Kinetics of formation of the 4,4′-bis-dimethylaminodiphenyl carbonium ion (BDC+) and its reaction with sulfhydryl residues

The use of 4,4′-bis-dimethylaminodiphenylcarbinol (BDC-OH) as an analytical reagent for sulfhydryl residues and as a specific chemical modification reagent for proteins is dependent upon the unique properties of the BDC⁺ cation present in aqueous buffers below a pH of 6.5. In the presence of aqueous buffers, pH 5.1, BDC⁺ exhibits a λ_max of 606 nm with an apparent molar absorption coefficient of 10,000 m^?1 cm^?1. Upon the addition of 4m guanidine hydrochloride this apparent coefficient is enhanced to 70,800 m^?1 cm^?1. The true molar extinction coefficient for BDC⁺ was determined to be 128,000 m^?1 cm^?1. The reaction of BDC⁺ with sulfhydryl residues of proteins or simple thiols is rapid and leads to a complex devoid of visible color. In the pH range 3.0–7.0, a complex equilibrium is established among the three species BDC-OH, BDC⁺, BDCH⁺⁺. The formation of this equilibrium is proton mediated, and is discussed in terms of the equilibrium, rate, and acid dissociation constants.     

The metallochromic indicator dye Arsenazo III forms 1: 1 complexes with caffeine

The metallochromic indicator dye, Arsenazo III, forms a 1:1 complex with caffeine, a methylxanthine. Binding is accompanied by a wavelength-dependent shift in the absorption spectrum of the dye. The magnitude of the absorption change is significant at wavelengths typically used to monitor intracellular calcium ion. The equilibrium constant for the caffeine-dye reaction is approx. 20 mM. The complex has a differential molar extinction coefficient of ?5.05 · 10³ M^?1 · cm^?1 at 630 nm.     

The dye absorption test as an indicator of the nutritive quality of heat-processed navy bean

Under standardized conditions, the absorption of cresol red dye by navy bean meal increased from approximately 2.0 mg g^?1 for raw samples up to 3.8 mg g^?1 for optimally cooked samples. Within this range, a pooled correlation coefficient of 0.93 was obtained between dye binding value and $\text{gain}\text{feed}$ ratio of rats fed on diets comprising, in total, 51 differently processed navy bean meals in five bio-assay experiments. Over-heating of navy bean, as judged by a deterioration in the $\text{gain}\text{feed}$ ratio of rats, caused no further change in dye binding value until samples charred, whereupon dye binding values of the order of 1.5 mg g^?1 were observed. The practicality of the test for indicating the nutritive quality of heat-processed navy bean is discussed in the light of these findings.     

An improved purification method and a further characterization of the 33-kilodalton protein of spinach chloroplasts

The 33-kDa protein was purified in a high yield from thylakoid membranes of spinach chloroplasts. The extinction coefficient and A^1%_1cm value at 276 nm of the protein were 22000 M^?1·cm^?1 and 6.8, respectively. The 33-kDa protein and a polypeptide appearing at 32 kDa in the SDS-polyacrylamide gel electrophoresis of thylakoid membranes were compared by peptide mapping after limited proteolysis. This indicates that the 32-kDa band is entirely due to the 33-kDa protein. The molar ratio of chlorophyll to the 33-kDa protein in the chloroplasts was estimated to be 300. This suggests that one photosynthetic unit possesses one or two molecules of the 33-kDa protein.     

