Ion Binding Mode Research Articles

Conformation, dynamics and ion-binding properties of single-chain polyuronates: a molecular dynamics study

In the present study, we report and compare sixteen explicit-solvent molecular dynamics simulations (10 ns) of homopolyuronate single chains corresponding to poly-β(1 → 4)-d-glucuronate (pGlcU), poly-β(1 → 4)-d-mannuronate (pManU), poly-α(1 → 4)-d-galacturonate (pGalU) and poly-α(1 → 4)-l-guluronate (pGlcU). Eight main simulations are performed at 300 K in the presence of Ca2+ counter-ions (neutralising amount), and starting from alternative regular two- and three-fold helical structures. Eight simulation variants probe the effect of an elevated temperature or of a different counter-ion environment. The chains are made formally infinite by application of artificial periodicity along the chain axis (octameric or nonameric repeat unit). The main observations made in these simulations are: (i) the glycosidic linkages (and local helical parameters) show an important flexibility (in time) and variability (along the chains), and regular helical structures only account for a limited fraction of the conformational ensembles populated at 300 K; (ii) for all system considered, the binding of Ca2+ counter-ions is essentially non-specific, with the formation of a dense counter-ion atmosphere around the chains (condensation), but no specific (tight-binding) interactions at well-defined coordination sites; (iii) the 32-, 95-, 21- and 21-helices appear to be the preferential regular helical forms for single chain pGlcU, pManU, pGalU and pGulU, respectively, in aqueous solution, with the possibility of a 31-helix for pGalU (these forms should be viewed in the sense of helical propensities). Taken together, these observations suggest that if chain dimers are appropriately described by the egg-box model (or any other structural model with similar qualitative features) chain–chain association within junction zones in gels must be accompanied by a substantial chain stiffening and a dramatic change in the ion-binding mode.

A spectroscopy approach for the study of the interactions of bioactive vanadium species with bovine serum albumin

The interest in biological functions (benefits or toxics effects) of vanadium species has grown enormously in recent years. In this work, different spectroscopic methods were applied to study the effects of the interaction of vanadyl and vanadate species with bovine serum albumin (BSA), considered as the most abundant plasma protein. UV–Vis, Fourier transform infrared (FT-IR), and FT-Raman spectroscopies were used to investigate changes in secondary and tertiary structures of BSA induced by the binding of oxovanadium(IV) and vanadate(V) species (VO 2+ and VO 3 - , respectively). Correlations between the metal ion binding mode, protein conformational transitions, and structural variations were established.

Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N–metal bonds

It was recently demonstrated spectroscopically that RNA/DNA nucleobases can bind to metal cations in aqueous solution through coordination bonds and covalent bonds. Nitrogen-15 (15N) NMR spectroscopy was employed and shown to be a powerful tool for determining the mode of metal ion binding to nitrogen atoms in RNA/DNA molecules. This review describes 15N NMR spectroscopic characteristics in accordance with the mode of metal ion binding to nitrogen atoms. The general rules for 15N chemical shift changes, which are applicable to the determination of the metal ion binding mode of N-metallated compounds, are also described.

Accelerating and Decelerating Effects of Metal Ions on Electron-Transfer Reduction of Quinones as a Function of Temperature and Binding Modes of Metal Ions to Semiquinone Radical Anions

The accelerating effect of Sc(3+) on the electron-transfer (ET) reduction of the p-benzoquinone derivative 1-(p-tolylsulfinyl)-2,5-benzoquinone (TolSQ) by 10,10'-dimethyl-9,9'-biacridine ((AcrH)(2)) at 233 K changes to a decelerating effect with increasing reaction temperature; the observed second-order rate constant k(et) decreases with increasing Sc(3+) concentration at high concentrations of Sc(3+) at 298 K. At 263 K the k(et) value remains constant with increasing Sc(3+) concentration. Such a remarkable difference with regard to dependence of k(et) on [Sc(3+)] between low and high temperatures results from the difference in relative activity of two ET pathways that depend on temperature, one of which affords 1:1 complex TolSQ*(-)-Sc(3+), and the other 1:2 complex TolSQ*(-)-(Sc(3+))(2) with additional binding of Sc(3+) to TolSQ*(-)-Sc(3+). The formation of TolSQ*(-)-Sc(3+) and TolSQ*(-)-(Sc(3+))(2) complexes was confirmed by EPR spectroscopy in the ET reduction of TolSQ in the presence of low and high concentrations of Sc(3+), respectively. The effects of metal ions on other ET reactions of quinones to afford 1:1 and 1:2 complexes between semiquinone radical anions and metal ions are also reported. The ET pathway affording the 1:2 complexes has smaller activation enthalpies DeltaH( not equal) and more negative activation entropies DeltaS( not equal) because of stronger binding of metal ions and more restricted geometries of the ET transition states as compared with the ET pathway to afford the 1:1 complexes.

