Interaction of myosin subfragment 1 with Cibacron Blue F3GA

Cibacron Blue F3GA and its immobilized derivatives have been shown before to bind and inhibit nucleotide-dependent enzymes and, among them, myosin subfragment 1. Experiments have been carried out to examine the mechanism of the subfragment 1--dye interaction. Binding of subfragment 1 to immobilized dye (Affi-Gel Blue) does not involve the ATP binding site on myosin. Subfragment 1 hydrolyzes MgATP and CaATP while bound to the Affi-Gel Blue column. Inactivated subfragment 1, which contains [3H]ADP noncovalently trapped at the active site, binds and elutes from the Affi-Gel Blue column in the same manner as unmodified, active protein. Free Cibacron Blue inhibits the ATPase activity of subfragment 1. The inhibition is pH, salt, and time dependent. Complete inhibition correlates with the noncovalent binding of four to five dye molecules per mole of subfragment 1. Three to four of these dye molecules can be preferentially removed from subfragment 1 in the presence of 1 M KCl without relieving the inhibition. This inhibition, which can be traced to one dye molecule per subfragment 1, is reversible and is facilitated in the presence of MgADP and MgATP, suggesting that the dye does not bind at the active site of subfragment 1. Our observations are explained in terms of hydrophobic and electrostatic protein--dye interactions.     

Interaction between transcobalamin II and immobilized Cibacron Blue F3GA

Human serum transcobalamin II (TC II), a vitamin B₁₂ (Cbl) transport protein, complexes with Cibacron Blue F3GA, a reactive blue dye which can bind to proteins that require nucleotides as cofactors. Apo-TC II and holo-TC II both bind, but intrinsic factor (IF) and R-type binders of Cbl do not. Other mammalian species TC II also complex with the dye. Greater than 87% of the applied TC II-CN-[⁵⁷Co]Cbl remains bound to the dye even at pH 4.0. At pH values below this, the CN-[⁵⁷Co]Cbl dissociates off TC II which remains bound to the dye. High salt concentrations will break the TC II-dye complex. Ionic forces were considered not to be involved since complexing also occurred at pH 9.0, 2.5 pH units above the isoelectric point of TC II. Failure to dissociate the TC II-dye complex with 50% glycerol makes hydrophobic interactions unlikely. In addition to the potential uses of TC II-Cibacron Blue F3GA complexes in a total scheme for protein purification, the possibility that TC II is a nucleotide-requiring protein should be explored.     

Dye-Ligand Affinity Chromatography: The Interaction of Cibacron Blue F3GA® with Proteins and Enzyme

Abstract

The dye Cibacron Blue F3GA has a high affinity for many proteins and enzymes. It has therefore been attached to various solid supports such as Sephadex, Sepharose, polyacrylamide, and the like. In the immobilized form the dye has rapidly been exploited as an affinity chromatographic medium to separate and purify a variety of proteins including dehydrogenases, kinases, serum albumin, interferons, several plasma proteins, and a host of other proteins. Such a diversity shown by the blue dye in binding several unrelated classes of proteins has generated considerable work in terms of studies of the chromophore itself and also the immobilized ligand. As a prelude to realizing the full potential of the immobilized Cibacron Blue F3GA, an understanding of the basic interactions of the dye with its surroundings must be gained. It has been recognized that the dye is capable of hydrophobic and/or electrostatic interactions at the instance of the ambient conditions. The study of interactions of the dye with salts, solvents, and other small molecules indicates the nature of the interactions of the dye with different kinds of groups at the interacting sites of proteins. The review will cover such interactions of the dye with the proteins, the interactions of the proteins with the immobilized ligand, and the media used to elute the bound protein in several cases, and thus consolidate the available information on such studies into a cogent and comprehensive explanation.     

