A novel procedure for identification of the folding/unfolding patterns of dimeric proteins

The unfolding of proteins has been widely used for investigating the thermodynamic properties of monomeric proteins but has been used infrequently for dimeric (or oligomeric) proteins, because of the inherent cooperation of denaturation and dissociation of the dimers (oligomers). Here, we introduce a thermodynamic parameter K_obs to discriminate the diverse folding patterns of dimeric proteins. K_obs remains constant as the protein concentration increases for the true one-step curve of unfolding pattern (A), increases and reaches a plateau for one-step curves with monomeric intermediate pattern (B), and increases steadily with no plateau for one-step curves with dimeric intermediate pattern (C).     

Activity coefficients of salts in highly concentrated protein solutions: I. Alkali chlorides in isoionic bovine serum albumin solutions

In order to understand the thermodynamic state of simple salts in living cells, the mean activity coefficients of LiCl, NaCl, KC1, RbCl, CsCl were determined in concentrated isoionic bovine serum albumin (BSA) solutions by use of the EMF method with ion exchange membrane electrodes. The protein concentration range extended up to 22 wt %, whereas the salt concentration was kept constant at 0.1 mole per kilogram water. These solutions may be regarded as crude but appropriate model systems for the cytoplasm of cells as far as type and magnitude of the macromolecular component influence on the chemical potential of the salts is concerned. The mean stoichiometric activity coefficients of the alkali chlorides in the isoionic BSA solutions decreased linearly with the protein molality; this decrease, however, did not exceed ca. 10% compared with the pure 0.1 molal salt solutions. Only very small differences in the behaviour of the different alkali chlorides were observed. The results may be interpreted by the superposition of the effects of specific Cl^? ion binding to BSA and BSA bound “non-solvent” water with probably electrostatic long range interactions of the BSA(Cl^?)_v polyions with the salt ions in solution. The resulting mean activity coefficients, corrected for ion binding and non-solvent water, showed a very slight linear dependence on the protein concentration. The departure from the value in the pure 0.1 molal salt solutions did not exceed ± 2%.     

Heme-linked ionization and chloride binding in intestinal peroxidase and lactoperoxidase.

Hog intestinal peroxidase and bovine lactoperoxidase exhibited similar spectral shifts upon pH alteration. From spectrophotometric titrations, it was found that there are hemelinked ionizations of pK_a = 4.75 in intestinal peroxidase and pK_a = 3.5 in lactoperoxidase. The apparent pK_a (pK_a′) increased with the increase in chloride concentration. The pK_a′ vs log[Cl^?] plots showed that the chloride forms complex with the acid forms of these enzymes with a dissociation constant (pK = 2.7). Although the dissociation constant (K_d) of the peroxidase-cyanide complexes is nearly independent of pH, cyanide competed with chloride in the acidic pH region. The slopes of logK_d vs log[Cl^?] were 1.0 for intestinal peroxidase and 0.5 for lactoperoxidase. The reaction of hydrogen peroxide with these peroxidases was also affected by chloride, similarly as the reaction with cyanide was. The results were explained by assuming that protonation occurs at the distal base and destroys the hydrogen bond between the base and a water molecule at the sixth coordinate position of the heme iron.     

Enantioselective DNA binding of iron(II) complexes of methyl-substituted phenanthroline

The enantioselective binding of [Fe(4,7-dmp)₃]²⁺ (dmp: 4,7-dimethyl-1,10-phenantroline) and [Fe(3,4,7,8-tmp)₃]²⁺ (tmp: 3,4,7,8-tetramethyl-1,10-phenanthroline) to calf-thymus DNA (ct-DNA) has been systematically studied by monitoring the circular dichroism (CD) spectral profile of the iron(II) complexes in the absence and presence of ct-DNA. The effect of salt concentration and temperature on the degree of enantioselectivity of the ct-DNA binding of the iron(II) complexes, i.e. the molar ratio of Δ- to Λ-enantiomer in the solution or vice versa has been rigorously evaluated. It is noticeable that Δ-[Fe(4,7-dmp)₃]²⁺ and Λ-[Fe(3,4,7,8-tmp)₃]²⁺ are preferentially bound to ct-DNA as reflected in their opposite CD spectral profiles. The preferential binding of the Λ-enantiomer of [Fe(3,4,7,8-tmp)₃]²⁺ to ct-DNA compared to that of the Δ-enantiomer is associated with the bulkiness of the ancillary ligands due to substitution of four hydrogen atoms in 1,10-phenanthroline for four methyl groups. The determination of enantiomeric inversion constant (K_inv) at various salt concentrations has revealed that the degree of enantioselectivity is salt concentration dependent, indicating that electrostatic interaction is involved in the enantioselective binding of the iron(II) complexes to ct-DNA. Although [Fe(4,7-dmp)₃]²⁺ and [Fe(3,4,7,8-tmp)₃]²⁺ exhibit an opposite pattern in the CD spectra, the degree of their enantioselectivity (K_inv) is not different from each other significantly. A thermodynamic study on the enantioselective binding of [Fe(4,7-dmp)₃]²⁺ to ct-DNA using the van’t Hoff plot of ln K_inv versus 1/T has demonstrated that the enthalpy change (ΔH°) in the inversion process from the Λ- to Δ-enantiomer of [Fe(4,7-dmp)₃]²⁺ ct-DNA is positive, indicating that the process is endothermic and thus entropically driven.     

