UDP-glucose dehydrogenase: substrate binding stoichiometry and affinity

Precise structural parameters of polyribonucleotides single stranded helices are determined as well as those of double stranded helices of poly 2′-O-methyl A and of poly A at neutral and acid pH. Infrared linear dichroism investigations indicate the similarity of the conformation of the sugar-phosphate backbone of these single and double stranded helices. The angles of the phosphate group for single stranded helix at neutral pH is found to be oriented at 48° for the 02P02 bisector and at about 65° for the 02–03 line to the helix axis. Similar values were found for double stranded poly A helix at acid pH. These structural parameters obtained for the first time on single stranded polynucleotide helices are proposed to be valid for other similar helical chains such as poly A segments of nuclear or messenger RNA and single stranded CCA acceptor end of transfer RNA.     

Resolution and reconstitution of Rhodospirillum rubrum pyridine dinucleotide transhydrogenase: localization of substrate binding sites.

Butanedione in the presence of borate buffer reversibly inhibits Rhodospirillum rubrum chromatophore transhydrogenase complex and the separated membrane-bound and soluble factor components of the complex. NADP⁺ completely protected against inactivation of the membrane-bound component, whereas NAD⁺ was without effect. Soluble factor was maximally protected only partially by either NAD⁺ or NADP⁺, but a mixture of the substrates afforded complete protection. NADP⁺-dependent association of soluble factor with factor-depleted membranes was markedly decreased after incubation of membranes with butanedione in the absence, but not in the presence, of NADP⁺. Soluble factor was bound to agarose-NAD and was eluted by NAD⁺, but not by NADP⁺. These results demonstrate the presence of at least three nicotinamide adenine dinucleotide binding sites on R. rubrum transhydrogenase complex, including separate NADP and NAD binding sites on soluble factor and a NADP binding site on the membrane-bound component.     

Biphasic saturations of binding proteins can be the result of a competitive inhibition of substrate fixation.

A mathematical model is proposed which explains some biphasic saturations of Binding Proteins by their substrates through an effect of a competitive inhibition. The inhibitor can be the substrate itself especially when the retention phenomenon is occuring. This model has been verified with two periplasmic Binding Proteins of Escherichia coli: the Glutamine Binding Protein and the Leucine-Isoleucine-Valine Binding Protein. A significant connection is found between experimental results and the hypothesis.     

Opiate binding in rat hearts: modulation of binding after hemorrhagic shock

[3H] Diprenorphine was used to measure binding in sectioned rat hearts. Saturable binding for concentrations up to about 20 nM was obtained in the right atrium and ventricle. Unlabeled diprenorphine displaced bound [3H] diprenorphine most effectively in the right atrium (up to 55%), as compared to less than 27% in the right ventricle and the remaining parts of the heart. Scatchard analysis of the binding in the right atrium revealed cooperative binding. The delta agonist [D-Ala2,D-Leu3] enkephalin, the kappa agonist ethylketocyclazocine, and levorphanol, but not the mu agonist [D-ala2,MePhe4,Gly-(ol)5] enkephalin or dextrophan competed variably with [3H]diprenorphine for the binding in the right atrium and ventricle. A significant decrease in binding was observed in the right atrium (-66%) and ventricle (-45%) of hearts removed from rats 2 h after hemorrhagic shock; 24 h after shock, recovery of binding was found. This novel observation suggests that the diprenorphine binding sites in the heart may be physiologically active receptors, involved in regulation of peripheral cardiovascular processes.     

Ligand-induced alterations in the reactivity of sulfhydryl groups and the structure of bovine liver glutamate dehydrogenase

The fluorogenic probe 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-C1) was employed as an environmentally sensitive reporter label for free sulfhydryl groups of bovine liver glutamate dehydrogenase. A maximum of six -SH groups per subunit was titrated in Tris and borate buffers (pH 7.8) in 2 h but there was no reaction in the presence of phosphate buffer. The rate and extent of -SH reactivity was changed significantly by one of the substrates and some allosteric effectors. Adenosine nucleotides, NADH, and α-ketoglutarate promoted conformational alterations in glutamate dehydrogenase such that -SH groups were rendered virtually unreactive in [enzyme-ADP], [enzyme-NADH], and [enzyme-α-ketoglutarate]binary complexes. GTP, a negative allosteric modulator, showed no effect on -SH exposure. Measurements of protein circular dichroism spectra and catalytic activity in conjunction with -SH reactivity demonstrated a direct relationship between structural stability, biological activity, and ligand-induced conformational changes. The ligands that strongly protected the enzyme from reaction with NBD-C1 concomitantly maintained its structural and functional integrity.     