Adsorption of papain with Cibacron Blue F3GA carrying chitosan-coated nylon affinity membranes

Covalent coupling of chitosan (CS) to activated nylon membrane was performed after the reaction of the microporous nylon membrane with formaldehyde. Non-specific adsorption on the CS-coated nylon membrane decreased greatly, compared with plain nylon membrane. The dye Cibacron Blue F3GA (CB F3GA) as a ligand was then covalently immobilized on the CS-coated membranes. Physical properties of the composite membrane and its applications in affinity membrane chromatography were examined. The contents of CS and CB F3GA-attached membranes were 89.6 mg/g nylon membrane and 146.1 micromol/g nylon membrane, respectively. These CB F3GA-attached composite membranes were used in the papain adsorption studies. Higher papain adsorption capacity, up to 235.3mg/g affinity membrane, was obtained. The adsorption isotherm fitted the Freundlich model well. Significant amount of the adsorbed papain (about 94.3%) was eluted by 1.0M NaSCN at pH 9.0. Experiments on regeneration and dynamic adsorption were also performed. It appears that CB F3GA-CS nylon membranes can be applied for papain separation without causing any denaturation.     

Hazards in the use of Cibacron Blue F3GA in studies of proteins.

Cibacron Blue F3GA from several commercial sources is shown to be heterogeneous. This crude dye inactivates both phosphoglycerate kinase and isoleucyl-tRNA synthetase. Purification of Cibacron Blue F3GA to homogeneity results in a dramatic decrease in inactivation of these enzymes. The inactivation is shown to be due to covalent modification of phosphoglycerate kinase and probably isoleucyl-tRNA synthetase by a minor component present in crude Cibacron Blue F3GA.     

Binding of Cibacron Blue F3GA to flavocytochrome b2 from baker's yeast.

1. Flavin-free cytochrome b2 has been prepared by rapid Sephadex filtration at acid pH. The method, which yields an apo-enzyme with high reconstitution potential and has several advantages over previously used procedures, is described in detail. 2. Flavin-free cytochrome b2 thus prepared is retained by blue-dextran-bound Sepharose. It can be eluted by an increase in ionic strength, by dilute ethylene glycol and specifically by low concentrations of FMN. The holoenzyme is not retarded at all. 3. Both flavin-free and holocytochrome b2 bind Cibacron blue F3GA with appearance of distinct difference spectra. Cibacron blue is an inhibitor for the holoenzyme, it shows mixed type inhibition with respect to lactate. 4. It is concluded that there are two types of binding sites for Cibacron blue F3GA on flavocytochrome b2. Both possess ionic and hydrophobic character; one of them, which is the flavin binding site, is only available in the absence of the cofactor. Taken together these results may mean that the enzyme possesses a local flavin-binding structure similar to the 'dinucleotide fold'.     

Repair of degraded duplex DNA from prehistoric samples using Escherichia coli DNA polymerase I and T4 DNA ligase.

The most notable feature of DNA extracted from prehistoric material is that it is of poor quality. Amplification of PCR products from such DNA is consequently an exception. Here we present a simple method for the repair of degraded duplex DNA using the enzymes Escherichia coli DNA polymerase I and T4 DNA ligase. Adjacent sequences separated by nicks do not split up into intact strands during the denaturation step of PCR. Thus the target DNA is refractory to amplification. The proposed repair of nicked, fragmented ancient DNA results in an increase of amplification efficiency, such that the correct base order of the respective nuclear DNA segment can be obtained.     

Lipase purification by affinity precipitation with a thermo-responsive polymer immobilized Cibacron Blue F3GA ligand

A thermo-responsive polymer (P_NNB) was synthesized with lower critical solution temperature 27.5°C and over 95% recovery. The adsorption of porcine pancreatic lipase on Cibacron Blue F3GA-conjugated P_NNB (P_NNB-CB) closely followed the bi-Langmuir adsorption isotherm. The maximum adsorption capacity was found at pH 5.0, with a ligand density of 18.4 μmol/g polymers. The optimized eluent was a 0.01 M phosphate buffer solution at pH 8.0 containing 20% ethylene glycol. Six adsorptiondesorption recycles indicated excellent reusability of the affinity adsorbent. P_NNB-CB was applied to separate porcine pancreatic lipase from its crude material giving a lipase activity recovery of 81.6% with a 16-fold purification factor. Lipase could be purified to single-band purity, according to gel electrophoresis. The purification strategy is therefore feasible and efficient for purifying proteins of interest.     

Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I

A DNA template containing a single ethyl phosphotriester was replicated in vitro by the bacteriophage T4 DNA polymerase and by Escherichia coli DNA polymerase I (DNA pol I). Escherichia coli DNA pol I bypassed the lesion efficiently, but partial inhibition was observed for T4 DNA polymerase. The replication block produced by the ethyl phosphotriester was increased at low dNTP concentrations and for a mutant T4 DNA polymerase with an antimutator phenotype, increased proofreading activity, and reduced ability to bind DNA in the polymerase active center. These observations support a model in which an ethyl phosphotriester impedes primer elongation by T4 DNA polymerase by decreasing formation of the ternary DNA polymerase–DNA–dNTP complex. When primer elongation is not possible, proofreading becomes the favored reaction. Apparent futile cycles of nucleotide incorporation and proofreading, the idling reaction, were observed at the site of the lesion. The replication block was overcome by higher dNTP concentrations. Thus, ethyl phosphotriesters may be tolerated in vivo by the up-regulation of dNTP biosynthesis that occurs during the cellular checkpoint response to blocked DNA replication forks.     

Interaction of DNA polymerase I of Escherichia coli with nucleotides. Antagonistic effects of single-stranded polynucleotide homopolymers

Binding of deoxyribonucleoside 5'-triphosphates to DNA polymerase I of Escherichia coli was measured by using a microscale nonequilibrium dialysis method. It allowed rapid and economic measurement of dissociation constants, with negligible interfering side reactions. A stoichiometry of 1 mol of nucleoside 5'-triphosphate/mol of DNA polymerase was measured, and the occurrence of a single binding site was established, for which the nucleotides competed in the binary complex with the polymerase. Binding affinities decreased in the order dGTP greater than or equal to dATP greater than dCTP congruent to dTTP. These results are in agreement with previous findings [Englund, P. T., Huberman, J. A., Jovin, T. M., & Kornberg, A. (1969) J. Biol. Chem. 244, 3038-3044] except that, in a few cases, values of dissociation constants were smaller by factors of 2-3. The cations Mg2+ and Mn2+, as well as spermine, slightly enhanced complex stability at low levels and decreased it at high concentrations, while NaCl and Hg2+ had only destabilizing effects. Recognition between nucleoside 5'-triphosphates and nucleotide templates was studied by titration of the polymerase-[3H]dGTP complex with polynucleotide homopolymers. Complementary poly(dC) did not affect binding of dGTP, and non-complementary templates caused rejection of the nucleotide. Rejection of dGTP followed a saturation dependence with an equivalence of 110 +/- 10 monomer units of polynucleotides bound per molecule of DNA polymerase. The results favor a model by which recognition arises chiefly from the stereogeometrical fit of complementary template and nucleoside 5'-triphosphate into a rigid binding site.     

Interaction of Escherichia coli DNA polymerase I with azidoDNA and fluorescent DNA probes: identification of protein-DNA contacts