An algebraic model for the kinetics of covalent enzyme inhibition at low substrate concentrations

This article describes an integrated rate equation for the time course of covalent enzyme inhibition under the conditions where the substrate concentration is significantly lower than the corresponding Michaelis constant, for example, in the Omnia assays of epidermal growth factor receptor (EGFR) kinase. The newly described method is applicable to experimental conditions where the enzyme concentration is significantly lower than the dissociation constant of the initially formed reversible enzyme–inhibitor complex (no “tight binding”). A detailed comparison with the traditionally used rate equation for covalent inhibition is presented. The two methods produce approximately identical values of the first-order inactivation rate constant (k_inact). However, the inhibition constant (K_i), and therefore also the second-order inactivation rate constant k_inact/K_i, is underestimated by the traditional method by up to an order of magnitude.     

Solid/gas biocatalysis: an appropriate tool to study the influence of organic components on kinetics of lipase-catalyzed alcoholysis

The influence of the addition of an extra component in a gaseous reaction medium, on the kinetics of alcoholysis of methyl propionate and n-propanol catalyzed by immobilized lipase B from Candida antarctica was studied in a continuous solid/gas reactor. In this reactor, the solid phase is composed of a packed enzymatic sample, which is percolated by gaseous nitrogen, simultaneously carrying gaseous substrates and additional components to the enzyme while removing reaction products. The system permits to set thermodynamic activity of all gaseous components (substrates or not) independently at the desired values. This allows in particular to study the influence of an extra added component at a constant thermodynamic activity value, contrary to classical solid/liquid system, which involves large variations of thermodynamic activity of added solvent, when performing full kinetic studies. Alcohol inhibition constant (K_I) and methyl propionate and propanol dissociation constants (K_MP and K_P) have been determined in the solid/gas reactor in the presence of 2-methyl-2-butanol, and compared with values previously obtained in the absence of added component and in the presence of water. Complementary experiments were carried out in the presence of an apolar compound (hexane) and led to the conclusion that the effect of added organic component on lipase-catalyzed alcoholysis is related to their competitive inhibitory character towards first substrate methyl propionate. The comparison of data obtained in liquid or with gaseous 2-methyl-2-butanol shows that lower K_MP and K_I are found in gaseous medium, which would correspond on the one hand to a lower acylation rate k₂, and on the other hand to a higher binding rate k₁ between substrate and free enzyme in gaseous medium.     

Reactions of the amino groups of RNAse A: IV. The effects of protein concentration

A study has been made of the effect of ribonuclease (RNAse) concentration on the properties of the amino groups. The biphasic dependence of pK on pH which has been established (Goldfarb and Martin, Bioorg. Chem.5, 137 (1976)). for 5 μM solution of RNAse also have been shown to occur for 50 μM solutions. In the lower pH range (7.5–8.5) the values of pK obtained with 50 μM solutions were similar to those obtained with 5 μM solutions (pK = 7.5) but the intrinsic constants were smaller. In the higher pH range (8.5–10) the pKs in the more concentrated solutions were larger than those found at the smaller concentration and the intrinsic constants were generally smaller. A quantitative study of the concentration vs k_i relation at pH 7.5 indicated a sigmoid relationship for all of the subsets with a constant maximum value equal to, and less than that at 5 μM RNAse and a constant minimum value above that at 20 μM. Parallel studies with oxidized RNAse gave parallel, although not identical, results from which it is proposed that the concentration effect does not arise totally from the three-dimensional structure of native RNAse.     

