Effect of sodium and potassium ions on conformation of linker parts of nucleosomes

The chromatin structure and DNA accessibility to proteins depend on the structure of linker DNA entering and exiting the nucleosome. Since DNA is a negatively charged polymer, the conformation of linker DNA, in turn, depends on the ionic microenvironment. In the present work, the effect of Na⁺ and K⁺ ions on the structure of mono nucleosome linker DNA was studiedby fluorescence microscopy of single complexes. It was revealed that nucleosomes adopt one of two conformational states, whose occupancy is significantly changed after the substitution of K⁺ ions by Na⁺. These changes are likely caused by different interaction of Na⁺ and K⁺ with DNA in the regions of DNA entry and exit of the nucleosome. Cation-dependent changes in the conformation of linker DNA may affect topological barriers in the nucleosome, structure of polynucleosome chromatin, and interactions with different protein factors.     

Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons

Internal Cs⁺, Na⁺, Li⁺, and, to a lesser degree, Rb⁺ interfere with outward current through the K pores in voltage clamped squid axons. Addition of 100 mM NaF to the perfusion medium cuts outward current for large depolarizations about in half, and causes negative conductance over a range of membrane voltages. For example, suddenly reducing membrane potential from +100 to +60 mv increases the magnitude of the outward current. Internal Cs⁺ and, to a small extent, Li⁺, also cause negative conductance. Na⁺ ions permeate at least 17 times less well through the K pores than K⁺, and Cs⁺ does not permeate measurably. The results strongly suggest that K pores have a wide and not very selective inner mouth, which accepts K⁺, Na⁺, Li⁺, Cs⁺, tetraethylammonium ion (TEA⁺), and other ions. The diameter of the mouth must be at least 8 A, which is the diameter of a TEA⁺ ion. K⁺ ions in the mouths probably have full hydration shells. The remainder of the pore is postulated to be 2.6–3.0 A in diameter, large enough for K⁺ and Rb⁺ but too small for Cs⁺ and TEA⁺. We postulate that Na⁺ ions do not enter the narrower part of the pore because they are too small to fit well in the coordination cages provided by the pore as replacements for the water molecules surrounding an ion.     

The Permeability of the Sodium Channel to Metal Cations in Myelinated Nerve

The relative permeability of sodium channels to eight metal cations is studied in myelinated nerve fibers. Ionic currents under voltage-clamp conditions are measured in Na-free solutions containing the test ion. Measured reversal potentials and the Goldman equation are used to calculate the permeability sequence: Na⁺ ≈ Li⁺ > Tl⁺ > K⁺. The ratio P_K/P_Na is 1/12. The permeabilities to Rb⁺, Cs⁺, Ca⁺⁺, and Mg⁺⁺ are too small to measure. The permeability ratios agree with observations on the squid giant axon and show that the reversal potential E_Na differs significantly from the Nernst potential for Na⁺ in normal axons. Opening and closing rates for sodium channels are relatively insensitive to the ionic composition of the bathing medium, implying that gating is a structural property of the channel rather than a result of the movement or accumulation of particular ions around the channel. A previously proposed pore model of the channel accommodates the permeant metal cations in a partly hydrated form. The observed sequence of permeabilities follows the order expected for binding to a high field strength anion in Eisenman's theory of ion exchange equilibria.     

Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations

Counterions are important constituents for the structure and function of nucleic acids. Using ⁷Li and ¹³³Cs nuclear magnetic resonance (NMR) spectroscopy, we investigated how ionic radii affect the behavior of counterions around DNA through diffusion measurements of Li⁺ and Cs⁺ ions around a 15-bp DNA duplex. Together with our previous data on ²³Na⁺ and ¹⁵NH₄⁺ ions around the same DNA under the same conditions, we were able to compare the dynamics of four different monovalent ions around DNA. From the apparent diffusion coefficients at varied concentrations of DNA, we determined the diffusion coefficients of these cations inside and outside the ion atmosphere around DNA (D_b and D_f, respectively). We also analyzed ionic competition with K⁺ ions for the ion atmosphere and assessed the relative affinities of these cations for DNA. Interestingly, all cations (i.e., Li⁺, Na⁺, NH₄⁺, and Cs⁺) analyzed by diffusion NMR spectroscopy exhibited nearly identical D_b/D_f ratios despite the differences in their ionic radii, relative affinities, and diffusion coefficients. These results, along with the theoretical relationship between diffusion and entropy, suggest that the entropy change due to the release of counterions from the ion atmosphere around DNA is also similar regardless of the monovalent ion types. These findings and the experimental diffusion data on the monovalent ions are useful for examination of computational models for electrostatic interactions or ion solvation.     

Dependence of the intracellular concentrations of univalent ions and hydrogenase activity on the salt composition and pH of the medium in the haloalkaliphilic sulfate-reducing bacterium <Emphasis Type="Italic">Desulfonatronum thiodismutans</Emphasis>

It has been shown that the intracellular concentrations of Na⁺, K⁺, and Cl^? ions in Desulfonatronum thiodismutans depend on the extracellular concentration of Na⁺ ions. An increase in the extracellular concentration of Na⁺ results in the accumulation of K⁺ ions in cells, which points to the possibility that these ions perform an osmoprotective function. When the concentration of the NaCl added to the medium was increased to 4%, the concentration gradient of Cl^? ions changed insignificantly. It was found that D. thiodismutans contains two forms of hydrogenase—periplasmic and cytoplasmic. Both enzymes are capable of functioning in solutions with high ionic force; however they exhibit different sensitivities to Na⁺, K⁺, and Li⁺ salts and pH. The enzymes were found to be resistant to high concentrations of Na⁺ and K⁺ chlorides and Na⁺ bicarbonate. The cytoplasmic hydrogenase differed significantly from the periplasmic one in having much higher salt tolerance and lower pH optimum. The activity of these enzymes depended on the nature of both the cationic and anionic components of the salts. For instance, the inhibitory effect of NaCl was less pronounced than that of LiCl, whereas Na⁺ and Li⁺ sulfates inhibited the activity of both hydrogenase types to an equal degree. The highest activity of these enzymes was observed at low Na⁺ concentrations, close to those typical of cells growing at optimal salt concentrations.     

Interactions des ions métalliques avec le DNA. IV. Fixation de i'ion cuivrique sur le DNA

The binding of cupric ion (Cu⁺⁺) to DNA was followed by spectrophotometry, melting profiles, and hydrodynamic techniques, in 0. 1M NaClO₄ and at pH 5. 6. A small amount of Cu⁺⁺ is bound specifically to bases (about 1 Cu⁺⁺ per 20 nucleotides), in agreement with polarographic and EPR data. A preferential stabilization of G–C pairs and only a slight increase of the flexibility of the molecule were observed. In 5 × 10^?3M NaClO₄, a higher number of nonhomogeneous binding sites is found by spectrophotometry. It is concluded that at least two types of sites are available for Cu⁺⁺. The first one, where Cu⁺⁺ is chelating N₇ of purines to phosphate, is observed only at low ionic strength and destabilizes the double helix. The second exists mainly at 0, 1M or higher ionic strength. All the sites are identical and could be attributed to two successive guanine residues in the same strand. Similar behavior was found for other divalent cations, e. g., Fe⁺⁺, Mn⁺⁺, and Co⁺⁺.     

