Protein concentration of cerebrospinal fluid by precipitation with Pyrogallol Red prior to sodium dodecyl sulphate-polyacrylamide gel electrophoresis

The Pyrogallol Red Molybdate (PRM) and Coomassie Brilliant Blue (CBB) protein dye-binding assays have been applied to samples of cerebrospinal fluid (CSF) to investigate protein concentration by dye precipitation prior to sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The protein concentration values of the CSF samples (N=62) showed good agreement between the PRM and CBB assays as indicated by linear regression analysis (y(PRM)=1.033x(CBB)+1.004 in units of mg/l, r=0.99) but the PRM assay was optimal for protein concentration as the PRM protein-dye complex was less soluble allowing protein recovery over a wider working range. Dye precipitation using PRM is recommended as a simple, rapid and economic method for protein concentration of samples of CSF prior to SDS-PAGE.     

Phospholipase A(2)-catalyzed membrane leakage studied by immobilized liposome chromatography with online fluorescent detection

Unilamellar liposomes composed of phosphatidylcholine with an entrapped self-quenching fluorescent dye, calcein, were immobilized in chromatographic gel beads by avidin-biotin binding. Bee venom phospholipase A(2) (PLA(2)) was applied in a small amount onto the immobilized liposome column. The release of calcein from the immobilized liposomes resulting from the catalyzed hydrolysis of the phospholipids was detected online by immobilized liposome chromatography (ILC) using a flow fluorescent detector. The PLA(2)-catalyzed membrane leakage of the immobilized liposomes as studied with ILC was found to be affected by the gel pore size used for immobilization, by liposome size, and as expected by the concentration of calcium, but was unaffected by the flow rate of ILC. The largest PLA(2)-induced calcein release from the liposome column was detected on large unilamellar liposomes immobilized on TSK G6000PW or Sephacryl S-1000 gel in the presence of 1 mM Ca(2+) in the aqueous mobile phase. Comparison with the PLA(2)-catalyzed membrane leakage in free liposome suspensions, we conclude that the fluorescent leakage from liposomes hydrolyzed by PLA(2) can be rapidly and sensitively detected by ILC runs using large amount of immobilized liposomes with entrapped fluorescent dye.     

A Coomassie blue-binding assay for the microquantitation of immobilized proteins

A sensitive assay procedure for the determination of microgram quantities of immobilized proteins is described. The procedure is based on the property of Coomassie blue G-250 to bind strongly yet reversibly to proteins. The assay involves incubation of the immobilized protein with a solution containing 0.1% Coomassie blue, 10% acetic acid, and 25% isopropyl alcohol in distilled water at room temperature followed by washing off of the unbound dye. The protein-bound dye is eluted with methanolic NaOH, acidified, and the absorbance is measured at 605 nm. The assay is highly reproducible and several proteins immobilized on various matrices could be conveniently assayed. Protein values determined by the dye-binding assay showed good agreement with those obtained by other procedures.     

Protein assay by Coomassie brilliant blue G-250-binding method is unsuitable for plant tissues rich in phenols and phenolases

Protein estimation in crude homogenates of plant tissues rich in phenols and phenolases was carried out by the dye-binding and, with recommended cautions, by the Lowry et al. methods and the two were compared. The dye-binding method gave grossly erroneous results with a high degree of variation when the homogenizing media differed; this was not due either to the interference by the components of the homogenizing media or to any shift in the absorbance maximum. While the reduced form of the "derived" polyphenolic compounds, generated during tissue homogenization, appeared to enhance dye binding with bovine serum albumin, their influence on the protein assay directly in crude homogenates was extremely diverse. Tissue homogenization in the absence of a reducing agent results in polyquinone-protein complexes which prevent optimal dye binding, resulting in low protein values, while the endogenous phenolics in a homogenate prepared in a mixture of cysteine and NaCl appear to suppress dye-protein complex formation. It is therefore our opinion that the dye-binding method is unsuitable for protein assay in phenol- and phenolase-rich plant tissues.     