Compensating Effects of Opposing Changes in Putrescine (2+) and K+Concentrations onlacRepressor-lacOperator Binding:in VitroThermodynamic Analysis andin VivoRelevance

Ion concentrations (K⁺, Glu⁻) in the cytoplasm of growingEscherichia colicells increase strongly with increases in the osmolarity of a defined growth medium. Whilein vitroexperiments demonstrate that the extent of protein-nucleic acid interactions (PNAI) depends critically on salt concentration,in vivomeasurements indicate that cells maintain a relatively constant extent of PNAI independent of the osmolarity of growth. How do cells buffer PNAI against changes in the cytoplasmic environment? At high osmolarity, the increase in macromolecular crowding which accompanies the reduction in amount of cytoplasmic water in growing cells appears quantitatively sufficient to compensate for the increase in [K⁺]. At low osmolarity, however, changes in crowding appear to be insufficient to compensate for changes in [K⁺], and additional mechanisms must be involved. Here we report quantitative determinations ofin vivototal concentrations of polyamines (putrescine(2+), spermidine(3+)) as a function of osmolarity (OsM) of growth, andin vitrobinding data on the effects of putrescine concentration on a specific PNAI (lacrepressor-lacoperator) as a function of [K⁺]. The total concentration of putrescine in cytoplasmic water decreases at least eightfold from low osmolarity (∼64 mmol (l H₂O)⁻¹at 0.03 OsM) to high osmolarity (∼8 mmol (l H₂O)⁻¹at 1.02 OsM). Over this osmotic range the total [K⁺] increases from ∼0.2 mol (l H₂O)⁻¹to ∼0.8 mol (l H₂O)⁻¹. We find that the effect of putrescine concentration on the repressor-operator interactionin vitrois purely competitive and is quantitatively described by a simple competition formalism in whichlacrepressor behaves as a specific-binding oligocation (Z_R=8±3). We demonstrate that this thermodynamic result is consistent with a structural analysis of the number of positively charged side-chains on two DNA binding domains of repressor which interact with the phosphodiester backbone of the operator site. Since this oligocation character of the binding surface of DNA-binding proteins appears to be general, we propose the competitive effects of putrescine and K⁺concentrations on the strength of specific binding are general. At low osmolarity, compensating changes in putrescine and K⁺concentration in response to changes in external osmolarity provide a general mechanism forE. colito vary cytoplasmic osmolarity while maintaining a constant extent of PNAI.     

Synthesis and biological evaluation of a new dysprosium(III) complex containing 2,9-dimethyl 1,10-phenanthroline

The binding of [Dy(dmp)₂Cl₃(OH₂)], where dmp is 2,9-dimethyl 1,10-phenanthroline, with Fish salmon DNA (FS-DNA) is investigated by absorption and emission spectroscopy, quenching studies, salt dependent, and gel electrophoresis. The binding constant (K_b) of the interaction is calculated as (1.27 ± .05) × 10⁵ M^?1 from absorption spectral titration data. The Stern–Volmer constant (K_SV), thermodynamic parameters involves ΔG°, ?H°, and ?S° are calculated by fluorescent data and Van’t Hoff equation. The thermodynamic studies show that the reaction for the binding of the complex with FS-DNA is endothermic and entropically driven (ΔS° > 0, ΔH° > 0). The effect of the complex concentration on FS-DNA cleavage reactions is also investigated by gel electrophoresis. Furthermore, the Dy(III) complex has been screened for its antibacterial activity. The experimental results suggest that the Dy(III) complex binds significantly to FS-DNA by hydrophobic groove binding mode and the complex has more efficient antibacterial activity compared to its metal salt.     

Microrespirometric characterization of activated sludge inhibition by copper and zinc

We have developed a novel microrespirometric method to characterize the inhibitory effects due to heavy metals on activated sludge treatment. This method was based on pulse dynamic respirometry and involved the injection of several pulses of substrate and inhibitors, of increasing concentration. Furthermore, we evaluated the inhibitory effects of heavy metals (copper and zinc), substrate and biomass concentrations, and pH on activated sludge activity. While higher biomass concentrations counteracted the inhibitory effects of both copper and zinc, higher substrate concentrations predominantly augmented the inhibitory effect of copper but no significant change in inhibition by zinc was observed. pH had a clear but relatively small effect on inhibition, partially explained by thermodynamic speciation. We determined the key kinetic parameters; namely, the half saturation constant (K _S ) and the maximum oxygen uptake rate (OUR _max ). The results showed that higher heavy metal concentrations substantially decreased K _S and OUR _max suggesting that the inhibition was uncompetitive.     

