The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods

The metallation of tetrapyrroles is believed to proceed via a sitting-atop (SAT) complex, in which some of the pyrrole nitrogen atoms are still protonated and the metal ion resides above the ring plane. No crystal structure of such a complex has been presented, but NMR and extended X-ray absorption fine structure (EXAFS) data has been reported for Cu(2+) in acetonitrile. We have used density functional calculations to obtain reasonable models for SAT complexes of porphyrins with Mg(2+), Fe(2+), and Cu(2+). The results show that there are many possible SAT complexes with 1-5 solvent molecules, one or two metal ions, and cis or trans protonation of the porphyrin ring. Many of these have similar energies and their relative stabilities vary with the metal ion. A complex with two cis pyrrolenine nitrogens atoms and 2-4 solvent molecules coordinated to Cu(2+) fits the NMR and EXAFS data best. However, we cannot fully exclude the possibility that what is observed is rather a mixture of a doubly protonated porphyrin and the copper porphyrin. Mg(2+) has a lower affinity for porphyrin and stronger affinity for water, so a complex with five water molecules and only one bond to porphyrin seems to be most stable. For Fe(2+), a cis structure with two first-sphere water molecules and four interactions to the porphyrin seems to be most likely.     

Characterization of dioxygenated cobalt(II)-carnosine complexes by Raman and IR spectroscopy

Raman and IR studies are carried out on carnosine (beta-alanyl-L-histidine, Carnos) and its complexes with cobalt(II) at different metal/ligand ratios and basic pH. Binuclear complexes that bind molecular oxygen are formed and information regarding the O-O bridge is obtained from the Raman spectra. When the Co(II)/Carnos ratio is 相似文献   

Sugar interaction with metal ions. The coordination behavior of neutral galactitol to Ca(II) and lanthanide ions

The crystal structures of CaCl(2).galactitol.4 H(2)O and 2EuCl(3).galactitol.14 H(2)O were determined to compare the coordination behavior of Ca and lanthanide ions. The crystal system of the Ca-galactitol complex, CaCl(2).C(6)H(14)O(6).4 H(2)O, is monoclinic, Cc space group. Each Ca ion is coordinated to eight oxygen atoms, four from two galactitol molecules and four from water molecules. Galactitol provides O-2, -3 to coordinate to one Ca(2+), and O-4, -5 with another Ca(2+), to form a chain structure. The crystal system of the Eu-galactitol complex, 2EuCl(3).C(6)H(14)O(6).14 H(2)O, is triclinic, P1; space group. Each Eu ion is coordinated to nine oxygen atoms, three from an alditol molecule and six from water molecules. Each galactitol provides O-1, -2, -3 to coordinate with one Eu(3+) and O-4, -5, -6 with another Eu(3+). The other water molecules are hydrogen-bonded in the structure. The similar IR spectra of Pr-, Nd-, Sm-, Eu-, Dy-, and Er-galactitol complexes show that those lanthanide ions have the same coordination mode to neutral galactitol. The Raman spectra also confirm the formation of metal ion-carbohydrate complexes.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to lanthanum and erbium ions

Lanthanide ions and erythritol form metal–alditol complexes with various structures. Lanthanum nitrate and erbium chloride coordinate to erythritol to give new coordination structures. The lanthanum nitrate–erythritol complex (LaEN), 2La(NO₃)₃·C₄H₁₀O₄·8H₂O, La³⁺ exhibits the coordination number of 11 (namely 11 polar atoms bound to one lanthanum) and is 11-coordinated to two hydroxyl groups from one erythritol molecule, six oxygen atoms from three nitrate ions and three water molecules. One erythritol molecule is coordinated to two La³⁺ ions and links the two metal ions together. The ratio of M:L is 2:1. The erbium chloride–erythritol complex (ErE), ErCl₂·C₄H₉O₄·2C₂H₅OH was obtained from ErCl₃ and erythritol in aqueous ethanol solution and the structure shows that deprotonation reaction occurs in the reaction process. The Er³⁺ cation is 8-coordinated with three hydroxyl groups of one erythritol molecule, two hydroxyl groups from another erythritol molecule, two ethanol molecules, and one chloride ion. Erythritol provides its three hydroxyl groups to one erbium cation and two hydroxyl groups to another erbium cation, that is, one hydroxyl group is coordinated to two metal ions and therefore loses its hydrogen atom and becomes a oxygen bridge. Another chloride ion is hydrogen bonded in the structure. The results indicate the complexity of metal–sugar coordination.     

