Developmental changes in bone mineral structure demonstrated by extended X-ray absorption fine structure (EXAFS) spectroscopy

EXAFS spectra have been recorded above the calcium K edge from bones of mice aged 3 days, 1 week, 1 month, 2 months and 7 months. Spectra indicated that the calcium ion environment in bone mineral changes during development. Results were compared with those obtained from amorphous calcium phosphate and a poorly crystalline hydroxyapatite matured from this amorphous calcium phosphate in the presence of water. Spectra from the older mice closely resembled those of the matured product but those from the younger mice were more like those from the freshly prepared amorphous calcium phosphate.     

Sulfur K-edge X-ray absorption spectroscopy as an experimental probe for S-nitroso proteins

X-ray absorption spectroscopy at the sulfur K-edge (2.4-2.6keV) provides a sensitive and specific technique to identify S-nitroso compounds, which have significance in nitric oxide-based cell signaling. Unique spectral features clearly distinguish the S-nitroso-form of a cysteine residue from the sulfhydryl-form or from a methionine thioether. Comparison of the sulfur K-edge spectra of thiolate, thiol, thioether, and S-nitroso thiolate compounds indicates high sensitivity of energy positions and intensities of XAS pre-edge features as determined by the electronic environment of the sulfur absorber. A new experimental setup is being developed for reaching the in vivo concentration range of S-nitroso thiol levels in biological samples.     

5 K extended X-ray absorption fine structure and 40 K 10-s resolved extended X-ray absorption fine structure studies of photolyzed carboxymyoglobin

A previous extended X-ray absorption fine structure (EXAFS) study of photolyzed carboxymyoglobin (MbCO) [Chance, B., Fischetti, R., & Powers, L. (1983) Biochemistry 22, 3820-3829; Powers, L., Sessler, J. L., Woolery, G. L., & Chance, B. (1984) Biochemistry 23, 5519-5523] has provoked much discussion on the heme structure of the photoproduct (MbCO). The EXAFS interpretation that the Fe-CO distance increases by no more than 0.05 A following photodissociation has been regarded as inconsistent with optical, infrared, and magnetic susceptibility studies [Fiamingo, F. G., & Alben, J. O. (1985) Biochemistry 24, 7964-7970; Sassaroli, M., & Rousseau, D. L. (1986) J. Biol. Chem. 261, 16292-16294]. The present experiment was performed with well-characterized dry film samples in which MbCO molecules were embedded in a poly(vinyl alcohol) matrix [Teng, T. Y., & Huang, H. W. (1986) Biochim. Biophys. Acta 874, 13-18]. The sample had a high protein concentration (12 mM) to yield adequate EXAFS signals but was very thin (40 micron) so that complete photolysis could be easily achieved by a single flash from a xenon lamp. Although the electronic state of MbCO resembles that of deoxymyoglobin (deoxy-Mb), direct comparison of EXAFS spectra indicates that structurally MbCO is much closer to MbCO than to deoxy-Mb.(ABSTRACT TRUNCATED AT 250 WORDS)     

Iron coordination structures of oxygen sensor FixL characterized by Fe K-edge extended x-ray absorption fine structure and resonance raman spectroscopy.

FixL is a heme-based O(2) sensor protein involved in a two-component system of a symbiotic bacterium. In the present study, the iron coordination structure in the heme domain of Rhizobium meliloti FixLT (RmFixLT, a soluble truncated FixL) was examined using Fe K-edge extended x-ray absorption fine structure (EXAFS) and resonance Raman spectroscopic techniques. In the EXAFS analyses, the interatomic distances and angles of the Fe-ligand bond and the iron displacement from the heme plane were obtained for RmFixLT in the Fe(2+), Fe(2+)O(2), Fe(2+)CO, Fe(3+), Fe(3+)F(-), and Fe(3+)CN(-) states. An apparent correlation was found between the heme-nitrogen (proximal His-194) distance in the heme domain and the phosphorylation activity of the histidine kinase domain. Comparison of the Fe-CO coordination geometry between RmFixLT and RmFixLH (heme domain of RmFixL), based on the EXAFS and Raman results, has suggested that the kinase domain directly or indirectly influences steric interaction between the iron-bound ligand and the heme pocket. Referring to the crystal structure of the heme domain of Bradyrhizobium japonicum FixL (Gong, W., Hao, B., Mansy, S. S., Gonzalez, G., Gilles-Gonzalez, M. A., and Chan, M. K. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 15177-15182), we discussed details of the iron coordination structure of RmFixLT and RmFixLH in relation to an intramolecular signal transduction mechanism in its O(2) sensing.     