Structural and physicochemical features on the metal-mediated base pairs

The chemical structure of the mercury-mediated T-T pair (T-Hg(I)I-T) was determined with (15)N NMR spectroscopy. In order to determine the chemical structure of the T-Hg(I)I-T pair, (15)N-(15)N J-coupling across a metal center (2JNN) was employed. Notably, this is the first observation of (2)J(NN) in a biological macromolecule (DNA duplex). This pairing mode was found to be a irregular metal ion-binding mode for DNA and RNA molecules, in which imino proton-metal exchange processes are included. Accordingly, (2)J(NN) is highly important for the determination of the chemical structures of metal-mediated base pairs.

Two Distinct Proton Binding Sites in the ATP Synthase Family

The F1F0 ATP synthase utilizes energy stored in an electrochemical gradient of protons (or Na+ ions) across the membrane to synthesize ATP from ADP and phosphate. Current models predict that the protonation/deprotonation of specific acidic c ring residues is at the core of the proton translocation mechanism by this enzyme. To probe the mode of proton binding, we measured the covalent modification of the acidic c ring residues with the inhibitor dicyclohexylcarbodiimide (DCCD) over the pH range from 5 to 11. With the H+-translocating ATP synthase from the archaeum Halobacterium salinarium or the Na+-translocating ATP synthase from Ilyobacter tartaricus, the pH profile of DCCD labeling followed a titration curve with a pKa around neutral, reflecting protonation of the acidic c ring residues. However, with the ATP synthases from Escherichia coli, mitochondria, or chloroplasts, a clearly different, bell-shaped pH profile for DCCD labeling was observed which is not compatible with carboxylate protonation but might be explained by the coordination of a hydronium ion as proposed earlier [Boyer, P. D. (1988) Trends Biochem. Sci. 13, 5-7]. Upon site-directed mutagenesis of single binding site residues of the structurally resolved c ring, the sigmoidal pH profile for DCCD labeling could be converted to a more bell-shaped one, demonstrating that the different ion binding modes are based on subtle changes in the amino acid sequence of the protein. The concept of two different binding sites in the ATP synthase family is supported by the ATP hydrolysis pH profiles of the investigated enzymes.

15N−15N J-Coupling Across HgII: Direct Observation of HgII-Mediated T−T Base Pairs in a DNA Duplex

N−N J-coupling across a metal center (2JNN) was clearly detected in a biological macromolecule (DNA duplex) for the first time. By using 2JNN, the base pairing mode of mercury-mediated T−T pairs (T−HgII−T) was definitely determined. This pairing mode was found to be a novel metal ion-binding mode for DNA and RNA molecules, in which imino proton−metal exchange processes are included. Accordingly, 2JNN is highly important for the determination of the chemical structures of metal-mediated base pairs.

Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length

Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg 2+) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.

Infrared Spectroscopy of Hydrated Amino Acids in the Gas Phase: Protonated and Lithiated Valine

We report here infrared spectra of protonated and lithiated valine with varying degrees of hydration in the gas phase and interpret them with the help of DFT calculations at the B3LYP/6-31++G** level. In both the protonated and lithiated species our results clearly indicate that the solvation process is driven first by solvation of the charge site and subsequently by formation of a second solvation shell. The infrared spectra of Val x Li+ (H2O)4 and Val x H+ (H2O)4 are strikingly similar in the region of the spectrum corresponding to hydrogen-bonded stretches of donor water molecules, suggesting that in both cases similar extended water structures are formed once the charge site is solvated. In the case of the lithiated species, our spectra are consistent with a conformation change of the amino acid backbone from syn to anti accompanied by a change in the lithium binding from a NO coordination to OO coordination configuration upon addition of the third water molecule. This change in the mode of metal ion binding was also observed previously by Williams and Lemoff [J. Am. Soc. Mass Spectrom. 2004, 15, 1014-1024] using blackbody infrared radiative dissociation (BIRD). In contrast to the zwitterion formation inferred from results of the BIRD experiments upon addition of a third water molecule, our spectra, which are a more direct probe of structure, show no evidence for zwitterion formation with the addition of up to four water molecules.