Interaction of copper(II) and nickel(II) with a bis-amide ligand functionalized with pyridine moieties: Thermodynamic and spectroscopic studies in aqueous solution

We synthesized a new bis-amide ligand derived from the l(+)-tartaric acid. We then determined its protonation constants and the stability constants of the copper(II) and nickel(II) chelates by potentiometry as well as ESI-MS and UV-Vis spectroscopy. We found that both metal ions are able to induce the deprotonation and the coordination of an amide nitrogen donor atom. In the case of copper complexes, the data show the formation of two major species: Cu₂(L₂H₋₃)⁺ and Cu₂(LH₋₄). EPR and XAS experiments led us to precise the relative structure of these compounds. In Cu₂(L₂H₋₃)⁺, each metal center is coordinated by pyridinic and amidic nitrogen atoms of one ligand and by nitrogen and oxygen atoms from pyridine and hydroxyl moieties from the other one. In Cu₂(LH₋₄), the copper centers are coordinated by pyridinic and amidic nitrogen atoms, as well as a deprotonated hydroxyl group of the ligand. In this latter complex, the lower value of the Cu-Cu distance determined from EXAFS experiments and compared to the one of the solid species likely involve the formation of an exogeneous hydroxyl bridge between the two copper centers. With Ni(II) ions, the only one major species is the mononuclear Ni(LH₋₂) complex, in which Ni(II) is held in an octahedral environment with the metal center chelated by the two pyridinic and the two amidic nitrogen atoms, and two oxygen atoms from water molecules.     

Coordination abilities of piperyd-1-yl-methane-1,1-diphosphonic acids towards zinc(II), magnesium(II) and calcium(II): potentiometric and NMR studies

The combination of the pH-metric and NMR studies is used to examine the stabilities and coordination modes as well as related structural aspects of zinc(II), magnesium(II) and calcium(II) complexation to piperyd-1-yl-methane-1,1-diphosphonic acid (1) and its derivatives containing a topologically modified piperidine ring (2-7). The studied compounds coordinate metal ions exclusively via the phosphonate functions with a nitrogen atom remaining protonated over the whole range of studied pH. Compounds 1-6 readily form soluble multinuclear complexes of type [M(3)(HL)(2)] and [M(3)(HL)(3)](3-) with Zn(2+) or [M(2)(H(2)L)(2)] with Ca(2+) and Mg(2+). These species are formed based on dimers consisting of two head-to-head arranged molecules linked by strong symmetrical hydrogen bonds. The placement of the two methyl groups at 2- and 6-positions on the piperidine ring precludes the molecular recognition via similar hydrogen bonds and accounts for different complexation properties of 7 compared to 1-6. The role that the metal coordination plays on conformation dynamics in 1-7 is also discussed.     

The environment of two metal ions surrounding the splice site of a group I intron.

Several divalent metal ions (Ca2+, Sr2+ and Pb2+) do not promote splicing, but instead induce cleavage at a single site in the conserved group I intron core in the absence of the guanosine cofactor at elevated pH, generating products with 5'-OH and 3'-phosphate ends. The reaction is competed by Mg2+, which does not cleave at this position, but hydrolyses the splice sites producing 3'-OH and 5'-phosphate ends. Mn2+ promotes both core cleavage and splice site hydrolysis under identical conditions, suggesting that two different metal atoms are involved, each responsible for one type of cleavage, and with different chemical and geometric requirements. Based on the core cleavage position and on the previously proposed coordination sites for Mg2+, we propose a structural location for two metal ions surrounding the splice site in the Michel-Westhof three-dimensional model of the group I intron core. The proposed location was strengthened by a first mutational analysis which supported the suggested interaction between one of the metal ions and the bulged residue in P7.     

