Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

Divalent metals associate with DNA in a site-selective manner, which can influence nucleosome positioning, mobility, compaction, and recognition by nuclear factors. We previously characterized divalent metal binding in the nucleosome core using hard (short-wavelength) X-rays allowing high-resolution crystallographic determination of the strongest affinity sites, which revealed that Mn²⁺ associates with the DNA major groove in a sequence- and conformation-dependent manner. In this study, we obtained diffraction data with soft X-rays at the Mn²⁺ absorption edge for a core particle crystal in the presence of 10 mM MnSO₄, mimicking prevailing Mg²⁺ concentration in the nucleus. This provides an exceptional view of counterion binding in the nucleosome through identification of 45 divalent metal binding sites.In addition to that at the well-characterized major interparticle interface, only one other histone-divalent metal binding site is found, which corresponds to a symmetry-related counterpart on the ‘free’ H2B α1 helix C-terminus. This emphasizes the importance of the α-helix dipole in ion binding and suggests that the H2B motif may serve as a nucleation site in nucleosome compaction. The 43 sites associated with the DNA are characterized by (1) high-affinity direct coordination at the most electrostatically favorable major groove locations, (2) metal hydrate binding to the major groove, (3) direct coordination to phosphate groups at sites of high charge density, (4) metal hydrate binding in the minor groove, or (5) metal hydrate-divalent anion pairing. Metal hydrates are found within the minor groove only at locations displaying a narrow range of high-intermediate width and to which histone N-terminal tails are not associated or proximal. This indicates that divalent metals and histone tails can both collaborate and compete in minor groove association, which sheds light on nucleosome solubility and chromatin compaction behavior.     

Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study

Four 20 ns molecular dynamics simulations have been performed with two counterions, K⁺ or Na⁺, at two water contents, 15 or 20 H₂O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K⁺ and Na⁺ binding to DNA are different. K⁺ binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na⁺ interacts preferentially with the phosphate groups. Increase of water causes a shift of both K⁺ and Na⁺ from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na⁺ organizes and immobilizes water structure around itself and near DNA while for K⁺ water is less organized and more dynamic.     

Probing the coordination properties of glutathione with transition metal ions (Cr2+,Mn2+,Fe2+,Co2+, Ni2+,Cu2+,Zn2+,Cd2+,Hg2+) by density functional theory

Complexes formed by reduced glutathione (GSH) with metal cations (Cr²⁺, Mn²⁺,Fe²⁺,Co²⁺,Ni²⁺,Cu²⁺,Zn²⁺,Cd²⁺,Hg²⁺) were systematically investigated by the density functional theory (DFT). The results showed that the interactions of the metal cations with GSH resulted in nine different stable complexes and many factors had an effect on the binding energy. Generally, for the same period of metal ions, the binding energies ranked in the order of Cu²⁺>Ni²⁺>Co²⁺>Fe²⁺>Cr²⁺>Zn²⁺>Mn²⁺; and for the same group of metal ions, the general trend of binding energies was Zn²⁺>Hg²⁺>Cd²⁺. Moreover, the amounts of charge transferred from S or N to transition metal cations are greater than that of O atoms. For Fe²⁺,Co²⁺,Ni²⁺,Cu²⁺,Zn²⁺,Cd²⁺ and Hg²⁺ complexes, the values of the Wiberg bond indices (WBIs) of M-S (M denotes metal cations) were larger than that of M-N and M-O; for Cr²⁺ complexes, most of the WBIs of M-O in complexes were higher than that of M-S and M-N. Furthermore, the changes in the electron configuration of the metal cations before and after chelate reaction revealed that Cu²⁺, Ni²⁺,Co²⁺ and Hg²⁺ had obvious tendencies to be reduced to Cu⁺,Ni⁺,Co⁺ and Hg⁺ during the coordination process.     

Effects of Ca2+ and other divalent cations on K+-evoked force production of slow muscle fibers from Rana esculenta and Rana pipiens