A colorimetric assay for gellan elaborated by Sphingomonas paucimobilis ATCC 31461

A colorimetric assay involving the dye toluidine blue O was developed to determine the concentration of the microbial heteropolysaccharide gellan elaborated by Sphingomonas paucimobilis ATCC 31461. Colour formation was linear up to a concentration of 0.7 mg/ml. The concentration of gellan produced in S. paucimobilis cultures was quantitated using this colorimetric dye-binding assay as well as the currently utilized gravimetric procedure, and comparable results were observed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparison of five techniques for the determination of protein content in mixed human saliva

This study was conducted to assess the relative accuracy of five different assay techniques for the determination of protein concentration in human mixed saliva. The protein concentration of paraffin-stimulated saliva from 20 individuals was determined using the biuret reaction, the Lowry assay, a modified Lowry technique using bicinchoninic acid, and two dye-binding assays. Using bovine serum albumin as the standard, mean values ranged from 0.67 to 2.37 mg/ml. The use of bovine serum albumin, trypsinogen, lysozyme, bovine pancreatic ribonuclease, and poly-L-lysine as standards with the five different assay techniques to measure protein concentration of pooled mixed saliva from the above subjects produced results ranging from 0.74 to 65.5 mg/ml. The protein concentration obtained for this saliva sample by amino acid analysis was consistent with the value obtained for the biuret reaction using any of the five different standard proteins. Thus, the protein concentration obtained for human saliva depends upon both the technique used and the protein standard.     

Interference of the detergent Tween 80 in protein assays.

The nonionic detergent Tween 80, which has been widely used to stimulate protein secretion in bacterial and fungal systems, caused interferences in three protein determination methods. The OD595 developed in the Coomassie blue dye-binding assay with a variety of purified proteins in the presence of Tween 80 was 1.6 to 3.4 times greater than that observed without detergent. These differences could not be attributed totally to the rapid color development in the assay with Tween 80 alone. Crude concentrated extracellular bacterial proteins shaken overnight with Tween 80 yielded an altered fractionation pattern on size exclusion chromatography and 10-fold increased color with an absorption spectrum in the dye-binding assay different from that of bacterial proteins shaken without detergent. In the bicinchoninic acid method, the detergent caused a 2- to 3-fold increase in OD562 due largely to contaminating peroxides which could be removed by treatment with catalase. In the Folin phenol method, the detergent caused a slight precipitate, but residual interference was not detectable in filtered assay mixtures.     

Determination of protein by Coomassie dye-binding in agarose gels

A variation of the Coomassie dye-binding assay for proteins is described. Protein samples were pipetted to the surface of agarose plates in uniformly sized spots and stained with Coomassie Blue G-250. The bound dye was determined by densitometric scanning using double wavelength and flying spot facilities. The response curves were linear in an about 10-fold concentration range with a lower detection limit of 0.5 microgram. No background correction was necessary because unbound dye and most substances known to interfere with other protein assays were removed during the staining and destaining of the agarose gels. Membrane proteins could be analyzed since the samples were applied as solutions in 1% sodium dodecyl sulfate.     

Covalent immobilization of proteins to N-hydroxysuccinimide ester derivatives of agarose. Effect of protein charge on immobilization

An uncharged N-hydroxysuccinimide ester derivative of agarose, Affi-Gel 10, exhibited excellent capacity for immobilization, at pH 7.5, of proteins having isoelectric points of 6.5--11.0. Under identical conditions, acidic proteins with isoelectric points of 3.3--5.9 did not couple well to this activated gel. Immobilization of acidic proteins increased in the presence of 80 mM CaCl2, or at a pH equal to or less than the isoelectric point. Affi-Gel 15, a new N-hydroxysuccinimide ester derivative of agarose containing a tertiary amine in the spacer arm, coupled acidic proteins efficiently at pH 7.5 but basic proteins coupled poorly. The immobilization of basic proteins to Affi-Gel 15 was increased to useful levels by increasing the ionic strength, or the pH, of the reaction medium. The lectin concanavalin A was efficiently immobilized using either activated gel, and the concanavalin A-agarose derivatives bound 3.9--4.1 mg ovalbumin/ml gel. These studies demonstrate that the charge of the protein relative to the charge of the gel is an important factor affecting the level of protein immobilization to active ester gels.     

