Coordination of Mn++ ions at contact sites between tRNA and aminoacyl-tRNA synthetase.

By means of PMR and ESR study the shielding of Mn⁺⁺ ions by aminoacyl-tRNA synthetase has been detected in the aminoacyl-tRNA synthetase - tRNA complex at pH 7.5. At pH 6 this effect was not observed. We propose that ions interact with certain aminoacyl-tRNA synthetase groups protonated when passing to slightly acid pH. The role of Mn⁺⁺ and Mg⁺⁺ ions in the formation of a functionally active complex tRNA-aminoacyl-tRNA synthetase is discussed.     

Effect of dipolar ions on the entropy-driven polymerization of tobacco mosaic virus protein

The effect of the dipolar ions, glycine, glycylglycine, and glycylglycylglycine on the polymerization of tobacco mosaic virus (TMV) protein has been studied by the methods of light scattering and ultracentrifugation. All three dipolar ions promote polymerization. The major reaction in the early stage is transition from the 4 S to the 20 S state. As in the absence of dipolar ions, the polymerization is enhanced by an increase in temperature; it is endothermic and therefore entropy-driven. The effect of the dipolar ions can be understood in terms of their action as salting-out agents; they increase the activity coefficient of TMV A protein, the 4 S material, and thus shift the equilibrium toward the 20 S state. The salting-out constants, K, for the reaction in 0.10 ionic strength phosphate buffer at pH 6.7 was found by the light scattering method to be 1.6 for glycine, 2.5 for glycylglycine, and 2.5 for glycylglycylglycine. A value of 2.7 was obtained by the ultracentrifugation method for glycylglycine in phosphate buffer at 0.1 ionic strength and pH 6.8 at 10 degrees C. For both glycine and glycylglycine, K increases when the ionic strength of the phosphate buffer is decreased. This result suggests that electrolytes decrease the activity coefficient of the dipolar ions, a salting-in phenomenon. However, the salting-in constants evaluated from these results are substantially higher than those previously determined by solubility measurements. The effect of glycine and glycylglycine on polymerization was studied at pH values between 6.2 and 6.8. The effectiveness of both dipolar ions is approximately 50% greater at pH 6.8 than at pH 6.2. The variation of the extent of polymerization with pH in the presence of the dipolar ions is consistent with the interpretation that approximately one hydrogen ion is bound for half of the polypeptide units in the polymerized A protein.     

Interaction of magnesium ions with poly A and poly U

The binding of Mg⁺⁺ to poly A and poly U has been measured quantitatively by using the metallochromic indicator calmagite. The method is described in detail. It is shown that there is electrostatic interaction between the binding sites, viz., the phosphate groups, and the intrinsic association constant, for the specific binding can be determined. After extrapolation to zero ionic strength we find that, for the binding of Mg⁺⁺ to poly A, k_int = 4 × 10⁴ and for that, to poly U, k_int = 3 × 10⁴. The intrinsic enthalpy of association is negative. The effect of Mg⁺⁺ on the secondary structure of poly A and poly U has been studied by measuring the ultraviolet absorbance, optical rotatory dispersion and viscosity as a function of the amount of added Mg⁺⁺ ions. It was found that Mg⁺⁺ promotes the formation of a more ordered secondary structure by neutralizing or screening the negative charges. It is concluded from the absorbance measurements that for poly A at pH ? 7 and for poly U at pH >xs 9 this ordering involves stacking of the bases. Likewise, in solutions of UDP with a pH around 10, base stacking occurs on addition of Mg⁺⁺.     

Coordination of iron ions in the form of histidinyl dinitrosyl complexes does not prevent their genotoxicity

Formation of dinitrosyl iron complexes (DNICs) was observed in a wide spectrum of pathophysiological conditions associated with overproduction of NO. To gain insight into the possible genotoxic effects of DNIC, we examined the interaction of histidinyl dinitrosyl iron complexes (HIS-DNIC) with DNA by means of circular dichroism. Formation of DNIC was monitored by EPR and FT/IR spectroscopy. Vibrational bands for aquated HIS-DNIC are reported. Dichroism results indicate that HIS-DNIC changes the conformation of the DNA in a dose-dependent manner in 10 mM phosphate buffer (pH 6). Increase of the buffer pH or ionic strength decreased the effect. Comparison of HIS-DNIC DNA interaction with the effect of hydrated Fe²⁺ ion revealed many similarities. The importance of iron ions in HIS-DNIC induced genotoxicity is confirmed by plasmid nicking assay. Treatment of pUC19 plasmid with 1 μM HIS-DNIC did not affect the plasmid supercoiling. Higher concentrations of HIS-DNIC induced single strand breaks. The effect was completely abrogated by addition of deferoxamine, a specific strong iron chelator. Our data reveal that formation of HIS-DNIC does not prevent DNA from iron-induced damage and imply that there is no direct interrelationship between iron–NO coordination and their mutual toxicity modulation.     