Quantitative determination of myeloperoxidase using tetramethylbenzidine as substrate

Tetramethylbenzidine, a noncarcinogenic, nonmutagenic derivative of benzidine, has been used as a substrate to assay myeloperoxidase. The assay is sensitive to 0.1 μg of enzyme and can be used to quantitate myeloperoxidase over a pH range of 4.4 to 7.4.     

Rapid procedures for determination of endo-N-acetyl-alpha-D-galactosaminidase in Clostridium perfringens, and of the substrate specificity of exo-beta-D-galactosidases

Culture fluid of Clostridium perfringens hydrolyzed the synthetic, chromogenic substrates beta-Gal-(1 leads to 3)-alpha-GalNAc-1 leads to OPh and beta-Gal-(1 leads to 3)-alpha-GalNAc-1 leads to OC6H4-NO2-o or -p to beta-Gal-(1 leads to 3)-GalNAc and the aglycon. Such assays facilitated the characterization and purification of this endo-N-acetyl-alpha-D-galactosaminidase activity. This activity was purified 1200-fold by fractionation with ammonium sulfate and chromatography on columns of Sephadex-G200, DEAE-Sephadex, and hydroxylapatite. The final preparation showed activity over a broad range of pH, with an optimum at 9.0, but less-pure material had two pH optima, 4.0 and 9.0. Another assay method, which employed the synthetic, chromogenic substrates beta-Gal-(1 leads to 3)-beta-GlcNAc-1 leads to OC6H4NO2-p, beta-Gal-(1 leads to 4)-beta GlcNAc-1 leads to OC6H4NO2-p, and beta-Gal-(1 leads to 6)-beta-GlcNAc-1 leads to OC6H4NO2-p, was developed for the rapid identification of the linkage specificity of exo-beta-D-galactosidases from any source via a coupled reaction with N-acetyl-beta-D-hexosaminidase.     

2-Mercaptoethanol as a substrate for liver alcohol dehydrogenase.

An activity was identified in a phosphate buffer extract of calf liver acetone powder which utilized 2-mercaptoethanol and NAD⁺ as substrates and formed NADH as one product. The activity responsible for catalyzing this reaction is associated with calf liver alcohol dehydrogenase based on copurification, similarity in pH optima, and similarity in response to chelating agents and other inactivating agents. Crystalline horse liver alcohol dehydrogenase also catalyzes the formation of NADH from NAD⁺ using 2-mercaptoethanol as the substrate. Although the K_m for mercaptoethanol is much lower than that for ethanol, 30 μm as compared to 0.625 mm, the maximum velocity with mercaptoethanol as the substrate is only 7% of that when ethanol is the substrate. Because of this difference in maximum velocity, 2-mercaptoethanol is an apparent competitive inhibitor with respect to ethanol with crystalline horse liver alcohol dehydrogenase, consistent with ethanol and 2-mercaptoethanol binding at the same site. The apparent K_i for 2-mercaptoethanol is 14 μm. 2-Butanethiol is a competitive inhibitor with respect to both 2-mercaptoethanol and ethanol with horse and beef liver alcohol dehydrogenases.     

Mutagenicity and irreversible binding of the hepatocarcinogen, 2,4-diaminotoluene.

Mutagenicity of 2,4-diaminotoluene (DAT) in the Salmonella mutagenicity assay was increased with liver fractions from phenobarbital (PB) or beta-naphthoflavone (BNF) treated rats. Substitutions of the hydrogens in the methyl group of 2,4-DAT with deuterium resulted in a decrease in mutagenicity. Incubation of rat liver microsomes with tritiated 2,4-DAT in the presence of NADPH led to the formation of irreversibly bound products to microsomal protein. The rates of binding were not increased using microsomes from PB or BNF-treated rats and was not altered by deuterium substitution in the methyl group. Addition of superoxide dismutase, glutathione (GSH) or rat liver supernatant reduced 2,4-DAT irreversible binding, whereas 2,4-DAT mutagenicity was unaffected by superoxide dismutase addition. Injection of tritiated 2,4-DAT 100 mg/kg to rats lead to its irreversible binding to liver protein and ribosomal RNA and to kidney protein in vivo, again protein binding was not increased after prior treatment with PB or BNF. No irreversible interaction of tritiated 2,4-DAT with DNA either in vitro or in vivo could be demonstrated.     

Scatchard plot: Common misinterpretation of binding experiments

The widespread misinterpretation in the literature of ligand-protein binding experiments which show upward curvature in Scatchard plots is emphasized. The most commonly encountered errors are discussed and references to the correct methods of resolution of upward-curved Scatchard plots are given.     