Near edge X-ray absorption fine structure spectroscopy (NEXAFS) of pigment-protein complexes: peridinin-chlorophyll a protein (PCP) of Amphidinium carterae

Peridinin-chlorophyll a protein (PCP) is a unique water soluble antenna complex that employs the carotenoid peridinin as the main light-harvesting pigment. In the present study the near edge X-ray absorption fine structure (NEXAFS) spectrum of PCP was recorded at the carbon K-edge. Additionally, the NEXAFS spectra of the constituent pigments, chlorophyll a and peridinin, were measured. The energies of the lowest unoccupied molecular levels of these pigments appearing in the carbon NEXAFS spectrum were resolved. Individual contributions of the pigments and the protein to the measured NEXAFS spectrum of PCP were determined using a “building block” approach combining NEXAFS spectra of the pigments and the amino acids constituting the PCP apoprotein. The results suggest that absorption changes of the pigments in the carbon near K-edge region can be resolved following excitation using a suitable visible pump laser pulse. Consequently, it may be possible to study excitation energy transfer processes involving “optically dark” states of carotenoids in pigment-protein complexes by soft X-ray probe optical pump double resonance spectroscopy (XODR).     

Plutonium(III) complexation by humic substances studied by X-ray absorption fine structure spectroscopy

We determined structural parameters for the near-neighbor surrounding of plutonium(III) in complexes with humic and fulvic acids at pH 1 and for the purpose of comparison also for the plutonium(III) aquo ion by means of X-ray absorption fine structure (XAFS) spectroscopy. It could be shown that in the complexes with humic substances as well as in the plutonium(III) aquo ion sample the trivalent oxidation state of plutonium was stable within the time of the experiment. In the humate and fulvate complexes, the plutonium(III) is surrounded by about eight oxygen atoms with an average Pu–O distance of 2.48 ± 0.02 Å. The structural parameters determined for plutonium(III)–humate and –fulvate complexes were compared to structural parameters of plutonium(III) and plutonium(IV) aquo ions.     

The local structure of solid diorganotin(IV) complexes formed with carbohydrates by X-ray absorption spectroscopy

Diethyltin(IV) complexes formed with carbohydrate ligands (aldoses, polyalcohols, sugar acids and disaccharides) containing the diethyltin(IV) moiety and the carbohydrate ligand in a 1:1 ratio were prepared. Their local structures were determined by extended X-ray absorption fine structure (EXAFS) in the solid state. The results showed that the dioxastannolane units are associated into an infinite chain polymer, in which tin(IV) is bound by two carbon atoms and three or four oxygen atoms either in highly distorted octahedral and trigonal bipyramidal arrangements or in a purely trigonal bipyramidal arrangement. The present structure models are consistent with the results of previous Mössbauer studies, proving the advantages of the use of the partial quadrupole splitting concept for the determination of the symmetry of the coordination sphere in tin(IV) organic complexes.     

Vanadium K-edge X-ray absorption spectroscopy of bromoperoxidase from Ascophyllum nodosum

Bromoperoxidase from Ascophyllum nodusum was the first vanadium-containing enzyme to be isolated. X-ray absorption spectra have now been collected in order to investigate the coordination of vanadium in the native, native plus bromide, native plus hydrogen peroxide, and dithionite-reduced forms of the enzyme. The edge and X-ray absorption near-edge structures show that, in the four samples studied, it is only on reduction of the native enzyme that the metal site is substantially altered. In addition, these data are consistent with the presence of vanadium(IV) in the reduced enzyme and vanadium(V) in the other samples. Extended X-ray absorption fine structure data confirm that there are structural changes at the metal site on reduction of the native enzyme, notably a lengthening of the average inner-shell distance, and the presence of terminal oxygen together with histidine and oxygen-donating residues.     