Interactions of DNA with divalent metal ions. I. 31P-nmr studies

³¹P-nmr has been used to investigate the specific interaction of three divalent metal ions, Mg²⁺, Mn²⁺, and Co⁺², with the phosphate groups of DNA. Mg²⁺ is found to have no significant effect on any of the ³¹P-nmr parameters (chemical shift, line-width, T₁, T₂, and NOE) over a concentration range extending from 20 to 160 mM. The two paramagnetic ions, Mn²⁺ and Co²⁺, on the other hand, significantly change the ³¹P relaxation rates even at very low levels. From an analysis of the paramagnetic contributions to the spin–lattice and spin–spin relaxation rates, the effective internuclear metal–phosphorus distances are found to be 4.5 ± 0.5 and 4.1 ± 0.5 Å for Mn²⁺ and Co²⁺, respectively, corresponding to only 15 ± 5% of the total bound Mn²⁺ and Co²⁺ being directly coordinated to the phosphate groups (inner-sphere complexes). This result is independent of any assumptions regarding the location of the remaining metal ions which may be bound either as outer-sphere complexes relative to the phosphate groups or elsewhere on the DNA, possibly to the bases. Studies of the temperature effects on the ³¹P relaxation rates of DNA in the absence and presence of Mn²⁺ and Co²⁺ yielded kinetic and thermodynamic parameters which characterize the association and dissociation of the metal ions from the phosphate groups. A two-step model was used in the analysis of the kinetic data. The lifetimes of the inner-sphere complexes are 3 × 10^?7 and 1.4 × 10^?5 s for Mn²⁺ and Co²⁺, respectively. The rates of formation of the inner-sphere complexes with the phosphate are found to be about two orders of magnitude slower than the rate of the exchange of the water of hydration of the metal ions, suggesting that expulsion of water is not the rate-determining step in the formation of the inner-sphere complexes. Competition experiments demonstrate that the binding of Mg²⁺ ions is 3–4 times weaker than the binding of either Mn²⁺ or Co²⁺. Since the contribution from direct phosphate coordination to the total binding strength of these metal ion complexes is small (～15%), the higher binding strength of Mn²⁺ and Co²⁺ may be attributed either to base binding or to formation of stronger outer-sphere metal–phosphate complexes. At high levels of divalent metal ions, and when the metal ion concentration exceeds the DNA–phosphate concentration, the fraction of inner-sphere phosphate binding increases. In the presence of very high levels of Mg²⁺ (e.g., 3.1M), the inner-sphere ? outer-sphere equilibrium is shifted toward ～100% inner-sphere binding. A comparison of our DNA results and previous results obtained with tRNA indicates that tRNA and DNA have very similar divalent metal ion binding properties. A comparison of the present results with the predictions of polyelectrolyte theories is presented.     

Lanthanide ions promote the hydrolysis of 2,3-Bisphosphoglycerate

The ³¹P NMR studies showed that lanthanide ions promote the site-specific hydrolysis of 2,3-Bisphosphoglycerate (BPG) at pH 7.4 by cleaving the 2 phosphomonoester bond. The effect of fourteen trivalent lanthanide ions and Sc³⁺, and Y³⁺ were compared by the percentage of hydrolysis obtained by determining the inorganic phosphate produced. All the trivalent lanthanide ions promote the hydrolysis, but Sc³⁺ not. Among them, Ce³⁺ affects the reaction mostly. This was mainly attributed to the autooxidation of Ce³⁺ to Ce⁴⁺, since the promoting effect of Ce³⁺ is related to the increasing Ce⁴⁺ amount in the solution and depressed by adding sulphite. Ce⁴⁺ promotes the hydrolysis more efficiently than Ce³⁺ do. The pseudo first-order rate constant for the hydrolysis of BPG by Ce(SO₄)₂ (18.7 mM) at pH 1 and pH 2, 37 °C is 3.1 h^–1 and 0.65 h^–1 respectively. A mechanism with a hydroxo species as reactive intermediate was proposed for the trivalent lanthanide ions. The site-specificity was explainable by this mechanism.     