Summary Slow muscle fibers were dissected from cruralis muscles of Rana esculenta and Rana pipiens. Isometric contractures were evoked by application of K⁺-rich Ringer's containing Ca²⁺, Ni²⁺, Co²⁺, Mn²⁺ or Mg²⁺. High (7.2 mmol/liter) external Ca²⁺ concentration raised, 0 Ca²⁺ lowered the K⁺ threshold. Replacing Ca²⁺ by Ni²⁺ or Co²⁺ had an effect similar to that of high Ca²⁺ Ringer's. In Mg²⁺ Ringer's the K⁺ concentration-response curve was flattened. These effects were observed already after short exposure times in both species of slow fibers. When Ca²⁺ was removed for long periods of time the slow fibers of R. esculenta lost their contractile response to application of high K⁺ concentrations much more quickly than those of R. pipiens, while the response to caffeine (20 mmol/liter) was maintained. Upon readmission of Ca²⁺ contractile ability was quickly restored in the slow fibers of both R. esculenta and R. pipiens, but the effects of Ni²⁺ (or Co²⁺, Mn²⁺ and Mg²⁺) were much larger in R. esculenta than in R. pipiens slow fibers. It is concluded that divalent cations have two different sites of action in slow muscle fibers. K⁺ threshold seems to be affected through binding to sites at the membrane surface; these sites bind Ni²⁺ and Co²⁺ more firmly than Ca²⁺. The second site is presumably the voltage sensor in the transverse tubular membrane, which controls force production, and where Ca²⁺ is the most effective species of the divalent cations examined.We are grateful to Mrs. S. Pelvay for technical assistance.     

Variable role of ions in two drug intercalation complexes of DNA

The crystal structures of the hexamer duplex d(CGTACG)₂ complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-Å resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co²⁺, Ba²⁺ and Na⁺ ions. They reveal at least two different types of coordination environments: (1) specific sites for Co²⁺ interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.     

External Ni<Superscript>2+</Superscript> and ENaC in A6 Cells: Na<Superscript>+</Superscript> Current Stimulation by Competition at a Binding Site for Amiloride and Na<Superscript>+</Superscript>

In cultured A6 monolayers from distal Xenopus kidney, external Ni²⁺ stimulated active Na⁺ uptake via the epithelial Na⁺ channel, ENaC. Transepithelial capacitance measurements ruled out exocytosis of ENaC-containing vesicles underlying the Ni²⁺ effect. Na⁺ current noise analysis was performed using the neutral Na⁺-channel blocker 6-chloro-3,5-diamino-pyrazine-2-carboxamide (CDPC) and amiloride. The analysis of CDPC-induced noise in terms of a three-state channel model revealed that Ni²⁺ elicits an increase in the number of open channels as well as in the spontaneous open probability. While Ni²⁺ had no influence on CDPC-blocker kinetics, the macroscopic and microscopic blocking kinetics of amiloride were affected. Ni²⁺ turned out to compete with amiloride for a putative binding site but not with CDPC. Moreover, external Na⁺—known to compete with amiloride and so producing the self-inhibition phenomenon—and Ni²⁺ exerted mutually exclusive analogous effects on amiloride kinetics. Na⁺ current kinetics revealed that Ni²⁺ prevents ENaC to be downregulated by self-inhibition. Co²⁺ behaved similarly to Ni²⁺, whereas Zn²⁺ did not. Attempts to disclose the chemical nature of the site reacting with Ni²⁺ suggested cysteine but not histidine as reaction partner.     

Studies on the interaction of metal ions with puruvate kinase from Ehrlich ascites-tumour cells and from rabbit muscle

1. Pyruvate kinase (ATP–pyruvate phosphotransferase, EC 2.7.1.40) from Ehrlich ascites-tumour cells was purified approximately fivefold by chromatography on DEAE-cellulose. The enzyme was shown to have an absolute requirement for one univalent and for one bivalent metal ion. 2. The univalent metal ion requirements were satisfied by K⁺, Rb⁺ or NH₄⁺; Na⁺ and Cs⁺ were weak activators but Li⁺ was inactive. 3. Ca²⁺ exhibited `non-competitive' and `apparent competitive' effects in relation to the K⁺ activation. 4. The bivalent metal ion requirements were satisfied by Mg²⁺, Mn²⁺ or Co²⁺; Ba²⁺, Sr²⁺, Ca²⁺, Ni²⁺, Be²⁺ and Cu²⁺ were inactive. Mn²⁺ and Co²⁺ were better activators than Mg²⁺. 5. The bivalent metal ion requirements of purified pyruvate kinase from rabbit muscle were satisfied by Mg²⁺, Mn²⁺, Co²⁺ and to a smaller extent by Ni²⁺. Mn²⁺ and Co²⁺ were better activators than Mg²⁺. 6. Ca²⁺ competitively inhibited the activation by Mg²⁺, Mn²⁺ and Co²⁺ for both the tumour and rabbit enzymes. 7. It is concluded that there are no significant differences in metal ion specificity between the tumour and rabbit enzymes. 8. The possible role of metal ions in regulating enzymic and metabolic activities is considered further.     