Selectivity sequences in a model calcium channel: role of electrostatic field strength

The energetics that give rise to selectivity sequences of ionic binding selectivity of Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺ in a model of a calcium channel are considered. This work generalizes Eisenman’s classic treatment (Biophys J 2(Suppl. 2):259, 1962) by including multiple, mobile binding site oxygens that coordinate many permeating ions (all modeled as charged, hard spheres). The selectivity filter of the model calcium channel allows the carboxyl terminal groups of glutamate and aspartate side chains to directly interact with and coordinate the permeating ions. Ion dehydration effects are represented with a Born energy between the dielectric coefficients of the selectivity filter and the bath. High oxygen concentration creates a high field strength site that prefers small ions, as in Eisenman’s model. On the other hand, a low filter dielectric constant also creates a high field strength site, but this site prefers large ions, contrary to Eisenman’s model. These results indicate that field strength does not have a unique effect on ionic binding selectivity sequences once entropic, electrostatic, and dehydration forces are included in the model. Thus, Eisenman’s classic relationship between field strength and selectivity sequences must be supplemented with additional information about selectivity filters such as the calcium channel that has amino acid side chains mixing with ions to make a crowded permeation pathway.     

A model of active transport of ions in hepatocytes

A mathematical model of the transport of basic ions (K⁺, Na⁺, Cl⁻) across the hepatocyte membrane has been created using the previously constructed models of active ion transport in biomembranes. The dependence of the resting potential on extracellular ion concentration has been established. Using the model, it is possible to independently calculate the resting potential at the biomembrane and the concentrations of sodium, potassium, and chlorine ions in the cell. The calculated internal concentrations of the ions are in good agreement with the corresponding experimental values.     

Effects of alkali ions on the circadian leaf movements of Oxalis regnellii

The influence of alkali ions on the circadian leaf movements of Oxalis regnellii Mig. was investigated. Ions were given to the oscillating system via the transpiration stream of cut stalks in nutrient medium. Chloride solutions of Rb⁺, Cs⁺, Na⁺ and K⁺ were tested and the results compared to previously published LiCl-results. The period of the circadian leaf movements was unaffected by a continual addition of Na⁺ or K⁺ to the nutrient medium (at least up to 40 mM). Rb⁺, in the concentration of 2.5 or 5 mM, caused a shortening of the period when applied continuously. Rb⁺ concentrations up to 60 mM were tested. Cs⁺ ions caused only lengthenings of the circadian period. Cs⁺ concentrations up to 40 mM were tested. Cs⁺ resembled Li⁺ in producing period lengthenings, but was not as effective as Li⁺ when compared on a concentration basis. Toxicity of the effective ions was in the following order: Li⁺Cs⁺Rb⁺, Rb⁺ pulses (50 mM, 4 h) phase-shifted the rhythm and caused advances. A phase response curve was determined and the maximum steady state advances were of the order of 1 h. The dual effect of the Rb⁺ ions is discussed and is assumed to be due to two counteracting processes, exemplified by Rb⁺-sensitive ATPase-controlled pumping processes and protein synthesis. For comparison, the effects of Rb⁺ and Li⁺ in human depressive disorders is also discussed in relation to their influence on circadian systems. It is emphasized that Rb⁺ and K⁺ behave differently and are not interchangeable in their action on circadian systems.     

Malaria parasites tolerate a broad range of ionic environments and do not require host cation remodelling

Malaria parasites grow within erythrocytes, but are also free in host plasma between cycles of asexual replication. As a result, the parasite is exposed to fluctuating levels of Na⁺ and K⁺, ions assumed to serve important roles for the human pathogen, Plasmodium falciparum. We examined these assumptions and the parasite's ionic requirements by establishing continuous culture in novel sucrose‐based media. With sucrose as the primary osmoticant and K⁺ and Cl^? as the main extracellular ions, we obtained parasite growth and propagation at rates indistinguishable from those in physiological media. These conditions abolish long‐known increases in intracellular Na⁺ via parasite‐induced channels, excluding a requirement for erythrocyte cation remodelling. We also dissected Na⁺, K⁺ and Cl^? requirements and found that unexpectedly low concentrations of each ion meet the parasite's demands. Surprisingly, growth was not adversely affected by up to 148 mM K⁺, suggesting that low extracellular K⁺ is not an essential trigger for erythrocyte invasion. At the same time, merozoite egress and invasion required a threshold ionic strength, suggesting critical electrostatic interactions between macromolecules at these stages. These findings provide insights into transmembrane signalling in malaria and reveal fundamental differences between host and parasite ionic requirements.     