Combination of extended X-ray absorption fine structure spectroscopy with lipidic cubic phases for the study of cation binding in bacteriorhodopsin

We have performed a quantitative X-ray absorption fine structure analysis of bacteriorhodopsin in purple membrane patches and in lipidic cubic phases regenerated with Mn²⁺. Lipidic cubic phases and purple membrane results have been compared, demonstrating that the lipidic cubic phase process does not introduce relevant distortions in the local geometry of the cation binding sites. For both samples, we have observed similarities for Mn²⁺ coordination in terms of type, number, and average distances of surrounding atoms, indicating a first coordination shell composed by 6 O atoms, and 3/4 C atoms located in the second coordination shell.     

Spectroscopic studies of zinc(II)- and cobalt(II)-associated Escherichia coli formamidopyrimidine-DNA glycosylase: extended X-ray absorption fine structure evidence for a metal-binding domain

Formamidopyrimidine-DNA glycosylase (Fpg) is a 30.2 kDa protein that plays an important role in the base excision repair of oxidatively damaged DNA in Escherichia coli. Sequence analysis and genetic evidence suggest that zinc is associated with a C4-type motif, C(244)-X(2)-C(247)-X(16)-C(264)-X(2)-C(267), located at the C-terminus of the protein. The zinc-associated motif has been shown to be essential for damaged DNA recognition. Extended X-ray absorption fine structure (EXAFS) spectra collected on the zinc-associated protein (ZnFpg) in the lyophilized state and in 10% frozen aqueous glycerol solution show directly that the metal is coordinated to the sulfur atom of four cysteine residues. The average Zn-S bond length is 2.33 +/- 0.01 and 2.34 +/- 0.01 A, respectively, in the lyophilized state and in 10% frozen aqueous glycerol solution. Fpg was also expressed in minimal medium supplemented with cobalt nitrate to yield a blue-colored protein that was primarily cobalt-associated (CoFpg). The profiles of the circular dichroism spectra for CoFpg and ZnFpg are identical, suggesting that the substitution of Co(2+) for Zn(2+) does not alter the structure of Fpg. A similar conclusion is reached upon the analysis of two-dimensional (15)N/(1)H HSQC spectra of uniformly (15)N-labeled samples of ZnFpg and CoFpg; the spectra are similar and display features characteristic of a structured protein. Biochemical assays with a 54 nt DNA oligomer containing 7, 8-dihydro-8-oxoguanine at a specific location show that CoFpg and ZnFpg are equally active at cleaving the DNA at the site of the oxidized guanine. EXAFS spectra of CoFpg indicate that the cobalt is coordinated to the sulfur atom of four cysteine residues with an average Co-S bond length of 2.28 +/- 0.01 and 2.29 +/- 0.01 A, respectively, in the lyophilized state and in 10% frozen aqueous glycerol solution. The structural similarity between CoFpg and ZnFpg suggests that it is biologically relevant to use the paramagnetic properties of Co(2+) as a structural probe.     

Cd(II)-ethylenediamine mono- and bimetallic complexes - Synthesis and characterization by Cd NMR spectroscopy and single crystal X-ray diffraction

Formation of three Cd(II)-ethylenediamine (en) complexes ([Cd(en)_n]²⁺, n = 1-3) in aqueous solution and in DMSO solvent has been established by means of ¹¹³Cd NMR spectroscopy. It is clearly shown that Cd(II)-en complexes form primarily in basic solutions. A correlation between the ¹¹³Cd NMR chemical shifts and the ethylenediamine (en) coordination number has been observed and discussed. Two single crystals with the composition [Cd₂(en)₅](ClO₄)₄ (1) and [Cd(en)₃](ClO₄)₂ (2) were prepared from aqueous solution, and their structures were determined by single crystal X-ray diffraction. Cd(II) ions are coordinated by six atoms in both compounds, 1 and 2: via five N-donor atoms and one O-donor atom forming a bimetallic complex 1, and via six N-donor atoms forming a distorted octahedral monometallic complex 2. Raman spectra of complexes 1 and 2 also provide additional evidence that the cis-form of the bridging en is present in complex 1.     

