Spin-resolved X-ray absorption near edge structure (XANES) simulation of metmyoglobin

Spin resolved multiple scattering (MS) calculations of Fe K-edge X-ray Absorption Near Edge Structure (XANES) of myoglobin are reported for the first time. The observed differences of the Fe K-edge XANES spectra of sperm whale metmyoglobin under spin transition as a function of temperature have been studied. The method allows one to compute separately spin effects and local structural effects. The results show that spin effects are confined in the absorption rising edge in the range 7111–7130 eV, while purely structural effects are dominant in the range 7130–7170 eV. Symmetry changes of the Fe coordination sphere mainly related to its movement towards the heme plane, coupled to an increase of axial asymmetry, can explain the XANES changes observed above 7130 eV without an appreciable change of the Fe-N_p distance. Received: 8 October 1997 / Revised version: 10 March 1998 / Accepted: 23 March 1998     

XANES Investigation of Dynamic Phase Transition in Olivine Cathode for Li‐Ion Batteries

Dynamic phase transformation in olivine LiFePO₄ involving formation of one or more intermediate or metastable phases is revealed by an in situ time‐resolved X‐ray absorption near edge structure (XANES) technique. The XANES spectra measured during relaxation immediately after the application of relatively high overpotentials, where metastable phases are expected, show a continuous shift of the Fe K‐edge toward higher energy. Surprisingly, the Fe K‐edge relaxes to higher energies after current interrupt regardless of whether the cell is being charged or discharged. This relaxation phenomenon is superimposed upon larger shifts in K‐edge due to changes in Fe^2+/Fe³⁺ ratio due to charging and discharging, and implies an intermediate phase of larger Fe? O bond length than any of the known crystalline phases. No intermediate crystalline phases are observed by X‐ray diffraction (XRD). A metastable amorphous phase formed during dynamic cycling and which structurally relaxes to the equilibrium crystalline phases over a time scale of about 10 min after cessation of charging/discharging current is consistent with the experimental observations.     

Synthesis, crystal structure, and DNA-cleaving behavior of 5-substituted benzene-1,3-bis(methylene)-spaced dinuclear copper(II) complexes

Three meta-dicopper complexes, 1-3, based on 5-substituted 1,3-xylylene spacer have been synthesized. These complexes are capable of inducing the transformation of supercoiled DNA (pUC19) to its nicked and linear DNA form in the presence of ascorbate, and their DNA nicking efficiency can be correlated to their DNA-binding ability. The cleavage mechanism is similar to that of the non-substituted meta-dicopper complex A. Amongst the three complexes, 5-(aminomethyl)-substituted complex 3 displayed a higher DNA-binding ability and nicking efficiency than unsubstituted complex A. The CD-spectroscopic study and structural analysis imply that the different CuCu distances and DNA binding modes induced by different 5-substituents on benzene-1,3-bis(methylene) spacer may be responsible for the different DNA cleaving behavior of meta-dicopper complexes.     

X-ray absorption near edge structure (XANES) for CO, CN and deoxyhaemoglobin: geometrical information

We use the recently developed multiple scattering theory to give a quantitative analysis of the X-ray absorption near edge structure (XANES) of haemoglobin and some of its substituents. We demonstrate that the XANES may contain information not provided by the extended X-ray absorption fine structure (EXAFS) part of the spectrum about the coordination geometry around the Fe atom, and in particular discuss the sensitivity of the XANES to the orientation of the CN group in HbCN. The anisotropy of the system leads to a strong dependence of the calculated spectrum on the polarisation of the X-rays. We show how this effect can be exploited in further XANES structural studies.     