Cobalt transport in nickel-resistant strains ofNeurospora crassa

Uptake of Co²⁺ by three nickel-resistant strains (Ni^R1, Ni^R2, and Ni^R3) ofNeurospora crassa that differed in resistance to Co²⁺ has been studied. Uptake was linear with Co²⁺ concentration (up to 1 mM), with time (up to 6 h), and with pH between 3 and 6. Uptake rates were in the order Ni^R2>Ni^R1>Ni^R3. In all strains, there was gradual increase in Co²⁺ uptake between 10° and 28°C, with a much sharper increase between 28° and 40°C. Metabolic inhibitors decreased Co²⁺ uptake partially in all strains, except for KF in Ni^R3. About 50–80 g Co²⁺/100 mg dry weight was surface bound. Ni²⁺, Zn²⁺, and Mn²⁺ competed with Co²⁺, the effects being strain specific. Mg²⁺ inhibited Co²⁺ uptake in all strains with preformed mycelia. In Ni^R1 and Ni^R2 only with young mycelia (40 h old) was Mg²⁺ inhibitory to Co²⁺ uptake,during growth in the presence of Co²⁺. The results suggested the presence of two transport systems for Co²⁺ in Ni^R1 and Ni^R2, only one of which was sensitive to Mg²⁺; in contrast, Ni^R3 had a single system, which was sensitive to Mg²⁺.     

Naked Eye Detection of Cr3+ and Co2+ Ions by Gold Nanoparticle Modified with Azomethine

This paper reports the synthesis of azomethine-modified gold nanoparticles with azomethine (azomethine-AuNPs) in aqueous media, which were characterized by FT-IR spectroscopy, ultraviolet–visible spectroscopy (UV-Vis), dynamic light scattering (DLS), thermogravimetric analysis (TGA), and transmission electron microscopy (TEM). The azomethine-AuNPs were employed as colorimetric for Cr³⁺ and Co²⁺ ions at pH 6.2–7.5 and 8.1–9.1, at room temperature in aqueous solution. In the presence of Cr³⁺ and Co²⁺, the azomethine-AuNPs induce aggregation of the nanoparticles. Upon aggregation, the surface plasmon absorption band red-shifts so that the nanoparticle solution appears a blue color. The sensitivity of azomethine-AuNPs towards other metal ions, Mg²⁺, Mn²⁺, Cr⁶⁺, Na⁺, Ni²⁺, Ag⁺, Al³⁺, Ca²⁺, Cd²⁺, Cu²⁺, Fe²⁺, Fe³⁺, Hg²⁺, Cd²⁺, K⁺, Co³⁺, Ni²⁺, Pb²⁺, and Zn²⁺ are negligible. This highly selective sensor allows a direct quantitative assay of Co²⁺ and Cr³⁺ with colorimetric detection limits of 83.22 and 108 nM, respectively.

     

Divalent Metal Cations upon Coordination to the N7 of Purines Differentially Stabilize the PyPuPu DNA Triplex due to Unequal Hoogsteen-type Hydrogen Bond Enhancement

Abstract

The PyPuPu triplexes consisting of CG*G triads are stabilized by alkaline earth cations (Ca²⁺, Mg²⁺) and transition metal cations (Mn²⁺, Co²⁺, Ni²⁺, Zn²⁺, Cd²⁺), while similar triplexes including TA*A triads are stabilized only by transition metal cations. We hypothesize that such a differential triplex stabilization by divalent metal cations can be the consequence of their coordination to the N7 of the third strand purines with concomitant polarization effects on the bases resulting in unequal Hoogsteen-type hydrogen bond enhancement.     

Response of the carotenoidless mutant Rhodobacter sphaeroides growing cells to cobalt and nickel exposure

The interaction of cobalt (Co²⁺) and nickel (Ni²⁺) ions with whole cells of the photosynthetic purple bacterium Rhodobacter sphaeroides strain R26 was investigated. Active and passive uptakes were examined in cells grown in the presence of increasing amounts of Co²⁺ and Ni²⁺. Inductively coupled plasma atomic emission spectroscopy (ICP-AES), pH titration, and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to assess the role of cell envelope and metabolism in accumulating the two heavy metals. The chosen microorganism was able to uptake cobalt and nickel up to 2.2 and 0.25 mg per gram of dried cells respectively, with the largest part found bound to the cell surface. Carboxylate groups lying on the cell wall of this Gram-negative bacterium proved to be the major candidates for binding protons and metal cations. Co²⁺ was found to interfere with Mg²⁺ extracellular immobilization and transport across the membrane, indicating that these ions share binding sites on the cell envelope and ion transport systems. According to the presence of a competition mechanism, bacterial growth experiments showed that high Mg²⁺ concentrations are able to rescue R. sphaeroides from Co²⁺ toxicity.     

