ratio of $\text{B}\text{A}$ appeared constant and close to 2, suggesting that A and B may be significant structural elements of complex II. Polyacrylamide gel electrophoresis of isolated TA-complex I gave rise to component C of M_r 60,000, but not to components A or B. Components A and B associated to a large M_r complex, designated as I′, which was revealed to an extent directly proportional to gel concentration. Similarly, component C aggregated to I″, as evidenced at elevated gel concentrations. In conclusion, it has been possible to define by gel electrophoresis three of the molecular species (A, B, and C) that comprise the glucocorticoid receptor, and the possible relationships between them.     

Affinity electrophoresis: New simple and general methods of preparation of affinity gels

Two simple and generally applicable methods of preparation of affinity gels for affinity electrophoresis in agarose and polyacrylamide gels are described. In the first method, amino ligands are coupled to periodate-oxidized agarose gel beads (Sepharose 4B), and homogeneous affinity gels are obtained after mixing the melted substituted beads with either melted agarose solution or with the polymerization mixture used for the preparation of polyacrylamide gels. This type of affinity gel was used for affinity electrophoresis of lectins (immobilized p-aminophenyl glycosides), ribonuclease (immobilized uridine 3′,5′-diphosphate 5′-p-aminophenyl ester), trypsin (immobilized p-aminobenzamidine), and double-stranded phage DNA fragments (immobilized acriflavine). Alternatively, heterogeneous affinity gels are prepared from the suspension of ligand-substituted agarose, dextran, or polyacrylamide gel beads in the polymerization solution normally used for preparation of polyacrylamide electrophoretic gels. This technique was used for affinity electrophoresis of lectins, ribonuclease, and trypsin on affinity gels containing appropriate ligands coupled to the gel beads “activated” by various methods. Applicability of affinity gels prepared by the two methods described above for affinity isoelectric focusing is demonstrated.     

The use of high-pressure liquid chromatography in the simultaneous assay of 11beta-hydroxylase and 18-hydroxylase in zona fasciculata-reticularis tissue of the rat adrenal cortex.

Certain reagents utilized in the formation of polyacrylamide gels are shown to interfere in the Lowry assay for protein. Acrylamide (3–30%) and potassium ferrocyanide (0.0015–0.0105%) produced a linear response in color formation. Both compounds are capable of reducing the phenol reagent in the absence of copper and the interference can be compensated for by employing the appropriate blank. An extract of polymerized and electrophoresed gels also interferes in the Lowry assay, however, this increased color formation cannot be corrected by using a gel extract blank. Under the conditions studied, filtration, centrifugation, and dialysis did not sufficiently remove the acrylamide fines responsible for the interference.     

Alkaline urea solubilization, two-dimensional electrophoresis and lectin staining of mammalian cell plasma membrane and plant seed proteins

Plasma membranes, isolated from Chinese hamster ovary cells and seed proteins from Arachis hypogaea (L.) were analyzed by two-dimensional electrophoresis. Polypeptides were solubilized without employing sodium dodecyl sulfate (SDS), using in its place 5 mm K₂CO₃ and 9.5 m urea. After addition of dithiothreitol and the nonionic detergent Nonidet P-40, more than 95% of the total protein remained in the supernatant fraction after the preparation was centrifuged at 100,000 g. The solubilization was comparable to that achieved with boiling SDS solution. This soluble material could be used directly for either isoelectric focusing or nonequilibrium pH gradient electrophoresis in narrow bore, tubular, polyacrylamide gels crosslinked by means of N,N′-diallyltartardiamide. Up to 750 μg of protein could be analyzed in one such 3 mm gel. Electrophoresis in polyacrylamide slab gels containing SDS was used for separations in the second dimension. The method allows large amounts of both basic and acidic insoluble proteins to be solubilized and then analyzed without employing SDS as a solubilizing agent. Classes of glycoproteins on the gels were detected by incubating with small volumes of ¹²⁵I-lectins in heat-sealed plastic bags. CHO cells contain several high molecular weight acidic glycoproteins that bind wheat germ agglutinin, but which do not stain with Coomassie blue. Several of the storage polypeptides in peanut seeds were also shown to bind wheat germ agglutinin and are probably, therefore, glycoproteins containing N-acetyl d-glucosamine.     