Structural and spectroscopic comparison of five-coordinate cobalt(II) and nickel(II) thiolato complexes with the related four-coordinate complexes

Five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co and Ni) (L1 = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate anion and HSMeIm = 2-mercapto-1-methylimidazole), were synthesized. These complexes were compared with the corresponding Cu(II) and Zn(II) complexes with the same ligands and were also compared with the related four-coordinate complexes [L1M(SC₆F₅)] (HSC₆F₅ = pentafluorobenzenthiol). All the complexes were characterized by X-ray crystallography and UV-Vis absorption, IR, ¹H NMR, and other spectroscopic techniques. All five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co, Ni, and Cu), form a distorted square pyramidal structure with a high spin state, and only [L1Zn(SMeIm)] takes a four-coordinate structure with a distorted tetrahedral configuration. The N21-M-S bond angles of the obtained five-coordinate complexes were proportional to the corresponding d value, which comes from between the equatorial basal plane with N4S ligand donor sets and metal ion. These observations and M-S bond distances affect on UV-Vis and far-IR spectral behavior.     

Similarity of the structure of ferritin and iron . dextran (imferon) determined by extended X-ray absorption fine structure analysis.

Ferritin, a natural complex of iron oxide encased in protein, and iron . dextran, a synthetic complex of iron oxide coated with dextran, have the similar properties of maintaining high concentrations of iron in solution at physiological pH and releasing iron relatively slowly in vivo. Extended x-ray absorption fine structure (EX-AFS) analysis was performed on each complex and compared to see if the structures of the iron cores were similar. The results obtained from the extended x-ray absorption fine structure technique show that the near-neighbor environment around the average iron atom in ferritin and iron . dextran is identical, within experimental uncertainty, for the first three shells. The similarity of the iron cores in both complexes may explain the similarity of iron release in vivo. Ferritin has a protein coat which is composed of 24 subunits arranged in a hollow sphere with six channels through which the iron may move during deposition and release. However, little is known about the requirements of the protein structure in ferritin for the maintenance of high concentrations of iron in a soluble, nontoxic form or about the role of the protein in the release of iron from ferritin. The results suggest that iron . dextran will be a useful model compound in studies of the relation of the iron core and protein in ferritin to function.     

Synthesis and characterization of Mg(II), Mn(II), Zn(II) and Cd(II) complexes with a new heptaaza Schiff base pendant-armed macrocycle: X-ray crystal structure, NMR and computational study

New 2-aminoethyl pendant-armed Schiff base macrocyclic complexes, [ML⁷]²⁺ (M = Mn(II), Mg(II), Zn(II) and Cd(II)), have been prepared via M(II) templated [1 + 1] cyclocondensation of 2,6-diacetylpyridine with a new branched hexamine, N,N,N′,N′-tetrakis(2-aminoethyl)-2,2-dimethylpropane-1,3-diamine. The ligand is a 16-membered pentaaza macrocycle having two 2-aminoethyl pendant arms [L⁷ is 2,14-dimethyl-6,10-bis(2-aminoethyl)-3,6,10,13,19-pentaazabicyclo[13.3.1]8,8-dimethylnonadeca-1(19),2,13,15,17-pentaene]. The crystal structures of [MnL⁷]²⁺ and [MgL⁷]²⁺ were determined from X-ray diffraction data. The geometry of the coordination sphere of complexes is a slightly distorted pentagonal bipyramid with the metal ion located within a pentaaza macrocycle and two pendant amines coordinating on opposite sides. All complexes were characterized by IR, microanalysis and except of [MnL⁷]²⁺ by ¹H NMR, ¹³C NMR, DEPT135, COSY(H, H) and HMQC spectroscopy. The data indicate that the structure is pentagonal bipyramidal in each case. The structure of all complexes has also been theoretically studied by ab initio Hartree-Fock and density functional theory methods.     