Binding energies of water to sodiated valine and structural isomers in the gas phase: the effect of proton affinity on zwitterion stability.

The structures of valine (Val) and methylaminoisobutyric acid (Maiba) bound to a sodium ion, both with and without a water molecule, are investigated using both theory and experiment. Calculations indicate that, without water, sodiated Val forms a charge-solvated structure in which the sodium ion coordinates to the nitrogen and the carbonyl oxygen (NO-coordination), whereas Maiba forms a salt-bridge structure in which the sodium ion coordinates to both carboxylate oxygens (OO-coordination). The addition of a single water molecule does not significantly affect the relative energies or structures of the charge-solvated and salt-bridge forms of either cluster, although in Maiba the mode of sodium ion binding is changed slightly by the water molecule. The preference of Maiba to adopt a zwitterionic form in these complexes is consistent with its higher proton affinity. Experimentally, the rates of water evaporation from clusters of Val.Na(+)(H(2)O) and Maiba.Na(+)(H(2)O) are measured using blackbody infrared radiative dissociation (BIRD). The dissociation rates from the Val and Maiba complexes are compared to water evaporation rates from model complexes of known structure over a wide range of temperatures. Master equation modeling of the BIRD kinetic data yields a threshold dissociation energy for the loss of water from sodiated valine of 15.9 +/- 0.2 kcal/mol and an energy of 15.1 +/- 0.3 kcal/mol for the loss of water from sodiated Maiba. The threshold dissociation energy of water for Val.Na(+)(H(2)O) is the same as that for the charge-solvated model isomers, while the salt-bridge model complex has the same water threshold dissociation energy as Maiba.Na(+)(H(2)O). These results indicate that the threshold dissociation energy for loss of a water molecule from these salt-bridge complexes is approximately 1 kcal/mol less than that for loss of water from the charge-solvated complexes.

Effect of metal ion and water coordination on the structure of a gas-phase amino acid.

The mode of metal ion and water binding to the amino acid valine is investigated using both theory and experiment. Computations indicate that without water, the structure of valine is nonzwitterionic. Both Li(+) and Na(+) are coordinated to the nitrogen and carbonyl oxygen (NO coordination), whereas K(+) coordinates to both oxygens (OO coordination) of nonzwitterionic valine. The addition of a single water molecule does not significantly affect the relative energies calculated for the cationized valine clusters. Experimentally, the rates of water evaporation from clusters of Val.M(+)(H(2)O)(1), M = Li, Na, and K, are measured using blackbody infrared radiative dissociation. The dissociation rate from the valine complex is compared to water evaporation rates from model complexes of known structure. These results indicate that the metal ion in the lithiated and the sodiated clusters is NO-coordinated to nonzwitterionic valine, while that in the potassiated cluster has OO coordination, in full agreement with theory. The zwitterionic vs nonzwitterionic character of valine in the potassiated cluster cannot be distinguished experimentally. Extensive modeling provides strong support for the validity of inferring structural information from the kinetic data.

Interaction of human serum albumin with oxovanadium ions studied by FT-IR spectroscopy and gel and capillary electrophoresis

