Accessibility and multivalency of immobilized Cibacron blue F3GA

The effect of immobilized dye concentration on protein complexation was observed using zonal chromatography. A monomeric protein, octopine dehydrogenase, was retained by a single interaction to a Sepharose CL-6B column containing 11.6 mM immobilized Cibacron blue F3GA. By contrast, a tetrameric protein, lactate dehydrogenase, was retained by the same column by multiple interactions. The degree of multiple interactions was found to systematically increase with increasing immobilized dye concentration. The concentration of immobilized dye accessible to protein was found to be inversely related to the concentration of ionic components in the solvent. Zonal chromatographic measurements of free dye and unconjugated matrix suggest that increasing the concentration of ionic components promotes the adsorption of immobilized dye to the adjacent matrix surface. Such adsorption markedly affects both the capacity of an immobilized dye column and the multiplicity of its interaction with oligomeric proteins.     

Effects of AMP and Cibacron blue F3G-A on the fructose 6-phosphate binding of yeast phosphofructokinase.

The positive effector 5′-AMP of yeast phosphofructokinase does not influence the binding of fructose 6-phosphate to the enzyme. Cibacron blue F3G-A considered an ATP analogue decreases the affinity of the enzyme to fructose 6-phosphate without exerting an effect on the cooperativity of fructose 6-phosphate binding. The peculiarities of the interactions of AMP and Cibacron blue with fructose 6-phosphate binding demonstrate compatibility of the allosteric kinetics with the binding behavior of the enzyme.     

Specific binding of Cibacron blue F3G-A to yeast phosphofructokinase.

The complex formation between the ATP-analogous reactive dye Cibacron blue F3G-A and yeast phosphofructokinase is accompanied by a red shift of the visible absorption spectrum. From the position of lambdamax of the dye-phosphofructokinase complex in the polarity scales obtained from model solvents it may be concluded that the chromophoric system is evidently located in a highly apolaric range of the enzyme protein. The spectrophotometric titration of yeast phosphofructokinase with Cibacron blue F3G-A yielded a sigmoidal binding curve, which can be described by the MONOD-WYMAN-CHANGEUX model.     

Affinity partitioning with polymer-bound Cibacron blue F3G-A for rapid,large-scale purification of phosphofructokinase from baker's yeast

Phosphofructokinase has been isolated in homogenous form from baker's yeast. The first two steps, fractional precipitation with polyethylene glycol and affinity partitioning in aqueous biphasic systems containing Cibacron blue F3G-A-polyethylene glycol, gave a 58-fold purification within 3 h. In these steps the amount of contaminating proteases was reduced by 2 orders of magnitude. After concentration using DEAE-cellulose followed by gel chromatography, homogeneous enzyme was obtained. The advantages of affinity partitioning for large-scale preparations are discussed.     

Active-site-directed inhibition of sucrose-phosphate synthase by Cibacron blue F3G-A and 1-deoxynojirimycin

Sucrose-phosphate synthase (SPS, E.C. 2.4.1.14) from spinach (Spinacia oleracea L.) was partially purified and the inhibition of the enzyme reaction by 1-deoxynojirimycin and Cibacron blue F3G-A analyzed. Cibacron blue was a high-affinity competitive inhibitor with respect to the substrate UDPglucose (K_i = 80 nM) and a mixed-type inhibitor with respect to fructose-6-phosphate. 1-Deoxynojirimycin was a mixed-type inhibitor of SPS with respect to UDPglucose [K_i(EI) = 5.8 mM] and a uncompetitive inhibitor with respect to fructose 6-phosphate. These results are discussed in relation to the mechanism of the reaction catalysed by SPS and the secondary structure of the enzyme.Abbreviations DN 1-deoxynojirimycin - Glc6P glucose-6-phosphate - Fru6P fructose-6-phosphate - SPS sucrose-phosphate synthase - UDPG1c UDPglucose We are grateful to M. Stitt (University of Heidelberg, Germany) for many helpful discussions and J. Harr and P. Bocion (both SANDOZ AGRO, Switzerland) for supporting the work.     