Affinity chromatography: purification of bovine trypsin and thrombin

Bovine trypsin has been purified by affinity chromatography on agarose beads containing covalently bound p-aminophenylguanidine, p-aminobenzamidine, or m-aminobenzamidine. Bovine thrombin was purified on a m-aminobenzamidine-agarose column containing a high concentration of the inhibitor. The values of the inhibition constant, K_i, for these inhibitors were determined for both enzymes and found to be 5–10 times poorer for thrombin than for trypsin. Only those benzamidines with low K_i values and coupled in high concentration to the agarose matrix were satisfactory for thrombin purification. Affinity-purified trypsin and thrombin were both greater than 90% active as measured by active site titration.     

Complexation of aluminium with (−) -epigallocathechin gallate studied by spectrophotometry

Complexation equilibria between Al(III) and (−)-epigallocathechin gallate (EGCG) in the presence of acetate buffer have been studied by spectrophotometry. The method is based on the competition between EGCG and buffer ligands for Al(III) ions. The apparent formation constant of the EGCG complex for Al(III), which could be determined by measuring the absorbance of the free EGCG, decreased with increasing acetate ion concentration at a fixed pH. This phenomenon has been quantitatively investigated and both types of complexes (EGCG and acetate) could be analyzed. The apparent formation constant of Al(III) complex with EGCG also decreased with decreasing pH at a fixed acetate ion concentration. The pH dependence of the apparent formation constant indicates the 1:1 competition between metal ions and hydrogen ions for the binding site of EGCG. The intrinsic formation constant of Al-EGCG complex, the proton association constant of EGCG and the formation constant of Al-acetate complex are found to be log K_Al-EGCG = 7.6 ± 0.1, log K_H-EGCG = 7.65 ± 0.03 and log K_Al-acetate = 2.07 ± 0.05 by a graphical analysis.     

The salt relations of marine and halophilic species of the unicellular green alga,Dunaliella

1. Comparisons were made of the effects of salt on the exponential growth rates of two unicellular algae,Dunaliella tertiolecta (marine) andDunaliella viridis (halophilic).
2. The algae contained glycerol in amounts which varied directly with the salt concentration of the growth media. The highest measured glycerol content ofD. tertiolecta was approximately equivalent to 1.4 molal and occurred in algae grown in 1.36 M sodium chloride. The highest glycerol content measured inD. viridis was approximately equivalent to 4.4 molal and occurred in algae grown in 4.25 M sodium chloride. Lower concentrations of free glucose, which varied inversely with extracellular salt concentration, were also detected.
3. It is inferred that Na⁺ is effectively excluded from the two algae. There was some evidence of a moderate uptake of K⁺.
4. Comparisons were made of erude preparations of the glucose-6-phosphate dehydrogenase and an NADP-specific glycerol dehydrogenase from each species and of the effects of salt and glycerol on the activities of these enzymes. It is concluded that the different salt tolerances of the two algae cannot be explained by generalized differences between their enzyme proteins.
5. Although intracellular glycerol must necessarily contribute to the osmotic status of the algae, its primary function in influencing their salt relations is considered to be that of a compatible solute, whereby glycerol maintains enzyme activity under conditions of high extracellular salt concentration and hence low (thermodynamic) water activity.

     

Dynamic light-scattering studies on thermal motions of native DNAs in solution

The basic character of dynamic light-scattering properties of native DNA was investigated on two DNA samples. The degree of non-single exponentiality of photocount correlation functions. C(t), and its dependence on Kquantitatively characterized by two methods. The spectral linewidth. Γ₃, determined from C(t) exhibits a K dependence near to but significantly different from the prediction for Rouse-Zimm (RZ) chains by Dubois-Violelte and De Gennes: It is inferred from data on λ-DNA that the exponent in She K dependence of the spectral linewidth for native DNA takes a value larger than 3 in the K region corresponding to the ‘K³’ region for RZ chains. These results are in good agreement with the prediction from the dynamic theory of semiflexible chains presented by one of us (K.S.). The apparent diffusion coefficients are fairly insensitive to DNA concentration and ionic strength at large K. On the other hand, it is indicated that the stiffness of native DNA may vary with temperature even in a temperature range substantially lower than thai of melting.     