THE EFFECT OF ACETATE BUFFER MIXTURES,ACETIC ACID,AND SODIUM ACETATE,ON THE PROTOPLASM,AS INFLUENCING THE RATE OF PENETRATION OF CRESYL BLUE INTO THE VACUOLE OF NITELLA

When living cells of Nitella are exposed to a solution of sodium acetate and are then placed in a solution of brilliant cresyl blue made up with a borate buffer mixture at pH 7.85, a decrease in the rate of penetration of dye is found, without any change in the pH value of the sap. It is assumed that this inhibiting effect is caused by the action of sodium on the protoplasm. This effect is not manifest if the dye solution is made up with phosphate buffer mixture at pH 7.85. It is assumed that this is due to the presence of a greater concentration of base cations in the phosphate buffer mixture. In the case of cells previously exposed to solutions of acetic acid the rate of penetration of dye decreases with the lowering of the pH value of the sap. This inhibiting effect is assumed to be due chiefly to the action of acetic acid on the protoplasm, provided the pH value of the external acetic acid is not so low as to involve an inhibiting effect on the protoplasm by hydrogen ions as well. It is assumed that the acetic acid either has a specific effect on the protoplasm or enters as undissociated molecules and by subsequent dissociation lowers the pH value of the protoplasm. With acetate buffer mixture the inhibiting effect is due to the action of sodium and acetic acid on the protoplasm. The inhibiting effect of acetic acid and acetate buffer mixture is manifested whether the dye solution is made up with borate or phosphate buffer mixture at pH 7.85. It is assumed that acetic acid in the vacuole serves as a reservoir so that during the experiment the inhibiting effect still persists.     

pH dependent effects of sodium ions on dextransucrase activity in Streptococcus mutans

Dextransuccrase (E.C 2.4.1.5) is a key enzyme in S. mutans for the metabolism of sucrose which helps in the adherence and accumulation of bacteria on tooth surface leading to the formation of dental caries. Dextransuccrase resembles in its catalytic properties with the brush boarder sucrase and exhibits pH dependent inhibitory and stimulatory effects in response to Na⁺. In this communication we studied the effect of monovalent cations on the activity of dextransuccrase from S. mutans. The percentage inhibition of dextransuccrase was 65% at 0.5 mM NaCl which enhanced to 90% at 20 mM sodium concentration. However there was no effect on dextransucrase activity in presence of other monovalent cations (Rb⁺, Cs⁺, and K⁺) tested. Enzyme activity was enhanced 20–24% in acidic pH but was strongly inhibited (59–89%) around neutral and alkaline pH by 0.5–2.0 mM sodium chloride. Upon dialysis, 86% of enzyme activity was restored to control values. There was no effect of 2 mM NaCl on glucosyltransferase activity of the enzyme. Kinetic studies revealed that enzyme showed biphasic effects in response to Na⁺ ions. At acidic pH the enzyme exhibited mixed type of activation affecting both Vmax and Km, while in alkaline pH, the enzyme showed V- type effect reducing Vmax by 74% without affecting Km. The effects of sodium ions on dextransuccrase activity were specific, thus it can be useful to block its catalytic activity, and reducing the cariogenic potential of S. mutans.     

Specific adsorption of phosphate ions on proteins evidenced by capillary electrophoresis and reversed-phase high-performance liquid chromatography

Specific adsorption of phosphate ions at pH=7.0 was studied on different proteins, either counter-ions of phosphate (lysozyme, lactoferrin) or co-ion of phosphate (α-lactalbumin). The theoretical electrophoretic mobility of globular proteins lysozyme and α-lactalbumin (apo and holo (+1 calcium per molecule) forms) was compared with those measured by capillary electrophoresis in phosphate at pH 7.0, versus the ionic strength (I) in the range 0–0.775 mol L⁻¹. The specific adsorption of phosphate ions was evidenced by difference. From the experimental charge number (Z^eff) of protein in phosphate medium, a phosphate content per protein molecule was determined at pH=7.0.