The synthesis of an azidoDNA duplex and its use to photolabel DNA polymerases have been previously described (Gibson & Benkovic, 1987). We now present detailed experiments utilizing this azidoDNA photoprobe as a substrate for Escherichia coli DNA polymerase I (Klenow fragment) and the photoaffinity labeling of the protein. The azidoDNA duplex is an efficient substrate for both the polymerase and 3'----5' exonuclease activities of the enzyme. However, the hydrolytic degradation of the azido-bearing base is dramatically impaired. On the basis of the ability of these duplexes to photolabel the enzyme, we have determined that the protein contacts between five and seven bases of duplex DNA. Incubation of azidoDNA with the Klenow fragment in the presence of magnesium results in the in situ formation of a template-primer with the azido-bearing base bound at the polymerase catalytic site of the enzyme. Photolysis of this complex followed by proteolytic digestion and isolation of DNA-labeled peptides results in the identification of a single residue modified by the photoreactive DNA substrate. We identify Tyr766 as the modified amino acid and thus localize the catalytic site for polymerization in the protein. A mansyl-labeled DNA duplex has been prepared as a fluorescent probe of protein structure. This has been utilized to determine the location of the primer terminus when bound to the Klenow fragment. When the duplex contains five unpaired bases in the primer strand of the duplex, the primer terminus resides predominantly at the exonuclease catalytic site of the enzyme. Removal of the mismatched bases by the exonuclease activity of the enzyme yields a binary complex with the primer terminus now bound predominantly at the polymerase active site. Data are presented which suggest that the rate-limiting step in the exonuclease activity of the enzyme is translocation of the primer terminus from polymerase to exonuclease catalytic sites.     

Either bacteriophage T4 RNase H or Escherichia coli DNA polymerase I is essential for phage replication.

Bacteriophage T4 rnh encodes an RNase H that removes ribopentamer primers from nascent DNA chains during synthesis by the T4 multienzyme replication system in vitro (H. C. Hollingsworth and N. G. Nossal, J. Biol. Chem. 266:1888-1897, 1991). This paper demonstrates that either T4 RNase HI or Escherichia coli DNA polymerase I (Pol I) is essential for phage replication. Wild-type T4 phage production was not diminished by the polA12 mutation, which disrupts coordination between the polymerase and the 5'-to-3' nuclease activities of E. coli DNA Pol I, or by an interruption in the gene for E. coli RNase HI. Deleting the C-terminal amino acids 118 to 305 from T4 RNase H reduced phage production to 47% of that of wild-type T4 on a wild-type E. coli host, 10% on an isogenic host defective in RNase H, and less than 0.1% on a polA12 host. The T4 rnh(delta118-305) mutant synthesized DNA at about half the rate of wild-type T4 in the polA12 host. More than 50% of pulse-labelled mutant DNA was in short chains characteristic of Okazaki fragments. Phage production was restored in the nonpermissive host by providing the T4 rnh gene on a plasmid. Thus, T4 RNase H was sufficient to sustain the high rate of T4 DNA synthesis, but E. coli RNase HI and the 5'-to-3' exonuclease of Pol I could substitute to some extent for the T4 enzyme. However, replication was less accurate in the absence of the T4 RNase H, as judged by the increased frequency of acriflavine-resistant mutations after infection of a wild-type host with the T4 rnh (delta118-305) mutant.     

Interaction of Cibacron Blue F3GA with glutamine synthetase: use of the dye as a conformational probe. 2. Studies using isolated dye fractions

By means of column chromatography on silicic acid, commercial preparations of Cibacron Blue F3GA have been resolved into four major subfractions (fractions I-IV). The difference spectrum between free dye and dye bound to any given form of Escherichia coli glutamine synthetase (GS) is different for each dye fraction. Moreover, uniquely different spectral perturbations are associated with the binding of any one dye fraction to the taut, relaxed, dissociated, or oxidized forms of GS. On the basis of the magnitude of the differences in the difference spectra between free dye and the dye-GS complexes, fraction II is most suitable for monitoring the interconversion of the relaxed and taut forms of GS. Fraction II can also be used to measure the fraction of oxidized (inactive) GS that is present in apparently homogeneous GS preparations. In contrast to the other three fractions, the difference spectrum obtained immediately following the binding of fraction I to GS undergoes a time-dependent change which is associated with the covalent attachment of the dye to the enzymes. Fractions II, III, and IV apparently bind to the nucleotide binding site on GS because the difference spectrum obtained with these fractions can be quenched by the subsequent addition of 1-2 mM ADP. The primary but not the secondary complex formed between GS and fraction I can also be destroyed by ADP.     