Biochemistry of selenium-derivatized naturally occurring and unnatural nucleic acids

Selenium (Se) can provide unique biochemical and biological functions, and properties to macromolecules, including protein and RNA. Although Se has not yet been found in DNA, identification of the presence of Se in natural tRNAs has led to discovery of the naturally occurring 2-selenouridine and 5-[(methylamino)methyl]-2-selenouridine (mnm(5)se(2)U). The Se-atoms at C(2) of the modified uridines are introduced by 2-selenouridine synthase via displacement of the S-atoms in the corresponding 2-thiouridine nucleotides of the tRNAs, and selenophosphate is used as the Se donor. The research indicated that mnm(5)se(2)U is located at the first or wobble position of the anticodons in several bacterial tRNAs, including tRNA(Lys), tRNA(Glu), and tRNA(Gln). The 2-seleno functionality on this modified nucleotide probably improves the translation accuracy and/or efficiency. These observations in vivo suggest that the presence of Se can provide natural RNAs with useful properties to better function and survival. To further investigate the biochemical and structural properties of Se-derivatized nucleic acids (SeNA), we have pioneered chemical and enzymatic synthesis of Se-derivatized nucleic acids, and introduced Se into both RNA and DNA at a variety of positions by atom-specific replacement of oxygen. This review outlines the recent advancements in chemical and biochemical syntheses, and studies of SeNAs, and their potential applications in structural and functional investigation of nucleic acids and their protein complexes.     

XAS analysis of a nanostructured iron polysaccharide produced anaerobically by a strain of Klebsiella oxytoca

A strain of Klebsiella oxytoca, isolated from acid pyrite-mine drainage, characteristically produces a ferric hydrogel, consisting of branched heptasaccharide repeating units exopolysaccharide (EPS), with metal content of 36 wt%. The high content of iron in the EPS matrix cannot be explained by a simple ferric ion bond to the sugar skeleton. The bio-generated Fe-EPS is investigated by X-ray absorption spectroscopy. Fe K-edge XANES analysis shows that iron is mostly in trivalent form, with a non-negligible amount of Fe(2+) in the structure. The Fe EXAFS results indicate that iron in the sample is in a mineralized form, prevalently in the form of nano-sized particles of iron oxides/hydroxides, most probably a mixture of different nano-crystalline forms. TEM shows that these nanoparticles are located in the interior of the EPS matrix, as in ferritin. The strain produces Fe-EPS to modulate Fe-ions uptake from the cytoplasm to avoid iron toxicity under anaerobic conditions. This microbial material is potentially applicable as iron regulator.     

The Fe-only nitrogenase from Rhodobacter capsulatus: identification of the cofactor, an unusual, high-nuclearity iron-sulfur cluster, by Fe K-edge EXAFS and 57Fe Mössbauer spectroscopy

Samples of the dithionite-reduced FeFe protein (the dinitrogenase component of the Fe-only nitrogenase) from Rhodobacter capsulatus have been investigated by 57Fe M?ssbauer spectroscopy and by Fe and Zn EXAFS as well as XANES spectroscopy. The analyses were performed on the basis of data known for the FeMo cofactor and the P cluster of Mo nitrogenases. The prominent Fourier transform peaks of the Fe K-edge spectrum are assigned to Fe-S and Fe-Fe interactions at distances of 2.29 A and 2.63 A, respectively. A significant contribution to the Fe EXAFS must be assigned to an Fe backscatterer shell at 3.68 A, which is an unprecedented feature of the trigonal prismatic arrangement of iron atoms found in the FeMo cofactor of nitrogenase MoFe protein crystal structures. Additional Fe...Fe interactions at 2.92 A and 4.05 A clearly indicate that the principal geometry of the P cluster is also conserved. M?ssbauer spectra of 57Fe-enriched FeFe protein preparations were recorded at 77 K (20 mT) and 4.2 K (20 mT, 6.2 T), whereby the 4.2 K high-field spectrum clearly demonstrates that the cofactor of the Fe-only nitrogenase (FeFe cofactor) is diamagnetic in the dithionite-reduced ("as isolated") state. The evaluation of the 77 K spectrum is in agreement with the assumption that this cofactor contains eight Fe atoms. In the literature, several genetic and biochemical lines of evidence are presented pointing to a significant structural similarity of the FeFe, the FeMo and and the FeV cofactors. The data reported here provide the first spectroscopic evidence for a structural homology of the FeFe cofactor to the heterometal-containing cofactors, thus substantiating that the FeFe cofactor is the largest iron-sulfur cluster so far found in nature.     