• •For lactoferrin (pI=8–9), the electrophoretic mobility (μ) was constant and negative, highlighting a charge reversal due to phosphate adsorption.
• •For α-lactalbumin (holo form) experimental μ was roughly constant and more negative than predicted. Z^eff increased continuously from −4 to −11 in the ionic strength range from 0.005 to 0.775 mol l⁻¹, respectively. Accordingly, one to six phosphates were bound per molecule, respectively.
• •For lysozyme, experimental electrophoretic mobility was positive but lower than predicted. Z^eff was only discrete values +5 for I in the range 0.001–0.020 mol l⁻¹ and about +3 in the range 0.050–0.500 mol l⁻¹, whereas the theoretical Z value was +7 at pH=7.0. Lysozyme bounds one phosphate at low ionic strength and about two — three at higher ionic strength.

Reversed-phase HPLC confirms that adsorption of phosphate is different for the three proteins.     

Model for prebiotic pyrophosphate formation: Condensation of precipitated orthophosphate at low temperature in the absence of condensing or phosphorylating agents

Summary The formation of pyrophosphate (PPi) by condensation of orthophosphate (Pi) at low temperature (37°C) in the absence of condensing or phosphorylating agents could have been an ancient process in chemical evolution. In the present investigation the synthesis of³²PPi from³²Pi was carried out at pH 8.0 and PPi was found in larger amounts in the presence of insoluble Pi (with calcium or manganese ions) than in its absence (with magnesium ions, or with no divalent cations present). After 10 days of incubation in the presence of precipitated calcium phosphate, about 1.6 nmol/ml of PPi was formed (0.057% yield relative to insoluble Pi). The hypothesis that the reaction is dependent on precipitated Pi was reinforced by the effect of adding dimethyl sulfoxide (2.1–9.9 M) in the presence of magnesium ions: the amount of magnesium phosphate precipitated in the presence of the organic solvent was proportional to the amount of PPi formed. The large and negative activation entropies found in aqueous media with calcium ions and in a medium containing 11.3 M dimethyl sulfoxide with magnesium ions suggest that the reaction was favored by a hydrophobic phenomenon at the surface of solid Pi. This reaction could serve as a model for prebiotic formation of PPi.     

The effect of fixed valence metal ions on the free radical process of epinephrine autoxidation

The physiologically active metal ions with fixed valence Ca²⁺ and Mg²⁺ were shown to accelerate epinephrine autoxidation at an alkaline pH, which proceeds via the known quinoid pathway and is accompanied by the generation of reactive oxygen species. A higher efficiency was observed for Ca²⁺ ions compared with Mg²⁺ ions. The activation of epinephrine autoxidation was evident from a decrease in the time of the initiation of the chain reaction to begin (i.e., the reaction lag) and an increase in the rate of both oxygen uptake and the formation of adrenochrome. Based on the observed effects, Ca²⁺ and Mg²⁺ cations were assumed to have the potential to play a role in the free radical processes that are associated with redox reactions in the cell and can also modulate the effect of epinephrine in the organism its oxidation via the quinoid pathway.     

Thermodynamics of the interaction of aluminum ions with DNA: implications for the biological function of aluminum

Aluminum is a known neurotoxic agent and its neurotoxic effects may be due to its binding to DNA. However, the mechanism for the interaction of aluminum ions with DNA is not well understood. Here, we report the application of isothermal titration calorimetry (ITC), fluorescence spectroscopy, and UV spectroscopy to investigate the thermodynamics of the binding of aluminum ions to calf thymus DNA (CT DNA) under various pH and temperature conditions. The binding reaction is driven entirely by a large favorable entropy increase but with an unfavorable enthalpy increase in the pH range of 3.5-5.5 and at all temperatures examined. Aluminum ions show a strong and pH-dependent binding affinity to CT DNA, and a large positive molar heat capacity change for the binding, 1.57 kcal mol(-1) K(-1), demonstrates the burial of the polar surface of CT DNA upon groove binding. The fluorescence of ethidium bromide bound to CT DNA is quenched by aluminum ions in a dynamic way. Both Stern-Volmer quenching constant and the binding constant increase with the increase of the pH values, reaching a maximum at pH 4.5, and decline with further increasing the pH to 5.5. At pH 6.0 and 7.0, aluminum ions precipitate CT DNA completely and no binding of aluminum ions to CT DNA is observed by ITC. Combining the results from these three methods, we conclude that aluminum ions bind to CT DNA with high affinity through groove binding under aluminum toxicity pH conditions and precipitate CT DNA under physiological conditions.     