Characterization of structure and metal ions specificity of Co2+-binding RNA aptamers

Studies on RNA motifs capable of binding metal ions have largely focused on Mg(2+)-specific motifs, therefore information concerning interactions of other metal ions with RNA is still very limited. Application of the in vitro selection approach allowed us to isolate two RNA aptamers that bind Co(2+) ions. Structural analysis of their secondary structures revealed the presence of two motifs, loop E and "kissing" loop complex, commonly occurring in RNA molecules. The Co(2+)-induced cleavage method was used for identification of Co(2+)-binding sites after the determination of the optimal cleavage conditions. In the aptamers, Co(2+) ions seem to bind to N7 atoms of purines, inducing cleavage of the adjacent phosphodiester bonds, similarly as is the case with yeast tRNA(Phe). Although the in vitro selection experiment was carried out in the presence of Co(2+) ions only, the aptamers displayed broader metal ions specificity. This was shown by inhibition of Co(2+)-induced cleavages in the presence of the following transition metal ions: Zn(2+), Cd(2+), Ni(2+), and Co(NH(3))(6)(3+) complex. On the other hand, alkaline metal ions such as Mg(2+), Ca(2+), Sr(2+), and Ba(2+) affected Co(2+)-induced cleavages only slightly. Multiple metal ions specificity of Co(2+)-binding sites has also been reported for other in vitro selected or natural RNAs. Among many factors that influence metal specificity of the Co(2+)-binding pocket, chemical properties of metal ions, such as their hardness as well as the structure of the coordination site, seem to be particularly important.     

Metal-ion environment in solid Mn(II), Co(II) and Ni(II) hyaluronates

Amorphous powders and films of some metal hyaluronate complexes of general composition (C14H20O11N)2 x xH2O (M = Mn2+, Ni2+ and Co2+) have been prepared at pH 5.5-6.0. The coordination geometry around the metal ions has been analyzed by EXAFS (extended X-ray absorption fine structure) and FTIR spectroscopy. Mn2+, Ni2+, and Co2+ ions are coordinated to carboxylate oxygen atoms and water molecules. The process of local geometry formation round the metal ions is sensitive to sample preparation.     

NMR study of a lymphocyte differentiating thymic factor. An investigation of the Zn(II)-nonapeptide complexes (thymulin)

Detailed investigations of a serum peptide (less than Glu1-Ala2-Lys3-Ser4-Gln5-Gly6-Gly7-Ser8-++ +Asn9) were carried out by 1H and 13C NMR spectroscopy to elucidate the structure of the complex formed with Zn(II), thymulin, which has been found to be active in vivo. These experiments were performed in dimethyl sulfoxide-d6 solution at different metal:peptide ratios. The results suggest the following conclusions. (i) The Zn(II) complexation corresponds to a fast exchange on the NMR time scale. (ii) The evolution of 1H and 13C NMR chemical shifts indicates the existence of two types of complexes: a 1:2 species associating two peptide molecules and one Zn(II) ion and a complex with 1:1 stoichiometry. The former is predominant for metal:peptide ratios below unity. (iii) In the 1:2 complex, Zn(II) is coordinated by the Ser4-O gamma H and Asn9-CO2- sites, while in the 1:1 complex, Ser8-O gamma H is the third ligand to the Zn(II) ion. The results are compared with those for the [Ala4] and [Ala8] analogues, and those for the complexes of thymulin with other metal ions (Cu2+ and Al3+) in terms of its biological activity. These comparative studies suggested that the 1:1 complex is the only conformation recognized by the antibodies.     