Molar extinction coefficients and other properties of an improved reaction center preparation from Rhodopseudomonas viridis

Reaction centers have been purified from chromatophores of Rhodopseudomonas viridis by treatment with lauryl dimethyl amine oxide followed by hydroxyapatite chromatography and precipitation with ammonium sulfate. The absorption spectrum at low temperature shows bands at 531 and 543 nm, assigned to two molecules of bacteriopheophytin b. The 600 nm band of bacteriochlorophyll b is resolved at low temperature into components at 601 and 606.5 nm. At room temperature the light-induced difference spectrum shows a negative band centered at 615 nm, where the absorption spectrum shows only a weak shoulder adjacent to the 600 nm band. The fluorescence spectrum shows a band at 1000 nm and no fluorescence corresponding to the 830 nm absorption band. Two molecules of cytochrome 558 and three of cytochrome 552 accompany each reaction center. The differential extinction coefficient (reduced minus oxidized) of cytochrome 558 at 558 nm was estimated as 20 ± 2 mM^?1 · cm^?1 through a coupled reaction with equine cytochrome c. The extinction coefficient of reaction centers at 960 nm was determined to be 123 ± 25 mM^?1 · cm^?1 by measuring the light-induced bleaching of P-960 and the coupled oxidation of cytochrome 558. The corresponding extinction coefficient at 830 nm is 300 ± 65 mM^?1 · cm^?1. The absorbance ratio $\text{a}{}_{\mathrm{<mtext>280</mtext><mtext>nm</mtext>}}\text{a}{}_{\mathrm{<mtext>830</mtext><mtext>nm</mtext>}}$ in our preparations was 2.1, and there was 190 kg protein per mol of reaction centers. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed three major components of apparent molecular weights 31 000, 37 000 and 41 000.     

Synthesis and characterization of 2′-azidoaminopterin as a potential photoaffinity label for folate-utilizing enzymes

A photoreactive analog of aminopterin, 2′-azidoaminopterin (VI), was synthesized and evaluated as a potential inhibitor and photoaffinity label of folate-utilizing enzymes. The compound was tightly bound to dihydrofolate reductase (DHFR) from escherichia coli (MB 1428) with K₁ equal to 3 × 10^?11M and to the enzyme from mouse (S-180) cells with K₁ approximately equal to 2 × 10^?10M. Dissociation constants measured by equilibrium dialysis using radioactive 2′-azidoaminopterin gave a value of K_D = 3.2 × 10^?9M for the bacterial enzyme. The presence of NADPH enhanced the affinity by more than an order of magnitude. Azidoaminopterin is also an inhibitor of thymidylate synthetase from Lactobacillus casei, competitive with methylene-tetrahydrofolate (K_i 7 × 10^?7M). Photolysis of the radioactive inhibitor in complex with DHFR from E. coli led to approximately 3% covalent incorporation of label into protein. The greater part of this attachment was nonspecific as shown by the lack of protection in the presence of methotrexate. Thymidylate synthetase from L. casei was not significantly inactivated upon photolysis in the presence of the inhibitor and deoxyuridylate. Model studies showed that photoreaction of the inhibitor led to covalent linkages with thiol, lysyl amino groups, and the hydroxyl groups of alcohols. Azidoaminopterin may be useful in labeling other enzymes of folate metabolism, although a minor photoproduct reacts nonspecifically with many proteins. The antifolate can be photoconjugated to polylysine as well as to proteins. The polylysine conjugates inhibit DHFR. Difference spectrum analysis of the photoproducts from the irradiation of the DHFR I complex indicates that water reacts efficiently with the enzyme-bound nitrene and must therefore have access to at least part of the bound p-aminobenzoyl group. This analysis suggests that azide analogs of protein ligands may be useful as reporter groups in probing the hydrophobicity of binding sites.     