The chick intestinal cytosol binding protein for 1,25-dihydroxyvitamin D3: A study of analog binding

The structural features of 1,25-dihydroxyvitamin D₃ that permit its high affinity binding to a 3.7 S protein from chick intestinal cytosol were determined in a series of binding and competition experiments analyzed by sucrose density gradient centrifugation. Optimal binding to the 3.7 S protein was achieved when both 1α- and 25-hydroxyls were present in the vitamin D₃ molecule. Modification of the side chain by the introduction of a methyl on C-24 and a double bond on C-22,23 (1,25-dihydroxyvitamin D₂) did not alter the binding of 1,25-dihydroxyvitamin D₃, but significantly diminished the binding of 25-hydroxyvitamin D₃. However, introduction of a hydroxyl on C-24 decreased the ability of either 1,25-dihydroxyvitamin D₃ or 25-hydroxyvitamin D₃ to compete, especially when the 24-hydroxyl was in the S configuration. These results reveal that the 3.7 S protein requires specific ligand structural features for binding and suggest that metabolite discrimination by the chick intestinal receptor system is likely located in the 3.7 S cytosol protein.     

Effect of albumin on binding and recovery of enzymes in affinity chromatography on Cibacron Blue

Bovine serum albumin appears to improve the specificity of Cibacron Blue F3GA in affinity chromatography of enzymes which interact with nucleotides. The action of bovine serum albumin may rest in its ability to selectively mask affinity sites in the dye, which are not specific for the nucleotide-binding region of the enzyme, while not seriously impairing binding nor its elution by nucleotides. Thus, the elution of Chlorella nitrate reductase from a Blue Sepharose chromatographic column by its coenzyme, NADH, fails, unless the column is first treated with bovine serum albumin. Such treatment also improves the recovery of some other nucleotide-binding enzymes tested.     

Sulfhydryl groups in urocanase: Relationship to nicotinamide adenine dinucleotide binding

This study concerned the role of the sulfhydryl groups in urocanase of Pseudomonas putida. When p-chloromercuribenzoate was added to the enzyme, two sulfhydryl groups reacted at once with little inhibition; the enzyme slowly became inhibited while further sulfhydryls reacted. After the p-chloromercuribenzoate inhibition occurred, if a thiol was subsequently added, most of the original activity was recovered. As the incubation time with p-chloromercuribenzoate was increased, the thiol became less effective in reversing the inhibition. However, if NAD⁺ (10 μm) was added with the thiol, 60–90% of the initial activity was restored even after long p-chloromercuribenzoate incubations. Restoration of activity by NAD⁺ was concentration dependent and specific for NAD⁺. Radioactive NAD⁺ could be bound to urocanase. These results confirm the coenzyme role for NAD⁺ in urocanase. In urea, p-chloromercuribenzoate titration of urocanase measured 11.9 -SH groups per molecule. Sulfite-modified enzyme treated with p-chloromercuribenzoate and dialyzed was substantially photoactivated in the presence of a thiol; that is, NAD⁺ was not required to restore activity. From these results, it is proposed that this enzyme contains two reactive —SH groups and that an essential —SH group is involved in NAD⁺ binding. Forces present in the sulfite-modified enzyme prevent the release of the NAD⁺ in the presence of mercurials.     

Thrombin-platelet interactions: an assessment of the roles of saturable and nonsaturable binding in platelet activation

Thrombin binds to platelets and induces platelet activation, but the relationship of binding to activation is not clear. To better define this relationship, we have analyzed parameters of binding and activation by alpha-thrombin and by three analogous proteases that activate platelets somewhat differently. The proteases were nitro-alpha-thrombin, a derivative with nitrated tyrosine, gamma-thrombin, a product of partial proteolysis of alpha-thrombin, and trypsin, a homologous protease. Nitro-alpha-thrombin and native alpha-thrombin activated platelets similarly, whereas gamma-thrombin and trypsin activated to a slightly lesser extent than alpha-thrombin and only after a distinctive delay. alpha-Thrombin and nitro-alpha-thrombin bound to platelets to about the same extent, but only alpha-thrombin showed evidence of saturable binding. Hirudin, a thrombin inhibitor, blocked both platelet activation and saturable binding by alpha-thrombin. With nitro-alpha-thrombin, hirudin blocked platelet activation, but it had no effect on binding. gamma-Thrombin and trypsin bound less than alpha-thrombin and with no evidence of saturable binding. There were identical relationships between the total amount bound and the extent of platelet activation for the four proteases (some show no saturable binding) but distinct differences in the relationships of total amount bound and the rate of activation; similar rates of activation required the binding of three to five times more gamma-thrombin or trypsin than alpha-thrombin. That is, without saturable binding, activation was slower. These data thus show a correlation between total amount bound and extent of activation but no correlation between amount saturably bound and the extent of platelet activation. Conversely, the rate of activation is more closely correlated with saturable binding than with total binding. We conclude that high-affinity saturable binding is not essential for thrombin-induced platelet activation but that it may accelerate the reaction.     