X-ray studies of the binding of Cibacron blue F3GA to liver alcohol dehydrogenase

The binding of Cibacron F3GA to orthorhombic crystals of liver alcohol dehydrogenase has been studied to 0.37-nm resolution. Similarities in the binding of this dye were found for rings B, C and D with the binding of the coenzyme NAD+. However, ring A of the dye and the nicotinamide ribose part of the coenzyme are quite differently bound to the enzyme.     

Affinity partitioning of phosphofructokinase from baker's yeast using polymer-bound Cibacron blue F3G-A

1. Phosphofructokinase from baker's yeast is partitioned between the phases of an aqueous two-phase system, containing dextran (Mr = 500000) and poly(ethyleneglycol) (Mr = 6000), in favour of the dextran-rich phase. By covalent binding of the dye Cibacron blue F3G-A to poly(ethyleneglycol) the enzyme can be extracted to the phase rich in this polymer, i.e. affinity partitioning. 2. The affinity partitioning effect, measured as the logarithmic increase of the partition coefficient by introducing polymer-bound Cibacron blue, depends on several factors. The influence of dye-polymer concentration, polymer concentration, polymer molecular weight, kind of salt and salt concentration, pH and temperature has been studied. 3. The effect of ATP, ADP, AMP, ITP, fructose 1,6-bis-phosphate and fructose 6-phosphate show large differences in the binding strength of these substances to the Cibacron blue binding sites. AMP cannot compete with Cibacron blue while ATP is strongly competing. 4. The use of affinity partitioning for enzyme isolation and determination of ligand binding is discussed, as well as possible mechanisms concerning this type of liquid/liquid extraction.     

A microassay for the determination of binding parameters of estrogen and androgen receptors employing affinity immobilization on Cibacron blue 3GA-Sepharose 6B

The problems of currently available ligand-binding assays for sex-steroid receptor proteins include the relatively large mass of tissue required, the interference by sex hormone-binding globulin (SHBG), and use in the androgen receptor (AR) assay of the unstable synthetic ligand methyltrienolone. To overcome these difficulties the stabilizing effect of the dye Cibacron blue 3GA on AR and estrogen receptor (ER) proteins, and its ability to bind to these proteins, was utilized in developing an assay system for each receptor that could be applied to small samples. Use of the affinity gel Cibacron blue 3GA-Sepharose 6B (Blue gel) for the immobilization of AR, ER, and the steroid ligands bound to these receptors in the standard two-tier column assay system enabled the use of a 1:100 (original tissue weight:volume) concentration, making possible full (5-7 point) Scatchard analysis on tissue specimens of a mass as low as 15-20 mg. Significant stabilization of AR and ER was observed and association constants for these receptors were of a similar order of magnitude to those obtained either by Sephadex LH-20 gel filtration or the dextran-coated charcoal adsorption technique. Inactivation by dilution was shown to be largely prevented based on results obtained with cytosol concentrations from 1:5 to 1:100 (original tissue weight:volume). Because Blue gel does not bind SHBG, the natural steroid 5 alpha-androstan-17 beta-ol-3-one (DHT) may be employed as a ligand in the AR assay.(ABSTRACT TRUNCATED AT 250 WORDS)     

Characterization of fragments of human albumin purified by Cibacron blue F3GA affinity chromatography.