Translational diffusion in the plasma membrane of sea urchin eggs

Translational diffusion in the plasma membrane of individual egg cells from the sea urchin species Paracentrotus lividus has been studied by fluorescence microphotolysis (FM). In order to probe the lipid phase of the membrane, procedures have been worked out by which the fluorescent analog 3,3′-dioctadecyl-oxatricarbocyanine (C₁₈diO) can be incorporated into the membrane. In the unfertilized egg a fraction R = 0.9 of C₁₈diO was mobile having an apparent diffusion coefficient of D = 6.0 × 10^?9 cm² sec^?1. Fifteen to twenty-five minutes after fertilization R and D were reduced to 0.8 and 2.7 × 10^?9 cm² sec^?1, respectively. In order to study diffusion of membrane proteins, procedures have been worked out by which the cell surface can be labeled with fluorescein-isothiocyanate (FITC). FITC binds to both the plasma membrane and the vitelline layer. Together with the vitelline layer two-thirds of the FITC-fluorescence could be removed from the egg surface. Gel electropherograms of isolated egg cortices showed various protein bands; however, only two of the protein bands were labeled with FITC. In the unfertilized egg a fraction R = 0.9 of the FITC-labeled membrane proteins was mobile having an apparent diffusion coefficient of D = 35 × 10^?11 cm² sem^?1. Fiteen to twenty-five minutes after fertilization R and D were reduced to 0.8 and 7.0 × 10^?11 cm² sec^?1, respectively. FITC-labeled proteins of the fertilization envelope were immobile. Our studies have shown (i) that the egg surface can be fluorescently labeled without blocking fertilization and early development, (ii) that the plasma membrane of unfertilized eggs is a fluid environment permitting a rapid movement of lipids and proteins, and (iii) that after fertilization a substantial degree of lipid and protein mobility is maintained.     

In Vitro Multiplication of Paedaria foetida L — A Rare Medicinal Plant

Paedaria foetida L, which has great medicinal value is facing danger of extinction. For its conservation, in vitro multiplication may prove one of the best techniques. Micropropagation of P. foetida has been achieved through the culture of nodal explants. The explants produced shoots on MS medium with 0.8% agar. This medium, however, caused high degree of browning of the explants and death of sprouted shoots. Agar free liquid MS medium with polyvinylpyrrolidone (PVP) proved better. Maximum shoot proliferation, free from callus and vitrification but with poor rooting could be obtained in liquid MS medium with PVP (0.8%), NAA (0.5 mg l^?1) and BA (2.0 mg l^?1). The best rooting occurred on semisolid MS medium containing 0.8% agar and 0.5 mg l^?1 IBA.     

Thermodynamics of mucopolysaccharide–dye binding. III. Thermodynamic and cooperativity parameters of acridine orange–heparin system

Binding isotherms for acridine orange (AO)–heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements. The evaluation of thermodynamic parameters indicates that the interactions of AO with heparins from several animal sources are similar to each other in magnitude. Binding is highly exothermic (ΔH = ?6 kcal mol^?1) and is stabilized by dye–polymer and dye–dye (coopertive) interactions, as well as by entropic factors (ΔS = +7 e.u.). The predominant stabilizing factor appears to be the electrostatic attraction between the AO cation and the heparin polyanion, although the other factors are important as well. At 24°C the value of the cooperative binding constants for the various heparins range from 8.8 to 11.3 × 10⁵M^?1, corresponding to a free energy of ?8 kcal mol^?1. The degree of cooperativity, which is a direct measure of dye–dye interaction, varies with polymer:dye ratio; the theoretical basis for this variation remains to be elucidated. Electrophoretic data indicate that each heparin sample consists of a mixture of species, each with its own charge density. This precludes definitive interpretation of observed small differences in the values of the thermodynamic parameters among the various samples until each sample can be resolved into its components.     