Study of mammalian ribosomal protein reactivity in situ. I. - Effect of 2-methoxy-5-nitrotropone on 40S and 60S subunits.

Liver ribosomes and subunits were reacted with increasing concentrations of 2-methoxy-5-nitrotropone. At low reagent concentrations (0.3 mM), the molar uptake by 60S subunits was more efficient than the uptake by 40S subunits, and the amount of reagent bound to 80S ribosomes was less than that bound to both free subunits considered together. At higher reagent concentrations, the molar uptake of both subunits was equivalent. Subunits and ribosomes remained fully active when reacted with up to 0.3 mM and 1 mM of the reagent, respectively. With 2 mM of the reagent, both subunits were half inactivated, although their sedimentation characteristics were unaltered. The reactivity of each ribosomal protein was assessed by two-dimensional gel electrophoresis and quantitative measurement of the unmodified proteins. From these results, considered together with the uptake characteristics and the inactivation curves, a number of tentative conclusions about ribosome topography can be drawn. The over-all sensitivity of the 60S subunits to the reagent is higher than that of the 40S subunits. Both subunits undergo a conformational change when they combine to form 80S ribosomes. Proteins S18, S20, S28 and L5, L9, L11, L15, L16, L25, L29, L30, L31, L34, L37 have NH2 groups exposed in native subunits. These groups are not essential for subunit function.     

Membrane receptors for Vicia graminea anti-N lectin and its binding to native and neuraminidase-treated human erythrocytes

Membrane receptors for Vicia graminea (Vg) lectin on human red cells were analyzed using deoxycholate lysates obtained from ¹²⁵I-erythrocyte membranes incubated with a purified lectin immobilized on Sepharose 4B. The glycoproteins (GP) specifically bound to the gel were eluted and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Using native erythrocytes the results obtained demonstrate that N red cells have exposed Vg receptors located on GPα (synonym glycophorin A) and GPδ (synonym glycophorin B) whereas on M erythrocytes the Vg receptors are restricted to GPδ. The presence of Vg receptors was also found on the hybrid glycoprotein (made of the N-ter of GPδ and C-ter of GPα) carried by St(a+) erythrocytes. A similar amount of radioactivity was bound to Vg-Sepharose incubated with neuraminidase-treated N or M membranes. The material eluted was tentatively identified as asialo GPα and asialo GPδ, suggesting that numerous receptors have been uncovered mainly on asialo GPα species from M erythrocytes. No glycoprotein component could be identified from the material eluted from Vg Sepharose incubated with native or neuraminidase-treated membrane from a Tn(+) individual. Scatchard plot analysis obtained from binding experiments at equilibrium with M, N, and St(a+) cells revealed the existence of at least two classes of receptors both on native and neuraminidase-treated erythrocytes. Desialylation of the M, N, and St(a+) erythrocytes resulted in an increase in the number of low- and high-affinity binding sites but had no significant effect on the association constants. However, high-affinity binding constants were about six times higher with N (7.07 × 10⁷ and 6.61 × 10⁷m^?1 for native and neuraminidase-treated N cells, respectively) as compared to M erythrocytes (1.13 × 10⁷ and 1.17 × 10⁷m^?1 for native and neuraminidase-treated M cells, respectively) whereas the low-affinity binding constants were similar for all types of cells (in the range of 0.1 to 0.3 × 10⁷m^?1). The number of Vg binding sites increases from 0.085 × 10⁵ to 0.8 × 10⁵ (high affinity) and from 2.10 × 10⁵ to 6.25 × 10⁵ (low affinity) per native and neuraminidase-treated N cell, respectively. On native and neuraminidase-treated M cells the number of Vg receptors increases from 0.011 × 10⁵ to 0.51 × 10⁵ (high affinity) and 0.13 × 10⁵ (low affinity), respectively. The large increase in the number of Vg receptors on neuraminidase-treated M cells is correlated with a large increase in agglutinability. Under similar treatment St(a+) cells behave like N erythrocytes whereas only 0.16 × 10⁵ Vg receptors of low affinity could be detected on neuraminidase-treated Tn erythrocytes. The results demonstrate that sialic acid is not required for binding and favor the view that the binding site of V. graminea lectin accommodates with two types of erythrocyte membrane receptors, one including both a contribution of polypeptide and oligosaccharide chains and a second which involves a simple interaction with sugar sequence Galβ1–3GalNAc available only when sialic acids are removed. The latter disaccharide is recognized by the Arachis hypogea lectin which therefore inhibits further binding of the V. graminea to neuraminidase-treated erythrocytes.