Iron overload of human colon adenocarcinoma cells studied by synchrotron-based X-ray techniques

Fast- and slow-proliferating human adenocarcinoma colorectal cells, HT-29 and HCA-7, respectively, overloaded with transferrin (Tf), Fe(III) citrate, Fe(III) chloride and Fe(II) sulfate were studied by synchrotron radiation total-reflection X-ray spectrometry (TXRF), TXRF-X-ray absorption near edge structure (TXRF-XANES), and micro-X-ray fluorescence imaging to obtain information on the intracellular storage of overloaded iron (Fe). The determined TfR1 mRNA expression for the investigated cells correlated with their proliferation rate. In all cases, the Fe XANES of cells overloaded with inorganic Fe was found to be similar to that of deliquescent Fe(III) sulfate characterized by a distorted octahedral geometry. A fitting model using a linear combination of the XANES of Tf and deliquescent Fe(III) sulfate allowed to explain the near edge structure recorded for HT-29 cells indicating that cellular overload with inorganic Fe results in a non-ferritin-like fast Fe storage. Hierarchical cluster analysis of XANES spectra recorded for Fe overloaded HT-29 and HCA-7 cells was able to distinguish between Fe treatments performed with different Fe species with a 95 % hit rate, indicating clear differences in the Fe storage system. Micro-X-ray fluorescence imaging of Fe overloaded HT-29 cells revealed that Fe is primarily located in the cytosol of the cells. By characterizing the cellular Fe uptake, Fe/S content ratios were calculated based on the X-ray fluorescence signals of the analytes. These Fe/S ratios were dramatically lower for HCA-7 treated with organic Fe(III) treatments suggesting dissimilarities from the Tf-like Fe uptake.     

Structure of the Fe-heme in the homodimeric hemoglobin from Scapharca inaequivalvis and in the T72I mutant: an X-ray absorption spectroscopic study at low temperature

The Fe site structure in the recombinant wild-type and T721 mutant of the cooperative homodimeric hemoglobin (HbI) of the mollusc Scapharca itnaequivalvis has been investigated by measuring the Fe K-edge X-ray absorption near edge structure (XANES) spectra of their oxy, deoxy and carbonmonoxy derivatives, and the cryogenic photoproducts of the carbonmonoxy derivatives at T = 12 K. According to our results, the Fe site geometry in T72I HbI-CO is quite similar to that of human carbonmonoxy hemoglobin (HbA-CO), while in native HbI-CO it seems intermediate between that of HbA-CO and sperm whale MbCO. The XANES spectra of oxy and deoxy derivatives are similar to the homologous spectra of human HbA, except for T72I HbI, for which the absorption edge is blue-shifted (about + 1 eV) towards the spectrum of the oxy form. XANES spectra of the cryogenic photoproducts of HbA-CO (HbA*), HbI-CO (HbI*) and mutant HbI-CO (T72I HbI*) were acquired under continuous illumination at 12 K. The Fe-heme structures of the three photoproducts are similar; however, while in the case of HbA* and HbI* the data indicate incomplete structural relaxation of the Fe-heme towards its deoxy-like (T) form, the relaxation in T72I HbI* is almost completely towards the proposed "high affinity" Fe-heme structure of T72I HbI. This evidence suggests that minor tertiary restraints affect the Fe-heme dynamics of T72I HbI, corresponding to a reduction of the energy necessary for the T --> R structural transition, which can contribute to the observed dramatic enhancement in oxygen affinity of this hemoprotein, and the decreased cooperativity.     

The solvation of bromide anion in acetonitrile: a structural study based on the combination of theoretical calculations and X-ray absorption spectroscopy

This work studies the solvation of bromide in acetonitrile by combining quantum mechanics, computer simulations and X-ray absorption near edge structure (XANES) spectroscopy. Three different sets of interaction potentials were tested, one of them derived from literature and the other two are simple modifications of the previous one to include specificities of the bromide–acetonitrile interactions. Results for microsolvation of bromide were obtained by quantum mechanical optimization and classical minimization of small clusters [Br(ACN) _n ]^?  (n = 9, 20). Analysis of molecular dynamics (MD) simulations has provided structural, dynamic and energetic aspects of the solvation phenomenon. The theoretical computation of Br K-edge XANES spectrum in solution using the structural information obtained from the different simulations has allowed the comparison among the three different potentials, as well as the examination of the main structural and dynamic factors determining the shape of the experimental spectrum.     