The oxygenation-linked binding of neutral red to spiny lobster hemocyanin. A structural study of the partially oxygenated protein

The structural change of lobster hemocyanin in cooperative O2 binding was studied by the dye-binding method. It was found that neutral red shows an O2-linked binding to hemocyanin with a higher affinity for the oxy form. The number of the dye-binding sites was estimated to be three in the hexameric molecule of oxyhemocyanin. The course of the structural change in the partially oxygenated hemocyanin was examined using the absorbance change of the bound dye as a measure. It was found that the fractional change in the dye binding was considerably greater than the degree of O2 saturation of hemocyanin. The three-state allosteric model, which was proposed for explanation of the O2 binding properties of lobster hemocyanin [N. Makino (1986) Eur. J. Biochem. 154, 49--55], was also consistent with the effects of the dye on the O2 binding to the native hemocyanin. On the basis of this model, the dye binding to partially oxygenated hemocyanin could be connected with the populations of the affinity states. It was inferred that the binding of neutral red reflects the quaternary structure of the protein. In contrast, O2 binding to the stripped (EDTA-treated) hemocyanin showed a considerable decrease in the cooperativity in the presence of the dye. The O2-binding isotherms could not be explained by the three-state model. It is suggested that the subunit interaction is partially blocked by the dye in the absence of divalent cations.     

Quantitation of immobilized proteins

A method for the quantitative determination of immobilized proteins based on the binding and subsequent elution of Coomassie Blue R is presented. Also presented is a method for the immobilization of proteins in solution by entrapment in polyacrylamide. These entrapped proteins are then available for use in the assay method presented. Other analytical procedures can also be performed on the entrapped proteins, either alone or in combination with the protein quantitation. The dye binding and elution method presented provides a sensitive and, in most applications, rapid method for the quantitative detection of immobilized proteins. Rather than immobilization being an obstacle to the assay method, this approach utilizes the advantages of immobilization for the removal of excess reagents. Application of this approach to several types of immobilized protein are presented.     

Measurement of protein in cell suspensions using the Commassie brilliant blue dye-binding assay

The direct measurement of protein in cell suspensions using the Coomassie brilliant blue dye-binding assay demonstrated markedly lower values compared to those obtained with the Lowry assay. It is shown that the addition of small amounts of Triton X-100 or NaOH to the cell suspensions prior to addition of the dye reagent corrected this discrepancy. Standards of soluble proteins may be used for the quantitation of protein in cell suspensions with the dyebinding assay provided that the same amounts of Triton X-100 or NaOH are added to both the standards and the samples.     

A rapid chromatographic technique for the detection of dye-binding proteins

A rapid and inexpensive assay for dye-binding proteins has been developed. It depends on the separation of free and protein-bound sulfobromophthalein in 1-ml columns of Sephadex G-25 due to differential adsorption of the dye to the protein and to the Sephadex. With bovine serum albumin the calibration curve is linear between 0.03 and 3 mg of protein and is not affected by the presence of moderate concentrations of salt.     

Sequential Limited Proteolysis of Myelin Basic Protein by Neutral Protease Activities of Bovine Brain

Acid extracts of delipidated white matter of bovine brain were prepared, and their proteolytic activities toward myelin basic protein (MBP) were evaluated at pH 3 and pH 7. This was done by measuring changes in total protein using a selective dye-binding assay, and by evaluating peptide patterns by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and densitometry. At pH 7 greater than 50% of total protein and about 75% of MBP were degraded after 48 h, whereas at pH 3 it was less than 20% altogether. Neutral proteolysis of MBP entailed up to 12 different proteolytic peptide fragments in the molecular weight range of 17.5 to 6 kd. Its enzymatic nature was verified using protease inhibitors, including N-ethylmaleimide, phenylmethylsulfonyl fluoride, o-phenanthroline, and EDTA, as well as pepstatin A and alpha 2-macroglobulin. Both transient changes in percentages of some intermediate peptides and differential effects of individual inhibitors on electrophoretic peptide patterns strongly suggest a sequential type of limited proteolysis. The results also indicate that acid extracts contained several endopeptidases of which a cysteine protease appears to initiate the breakdown of MBP.     

An Update on Protein Stains: Amido Black,Coomassie Blue G,and Coomassie Blue R

Samples of amido black, Coomassie blue G, and Coomassie blue R obtained over a number of years were tested for dye content, impurities, and effectiveness for staining proteins after polyacrylamide gel electrophoresis and for protein dye-binding assays. Some impurities produced reactions resembling metachromasia with specific proteins, although instances of true metachromatic staining are also reported. Several simple assays are given for determining dye content and relative levels of impurities. Recommendations are made for selecting batches of commercial dyes which are most likely to perform satisfactorily.     