Poly-N-acryloyl-Tris gels as anticonvection media for electrophoresis and isoelectric focusing

We describe in detail the synthesis of an acrylic monomer, N-acryloyl-tris(hydroxy-methyl)aminomethane (NAT), which was successfully used for the preparation of gels for electrophoresis and isoelectric focusing. The polymerization kinetics and transparency of the poly(NAT) gels crosslinked by N,N'-methylenebisacrylamide (Bis) are also shown. Poly(NAT)-Bis gradient (4-24%) gel resolves proteins according to their size. The exclusion limit of this gel is slightly over 3 X 10(6), which is more than threefold higher than the exclusion limit of the polyacrylamide gradient gel of the same concentration. The gel made of 6% NAT and 3% Bis represents a suitable matrix for isoelectric focusing. These results demonstrate that poly(NAT)-Bis gels could be advantageously used in those applications where the extensive sieving by the polyacrylamide matrix is not desir desirable.     

Purification and characterization of an extracellular laccase from a Pseudomonas sp. LBC1 and its application for the removal of bisphenol A

The Pseudomonas sp. LBC1 produced extracellular laccase when grown in the nutrient broth. The enzyme was purified using acetone precipitation and an anion-exchange chromatography. The molecular weight of the purified laccase was estimated as 70 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis. An enzyme showed maximum substrate specificity towards o-tolidine than other substrates of laccase including 2,2′-azinobis, 3-ethylbenzothiazoline-6-sulfonic acid, hydroquinone, N,N′-dimethyl phenylene diamine, syringic acid and veratryl alcohol. The optimum pH and temperature for the laccase activity were 4.0 and 40 °C, respectively. Cyclic voltammogram revealed the redox potential of purified enzyme as 0.30 V. The laccase was stable up to 40 °C and within pH range 6.0–8.0. Sodium azide and EDTA strongly inhibited laccase activity. The purified laccase completely degraded the higher concentration of bisphenol A within 5 h. Biodegradation metabolites of bisphenol A were characterized by using FTIR, HPLC and GC–MS.     

Characterization of a Platelet-Derived Growth Factor Receptor on Swiss 3T3 Cells by Affinity Crosslinking

Abstract

Crosslinking experiments with various bifunctional reagents were used to investigate the nature and fate of the platelet growth factor (PDGF) receptor on Swiss mouse 3T3 cells. With ethylene glycol bis succinimidyl succinate (EGS) two bands with Mr 205′000 and Mr 190′000 were labeled at equal intensity, while with disuccinimidyl suberate (DSS) and the photoactivatable pazidophenylglyoxal (pAPG) almost exclusively the latter band was labeled, when analyzed by SDS polyacrylamide gel electrophoresis under reducing conditions. Evidence is presented that the Mr 190′000 band represents a Mr 175′000 receptor protein crosslinked to a single chain of the PDGF-dimer and the Mr 205′000 species the same Mr 175′000 protein crosslinked to both chains of PDGF. Pretreatment of cells with tunicamycin generated a third labeled band with Mr 150′000, while pretreatment with neuraminidase resulted in a shift of the Mr 205′000 and 190′000 bands by 5′000. This shows that the PDGF receptor is a sialoglycoprotein, consisting of a Mr β 135′000 proteinaceous core and a Mr β 40′000 carbohydrate moiety containing sialic acid. The virtually unchanged labeling intensity seen with tunicamycin and neuraminidase pretreated cells further suggests that the carbohydrate portion of the receptor is not required for PDGF binding. Finally, the crosslinking technique was used to show that at 37°C preformed ¹²⁵I-PDGF receptor complexes disappear from the cell surface with a t_1/2 β 8 min.     

Thermally induced protein gelation: gelation and rheological characterization of highly concentrated ovalbumin and soybean protein gels

In order to optimize the use of proteins as functional ingredients in foods, one needs more insight into the effects of environmental conditions (pH, ionic strength, and temperature) on the functional properties of protein. This paper summarizes the results of an extensive study on heat-induced gelation of ovalbumin (egg-white protein) and soybean protein in the concentration range from 10 to 35 g/100 g. It was the aim of the study to relate the rheological properties of thermally induced protein gels to the microstructure of the gel and the physicochemical properties of the constituent protein. The gelling behavior of the protein was quantified with rheological techniques, and the physical properties of the gels were determined, at small and large deformations. From the swelling/dissolving behavior of the gels in various media, the nature of the crosslinks was determined qualitatively. The microstructure of the gels was determined with electron microscopy. Nmr-spectroscopy was applied in order to elucidate changes in conformation during heating. It was found that the formation of a continuous covalently crosslinked network is not a prerequisite for thermally-induced protein gelation. The properties of a gel strongly depend on the pH at which the gel is formed. When heat-set at high pH(pH～10), a homogeneous, strong, and almost transparent gel is formed, consisting of flexible crosslinked protein gels. Heat-setting at low pH (pH 5) leads to the formation of a heterogeneous and weak gel, which easily exudes water. This gel consists of crosslinked aggregated protein. The ionic strength of the solvent in which the protein is dissolved and heat-set has a much lower effect on gel properties.     