Univalent ions in phospholipid model membranes: Thermodynamic and hydration aspects

By means of differential scanning calorimetry, effects of systematic series of Group I and VII ions on the phase state of model multibilayer dimyristoylphosphatidylcholine (di(14:0)PC) membranes have been studied at a lipid/ion molar ratio of 3/1. The sign-changing correlations between the ionic radii of cations and temperature shifts of di(14:0)PC phase transition were obtained. For cosmotropic Li⁺ and Na⁺, the observed shifts were positive (LiCl: ΔT _m = 0.6°C; ΔT _p = 1.9°C), whereas chaotropic K⁺ and Rb⁺ presence resulted in negative shifts (RbCl: ΔT _m = ?0.3°C; ΔT _p = ?2.5°C). The anions (Cl^?, Br^?, I^?) showed a similar effect increasing with the ion chaotropicity. An essentially weaker effect of Cs⁺ as compared to other alkali metal ions (CsCl: ΔT _m ≈ 0°C; ΔT _p = ?0.1°C) can be one of the reasons of its accumulation in living organisms. Generalization of all available data allowed us to specify some important factors of lipid-ion interactions that should be taken into account in further investigations in this field.     

Effect of tetramethylammonium ions on conformational changes of DNA in the premelting temperature range

The reversible conformational change of DNAs and polydeoxyribonucleotides occurring before melting was followed by circular dichroism. Δθ/δT, the rate of change of ellipticity θ with temperature, was used mainly as a measure of this premelting phenomenon. If sodium ions were replaced by tetramethylammonium ions Δθ/δT decreased for poly (dA) poly (dT) and poly (dA.dT) poly (dT.dA), but increased for poly (dG.dC) poly (dC.dG). DNAs of different base composition showed no more premelting (Δθ/ΔT ~ 0) even at low molarities of TMACl provided the Na/TMA ratio was very small. For all cases studied the θ values at 0°C and at a given ionic strength were smaller in NaCl than in TMACl. When studying the series of ammonium ions from NH⁺₄ to (C₂H₅)₄,N⁺ the Δθ/ΔT values first decreased, going through zero with TMA⁺ io and then increased again. A tentative and qualitative explanation of our results can be given: (a) Hydration of the polymers increases in presence of TMA ions and their average stability decreases; locally, however, (AT) pairs are preferentially stabilized by TMA ions owing to a specific interaction at the level of O₂ of thymine. (b) In order to explain the different behaviour of (AT) polymers and DNA, it is assumed that only the B structure is able to accommodate TMA ions in the small groove of the double stranded helix.     

Identification of Electric-Field-Dependent Steps in the Na,K-Pump Cycle

The charge-transporting activity of the Na⁺,K⁺-ATPase depends on its surrounding electric field. To isolate which steps of the enzyme’s reaction cycle involve charge movement, we have investigated the response of the voltage-sensitive fluorescent probe RH421 to interaction of the protein with BTEA (benzyltriethylammonium), which binds from the extracellular medium to the Na⁺,K⁺-ATPase’s transport sites in competition with Na⁺ and K⁺, but is not occluded within the protein. We find that only the occludable ions Na⁺, K⁺, Rb⁺, and Cs⁺ cause a drop in RH421 fluorescence. We conclude that RH421 detects intramembrane electric field strength changes arising from charge transport associated with conformational changes occluding the transported ions within the protein, not the electric fields of the bound ions themselves. This appears at first to conflict with electrophysiological studies suggesting extracellular Na⁺ or K⁺ binding in a high field access channel is a major electrogenic reaction of the Na⁺,K⁺-ATPase. All results can be explained consistently if ion occlusion involves local deformations in the lipid membrane surrounding the protein occurring simultaneously with conformational changes necessary for ion occlusion. The most likely origin of the RH421 fluorescence response is a change in membrane dipole potential caused by membrane deformation.     