An Update on Protein Stains: Amido Black, Coomassie Blue G, and Coomassie Blue R

Samples of amido black, Coomassie blue G, and Coomassie blue R obtained over a number of years were tested for dye content, impurities, and effectiveness for staining proteins after polyacrylamide gel electrophoresis and for protein dye-binding assays. Some impurities produced reactions resembling metachromasia with specific proteins, although instances of true metachromatic staining are also reported. Several simple assays are given for determining dye content and relative levels of impurities. Recommendations are made for selecting batches of commercial dyes which are most likely to perform satisfactorily.     

Kinetic properties of phenylalanine ammonia-lyase from sunflower (Helianthus annuus L.) hypocotyls.

Phenylalanine ammonia-lyase (PAL) from sunflower hypocotyls has been partially purified by selective precipitation with ammonium sulfate and molecular gel filtration on Sephacryl S-300. Kinetic assays carried out with this partially purified PAL preparation revealed that the enzyme did not show a homogeneous kinetic behaviour. The observed kinetic pattern and parameters (Km and Vmax) depended on the assay conditions used and the protein concentration added to the assay mixture. PAL displayed Michaelian or negative cooperativity kinetics. Such behaviour can be explained by the existence of an association-dissociation process of PAL-protein subunits. The presence of mono-, tri- and tetrameric forms of PAL has been assessed by molecular gel filtration on Sephacryl S-200, using different elution conditions.     

Affibody protein capture microarrays: synthesis and evaluation of random and directed immobilization of affibody molecules

Affibody molecules, 58-amino acid three-helix bundle proteins directed to different targets by combinatorial engineering of staphylococcal protein A, were used as capture ligands on protein microarrays. An evaluation of slide types and immobilization strategies was performed to find suitable conditions for microarray production. Two affibody molecules, Z(Taq) and Z(IgA), binding Taq DNA polymerase and human IgA, respectively, were synthesized by solid phase peptide synthesis using an orthogonal protection scheme, allowing incorporation of selective immobilization handles. The resulting affibody variants were used for random surface immobilization (through amino groups) or oriented surface immobilization (through cysteine or biotin coupled to the side chain of Lys58). Evaluation of the immobilization techniques was carried out using both a real-time surface plasmon resonance biosensor system and a microarray system using fluorescent detection of Cy3-labeled target protein. The results from the biosensor analyses showed that directed immobilization strategies significantly improved the specific binding activity of affibody molecules. However, in the microarray system, random immobilization onto carboxymethyl dextran slides and oriented immobilization onto thiol dextran slides resulted in equally good signal intensities, whereas biotin-mediated immobilization onto streptavidin-coated slides produced slides with lower signal intensities and higher background staining. For the best slides, the limit of detection was 3 pM for IgA and 30 pM for Taq DNA polymerase.     

Isolation of carcinogenic aminoazo dye-binding protein and its identification as alcohol dehydrogenase

A major carcinogenic aminoazo dye-binding protein having Ip of 9.7 (isoelectric focusing) was isolated from the liver cytosol of rats given 40 mg 3'MeDAB. The protein has the molecular weight of 6.8 × 10⁴ (gel-filtration) and two subunits of about 3.9 × 10⁴ molecular weight (SDS-polyacrylamide gel electrophoresis). The amino acid composition was similar to that reported for liver alcohol dehydrogenase of animals. The enzymatic activity was shown to be associated consistently with the dye-binding protein fractions throughout the purification steps suggesting identity of the dye-binding protein as liver alcohol dehydrogenase.     

Interaction of bromophenol blue with serum albumin: criteria for using dyes for assessing the state and quantity of protein

The optical properties of the complexes of the pH-dependent dye bromophenol blue (BPB) with human serum albumin were investigated by the spectrophotometric method. The solvatochromic longwave displacement of bound BPB-2 absorption and BPB-1/BPB-2 redistribution were shown to form the optical signal of complexes. Because of the distortion of the bound BPB-2 signal its quantity was determined as delta A630 = A630 - A660 and the use of lambda max as structural parameter was limited to low pH less than or equal to 3. The conclusion was made that BPB is inapplicable as a structural probe on account of low structural dependence of delta A630 and pH-limitation of lambda max used. The maximal absorption delta Amax = Amax - A660 and its structural independence were obtained in the region of 70-100% occupation of the dye-binding centers of the protein. It is the optimal conditions for the quantitative determination of protein. After maximal dye binding (15-16 molecules of BPB per 1 molecule of albumin) the aggregation and precipitation of the complexes occurred.