Trehalase from the cellular slime mold Dictyostelium discoideum: Purification and characterization of the homogeneous enzyme from myxamoebae

Trehalase (α-α′-trehalose 1-d-glucohydrolase, EC 3.2.1.28) was solubilized from myxamoebae of the cellular slime mold Dictyostelium discoideum by a freeze-thaw cycle and was subsequently purified to homogeneity using the techniques of ethanol fractionation, molecular sieve chromatography, DEAE-cellulose ion-exchange chromatography, chromatofocusing, and preparative polyacrylamide disc gel electrophoresis. The 1000-fold purified enzyme had a specific activity of about 104 units/mg, which was accompanied by a net recovery of 5 to 7% of the original activity. The purified enzyme was maximally active at pH 5.5, showed high specificity for trehalose, and exhibited a typical hyperbolic response as a function of trehalose concentration with a K_m of 1.2 mm. The enzyme was maximally active at 50 °C and had an energy of activation of 12–13 kcal/mol. Thermal stability studies demonstrated that full enzymatic activity was recovered following a 5-min incubation of trehalase at temperatures up to 45–50 °C. Analysis of various compounds for inhibitory effects indicated that Tris and urea were slightly effective, reducing enzymatic activity by 28 and 6% at concentrations of 100 and 10 mm, respectively. Of five heavy metals tested, HgCl₂ was the most inhibitory, reducing activity by 58% when present at a final concentration of 1.0 mm. Enzymatic activity was not affected by any adenine derivative examined (e.g., ATP, ADP, AMP, cAMP, adenosine, and adenine). The molecular weight of the native enzyme was determined by molecular sieve chromatography, pore gradient electrophoresis, and electrophoresis as a function of acrylamide concentration. All three methods yielded a value of about 10⁵ ± 5 × 10³. Estimation of the subunit or monomer molecular weight by sodium dodecyl sulfate-gel electrophoresis indicated a value of 95–100 × 10³. The isoelectric point as determined in 7.5% polyacrylamide gels with pH 3–10 ampholytes was 7.2–7.3. The purified enzyme adsorbed to concanavalin A-Sepharose in the presence of KCl (0.1 m) and was eluted with α-methylmannoside, thereby suggesting an association between trehalase and carbohydrate. In agreement with this conclusion was the observation that trehalase could be specifically stained for carbohydrate with the Alcian blue and periodic acid-Schiff's reagents following polyacrylamide disc gel electrophoresis.     

Isolation of a plant glycoprotein involved with control of intercellular recognition

A recognition molecule was isolated from stigmas of S-allele genotype S₂S₂ of Brassica oleracea var. capitata L. After Sephadex chromatography, it eluted as a single symmetrical peak during diethylaminoethane-cellulose chromatography. A high degree of purity was affirmed by: sedimentation as a single peak during ultracentrifugation through 5 to 20% sucrose gradients; elution as a single peak from Sephadex G-100; visualization as a single band which stains with Coomassie blue and periodic acid Schiff reagent after electrophoresis on polyacrylamide gels. Other criteria supporting the conclusion that it is a glycoprotein are: (a) the highly purified preparation is anthrone-positive and has a Lowry protein to anthrone-positive carbohydrate ratio of 1.3; (b) the preparation contains arabinose, galactose, glucose, and mannose, although it is not precipitated by concanavalin A; (c) the immunological properties of the molecule are lost following protease treatment, and it has a molecular weight of 90,000 by Sephadex gel-filtration analysis and 54,500 by velocity sedimentation analysis.     

An improved staining procedure for the detection of the peroxidase activity of cytochrome P-450 on sodium dodecyl sulfate polyacrylamide gels

The use of 3,3′,5,5′-tetramethylbenzidine-H₂O₂ as a stain for the peroxidase activity of cytochrome P-450 (or cytochrome P-450 in sodium dodecyl sulfate polyacrylamide gels is described in this report. This reagent can be used to detect very low levels of heme-associated peroxidase activity. The blue-stained bands on polyacrylamide gels are distinet, and the color is stable. The stained gels can be photographed or scanned at 690 nm because the gel background remains clear. The stain is easily removed from the gels to permit subsequent protein staining. Staining first for peroxidase activity has no effect on the subsequent protein staining profile. The peroxidase activity of cytochrome P-450 (or cytochrome P-420) in immunoprecipitates in Ouchterlony double diffusion plates can also be detected using this reagent.     

Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA

Complex mixtures of RNA molecules may be separated by two-dimensional electrophoresis on polyacrylamide gel slabs. The first dimension of the separation is carried out on acid gels in the presence of a high urea concentration, the second on more concentrated gels buffered at pH 8. The method has been applied to the complete separation of RNA fractions obtained after a preliminary gel electrophoresis of partial enzymic digests of ³²P-labeled bacteriophage RNA. Another application is the fractionation of partial digests as obtained in sequence determination of RNA molecules. Spots are detected by autoradiography and extracted by a simple micro procedure which yields the material in a concentrated form suitable for sequence analysis by fingerprinting.     