Heavy metal ions affect the activity of DNA glycosylases of the Fpg family

Prokaryotic enzymes formamidopyrimidine-DNA glycosylase (Fpg) and endonuclease VIII (Nei) and their eukaryotic homologs NEIL1, NEIL2, and NEIL3 define the Fpg family of DNA glycosylases, which initiate the process of repair of oxidized DNA bases. The repair of oxidative DNA lesions is known to be impaired in vivo in the presence of ions of some heavy metals. We have studied the effect of salts of several alkaline earth and transition metals on the activity of Fpg-family DNA glycosylases in the reaction of excision of 5,6-dihydrouracil, a typical DNA oxidation product. The reaction catalyzed by NEIL1 was characterized by values K _m = 150 nM and k _cat = 1.2 min⁻¹, which were in the range of these constants for excision of other damaged bases by this enzyme. NEIL1 was inhibited by Al³⁺, Ni²⁺, Co²⁺, Cd²⁺, Cu²⁺, Zn²⁺, and Fe²⁺ in Tris-HCl buffer and by Cd²⁺, Zn²⁺, Cu²⁺, and Fe²⁺ in potassium phosphate buffer. Fpg and Nei, the prokaryotic homologs of NEIL1, were inhibited by the same metal ions as NEIL1. The values of I₅₀ for NEIL1 inhibition were 7 μM for Cd²⁺, 16 μM for Zn²⁺, and 400 μM for Cu²⁺. The inhibition of NEIL1 by Cd²⁺, Zn²⁺, and Cu²⁺ was at least partly due to the formation of metal-DNA complexes. In the case of Cd²⁺ and Cu²⁺, which preferentially bind to DNA bases rather than phosphates, the presence of metal ions caused the enzyme to lose the ability for preferential binding to damaged DNA. Therefore, the inhibition of NEIL1 activity in removal of oxidative lesions by heavy metal ions may be a reason for their comutagenicity under oxidative stress.     

Super-high-affinity binding site for [3H]diazepam in the presence of Co2+, Ni2+, Cu2+, OR Zn2+

Chloride salts of Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Cr³⁺, Mn²⁺, Fe²⁺, and Fe³⁺ had no effect on [³H]diazepam binding. Chloride salts of Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺ increased [³H]diazepam binding by 34 to 68% in a concentration-dependent fashion. Since these divalent cations potentiated the GABA-enhanced [³H]diazepam binding and the effect of each divalent cation was nearly additive with GABA, these cations probably act at a site different from the GABA recognition site in the benzodiazepine-receptor complex. Scatchard plots of [³H]diazepam binding without an effective divalent cation showed a single class of binding, with a Kd value of 5.3 mM. In the presence of 1 mM Co²⁺, Ni²⁺, Cu²⁺, or Zn²⁺, two distinct binding sites were evident with apparent Kd values of 1.0 nM and 5.7 nM. The higher-affinity binding was not detected in the absence of an effective divalent cation and is probably a novel, super-high-affinity binding site.     

Blockade by nickel ions of phasic contraction to K+ and high affinity calcium of ileal longitudinal muscle of guinea-pig

1. Preincubation with 1 or 2mM Ni²⁺ inhibited dose-dependently the ileal phasic response to K⁺ (60 mM) without appreciable effects on the tonic response. Ni²⁺ above 3mM inhibited the tonic response.2. Ni²⁺ inhibited the high affinity Ca²⁺ sites than the low affinity sites during K⁺ contraction.3. After treatment with Ni²⁺, the K⁺ response was fairly restored by a wash with normal medium. The nickel bound to the ileal cells was almost eliminated with the washing.4. This probably indicates that Ni²⁺ mainly inhibited the K⁺-induced phasic tension by reducing Ca²⁺ release rather than Ca²⁺ influx.     

The effect of amphotericin B on the permeability of lipid bilayers to divalent trace metals

In this study amphotericin B released the divalent trace metals Zn²⁺, Co²⁺, Cu²⁺, Ni²⁺, Mn²⁺, Fe²⁺, Cd²⁺ and Pb²⁺ from multilamellar liposomes containing cholesterol. This observation is consistent with amphotericin B channels being permeable to these metals, and it is proposed, therefore, that the antibiotic may be useful in investigating the metabolism of these elements.     