Studies on nucleic acids. VIII. Changes in the stability of DNA secondary structure by interaction with divalent metal ions

The melting temperature of a natural DNA is decreased in the presence of increasing amounts of copper ions, whereas other divalent metal ions stabilize the DNA secondary structure at low ionic strength. At 1.28 × 10^?4M, Cu²⁺ produces a decrease of T_m depending on base composition. At very low Cu²⁺ concentrations (0.5 Cu²⁺/2 DNA-P) a stabilization of the DNA conformation appears due to an interaction between Cu²⁺ and phosphate groups of the DNA molecule. In this case the normal trend of GC dependence of T_m exists similar to that with Na⁺ and Mg²⁺ as counterions. If copper ions are in excess, the observed destabilization is stronger for DNAs rich in guanine plus cytosine than for those rich in adenine plus thymine. A sharp decrease of T_m occurs between 0.5–0.8 Cu²⁺/2 DNA-P and 1.5 Cu²⁺/2 DNA-P. The breadth of the transition decreases at high Cu²⁺ concentration with further addition of copper ions. Denaturation and renaturation experiments indicate that Cu²⁺ ions exceeding the phosphate equivalents interact with the bases and reduce the forces of the DNA helix conformation. Evidence is presented, that the destabilization effect produced by Cu²⁺ is possibly due to an interaction with guanine sites of the DNA molecule.     

Helix-coil transition in nucleoprotein. Effect of ionic strength on thermal denaturation of polylysine-DNA complexes

Thermal denaturation of direct-mixed and reconstituted polylysine–DNA complexes in 2.5 × 10^?4 M EDTA, pH 8.0 and various concentrations of NaCl has been studied. For both complexes, increasing ionic strength of the solution raises T_m, the melting temperature of free base pairs. The linear dependence of T_m on log Na⁺ indicates that the concept of electrostatic shielding on phosphate lattice of an infinitely long pure DNA by Na⁺ can be applied to short free DNA segments in a nucleoprotein. For a direct-mixed polylysine–DNA complex, the melting temperature of bound base pairs T_m′ remains constant at various ionic strengths. On the other hand, the T_m′ in a reconstituted polylysine–DNA complex is shifted to lower temperature at higher ionic strength. This phenomenon occurs for reconstituted complex with long polylysine of one thousand residues or short polylysine of one hundred residues. It is shown that such a decrease of T_m′ is not due to a reduction of coupling melting between free and bound regions in a complex when the ionic strength is raised. It is also not due to intermolecular or intramolecular change from a reconstituted to a direct-mixed complex. It is suggested that this phenomenon is due to structural change on polylysine-bound regions by ionic strength. It is suggested further that Na⁺ may replace water molecules and bind polylysine-bound regions in a reconstituted complex. Such a dehydration effect destabilizes these regions and lowers T_m′. This explanation is supported by circular dichroism (CD) results.     