Spectroscopic and electronic structure studies of the role of active site interactions in the decarboxylation reaction of alpha-keto acid-dependent dioxygenases

The alpha-ketoglutate (alpha-KG)-dependent dioxygenases are a large class of mononuclear non-heme iron enzymes that require Fe(II), alpha-KG and dioxygen for catalysis, with the alpha-KG cosubstrate supplying the two additional electrons required for dioxygen activation. A sub-class of these enzymes exists in which the alpha-keto acid is covalently attached to the substrate, including (4-hydroxy)mandelate synthase (HmaS) and (4-hydroxyphenyl)pyruvate dioxygenase (HPPD) which utilize the same substrate but exhibit two different general reactivities (H-atom abstraction and electrophilic attack). Previous kinetic studies of Streptomyces avermitilis HPPD have shown that the substrate analog phenylpyruvate (PPA), which only differs from the normal substrate (4-hydroxyphenyl)pyruvate (HPP) by the absence of a para-hydroxyl group on the aromatic ring, does not induce a reaction with dioxygen. While an Fe(IV)O intermediate is proposed to be the reactive species in converting substrate to product, the key step utilizing O(2) to generate this species is the decarboxylation of the alpha-keto acid. It has been generally proposed that the two requirements for decarboxylation are bidentate coordination of the alpha-keto acid to Fe(II) and the presence of a 5C Fe(II) site for the O(2) reaction. Circular dichroism and magnetic circular dichroism studies have been performed and indicate that both enzyme complexes with PPA are similar with bidentate alpha-KG coordination and a 5C Fe(II) site. However, kinetic studies indicate that while HmaS reacts with PPA in a coupled reaction similar to the reaction with HPP, HPPD reacts with PPA in an uncoupled reaction at an approximately 10(5)-fold decreased rate compared to the reaction with HPP. A key difference is spectroscopically observed in the n-->pi( *) transition of the HPPD/Fe(II)/PPA complex which, based upon correlation to density functional theory calculations, is suggested to result from H-bonding between a nearby residue and the carboxylate group of the alpha-keto acid. Such an interaction would disfavor the decarboxylation reaction by stabilizing electron density on the carboxylate group such that the oxidative cleavage to yield CO(2) is disfavored.     

Limonoids with an Oxygen Bridge between C(1) and C(29) from the Seeds of a Krishna Mangrove,Xylocarpus granatum

Ten limonoids, named granatumins L–U ( 1 – 10 , resp.), were isolated from the seeds of an Indian mangrove, Xylocarpus granatum, collected in the estuary of Krishna, Andhra Pradesh. The structures of these compounds were established on the basis of spectroscopic data. The relative configuration of granatumin L ( 1 ) was confirmed by a single‐crystal X‐ray diffraction analysis. Granatumins L–T ( 1 – 9 , resp.) belong to the small group of limonoids with an oxygen bridge between C(1) and C(29), while granatumin U ( 10 ) is a 28‐Me‐oxidized mexicanolide. This is the first report of limonoids with an O‐bridge between C(1) and C(29) from the Indian X. granatum. The pronounced structural diversity of limonoids from this mangrove might originate from environmental factors.     

Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences

X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations have been jointly applied to the study of the Cu,Zn superoxide dismutase from Haemophilus ducreyi (HdSOD) in interaction with the carbon monoxide molecule. The configurational flexibility of the Fe(II)-heme group, intercalated between the two subunits, has been sampled by MD simulations and included in the XANES data analysis without optimization in the structural parameter space. Our results provide an interpretation of the observed discrepancy in the Fe-heme distances as detected by extended X-ray absorption fine structure (EXAFS) spectroscopy and the classical XANES analysis, in which the structural parameters are optimized in a unique structure. Moreover, binding of the CO molecule to the heme induces a long range effect on the Cu,Zn active site, as evidenced by both MD simulations and in vitro experiments. MD simulation of the CO bound system, in fact, highlighted a structural rearrangement of the protein-protein hydrogen bond network in the region of the Cu,Zn active site, correlated with an increase in water accessibility at short distance from the copper atom. In line, in vitro experiments evidenced an increase of copper accessibility to a chelating agent when the CO molecule binds to the heme group, as compared to a heme deprived HdSOD. Altogether, our results support the hypothesis that the HdSOD is a heme-sensor protein, in which binding to small gaseous molecules modulates the enzyme superoxide activity as an adaptive response to the bacterial environment.     