Controlled limited proteolysis of human plasma albumin (0.3 mM; 37 degrees C; 15 min; pH 3.7) with pepsin [pepsin/albumin, 1:1000 (w/w)] in the presence of octanoic acid (4.2 mM) yields at least 14 fragments in the range of 5000--56000 Da. By utilizing a combination of conventional and affinity-chromatographic procedures, two fragments with mol. wts. 25000 and 27000 were purified to more than 99% homogeneity. The larger fragment consists of a continuous polypeptide chain and has been shown to contain the primary bilirubin-binding site. The small fragment contains an internal cleavage site. On the basis of amino acid compositions, N-terminal sequences, C-terminal sequences, molecular weights and other internal markers the locations of these fragments within the known sequence of human albumin were determined to be residues 49--308 for the 27000 Da peptide and 309--585 for the 25000 Da peptide. Peptide 309--585 contains an internal cleavage site and appears to be missing residues 408--423. These non-overlapping fragments should be useful for investigations of individual ligand-binding sites and for the determination of antigenic sites.     

Interaction of Cibacron Blue F3GA with Escherichia coli DNA polymerase I and with T4 DNA polymerase.

Individual rapid procedures for the enrichment of Escherichia coli DNA polymerase I and of bacteriophage T4 DNA polymerase free of endonuclease activity are described using Blue dextran-Sepharose chromatography. The blue dye of Blue dextran-Sepharose selectively binds to the deoxynucleoside triphosphate substrate site of the E. coli but not the T4 enzyme indicating that the catalytic sites of these two enzymes which catalyze the same polymerization reaction in vitro are quite distinct.     

Affinity interaction of hydroxypyruvate reductase from Methylophilus spp. with Cibacron blue F3GA-derived poly(HEMA EGDMA) microspheres: partial purification and characterization

A methylotrophic hydroxypyruvate reductase was partially purified and characterized from Methylophilus spp. using the biomimetic dye, Cibacron Blue F3FA attached to poly(HEMA-EGDMA) microspheres. The absorption capacities of the dye-affinity microspheres were determined by changing pH and the concentration of the proteins in the adsorption medium. Hydroxypyruvate reductase was desorbed from the dye-affinity support specifically with 2 mM NADH solution. The enzyme was purified 10·4-fold with 47% yield. The molecular mass and subunit molecular mass of the enzyme was estimated to be 75 kDa and 37 kDa on the basis of its mobility in polyacrylamide and SDS-polyacrylamide gels, respectively. This suggested a homogeneous dimer structure. The optimal pH was between 5·0 and 7·0, and the maximum enzyme activity was obtained at 50°C. The K_m values of hydroxpyruvate reductase were 0·222 mM for hydroxpyruvate and 0·067 mM for NADH.     

Interaction of Cibacron blue F3GA and polynucleotides with ricin A-chain, 60 S ribosomal subunit-inactivating protein

Cibacron blue F3GA, a sulfonated polyaromatic blue dye, inhibited the ability of ricin A-chain to inactivate ribosomes. Difference-spectroscopic study revealed that the dye bound to the A-chain (Kd = 0.72 microM), producing a difference spectrum with a single maximum at 688 nm and two minima at 585 and 628 nm. Such a significant difference spectrum was not observed in the presence of ricin B-chain or intact ricin, neither of which can inactivate ribosomes. Modification of arginine residues in the A-chain with phenylglyoxal showed a correlation between the loss of inhibitory activity on protein synthesis and the loss of difference absorbance produced by the dye-A-chain interaction. Both losses occurred significantly at an early stage of the modification. Furthermore, the dye protected the A-chain against a loss of its inhibitory activity resulting from the modification of arginine residues. These results suggest that the same arginine residues participate both in the interaction with the dye and in the inactivation of ribosomes. Based on these data, the dye appears to interact with the active site of the A-chain. Addition of several polynucleotides, namely rRNA, tRNA, poly(U) and DNA, to the dye-A-chain complex resulted in a marked displacement of the dye, whereas mono- and dinucleotides had little or no effect on the dye-A-chain interaction. These findings indicate the possible existence of a polynucleotide binding site in the active site of the A-chain. A combination of these and other results suggests that the A-chain recognizes and acts on some part of RNA of the 60 S ribosomal subunit.     