Sorption of Heavy Metal Cations by Corn Mitochondria and the Effects on Electron and Energy Transfer Reactions

The passive sorption of Pb⁺², Cd⁺², Zn⁺², Co⁺², Ni⁺², and Mn⁺² by isolated corn mitochondria was determined, and, except for Pb⁺², the maximum sorption for each cation was about 58 nmol per milligram of protein. Sorption of Pb⁺² was apparently ten times greater, but precipitation may have been the cause of this larger value. The effects of Pb⁺², Cd⁺², Zn⁺², Co⁺², and Ni⁺² on acceptorless rates of electron transport for three substrates were determined. Greater than 50% inhibitions of oxidation were observed for succinate after additions of >0.1 mM Cd⁺², Zn⁺², or Pb⁺²: for NADH after additions of >0.5 mM Cd⁺² or Zn⁺²; and for malate + pyruvate after additions of >0.1 mM Cd⁺². Some inhibition of the rate of substrate oxidation was observed for most cations at higher concentrations. Coupling, as measured by ADP/O ratios, was inhibited at lowest concentrations by Cd⁺² or Zn⁺² and at higher concentrations by Co⁺² or Ni⁺². Substantial swelling of mitochondria oxidizing succinate was observed following additions of O.1 mM Cd⁺² or Pb⁺², Correlations are drawn between the effects of Pb⁺², Cd⁺², Zn⁺², Co⁺², and Ni⁺² and their sorption to mitochondrial membranes.     

Studies on the advent of ureotelism. The effects of bivalent cations on the capacity of the hepatic arginase of the Mexican axolotl to hydrolyse endogenous arginine

1. The effects of 19 bivalent cations on the activity, stability and capacity to hydrolyse endogenous arginine of axolotl liver arginase were studied. 2. It was found that Fe²⁺, Co²⁺, Ni²⁺ and Zn²⁺, as well as Mn²⁺, stabilize the enzyme and render it able to hydrolyse endogenous arginine. 3. By using different concentrations of Co²⁺ and Ni²⁺ it was possible to dissociate the effect of each of the metal ions on the activity and stability of arginase from that on its capacity to hydrolyse endogenous arginine. 4. The effects of Mn²⁺, Co²⁺ and Ni²⁺ on the activity and stability of arginase in the homogenate were also observed with purer preparations of the enzyme. 5. It is suggested that the capacity to hydrolyse endogenous arginine is a consequence of the integration of arginase with the arginine-formation sites.     

Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability

BackgroundDenaturants, namely, urea and guanidinium chloride (GdmCl) affect the stability as well as structure of DNA. Critical assessment of the role of hydrogen bonding of these denaturants with the different regions of DNA is essential in terms of its stability and structural aspect. However, the understanding of the mechanistic aspects of structural change of DNA induced by the denaturants is not yet well understood.MethodsIn this study, various spectroscopic along with molecular dynamics (MD) simulation techniques were employed to understand the role of hydrogen bonding of these denaturants with DNA bases in their stability and structural change.Results and conclusionIt has been found that both, GdmCl and urea intrude into groove region of DNA by striping surrounding water. The hydrogen bonding pattern of Gdm⁺ and urea with DNA bases in its groove region is multimodal and distinctly different from each other. The interaction of GdmCl with DNA is stabilized by electrostatic interaction whereas electrostatic and Lennard-Jones interactions both contribute for urea. Gdm⁺ forms direct hydrogen bond with the bases in the minor groove of DNA whereas direct and water assisted hydrogen bond takes place with urea. The hydrogen bond formed between Gdm⁺ with bases in the groove region of DNA is stronger than urea due to strong electrostatic interaction along with less self-aggregation of Gdm⁺ than urea. The distinct hydrogen bonding capability of Gdm⁺ and urea with DNA bases in its groove region affects its width differently. The interaction of Gdm⁺ decreases the width of the minor and major groove which probably increases the strength of hydrogen bond between the Watson-Crick base pairs of DNA leading to its stability. In contrast, the interaction of urea does not affect much to the width of the grooves except the marginal increase in the minor groove width which probably decreases the strength of hydrogen bond between Watson Crick base pairs leading to the destabilization of DNA.General significanceOur study clearly depicts the role of hydrogen bonding between DNA bases and denaturants in their stability and structural change which can be used further for designing of the guanidinium based drug molecules.