Effect of calcium (II) and magnesium (II) ions on the 18-23 gamma-carboxyglutamic acid containing cyclic peptide loop of bovine prothrombin. An AMBER molecular mechanics study

The effect of calcium (II) and magnesium (II) ions on the conformation of the 18-23 cyclic peptide loop of bovine prothrombin are investigated by the molecular mechanics program AMBER (Assisted Model Building with Energy Refinement). The work is an extension of an earlier paper (Eastman et al., Int. J. Peptide Protein Res. 27, 1986, 530-553) that employed the program ECEPP (Empirical Conformational Energy Program for Peptides). In the absence of either metal ion, or in the presence of either one Ca(II) or one Mg(II) ion, the lowest-energy forms found by AMBER have the Gla21-Pro22 peptide bond in a trans conformation. In the presence of two Ca(II) or Mg(II) ions, the loop form of lowest energy is decidedly cis. The coordination about the Ca(II) and Mg(II) ions is different in both the single and double metal cases. In addition, the peptide chains that emerge from the loop are oriented parallel to each other in the lowest-energy complex with two Ca(II) ions, but are not parallel in the lowest-energy complex with two Mg(II) ions.     

DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action

The catalytic properties of DNA gyrase, an A 2B 2 complex, are modulated by the presence of divalent metal ions. Using circular dichroism, protein melting experiments and enzyme activity assays, we investigated the correlation between the A 2B 2 conformation, the nature of the metal ion cofactor and the enzyme activity in the presence and absence of DNA substrate. At room temperature, DNA gyrase structure is not appreciably affected by Ca (2+) or Mg (2+) but is modified by Mn (2+). In addition, metal ions strongly affect the enzyme's thermal transitions, rendering the A 2B 2 structure more flexible. Using the B subunit, we were able to identify two distinct complexes with manganese ions. The first one exhibits a 1:1 stoichiometry and is not affected by the presence of DNA. The second complex is associated with a large protein structural modification that can be remarkably modulated by addition of the DNA substrate. This behavior is conserved in the reconstituted protein. Studies with two GyrB mutants indicate that Mn (2+) interference with the TOPRIM region modulates gyrase supercoiling activity. In particular, considering the need for two divalent metal ions for an efficient catalytic cleavage of the phosphodiester bond, our data suggest that residue D500 participates in the first complexation event (DNA-independent), whereas residue D498 is involved mainly in the second process. In conclusion, a combination of the ion features (ionic size, electronegativity, coordination sphere) operating at the level of the catalytic region and of the ion-driven modifications in overall enzyme structure and flexibility contribute to the mechanism of gyrase activity. An effectual role for DNA recruiting the second catalytic metal ion is envisaged.     

Metal-ion interactions with sugars. Crystal structures and FT-IR studies of the LaCl3-ribopyranose and CeCl3-ribopyranose complexes

Single crystals of LaCl3.C5H10O5.5H2O (1) and CeCl3.C5H10O5.5H2O (2) were obtained from ethanol-water solutions and their structures determined by X-ray. The two complexes are isomorphous. Two configurations of complex 1 or complex 2, as a pair of isomers, were found in each single crystal in a disordered state. The ligand of one of the isomer is alpha-D-ribopyranose in the 4C1 conformation, the ligand of the other is beta-D-ribopyranose in the 1C4 conformation. For complex 1, the alpha:beta anomeric ratio is 51:49, and for complex 2, the ratio is 52:48. Both ligands of the two isomers provide three hydroxyl groups in ax-eq-ax orientation for coordination. The Ln3+ (Ln = La or Ce) ion is nine-coordinated with five Ln-O bonds from water molecules, three Ln-O bonds from hydroxyl groups of the D-ribopyranose, and one Ln-Cl bond from chloride ion. The hydroxyl groups, water molecules, and chloride ions form an extensive hydrogen-bond network. The IR spectral C-C, O-H, C-O, and C-O-H vibrations were observed to be shifted in both the two complexes and the IR results are in accord with those of X-ray diffraction.     

Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations

Counterions are required for RNA folding, and divalent metal ions such as Mg(2+) are often critical. To dissect the role of counterions, we have compared global and local folding of wild-type and mutant variants of P4-P6 RNA derived from the Tetrahymena group I ribozyme in monovalent and in divalent metal ions. A remarkably simple picture of the folding thermodynamics emerges. The equilibrium folding pathway in monovalent ions displays two phases. In the first phase, RNA molecules that are initially in an extended conformation enforced by charge-charge repulsion are relaxed by electrostatic screening to a state with increased flexibility but without formation of long-range tertiary contacts. At higher concentrations of monovalent ions, a state that is nearly identical to the native folded state in the presence of Mg(2+) is formed, with tertiary contacts that involve base and backbone interactions but without the subset of interactions that involve specific divalent metal ion-binding sites. The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA.     

NMR investigation of the copper(II)-carnosine complex in water solution

The predominant species in water solution of excess carnosine and Cu2+ ions was characterized by measuring 13C and 1H spin-lattice and spin-spin relaxation rates. Four peptide molecules were calculated to be coordinated to the metal through the imidazole nitrogen. Evaluation of ion-proton distances demonstrated that metal complexation does not involve severe changes in conformation of the peptide.     

Binding ability of a HHP-tagged protein towards Ni2+ studied by paramagnetic NMR relaxation: The possibility of obtaining long-range structure information

The binding ability of a protein with a metal binding tag towards Ni(2+) was investigated by longitudinal paramagnetic NMR relaxation, and the possibility of obtaining long-range structure information from the paramagnetic relaxation was explored. A protein with a well-defined solution structure (Escherichia coli thioredoxin) was used as the model system, and the peptide His-His-Pro (HHP) fused to the N-terminus of the protein was used as the metal binding tag. It was found that the tag forms a stable dimer complex with the paramagnetic Ni(2+) ion, where each metal ion binds two HHP-tagged protein molecules. However, it was also found that additional sites in the protein compete with the HHP-tag for the binding of the metal ion. These binding sites were identified as the side chain carboxylate groups of the aspartic and glutamic acid residues. Yet, the carboxylate groups bind the Ni(2+) ions considerably weaker than the HHP-tag, and only protons spatially close to the carboxylate sites are affected by the Ni(2+) ions bound to these groups. As for the protons that are unaffected by the carboxylate-bound Ni(2+) ions, it was found that the long-range distances derived from the paramagnetic relaxation enhancements are in good agreement with the solution structure of thioredoxin. Specifically, the obtained long-range paramagnetic distance constraints revealed that the dimer complex is asymmetric with different orientations of the two protein molecules relative to the Ni(2+) ion.     

Multiple scattering x-ray absorption studies of Zn2+ binding sites in bacterial photosynthetic reaction centers

Binding of transition metal ions to the reaction center (RC) protein of the photosynthetic bacterium Rhodobacter sphaeroides has been previously shown to slow light-induced electron and proton transfer to the secondary quinone acceptor molecule, Q(B). On the basis of x-ray diffraction at 2.5 angstroms resolution a site, formed by AspH124, HisH126, and HisH128, has been identified at the protein surface which binds Cd(2+) or Zn(2+). Using Zn K-edge x-ray absorption fine structure spectroscopy we report here on the local structure of Zn(2+) ions bound to purified RC complexes embedded into polyvinyl alcohol films. X-ray absorption fine structure data were analyzed by combining ab initio simulations and multiparameter fitting; structural contributions up to the fourth coordination shell and multiple scattering paths (involving three atoms) have been included. Results for complexes characterized by a Zn to RC stoichiometry close to one indicate that Zn(2+) binds two O and two N atoms in the first coordination shell. Higher shell contributions are consistent with a binding cluster formed by two His, one Asp residue, and a water molecule. Analysis of complexes characterized by approximately 2 Zn ions per RC reveals a second structurally distinct binding site, involving one O and three N atoms, not belonging to a His residue. The local structure obtained for the higher affinity site nicely fits the coordination geometry proposed on the basis of x-ray diffraction data, but detects a significant contraction of the first shell. Two possible locations of the second new binding site at the cytoplasmic surface of the RC are proposed.     

Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes

Crystal structures of metal-product complexes of fructose 1, 6-bisphosphatase (FBPase) reveal competition between AMP and divalent cations. In the presence of AMP, the Zn(2+)-product and Mg(2+)-product complexes have a divalent cation present only at one of three metal binding sites (site 1). The enzyme is in the T-state conformation with a disordered loop of residues 52-72 (loop 52-72). In the absence of AMP, the enzyme crystallizes in the R-state conformation, with loop 52-72 associated with the active site. In structures without AMP, three metal-binding sites are occupied by Zn(2+) and two of three metal sites (sites 1 and 2) by Mg(2+). Evidently, the association of AMP with FBPase disorders loop 52-72, the consequence of which is the release of cations from two of three metal binding sites. In the Mg(2+) complexes (but not the Zn(2+) complexes), the 1-OH group of fructose 6-phosphate (F6P) coordinates to the metal at site 1 and is oriented for a nucleophilic attack on the bound phosphate molecule. A mechanism is presented for the forward reaction, in which Asp74 and Glu98 together generate a hydroxide anion coordinated to the Mg(2+) at site 2, which then displaces F6P. Development of negative charge on the 1-oxygen of F6P is stabilized by its coordination to the Mg(2+) at site 1.     

A multi-approach study of the interaction of the Cu(II) and Ni(II) ions with alanylglycylhistamine, a mimicking pseudopeptide of the serum albumine N-terminal residue

The protonation equilibria of alanylglycylhistamine (Ala-Gly-Ha) and the complexation of this ligand with Cu(II) and Ni(II) have been studied by pH-potentiometry, 1H and 14N NMR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), UV-Vis spectrophotometry and electron paramagnetic resonance (EPR). From pH approximately 2-12, the following complexes: MLH, MLH(-1), MLH(-2) and MLH(-3) are successively formed in aqueous solutions, the ligand under its neutral form being noted L. At physiological pH, the MLH(-2) complex is predominant. The coordination in this complex is assumed by one amino, two deprotonated peptide and one imidazole nitrogen atoms. The ESI-MS study confirmed the formation of the MLH(-1), MLH(-2) and MLH(-3) complexes. The structure of MLH(-2) was determined by single crystal X-ray analysis. CD and UV-Vis techniques allowed us to propose that the imidazole-N3 nitrogen acts as the anchor group for the coordination to the metal(II) ions rather than the amino group. At high pH values, the further deprotonation of the N-H imidazole group, leading to the formation of MLH(-3), occurs, as revealed by 1H NMR spectroscopy.     

CCK8 peptide derivatized with diphenylphosphine for rhenium labelling: synthesis and molecular mechanics calculations.

A novel CCK8 derivative bearing a chelating agent at its N- end and its oxo-rhenium(V) complex have been synthesized and characterized. The chelating agent N-[N-13-(diphenylphosphino)propionyl]glycyl]cysteine (PN2S) ligand, the coordination set of which is made by the phosphorus atom of phosphine, the nitrogen atoms of the two amido groups and the sulphur atom of cysteine, has been used due to its high affinity towards the oxo-rhenium(V) moiety. Molecular modelling studies indicate that the CCK8 peptide adopts the right conformation for cholecystokinin receptor binding, and that modifications on the N-terminal side of CCK8 obtained by introducing chelating agents and its metal complexes should not affect the interaction with CCK(A) receptor.