Some oxovanadium compounds have shown potential to inhibit RNase activity, while at the same time not inhibiting DNase activity. Some vanadyl complexes also inhibit protein synthesis in rabbit reticulocytes, but induce activation of protein–tyrosine kinase. To gain an insight into the interaction of oxovanadium ions with proteins, the present study was designed to examine the bindings of VOSO4and NaVO3salts with human serum albumin (HSA) in aqueous solution at physiological pH with metal ion concentrations of 0.0001 to 1 mM and HSA (fatty acid free) concentration of 2% w/v. Gel and capillary electrophoresis (CE) and Fourier transform infrared (FT-IR) spectroscopic methods were used to determine the metal ion binding mode, association constant, and the secondary structure of the protein in the presence of the oxovanadium compounds. Gel electrophoresis results showed that a maximum of 20 vanadyl cations (VO2+) are bound per HSA molecule with strong (K1= 7.0 × 107M–1) and weak (K2= 6.5 × 105M–1) bindings. Similarly, capillary electrophoresis showed two major bindings for vanadyl cation with K1= 1.2 × 108M–1and K2= 8.5 × 105M–1, whereas vanadate (VO–3) has only a weak binding affinity (K = 6.0 × 103M–1) with HSA molecule. The VO–3binds mainly to the lysine ε-amino NH+3groups, while VO2+binds possibly to the histidine nitrogen atom and the N-terminal of the α-amine residue. Infrared spectroscopic analysis showed metal ion binding results in major protein secondary structural changes from that of the α-helix (55.0 to 43–44%) to the β-sheet (22.0 to 23–26%), β-antiparallel (12.0 to 13–16%), and turn (11.0 to 17–18%), at high metal ion concentration. The observed spectral changes indicate a partial unfolding of the protein structure, in the presence of oxovanadium ions.Key words: oxovanadium, protein, binding mode, binding constant, secondary structure, electrophoresis, FT-IR spectroscopy.

Interaction of RNase A with VO3- and VO2+ Ions. Metal Ion Binding Mode and Protein Secondary Structure

Some of vanadyl complexes have shown potential to inhibit RNase activity by acting as transition state analogue, while at the same time not inhibiting DNase. To gain an insight into the interaction of protein with vanadate (VO3) and vanadyl (VO2+) ions, the present study was designed to examine the binding of ribonuclase A (RNase A) with NaVO3 and VOSO4 in aqueous solution at physiological pH with metal ion concentrations of 0.001 mM to 1 mM, and protein concentration of 2% w/v. Absorption spectra and Fourier transform infrared (FTIR) spectroscopy with self-deconvolution and second derivative resolution enhancement were used to determine the cation binding mode, association constant and the protein secondary structure in the presence of vanadate and vanadyl ions in aqueous solution. Spectroscopic results show that an indirect metal ion interaction occurs with the polypeptide C = O, C-N (via H2O) with overall binding constants of K(VO3-) = 3.93×102 M−1 and K(VO2+) = 4.20×103 M−1. At high metal ion concentrations, major protein secondary structural changes occur from that of the α-helix 29% (free enzyme) to 23–24%; β-sheet (pleated and anti) 50% (free enzyme) to 64–66% and turn 21% (free enzyme) to 10–12% in the metal-RNase complexes. The observed structural changes indicate a partial protein unfolding in the presence of high metal ion concentration.

Interaction of metal ions with poly(1,3-propylene phosphate) ? a synthetic analogue of natural teichoic acids

The binding of metal ions to poly(1,3-propylene phosphate), (PPP), which can be considered as a synthetic analogue of natural teichoic acids, was examined. Infrared spectra of PPP in different ionic forms and of different degrees of polymerization were analyzed and some information on metal ion binding modes in M(I)-PPP and M(II)-PPP complexes, both in the condensed state as well as in aqueous solution, was obtained. It is concluded that the binding modes of sodium, potassium, cesium, calcium, and magnesium ions to phosphate groups of PPP are the same or similar and/or complexes of the same or similar structure are formed. In aqueous solution the analyzed metal ions are bound to poly(alkylene phosphate) chains mainly in the form of “outer sphere” complexes.

A comparative study of Fe(II) and Fe (III) ions complexation with proteins of the light-harvesting complex of chloroplast thylakoid membranes

The interactions of Fe(II) and Fe(III) ions with proteins of the light-harvesting complex (LHC-II) of chloroplast thylakoid membranes were studied in aqueous solution with metal ion concentrations of 0.01 to 20 mM, using the Fourier Transform infrared (FTIR) difference spectroscopic technique. Correlations between spectral changes and metal ion binding mode, protein conformational transitions, and structural variations were established. FTIR difference spectroscopic results have shown the presence of a strong iron-protein complexation at high metal ion concentrations (5–20 mM), while at low cation concentrations (0.01–1 mM) metal-protein binding is less significant. Fe(III) ion binding was mainly through the protein carbonyl groups, whereas Fe(II) coordination was via both C=O and CN donor atoms. A comparison between the Fe-protein and Hg-protein complexes of the LHC-II systems indicated the presence of a strong metal-sulfur binding for the Hg(II) ion with no significant Fe-sulfur interaction. Major conformational changes from that of the α-helix to β-sheet and turn structures were observed for the protein in the presence of both Fe(II) and Fe(III) ions at high cation concentrations (5–20 mM).