Fluorescence of free and protein-bound Auramine O

The spectral properties and binding of Auramine O were studied as a model for the binding of cationic ligands to proteins. The dye was fluorescent in H₂O with a quantum yield of 4 × 10^?5, but the emission became blue-shifted and more intense in less polar solvents, as in the case of more common fluorescent probes. Emission increased where dye motion was restricted, e.g., when bound to proteins, in glycerol solutions, dried on filter paper, or embedded in ice. The amount of solvent spectral shift was probably limited by the short lifetime of free dye emission, which was estimated to be of the order of picoseconds. Auramine O was bound by yeast alcohol dehydrogenase and serum albumins of different species. Fluorescence enhancement and equilibrium dialysis measurements showed the number of dyes bound per molecule of protein and the association constants to be 2 and 1.2 × 10⁴m^?1 for yeast alcohol dehydrogenase and 1 and 0.23–1.9 × 10⁴m^?1 for the albumins. The Auramine O complex with liver alcohol dehydrogenase, described by Conrad et al. [Biochemistry9, 1540–1546 (1970)], had peak emission at 520 nm, further to the red than any of the other complexes studied, suggesting a relatively polarizable binding environment. NaCl did not displace the dye, but enhanced its fluorescence in the complex. The fluorescence was sensitive to protein conformational changes brought about by urea. A literature survey suggests that cationic organic ligands bind strongly to the active site of only those enzymes which have cationic substrates, and bind only weakly to noncatalytic sites in other enzymes. The significance and advantages of cationic fluorescent probes of proteins are discussed.     

Interaction of the dye Congo red with fibrils of lysozyme,beta2-microglobulin,and transthyretin

Interaction of the dye Congo red (CR) with fibrils of three model proteins—hen egg lysozyme, recombinant human beta 2-microglobulin (b2M), and recombinant human transthyretin (TTR)—has been investigated using spectrophotometry. Considerable amounts of impurities were detected in the commercial dye formulation. A procedure of dye purification has been developed. The molar extinction coefficient of the dye at 490 nm (ε₄₉₀) has been measured; the coefficient was 3.3 × 10⁴ M^–1 cm^–1 at pH > 6.0. The formation of a complex between CR and the fibrils was accompanied by a change in the absorption spectrum of the dye in the visible wavelength range. Titration of fibril solutions with excessive amounts of dye showed that the number of CR molecules bound to a protein monomer within the lysozyme fibrils was close to five, whereas the respective ratio for b2M was close to four, and the ratio for TTR fibrils was close to four molecules per protein subunit.     

Biodegradation of the textile dye Mordant Black 17 (Calcon) by Moraxella osloensis isolated from textile effluent-contaminated site

The bacterium with dye degrading ability was isolated from effluent disposal sites of textile industries, Tirupur and was identified as Moraxella osloensis based on the biochemical and morphological characterization as well as 16S rRNA sequencing. This organism was found to decolorize 87 % of Mordant Black 17 at 100 mg l^?1 under shake culture condition compared to 92 % under stationary culture condition. Maximum degradation of the dye by M. osloensis was achieved when the mineral salt medium was supplemented with 0.5 % glucose and 0.1 % ammonium nitrate at 35 °C. Degradation of dye was found to follow first order kinetics with the k value of 0.06282 h^?1 and a R² value of 0.955. Analyses for the identification of intermediate compounds confirmed the presence of naphthalene, naphthol, naphthoquinone, salicylic acid and catechol. Based on this finding a probable pathway for the degradation of Mordant Black 17 by M. osloensis has been proposed.     

Arsenazo I and tetramethylmurexide as optical calcium indicators

Calcium-binding stoichiometry, dissociation equilibrium constants at zero ionic strength (K⁰), and molar extinction difference coefficients (Δ?_λ) at the wavelength λ of the metallochromic indicators arsenazo I (ArsI) and tetramethylmurexide (TMX) were reevaluated with a computerized method based on mass conservation and thermodynamic consistency checks. This new method is shown to provide a more critical assessment of the assumed calcium-dye complexing model than is afforded by the commonly used reciprocal-plot method. The analyses of spectrophotometric Ca titrations confirm that both dyes form only 1:1 complexes in aqueous solution. For TMX, K⁰ = 1.3 × 10^?3m and Δ?₄₈₀ = 1.5 × 10⁴m^?1 cm^?1; for ArsI, K⁰ = 5.8 × 10^?3m and Δ?₅₆₂ = 1.8 × 10⁴m^?1 cm^?1 at pH 7.0 and T = 293°K. The discriminatory power of the analytical method is demonstrated by comparison of these results with those found for a different dye, arsenazo III, which complexes Ca in 1:1, 1:2, and 2:1 forms.     