Cibacron blue 3G-A inhibits cell separation of gram-positive bacteria

A triazine dye, Cibacron blue 3G-A (CB), is an inhibitor of cell separation of staphylococcal spp. therefore, we examined the effect of CB on growth of grampositive bacteria other than Staphylococcus. CB added to the medium of growing cultures of strains of genus Micrococcus, Streptococcus, Lactobacillus and Bacillus caused inhibition of cell separation. Moreover, in case of Bacillus and Lactobacillus, individual cells were elongated as filament. Strains of the genus Micrococcus were as sensitive to CB as genus Staphylococcus in which the minimum concentrations of CB needed for inhibition of cell separation ranged from 15 to 100 M. Other strains belong to genus Streptococcus, Bacillus and Lactobacillus were less sensitive; the minimum concentrations were 100 M–25 mM.     

Use of Cibacron Blue--Sepharose 6B to detect modifications of the non-allosteric 6-phosphofructokinase from Escherichia coli K-12

In crude cell-free extracts of aerobically grown E. coli K-12, the non-allosteric form of 6-phosphofructokinase has a tetrameric molecular weight 140 000 with a low affinity (less than 5%) for the blue dextran chromophore--Cibacron Blue. The allosteric form has the same tetrameric molecular weight, but possesses a strong affinity for the blue dextran chromophore. Under conditions of prolonged storage, purification procedures of mild heat treatment (50 degrees C), the non-allosteric form converts to an active dimer (mol. wt 67 000), which binds to Cibacron Blue (less than 90%). Acid precipitation plus heat treatment prevents the conversion to the dimeric form and retains low Cibacron Blue affinity. These results are consistent with the isolation of a low molecular weight form and suggest that the inherent lability of this enzyme might be due to both non-specific proteolytic modification and a weak quaternary structure.     

A general method for fractionation of plasma proteins. Dye-ligand affinity chromatography on immobilized Cibacron blue F3-GA.

The chromatographic behaviour of 27 different plasma proteins on fractionation of human plasma on immobilized Cibacron Blue F3-GA was studied. The column was eluted by using a three-step procedure. First, a low-molarity buffer (30 mM-H3PO4/Na3PO4, pH 7.0, I0.053) was used, then a linear salt gradient (0-1 M-NaCl in the buffer above) was applied, followed by a wash with two bed volumes of 1.0 M-NaCl. Finally, bound proteins were 'stripped' with 0.5 M-NaSCN. Up to 1 ml of whole plasma could be loaded per 5 ml bed volume. No denaturation of proteinase inhibitors or complement fractions was observed. The recovery of individual proteins ranged between 52 and greater than 95%. Enrichment of four individual plasma components (alpha 1-antitrypsin, caeruloplasmin, antithrombin III and haemopexin) was between 10-fold and 75-fold. These results indicate that chromatography on immobilized Cibacron Blue F3-GA can be a useful initial step in the purification of plasma proteins.     

The kinetic mechanism of phage T4 DNA-[N6-adenine]-methyltransferase

Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the GATC recognition site catalyzed by the phage T4 DNA-[N6-adenine]-methyltransferase (MTase) [EC 2.1.1.72] showed that the reverse reaction is at least 500 times slower than the direct one. The overall pattern of product inhibition corresponds to an ordered steady-state mechanism following the sequence SAM decreases DNA decreases metDNA increases SAH increases (S-adenosyl-L-homocysteine). Pronounced inhibition was observed at high concentrations of the 20-meric substrate duplex, which may be attributed to formation of a dead-end complex MTase-SAH-DNA. In contrast, high SAM concentrations proportionally accelerated the reaction. Thus, the reaction may include a stage whereby the binding of SAM and the release of SAH are united into one concerted event. Computer fitting of alternative kinetic schemes to the aggregate of experimental data revealed that the most plausible mechanism involves isomerization of the enzyme.     