The effects of Cu2+ and Pb2+ on the solution structure of calf thymus DNA: DNA condensation and denaturation studied by Fourier transform ir difference spectroscopy.

The interaction of calf thymus DNA with Cu2+ and Pb2+ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established. Spectroscopic evidence has shown that at low metal/DNA (P) molar ratios 1/80 and 1/40, copper and lead ions bind mainly to the PO2- of the backbone, resulting in increased base-stacking interaction and duplex stability. The major copper ion base binding via G-C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A-T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal-DNA binding also results in DNA condensation. No major departure from the B-family structure was observed, upon DNA interaction with these metal ions.

Complexation of copper and zinc ions with proteins of a light-harvesting complex (LHC-II) of chloroplast thylakoid membranes studied by FT-IR spectroscopy

Abstract The interaction of Zn(II) and Cu(II) ions with the light-harvesting proteins (LHC-II) of chloroplast thylakoid membranes was studied in aqueous solution with metal ion concentrations of 0.01 to 20mM, using Fourier transform-infrared (FT-IR) spectroscopy. Analyses of the metal ion binding mode and protein conformational variations were carried out and correlations between spectral changes and metal—protein complexation were established. Infrared difference spectroscopic results revealed the presence of a strong metal—protein interaction at high metal ion concentrations, while at low concentrations complexation was negligible. The binding of Zn and Cu ions was found to be with the protein carbonyl groups at low metal ion concentrations, whereas CO and CN groups were the main coordination sites at higher concentrations. A major conformational variation from α-helix to β-sheet and turn structures was observed in the presence of a concentrated metal ion solution.

Interaction of toxic metal ions Cd 2+, Hg 2+, and Pb 2+ with light-harvesting proteins of chloroplast thylakoid membranes. An FTIR spectroscopic study

The interaction of divalent metal ions Cd, Hg, and Pb with the light-harvesting proteins (LHC-II) of chloroplast thylakoid membranes was investigated in aqueous solution with metal ion concentrations of 0.01 to 20 mM, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between the metal ion binding mode, protein conformational transitions, and structural variations are established. Infrared difference spectroscopic evidence has shown strong Hg ion binding with different protein subunits at very low metal ion concentration with drastic structural modifications of interacted proteins. The Cd ion binding was observed at higher metal ion concentration with major protein conformational changes, while Pb ion interaction was less effective on protein conformation. The major metal ion binding sites were those of the protein carbonyl group or the nitrogen atom and/or both, while the sulphur donor sites were also the target of Hg-protein complexation.

Crystallographic determination of lanthanide ion binding to troponin C

X-ray intensity data to 2.8 Å resolution were collected from each of three crystals of turkey skeletal troponin C(TnC) that had been soaked individually in solutions containing the lanthanide ions europium, thulium and lutetium. Each of the resulting difference electron density maps computed for the three data sets showed three lanthanide ion-binding sites on the TnC molecule. Two of the sites are approximately coincident with the Ca 2+ positions in binding loops III and IV and the third site is near the Ca 2+-free loop I. The mode of ion binding in loop I is different from that commonly observed for Ca 2+ in the Ca 2+-binding proteins.

The Separation of Platinum Group Metals (PGM) in Chloride Media by Isothiouronium Resins

Abstract Styrene-divinylbenzene copolymers incorporating isothiourea functional groups show a remarkable affinity for platinum-group-metal (PGM) ions in chloride media, The mode of ion binding to the resin depends on the equilibria between isothiourea (free base) form and isothiouronium (conjugated acid) form, This in return is related to matrix structure, A. resin, Monivex, which shows high binding capacities for PGM ions in high acidities (2–6M HC1) is described. Equilibrium, rate and selectivity data, as well as process application data is presented and discussed, Electron microprobe studies are used to follow chemical changes in resin beads and ion regeneration patterns.