Effects of liming on phosphate availability in acid soils

Summary The critical factors involved in the plant-soil-phosphorus-lime interaction are outlined and discussed. Conflicting reports suggest that the prior liming of highly weathered acid soils can result in an increase, a decrease, or no change in the availability of applied phosphate. Adsorption of phosphate by amphoteric soil surfaces generally decreases slowly as the pH is raised from 4.0 to 7.0. However, in soils initially high in exchangeable Al³⁺, liming results in the formation of new, highly active, phosphate adsorbing surfaces as the Al³⁺ ions precipitate as insoluble polymeric hydroxy-Al cation species. Thus, if an acid soil is reacted with lime and then phosphate, without intervening air drying, liming can increase phosphate adsorption. If the same limed soil is air dried before reaction with phosphate (e.g. adsorption isotherm studies), liming decreases phosphate adsorption. Apparently, air drying alters the surface characteristics of recently limed soils, probably by promoting the crystallization of the hydroxy-Al cation polymers as gibbsite.An important phenomenon, which is often overlooked, is that liming can increase phosphate availability by stimulating mineralization of soil organic phosphorus. However, at high soil pH values, the precipitation of insoluble calcium phosphates can decrease phosphate availability. Since Al toxicity is characterised by the inhibition of the uptake, translocation and utilization of phosphate by plants, liming often increases the utilization of soil phosphate by plants through amelioration of Al toxicity.When making lime recommendations or interpreting the data collected from lime-phosphate experiments, it is important to consider all the complex interacting soil and plant factors involved.     

Effect of pH, ionic strength and univalent inorganic ions on the reconstitution of aspartate aminotransferase

1. The effect of pH change on the reconstitution of aspartate aminotransferase (EC 2.6.1.1), i.e. the reactivation of the apoenzyme with coenzyme (pyridoxal phosphate and pyridoxamine phosphate), was studied in the pH range 4.2-8.9 by using three buffer systems at concentrations ranging from 0.025 to 0.1m. 2. Although the profile of the reconstitution rate-pH curve in the range pH5.2-6.8 (covered by sodium cacodylate-HCl buffer) reflects the influence of the H(+) concentration on the reconstitution process, the profile of the curve in the pH ranges 4.2-5.6 and 7.2-8.25 (covered respectively by sodium acetate-acetic acid and Tris-HCl buffers) appears to be influenced by the ionic strength of the buffer. 3. The reconstitution is also influenced by univalent inorganic ions such as halide ions and, to a lesser extent, alkali metal ions, which are known to alter the water structure.     

The competition transport of sodium ions and protons in the cytoplasmic access channel of the Na+,K+-ATPase

The changes in capacitance and conductance of lipid bilayer membranes have been studied with adsorbed membrane fragments containing Na⁺,K⁺-ATPase. These changes have been initiated by fast release of protons from a bound form (“caged H⁺”) induced by an UV flash. The changes of the capacitance in the presence of Na⁺,K⁺-ATPase were affected by the frequency of the applied voltage, pH and the concentration of sodium ions. Addition of sodium ions altered the changes of capacitance caused by a pH jump in the medium due to caged H⁺ photolysis, and the magnitude and sign of this effect depended on the initial pH. These results are explained by competitive binding of sodium ions and protons to the ion-binding sites of the Na⁺,K⁺-ATPase at its cytoplasmic side. The pH at which the sign of the sodium ion effect changed allows the evaluation of the pK of the proton binding site, which is about 7.6.     