Unusual properties of two branched RNA''s with circular and linear components.

Irradiation with ultraviolet light was used to create two nonlinear RNA molecules. Circular potato spindle tuber viroid (PSTV) RNA was crosslinked at a single site to generate a figure eight-shaped molecule; 5S rRNA from HeLa cells was transformed into an alpha-shaped molecule with a small circular element and two arms (1). Crosslinked RNA's could be separated from their untreated counterparts by electrophoresis in polyacrylamide gels containing urea. The gel mobility of crosslinked PSTV was not altered by boiling, treatment with E. coli RNase III or glyoxalation. However, mild nuclease digestion ("nicking") produced derivatives which migrated more slowly than the starting material in gels of certain polyacrylamide concentrations, but not in others. Limited nuclease digestion of crosslinked 5S rRNA did not generate any detectable products with reduced mobility in the gels tested. Thus, the ability of the "nicking assay" to reveal circular elements within nonlinear RNA's can vary depending upon the composition of the gel chosen for analysis and on the size of the circular element relative to the rest of the molecule.     

A new enzymatic staining method for the detection of radish beta-fructosidase in gel electrophoresis

Optimum conditions for β-fructosidase detection in polyacrylamide and agarose gels are defined from comparison of zymograms obtained with two staining methods including an original one. Under all conditions tested in the present study detection has been improved with the new staining procedure. The new staining medium developed here uses two intermediary enzymes: glucose oxidase and peroxidase, 3.3′-diaminobenzidine as final acceptor, and sucrose as substrate for β-fructosidase. β-Fructosidase zymogram is obtained either by gel immersion in this staining solution, or when highly crosslinked polyacrylamide separating gels are used, by overlaying the slab within a thin buffered agarose gel containing staining chemicals (“sandwich technique”). Examples are presented to illustrate the general principles involved and indicate the conditions necessary for optimal development of this precise and specific technique.     

Visualization by chilling of protein bands in polyacrylamide gels containing 8 M urea: preparation and quantitation of foot-and-mouth disease virus capsid proteins

Protein bands become visible in polyacrylamide gels containing 8 m urea after chilling the gels in air for 5 to 10 min at ?70°C. Urea appears to crystallize preferentially as opaque bands in regions of the gel where protein reduces the amount of free water available as solvent for the urea molecules. Thus detected, the gel sections containing protein bands from foot-and-mouth disease virus can be immediately cut out, and their proteins obtained by electrophoretic elution or extraction procedures. Analysis of the proteins for purity and concentration is then carried out by electrophoresing measured aliquots on analytical gels, staining with Coomassie brilliant blue, scanning the gels for absorbance at 600 nm, and converting peak areas to micrograms of protein using Folin phenol standard curves determined for each purified capsid protein. The most basic capsid protein and its in virion proteolytic-cleavage products stain metachromatically.     

The subunit interface of the Escherichia coli ribosome: Identification of proteins at the interface between the 30 S and 50 S subunits by crosslinking with 2-iminothiolane

The 70 S ribosomes of Escherichia coli were treated with 2-iminothiolane with the resultant addition of 110 sulfhydryl groups per ribosome. The modified ribosomes were oxidized to promote disulfide bond formation, some of which formed intermolecular crosslinks. About 50% of the crosslinked 70 S ribosomes did not dissociate when exposed to low concentrations of magnesium in the absence of reducting agent. Dissociation took place in the presence of reducing agents, which indicated that the subunits had become covalently linked by disulfide linkages. Proteins extracted from purified crosslinked 70 S ribosomes were first fractionated by polyacrylamide/urea gel electrophoresis. The proteins from sequential slices of these gels were analyzed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Monomeric proteins derived from crosslinked dimers appeared below the diagonal containing non-crosslinked proteins, since the second electrophoresis, but not the first, is run under reducing conditions to cleave the crosslinked species. Final identification of the proteins in each dimer was made by radioiodination of the crosslinked proteins, followed by two-dimensional polyacrylamide/urea gel electrophoresis in the presence of non-radioactive total 70 S proteins as markers. This paper describes the identification of 23 protein dimers that contained one protein from each of the two different ribosomal subunits. The proteins implicated must have some part of their structure in proximity to the other ribosomal subunit and are therefore defined as “interface proteins”. The group of interface proteins thus defined includes 50 S proteins that are part of the 5 S RNA: protein complex and 30 S proteins at the initiation site. Correlations between the crosslinked interface proteins and other functional data are discussed.