Kinetics of interaction of some α- and β-D-monosaccharides with concanavalin A

The rates of formation and dissociation of concanavalin A with some 4-methylumbelliferyl and p-nitrophenyl derivatives of α- and β-D-mannopyranosides and glucopyranosides were measured by fluorescence and spectral stopped-flow methods. All process examined were uniphasic. The second-order formation rate constants varied only from 6.8 · 10⁴ to 12.8 · 10⁴ M^?. s^?1, whereas the first-order dissociation rate constants ranged from 4.1. to 220 s^?1, all at ph 5.0, I = 0.3 M, and 25°C. Dissociation rates thus controlled the value of binding constant. The effect of temperature on these reactions was examined, from which enthalpies and entropies of activation and of reaction could be calculated. The effects of pH at 25°C on the reaction rates of 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside with concanavalin A were examined. The value of the binding constant K_ap (derived from the kinetics) at any pH could be related to the intrinsic binding constant K by the expression K_ap = K_aK(K_a + [H⁺])^?1. The values of K_a, the ionization constant of the protein segment responsive to sugar binding, were 3 · 10^?4 M and 1 · 10^?4 M for 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside, respectively. The binding constant of p-nitrophenyl α-D-mannopyranoside is surprisingly much less sensitive to a pH change from 5.0 to 2.7. Ionic strength had little effect on the binding characteristics of 4-methylumbelliferyl α-D-mannopyranoside to concanavalin A at pH 5.2 and 25°C.     

PHOSPHATE ION AS A PROMOTER CATALYST OF RESPIRATION

The active component of phosphate solutions, in relation to promoter action on oxidising enzymes, is the PO₄ ^'''''' ion. This is shown by the demonstration of a hyperbolic relationship between per cent production of CO₂ (of Elodea) and pPO₄, the measure of the phosphate ion potential. This is consistent with the rate of respiration as affected by changing pPO₄ through change of total phosphate concentration while pH is kept constant. The equation for this relationship is (CO₂ – a) (pPO₄ – b)ⁿ = K where a, b, n, and K are constants and n = 1. The same relationship to phosphate ion concentration, expressed by the equation (Activity of enzyme) (pPO₄)ⁿ = K, where n and K are constants and n varies from 1 to 6 under different conditions, appears to hold for some other enzyme actions, including those of peroxidase and pancreatic lipase.     

Growth Kinetics of Attached Iron-Oxidizing Bacteria

A model of growth and substrate utilization for ferrous-iron-oxidizing bacteria attached to the disks of a rotating biological contactor was developed and tested. The model describes attached bacterial growth as a saturation function in which the rate of substrate utilization is determined by a maximum substrate oxidation rate constant (P), a half-saturation constant (K_s), and the concentration of substrate within the rotating biological contactor (S₁). The maximum oxidation rate constant was proportional to flow rate, and the substrate concentration in the reactor varied with influent substrate concentration (S₀). The model allowed the prediction of metabolic constants and included terms for both constant and growth-rate-dependent maintenance energies. Estimates for metabolic constants of the attached population of acidophilic, chemolithotrophic, iron-oxidizing bacteria limited by ferrous iron were: maximum specific growth rate (μ_max), 1.14 h⁻¹; half-saturation constant (K_s) for ferrous iron, 54.9 mg/liter; constant maintenance energy coefficient (m₁), 0.154 h⁻¹; growth-rate-dependent maintenance energy coefficient (m′), 0.07 h⁻¹; maximum yield (Y_g), 0.063 mg of organic nitrogen per mg of Fe(II) oxidized.     

Gallic acid oxidation by turnip peroxidase

Both ellagic and gallic acids non competitively inhibited guaiacol oxidation by turnip peroxidase. The K_i values were 3 and 26 μm for ellagic and gallic acid respectively. Enzymatic oxidation of gallic acid by the isolated major turnip peroxidase was characterized with respect to spectral behaviour, affinity constant and pH effect. The K_m for H₂O₂ and gallic acid are 2.5 and 8.0 mM for turnip peroxidase. The pH optimum for gallic acid oxidation is about 6.5 and the rate constant k₄ decreased with the increase of pH in presence of both guaiacol and Gallic acid. When the gallic acid oxidation products were subjected to chromatographic analysis, it was found to be converted mainly to ellagic and an unknown quinone.     

Cat Heart Muscle in Vitro : VI. Potassium exchange in papillary muscles

The exchange of cell K with K⁴², J _K, has been measured in cat right ventricular papillary muscle under conditions of a steady state with respect to intracellular K concentration. Within the limits of the measurement, all of cell K exchanged at a single rate. Cells from small cats are smaller and have larger surface/volume ratios than cells from large cats. The larger surface/volume ratio results in larger flux values. J _K increases in an approximately linear manner as the external K concentration is increased twentyfold, from 2.5 to 50 mM, at constant intracellular K concentration. The permeability for K ions, P _K, calculated from the influx and membrane potential, remains very nearly constant over this range of external K concentrations. J _K is not affected by replacement of O₂ by N₂, or by stimulated contractions at 60 per minute, but K influx decreases markedly in 10^-5 M and 10^-8 M ouabain.