An alternative 7-ethoxyresorufin o-deethylase activity assay: A continuous visible spectrophotometric method for measurement of cytochrome P-450 monooxygenase activity

A procedure to directly measure the cytochrome P-450-dependent 7-ethoxyresorufin O-deethylase activity with a visible spectrophotometer is described and compared to the standard fluorometric method. The two assays yielded identical results with both β-naphthoflavone-treated mammalian (rat) and fish (scup, Stenotomus chrysops) liver microsomes. The assay takes advantage of a clean distinction in visible absorption spectra obtained for highly purified 7-ethoxyresorufin (substrate) and resorufin (enzymatic product). The purification and characterization of resorufin, the enzymatic product, are detailed, and its extinction coefficient (ε₅₇₂ = 73 mm^?1 cm^?1) provides for an accurate quantitation of enzyme activity. The large visible extinction coefficient of the product chromophore provides a high sensitivity for low-activity samples. The application of this enzyme assay in a visible spectrophotometer, along with the considerable evidence that a single aromatic hydrocarbon-inducible cytochrome P-450 isozyme is responsible for the catalysis, enhances the utility of this substrate in microsomal monooxygenase assays. The utility of the visible assay is further demonstrated by the simple determinations of the coupling ratio for 7-ethoxyresorufin oxidation in scup liver microsomes and the K_I for 7,8-benzoflavone and phenylimidazole inhibition of the enzymatic reaction.     

Streptokinase-polyethylene glycol conjugates with increased stability and reduced side effects

Covalent SK-PEG2 and SK-PEG5 conjugates with various degrees of modification of the protein amino groups were obtained by variation of the duration of streptokinase (SK) incubation with activated polyethylene glycol (M 2 and 5 kDa, PEG2 and PEG5); their properties were studied in comparison with the properties of unmodified SK in vitro. SK-PEG2 and SK-PEG5 conjugates with the highest stability in plasma retaining 80% of initial fibrinolytic activity were formed at modification degrees of 54 and 52%, respectively. Interaction of the conjugates with equimolar plasminogen resulted in the formation of plasmin (Pm) activator complexes Pm·SK-PEG2 and Pm·SK-PEG5 with the maximum amidase activity being the same as that of Pm complex with native SK. Catalytic efficiency of plasminogen activation (k _Pg/K _Pg) was found to be slightly higher (2.84 min^?1 μM^?1) in case of Pm·SK-PEG2 complex and slightly lower, in case of the Pm·SK-PEG5 complex (1.17 min^?1 μM^?1), if compared to that of the unmodified complex Pm·SK (2.1 min^?1 μM^?1). Investigation of lysis kinetics of human plasma clot and depletion of plasminogen and fibrinogen plasma levels under the effect of equal doses of SK in free and conjugated forms demonstrated that SK-PEG2 and SK-PEG5 conjugates possess high thrombolytic activity (89 and 72% to the activity of free SK, respectively) and cause 3.5–4-fold lower side effects than free SK. The SK-PEG2 and SK-PEG5 conjugates with increased stability in plasma and reduced side effects may be used in therapy of thrombotic disorders.     

Identification of cyclic guanosine monophosphate-binding proteins in Drosophila by direct photoaffinity labeling

A procedure for direct photoaffinity labeling with [³²P]cGMP has been used to identify cGMP-binding proteins in Drosophila. This method provides better sensitivity and resolution than previously described direct methods, because the proteins can be visualized by autoradiography following sodium dodecyl sulfate-gel electrophoresis. Labeling is observed with cGMP concentrations as low as 4 × 10^?8m and is specific for cGMP. The sensitivity of the technique is sufficient to permit detection of cGMP-binding proteins in crude extracts. With this technique a single cytoplasmic cGMP-binding protein of subunit M_r 108,000 has been identified in Drosophila embryos and cultured cells.     