Syntheses, characterization and antimicrobial activity of the first complexes of Zn(II), Cd(II) and Co(II) with N-benzyloxycarbonylglycine: X-ray crystal structure of the polymeric Cd(II) complex

For the first time, complexes of Zn(II), Cd(II) and Co(II) (1-3) with N-benzyloxycarbonylglycine have been synthesized and characterized. The complexes adopt tetrahedral, pentagonal-bipyramidal and octahedral geometry, respectively. The structure of the polymeric cadmium complex was resolved by single crystal X-ray analysis. The cadmium ion has a distorted pentagonal-bipyramidal coordination formed by two water molecules and two N-benzyloxycarbonylglycinato ligands (N-Boc) coordinated in different fashions, one as bidentate and the second connecting three cadmium atoms. In a rather complicated 2D supramolecular structure, the phenyl rings interact mutually exclusively by the CH?π interactions.Investigation of the antimicrobial activity of the obtained complexes and N-benzyloxycarbonylglycine revealed that the ligand does not inhibit the growth of Candida albicans, whereas the newly synthesized complexes suppress the growth of this human fungal pathogen.     

Evidence for synergistic anion binding to iron in ovotransferrin complexes from resonance Raman and extended X-ray absorption fine structure analysis

The 2,3-dihydroxybenzoate and thioglycolate complexes of iron(III)-ovotransferrin have been studied with resonance Raman and extended x-ray absorption fine structure spectroscopies, respectively, to obtain evidence for the coordination of the synergistic anion to the iron center. The dihydroxybenzoate complex exhibits resonance-enhanced Raman vibrations arising from both the endogenous tyrosinates and the added dihydroxybenzoate. A comparison of the extended x-ray absorption fine structure spectra of the carbonate and thioglycolate complexes shows a large feature at about 1.95 A assigned to Fe-(O,N) interactions. The latter complex exhibits an added feature at 2.32 A assigned to an Fe-S interaction. These experiments demonstrate that the Lewis base functions in the synergistic anions coordinate to the iron in ovotransferrin.     

Synthesis, characterization and crystal structures of Cd(II) and Zn(II) complexes with 2,2′-biimidazole

The reactions of zinc and cadmium salts with 2,2′-biimidazole (H₂biim) yielded a series of compounds in which the ligand is coordinated in the chelating bidentate mode. ZnCl₂ and [Ag(H₂biim)](NO₃) in methanol in a 2:1 proportion produced Zn(H₂biim)Cl₂, in which the metal has a distorted tetrahedral coordination. A 1:2 ratio led to [Zn(H₂biim)₂(CH₃OH)₂](NO₃)₂, containing an octahedrally coordinated Zn(II) center with the O-bonded methanol ligands occupying trans positions. The corresponding [Cd(H₂biim)₂(CH₃OH)₂](NO₃)₂ compound was obtained from CdCl₂. By starting with Cd(NO₃)₂ and Cd(ClO₄)₂ in aqueous media, the related octahedral bis-chelate compounds [Cd(H₂biim)₂(NO₃)(H₂O)](NO₃) and Cd(H₂biim)₂(ClO₄)₂, respectively, were isolated, the apical positions being filled by perchlorate oxygens in the latter case. With Cd(BF₄)₂, the glass container participated in the reaction and a tris-chelate complex [Cd(H₂biim)₃]₂(SiF₆)(BF₄)₂ · 6EtOH was isolated. The [Cd(H₂biim)₃]²⁺ and ions define an extended hydrogen-bonded network, in which ions surrounded by disordered ethanol molecules occupy large cavities. The two free N-H groups provide H₂biim with a unique ability to form hydrogen bonds and their interactions with counter anions or other acceptors play a determining role in controlling molecular packing. The IR spectra of all compounds are discussed.     

Structural investigations by extended X-ray absorption fine structure spectroscopy of the iron center of mitochondrial aconitase in higher plant cells.