Single turnover kinetics of phage T4 DNA-(N6-adenine)methyltransferase

Interaction of T4 DNA-(N6-adenine)-methyltransferase [EC 2.1.1] was studied with a variety of synthetic oligonucleotide substrates containing the native recognition site GATC or its modified variants. The data obtained in the decisecond and second intervals of the reaction course allowed for the first time the substrate methylation rates to be compared with the parameters of the steady-state reaction. It was established that the substrate reaction proceeds in two stages. Because it is shown that in steady-state conditions T4 MTase forms a dimeric structure, the following sequence of events is assumed. Upon collision of a T4 MTase monomer with an oligonucleotide duplex, an asymmetrical complex forms in which the enzyme randomly oriented relative to one of the strands of the specific recognition site catalyzes a fast transfer of the methyl group from S-adenosylmethionine to the adenosine residue (k1 = 0.21 s-1). Simultaneously, a second T4 MTase subunit is added to the complex, providing for the continuation of the reaction. In the course of a second stage, which is by an order of magnitude slower (k2 = 0.023 s-1 for duplex with the native site), the dimeric T4 MTase switches over to the second strand and the methylation of the second residue, target. The rate of the methyl group transfer from donor, S-adenosylmethionine, to DNA is much higher than the overall rate of the T4 MTase-catalyzed steady-state reaction, although this difference is considerably less than that shown for EcoRI Mtase. Substitutions of bases and deletions in the recognition site affect the substrate parameters in different fashions. When the GAT sequence is disrupted, the proportion of the initial productive enzyme-substrate complexes is usually sharply reduced. The flipping of the adenosine residue, a target for the modification in the recognition site, revealed by fluorescence titration, upon interaction with the enzyme supports the existing notions about the involvement of such a DNA deformation in reactions catalyzed by various DNA-MTases.     

The Kinetic Mechanism of Phage T4 DNA-[N6-Adenine]-Methyltransferase

Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the GATC recognition site catalyzed by the phage T4 DNA-[N6-adenine]-methyltransferase (MTase) [EC 2.1.1.72] showed that the reverse reaction is at least 500 times slower than the direct one. The overall pattern of product inhibition corresponds to an ordered steady-state mechanism following the sequence SAMDNAmetDNASAH (S-adenosyl-L-homocysteine). Pronounced inhibition was observed at high concentrations of the 20-meric substrate duplex, which may be attributed to formation of a dead-end complex MTase–SAH–DNA. In contrast, high SAM concentrations proportionally accelerated the reaction. Thus, the reaction may include a stage whereby the binding of SAM and the release of SAH are united into one concerted event. Computer fitting of alternative kinetic schemes to the aggregate of experimental data revealed that the most plausible mechanism involves isomerization of the enzyme.     

A differential scanning calorimetric study of the binding of sulfate ion and of Cibacron blue F3GA to yeast phosphoglycerate kinase

In continuation of earlier work [Hu, C. Q., & Sturtevant, J.M. (1987) Biochemistry 26, 178-182], differential scanning calorimetry has been employed in a study of the effects on the thermal denaturation of yeast phosphoglycerate kinase of two inhibitors of the enzyme, sulfate ion and the dye Cibracron blue F3GA. Sulfate ion, as is usual with ligands that dissociate during unfolding of the host protein, raises t1/2, the temperature of half-completion of the denaturation, has only a modest effect, stemming from the enthalpy of dissociation of the ligand, on the enthalpy of denaturation, and has little or no effect on the heat capacity change resulting from denaturation. In sharp contrast, Cibacron blue F3GA lowers t1/2 and drastically decreases both the enthalpy and heat capacity changes due to denaturation. The DSC results with sulfate ion are consistent with previous kinetic data [Scopes, R. K. (1978) Eur. J. Biochem. 91, 119-129; Khamis, M. H., & Larsson-Raznikiewicz, M. (1981) Biochim. Biophys. Acta 657, 190-194], which indicate two binding sites for sulfate ion at one of which the ligand acts as a competitive inhibitor. The results with Cibacron blue F3GA indicate that the dye induces a major destabilizing structural change in the enzyme in addition to rendering it enzymically inactive.