The absorbance coefficient of beef heart cytochrome c1

Isolated cytochrome c₁ contains endogenous reducing equivalents. They can be removed by treating the protein with sodium dithionite followed by chromatography. This treatment has no effect on the reaction with cytochrome c, nor does it alter the optical spectrum, or the polypeptide or amino acid composition of the protein. Both the titration of dithionite-treated ferrocytochrome c₁ with potassium ferricyanide and the anaerobic titration of dithionite-treated ferricytochrome c₁ with NADH in the presence of phenazine methosulphate lead to the same value for the absorbance coefficient of cytochrome c₁ : 19.2 mM^?1 · cm^?1 at 552.4 nm for the reduced-minus-oxidised form. This value was also obtained when the haem content was determined by comparing the spectra of the reduced pyridine haemochromes of cytochrome c and cytochrome c₁. Comparison of the optical spectra of cytochrome c and cytochrome c₁ by integration shows equal transition moments for the transitions in the porphyrin systems of both proteins. A set of equations is presented with which the concentration of the cytochromes aa₃, b, c and c₁ can be calculated from one reduced-minus-oxidised difference spectrum of a mixture of these proteins.     

A fluorescence spectroscopy assay for real-time monitoring of enzyme immobilization into mesoporous silica particles

Mesoporous silica particles are used as support material for immobilization of enzymes. Here we investigated a fluorescence-based assay for real-time monitoring of the immobilization of lipase, bovine serum albumin, and glucose oxidase into micrometer-sized mesoporous silica particles. The proteins are labeled with the dye epicocconone, and the interaction with the particles is observed as an increase in emission intensity of the protein–dye conjugates that can be quantified if correcting for a comparatively slow photobleaching. The immobilization occurs in tens of minutes to hours depending on particle concentration and type of protein. In the limit of excess particles over proteins, the formation of the particle–protein complexes can be described by a single exponential growth for all three investigated proteins, and the fitted pseudo-first-order rate constant increases linearly with particle concentration for each protein type. The derived second-order rate constant k varies with the protein hydrodynamic radius according to k ∼ R_H^{−4.70±0.01}, indicating that the rate-limiting step at high particle concentrations is not the diffusional encounter between proteins and particles but rather the entry into the pores, consistent with the hydrodynamic radii of the three proteins being smaller but comparable to the pore radius of the particles.     

Properties of photochemical reaction centers purified from Rhodopseudomonas gelatinosa

Reaction centers were isolated from a carotenoidless mutant of Rhodopseudomonas gelatinosa by hydroxyapatite chromatography of purified chromatophores treated with lauryl dimethyl amine oxide. Absorption spectra and spectra of light-induced absorbance changes are similar to those of reaction centers from Rhodopseudomonas sphaeroides. The ratio of absorbance at 280 nm to that at 799 nm was 1.8 in the purest preparations. The extinction coefficient at the 799 nm absorption maximum was estimated to be 305 ± 20 mM^?1 · cm^?1. The molecular weight based on protein and chromophore assays was found to be 1.5 · 10⁵; the reaction center protein accounted for 6% of the total membrane protein. These reaction centers contained no cytochrome and showed just two components of apparent molecular weights 33 000 and 25 000 in polyacrylamide gel electrophoresis. The chromatophores contained 42 molecules of antenna bacteriochlorophyll for each reaction center.     

Hydrational and intrinsic compressibilities of globular proteins

Partial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 ± 3) × 10^?6 bar ^?1 for the isothermal compressibility coefficient of the protein interior at 25°C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x-ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 × 10^?6 bar ^?1, which is 20% less than that of pure water. © 1993 John Wiley & Sons, Inc.