Analytical evaluation of the purity of commercial preparations of Cibacron Blue F3GA and related dyes

The composition and purity of three commercial preparations of the widely used affinity chromatography ligand Cibacron Blue F3GA have been evaluated by TLC and by paired-ion reversed-phase HPLC and were found to contain several chromophoric species. Stepwise synthesis of the reported dye structure showed that only one commercial preparation contained any actual Cibacron Blue F3GA, and that it was present only in minor amounts. In all three preparations the major component appears to be the dichlorotriazinyl precursor of Cibacron Blue F3GA. Commercial samples of the related dyes Procion Blue MX-3G and Procion Blue MX-R are also highly heterogeneous. In addition, our experiments suggest that TLC results must be evaluated carefully to ensure that catalytic surface activity of alumina and silica has not created ghost bands.     

天花粉蛋白与CibacronBlueF_3GA结合特性的研究

 天花粉蛋白与ＣｉｂａｃｒｏｎＢｌｕｅＦ_３ＧＡ结合特性的研究何贤辉,柯一保,孙汛,聂慧玲（中国科学院上海细胞生物学研究所,上海２０００３１）天花粉蛋白（Ｔｒｉｃｈｏｓａｎｔｈｉｎ,简称ＴＣ８）是从葫芦科植物栝楼（Ｔｂｅｈｏｓａｎｔｈｅｓｋｉｒｉｌｏｗ?..     

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.     

Interaction of Cibacron Blue F3GA with glutamine synthetase: use of the dye as a conformational probe. 1. Studies using unfractionated dye samples

Cibacron Blue F3GA dye has been used to probe subtle conformational changes in protein structure associated with the conversion of Escherichia coli glutamine synthetase (GS) between relaxed, taut, oxidized, and dissociated forms. Binding of the dye to each form of the enzyme elicits a different spectral perturbation of the dye which can be detected by difference spectroscopy. By following time-dependent changes in the difference spectrum associated with the binding of dye to the enzyme, it was demonstrated that dissociation of subunits provoked either by urea or by relaxation of the enzyme at pH 8.5 is a multiphasic process. In the presence of 3-4 M urea, dissociation of taut GS is associated with an almost instantaneous, transient increase in absorbancy of the difference spectrum at 638 nm and, after a lag, by a progressive decrease in absorbancy at 585 nm and an increase at 700 nm. The kinetics of these changes vary as a function of temperature, pH, and the concentrations of KCl, MnCl2, and urea, probably reflecting differences in the rates of GS relaxation and in the formation of aggregates of intermediate sizes. Results of direct binding measurements show that the taut and relaxed forms of GS can bind only 1-1.3 equiv of dye per subunit, whereas dissociated subunits bind up to 3.0 equiv per subunit. The Kd of the dye-taut GS complex as calculated from binding data was 0.55 microM. The binding of dye to taut GS was inhibited by its substrate, ADP, and by the allosteric effectors AMP and tryptophan. On the basis of the abilities of ADP, AMP, and tryptophan to inhibit the binding of dye to GS, dissociation constants of the respective GS-ligand complexes were 2.4, 121, and 1170 microM, respectively, in good agreement with previously determined values. From the difference spectra obtained between a given concentration of dye in a 5.0-cm cell and 10 times that concentration in a 0.5-cm cell, it was established that at concentrations greater than 5 microM a significant fraction of the dye is present as stacked aggregates. Because only the dye monomer binds to GS, the difference spectrum between dye and dye bound to GS is due in part to GS-promoted shifts in the equilibrium between stacked and unstacked dye molecules. Consequently, with increasing dye concentrations, the amplitude of the dye vs. dye + GS difference spectrum can continue to increase, even after the GS becomes saturated with dye.(ABSTRACT TRUNCATED AT 400 WORDS)