Transport of magnesium ions in the phloem of Ricinus communis L. seedlings

During growth of Ricinus communis seedlings, magnesium ions are mobilized in the endosperm, taken up by and accumulated to very high levels (150 μmol·g FW^?1) in the cotyledons, and translocated to hypocotyl and roots. The magnesium gain from days 6 to 7 in the cotyledons and the seedling axis necessitates a total up-take rate of 600 nmol·h^?1-seedling^?1 and the phloem translocation rate must amount to 200 nmol·h^?1. seedling^?1. The phloem loading of magnesium and the regulatory properties of this process were investigated, making specific use of the ability to collect pure phloem sap from the cut hypocotyl of 6-d-old Ricinus seedlings. The concentration of magnesium in sieve-tube sap (5 mM) was fairly constant under many incubation conditions, e.g. incubation in magnesium-free buffer, incubation with different cations (K⁺, Na⁺, NH ₄ ⁺ ) or anions (Cl^?, NO ₄ ^- , SO ₄ ^2- ), or incubation with sucrose and amino acids. Even addition of magnesium chloride to the cotyledons did not enhance phloem loading of magnesium ions. Therefore the high magnesium content of the cotyledons was sufficient for continuous phloem loading of magnesium, irrespective of external ionic conditions. Also, the flow rate of sieve-tube sap did not influence the magnesium concentration in the sap. Only the incubation with sulfate and phosphate ions increased the magnesium-ion concentration in the phloem. Magnesium sulfate offered to the cotyledons caused a threefold increase of magnesium ions in the sieve-tube sap, which was inhibited by Na⁺, NH ₄ ⁺ and Ca²⁺ in rising order, but not by K⁺. Incubation with phosphate for a prolonged period (8 h) led to an increased mobilization of intra-cotyle-donary magnesium and an enhanced phloem loading of mobilized magnesium. It is concluded that phosphate availability is a decisive factor for mobilization and translocation of magnesium ions within the plant.     

L'induction du rythme endogène de sporulation chez Aspergillus niger: Rõles du rapport glucose/potassium et de micro-éléments

In Aspergillus niger Van Tieghem cultivated on a synthetic medium, the induction of an endogenous rhythm of sporulation and its perpetuation depend on the glucose K⁺ balance in the medium, an excess of one of them suppressing the oscillations. In its inducing effect on the rhythm K⁺ is partially replaced by Rb⁺, but not by Na⁺, Li⁺ or Cs⁺. While the glucose K⁺ balance is favourable for the manifestation of the rhythm, the addition of increasing levels of Na⁺, Li⁺ or Cs⁺ do not modify the period length. Nevertheless, at 0.3 M of Na⁺ or Li⁺ and 0.03 M of Cs⁺ rhythm disappears. The amplitude of oscillations depends on the level of the micro-elements furnished, especially on Mn²⁺. EDTA (1 × 10^?3M) inhibits the rhythm.     

Conversion of monensin from an ionophore to an inhibitor of Na+ uptake by SV3t3 membrane vesicles as a function of Na+ concentration

Monensin is a Na⁺ ionophore in membrane vesicles from SV3T3 cells; but its ability to stimulate Na⁺ flux is inhibited by increasing concentrations of Na⁺. At greater than 20-mM Na⁺, monensin inhibits Na⁺ uptake by the vesicles. Cs⁺ and NH₄⁺ also cause monensin to inhibit Na⁺ uptake, but general alterations in ionic strength do not convert the ionophore to an inhibitor. Monensin does not cause Na⁺ loss during collection of the vesicles on filters; nor is inhibition the result of the vesicle lumen being made alkaline by H⁺ loss in exchange for Na⁺. The specificity for cation and ionophore indicates that a precise interaction between the cation, ionophore, and membrane is required for inhibition.     

A parallel stranded G‐quadruplex composed of threose nucleic acid (TNA)

G‐rich sequences can adopt four‐stranded helical structures, called G‐quadruplexes, that self‐assemble around monovalent cations like sodium (Na⁺) and potassium (K⁺). Whether similar structures can be formed from xeno‐nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α‐l ‐threofuranosyl nucleic acid) to adopt a four‐stranded helical structure based on a planar G‐quartet motif. Using native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) and solution‐state nuclear magnetic resonance (NMR) spectroscopy, we show that despite a backbone repeat unit that is one atom shorter than the backbone repeat unit found in DNA and RNA, TNA can self‐assemble into stable G‐quadruplex structures that are similar in thermal stability to equivalent DNA structures. However, unlike DNA, TNA does not appear to discriminate between Na⁺ and K⁺ ions, as G‐quadruplex structures form equally well in the presence of either ion. Together, these findings demonstrate that despite a shorter backbone repeat unit, TNA is capable of self‐assembling into stable G‐quadruplex structures.