We have obtained iron K-edge extended x-ray absorption fine structure spectra of the plant mitochondrial aconitase in its active state, in the presence (aconitase (+)) and absence (aconitase (-)) of the substrate citrate. Analysis of the data indicates that oxygens are present in the first coordination shell, at an average Fe-O distance of 1.96/1.98 A (aconitase (+)/aconitase(-)). Part of these oxygens is provided by the citrate, which binds at 1.99 A from the iron in aconitase (+). The second shell (sulfur) contribution is split and is consistent with Fe-S distances of 2.30/2.29 and 2.56/2.59 A, and the third shell (iron) is consistent with an Fe-Fe distance of 2.83/2.84 A. Both Fe-S and Fe-Fe distances are longer than similar distances found in most Fe-S centers. A strong scattering at approximately 5 A has been identified as originating from an iron atom which is near to, but not part of, the Fe-S cluster. These data indicate that active plant mitochondrial aconitase contains a novel type of iron center.     

Zn(II)-113Cd(II) and Zn(II)-Mg(II) hybrids of alkaline phosphatase. 31P and 113Cd NMR

Methods have been developed for the addition of different metal ion species to the three distinct pairs of metal sites (A, B, and C) found in the dimer of apoalkaline phosphatase. This allows the preparation of hybrid alkaline phosphatases in which A and B sites of each monomer contain two different species of metal ion or the A and B sites of one monomer contain the same species of metal ion, while the adjacent monomer contains a second species. The following hybrids have been characterized in detail: (Zn(II)ACd(II)B)2 alkaline phosphatase, (Zn(II)AMg(II)B)2 alkaline phosphatase, (Cd(II)AZn(II)B)2 alkaline phosphatase, and (Zn(II)AZn(II]B)(Cd(II)ACd(II)B) alkaline phosphatase. 31P and, where appropriate, 113Cd NMR have been used to monitor the behavior of the covalent (E-P) and noncovalent (E X P) phosphointermediates and of the A and B metal ions. From the pH dependencies of the E-P in equilibrium E X P in equilibrium E + Pi equilibria, it is clear that A site metal is the dominant influence in dephosphorylation of E-P and may have a coordinated water molecule, which ionizes to ZnOH- at a low pH providing the nucleophile for dephosphorylation. A site metal also serves to coordinate phosphate in the E X P complex. B site metal has a much smaller effect on dephosphorylation rates, although it does dramatically alter the Pi dissociation rate, which is the rate-limiting step for the native enzyme at alkaline pH, and is probably important in neutralizing the charge on the phosphoseryl residue, thus potentiating the nucleophilic attack of the OH- bound at A site. Phosphate dissociation is slowed markedly by replacement of B site zinc by cadmium. There is clear evidence for long range effects of subunit-subunit interactions, since metal ion and phosphate binding at one active center alters the environments of A and B site metal ions and phosphoserine at the other active site.     

Characterization of main sulfur source of wood-degrading basidiomycetes by S K-edge X-ray absorption near edge spectroscopy (XANES)

The main wood degraders in aerobic terrestrial ecosystems belong to the white- and brown-rot fungi, where their biomass can be created on wood decay only. However, total sulfur (S) concentration in wood is very low and only little is known about the different sulfur compounds in wood today. Sulfur-starved brown-rot fungi Gloeophyllum trabeum and Oligoporus placenta were incubated on sterilized pine wood blocks whereas Lentinus cyathiformis and the white-rot fungi Trametes versicolor were incubated on sterilized beech wood blocks. After 19 weeks of incubation, the S oxidation status was analyzed in wood, in degraded wood, and in biomass of wood-degrading fungi by synchrotron based S K-edge XANES, and total S and sulfate were quantified. Total sulfur and sulfate content in pine wood blocks were approximately 50 and 1 ??g g⁻¹, respectively, while in beech wood approximately 100 and 20 ??g g⁻¹ were found, respectively. Sulfur in beech was dominated by sulfate-esters. In contrast, pine wood also contained larger amounts of reduced S. Three out of four selected fungi caused a reduction of the S oxidation state in wood from oxidized S (sulfate-ester, sulfate) to intermediate S (sulfonate, sulfoxide) or reduced S (thiols, e.g., proteins, peptides, enzyme cofactors). Only O. placenta shifted thiol to sulfonate. Growth experiments of these fungi on selective minimal media showed that in particular cysteine (thiol), sulfonates, and sulfate enhanced total mycelium growth. Consequently, wood-degrading fungi were able to utilize a large variety of different wood S sources for growth but preferentially transformed in vivo sulfate-esters and thiol into biomass structures.