The role of calcium ions and the thioredoxin system in regulation of spinach chloroplast fructosebisphosphatase

Illumination of isolated type A spinach chloroplasts causes a rapid increase in their activity of fructosebisphosphatase, as assayed at physiological substrate and Mg²⁺ concentrations. Activation is accelerated by addition of dihydroxyacetone phosphate to the chloroplasts and decreased by inorganic phosphate concentrations greater than those optimal for CO₂ fixation. At all times, measured fructosebisphosphatase activity was greater than was necessary to account for the observed rates of CO₂ fixation. Activation of purified fructosebisphosphatase $\text{in vitro}$ by dithiothreitol or reduced thioredoxin is extremely slow, but is greatly accelerated in the presence of physiological concentrations of Mg²⁺ and fructosebisphosphate if Ca²⁺ ions are present. Increased concentrations of fructosebisphosphate greatly increase the rate and extent of activation whereas in the absence of fructosebisphosphate Ca²⁺ ions have no effect. Neither inorganic phosphate nor dihydroxyacetone phosphate significantly affect the rate of activation. Ca²⁺ ions strongly inhibit the activity of the activated form of fructosebisphosphatase. It is proposed that free Ca²⁺ ions within chloroplasts are involved in preventing fructosebisphosphatase from functioning in the dark, and that free and/or bound Ca²⁺ facilitates the rapid reductive activation of this enzyme when the light is turned on again.     

Anti-fibrillogenic and fibril destabilizing effects of metal ions on cystatin fibrils

Metals such as Cu²⁺, Fe³⁺, and Zn²⁺ are major contributors to the biology of a brain in stages of health, aging, and disease because of their unique effects on both protein structures (misfolding) and oxidative stress. The relationship between metal ions and neurodegenerative diseases is very complicated. Our study highlights how metal ions influence amyloid formation at low pH and on preformed amyloid fibrils. By using thioflavin T assay, ANS fluorescence, Congo red assay, circular dichroism, and microscopy to elucidate the effects of Cu²⁺, Fe³⁺, and Zn²⁺ on goat brain cystatin (GBC) aggregation at low pH. Results showed that Cu²⁺ and Fe³⁺ inhibit fibril formation of GBC by promoting amorphous aggregates. However, Zn²⁺ exclusively promotes fibril formation at low pH, leading to the formation of more ordered aggregates. Furthermore, the combined results of these complementary methods also suggested that Cu²⁺ and Fe³⁺ destabilize the β-sheet secondary structure of preformed amyloid fibrils of GBC.     

A continuous spectrophotometric assay for arylsulfatase activity,dependent on the formation of complexes between cupric ions and nitrocatechols

The nitrocatechols 2-hydroxy-5-nitrophenol and 2-hydroxy-5-methyl-4-nitrophenol formed strongly colored complexes with cupric ions, the dissociation constants of these complexes being 1.61 and 1.74 × 10^?4m, respectively. Complex formation with 2-hydroxy-5-methyl-4-nitrophenol was independent of pH between pH 5.4 and 7.2. The aryl-sulfate sulfohydrolase (EC 3.1.6.1) from the New Zealand mollusk, Haliotis iris, was not inhibited by low concentrations of cupric ion so that the enzymatic hydrolysis of sulfate esters of the above nitrocatechols could be monitored continuously in the presence of cupric ions, by following the formation of the yellow complexes. Assay methods based on this phenomenon gave results identical with those obtained by the discontinuous method of alkaline development. Rate measurements were linearly related to enzyme concentration whichever assay method was used. At very high pH, cupric ions decreased the intensity of color of the nitrocatechol anions.     

Effect of monovalent and divalent ions upon the activity of nisin againstMicrococcus flavus

Effect of monovalent and divalent ions on the activity of nisin againstMicrococcus flavus has been studied and Mg²⁺ ions have been found to reverse the effect of nisin. The protection by Mg²⁺ ions has been found to be due to complex formation with the antibiotic.     

Standard free energy maps for the hydrolysis of ATP as a function of pH and metal ion concentration: comparison of metal ions

The observed equilibrium constant K_obs for the hydrolysis of ATP to ADP and inorganic phosphate has been calculated as a function of pH and metal ion concentration pM (- log [M]) at 25 °C and μ = 0.2 with the use of literature values of the acid dissociation and complex dissociation constants for the phosphates.The resulting standard free energy changes ΔG °′ are presented by means of contour diagrams for the range pH 4–10 and pM 1–7. These maps summarize the results of some 1900 calculations per diagram, and clearly simulate a differential effect of the metal ions of interest, including Mg²⁺, Ca²⁺, Sr²⁺, Mn²⁺, Li⁺, Na⁺ and K⁺, on the equilibrium hydrolysis of ATP.