Structural Evolution During Perovskite Crystal Formation and Degradation: In Situ and Operando X‐Ray Diffraction Studies

This review provides an update on the progress in understanding formation and degradation mechanisms in halide perovskites for photovoltaic applications, as supported by in situ and operando X‐ray scattering techniques. The value of these real‐time analyses is particularly high for gaining insights into the structural evolution during crystal formation and decomposition upon exposure to external stress factors. This type of analysis reveals the pathways between starting and end points of a process rather than being limited to comparing states before and after the process. Special attention is put on the successful efforts toward upscaling including deposition techniques that are compatible to roll‐to‐roll processing. These processes are realized using fast annealing procedures. The development of these processes strongly benefited from in situ studies exploring the direct transition from precursor to perovskite without going through observable crystalline intermediate phases. A particular focus of this review is the benefit of using in situ and operando X‐ray scattering techniques to better understand and ultimately improve device stability. The difference between structural stability of thin films and structural stability under device operation is highlighted, convincingly demonstrating the indispensability of operando studies.     

An EXAFS study of the interaction of substrate with the ferric active site of protocatechuate 3,4-dioxygenase

X-ray crystallographic studies of the intradiol cleaving protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa have shown that the enzyme has a trigonal bipyramidal ferric active site with two histidines, two tyrosines, and a solvent molecule as ligands [Ohlendorf, D.H., Lipscomb, J.D., & Weber, P.C. (1988) Nature 336, 403-405]. Fe K-edge EXAFS studies of the spectroscopically similar protocatechuate 3,4-dioxygenase from Brevibacterium fuscum are consistent with a pentacoordinate geometry of the iron active site with 3 O/N ligands at 1.90 A and 2 O/N ligands at 2.08 A. The 2.08-A bonds are assigned to the two histidines, while the 1.90-A bonds are associated with the two tyrosines and the coordinated solvent. The short Fe-O distance for the solvent suggests that it coordinates as hydroxide rather than water. When the inhibitor terephthalate is bound to the enzyme, the XANES data indicate that the ferric site becomes 6-coordinate and the EXAFS data show a beat pattern which can only be simulated with an additional Fe-O/N interaction at 2.46 A. Together, the data suggest that the oxygens of the carboxylate group in terephthalate displace the hydroxide and chelate to the ferric site but in an asymmetric fashion. In contrast, protocatechuate 3,4-dioxygenase remains 5-coordinate upon the addition of the slow substrate homoprotocatechuic acid (HPCA). Previous EPR data have indicated that HPCA forms an iron chelate via the two hydroxyl functions.(ABSTRACT TRUNCATED AT 250 WORDS)     

Fe(II)/α-Ketoglutarate-Dependent Hydroxylases and Related Enzymes

Fe(II)/α-ketoglutarate (αKG)-dependent hydroxylases catalyze an amazing diversity of reactions that result in protein side-chain modifications, repair of alkylated DNA/RNA, biosynthesis of antibiotics and plant products, metabolism related to lipids, and biodegradation of a variety of compounds. These enzymes possess a β-strand “jellyroll” structural fold that contains three metal-binding ligands found in a His¹-X-Asp/Glu-X_n-His² motif. The cosubstrate, αKG, chelates Fe(II) using its C-2 keto group (binding opposite the Asp/Glu residue) and C-1 carboxylate (coordinating opposite either His¹ or His²). Oxidative decomposition of αKG forms CO₂ plus succinate and leads to the generation of an Fe(IV)-oxo or other activated oxygen species that hydroxylate the primary substrate. The reactive oxygen species displays alternate reactivity in related enzymes that catalyze desaturations, ring expansions, or ring closures. Other enzymes resemble the Fe(II)/αKG-dependent hydroxylases in terms of protein structure or chemical mechanism but do not utilize αKG as a substrate. This review describes the reactions catalyzed by this superfamily of enzymes, highlights key active site features revealed by structural studies, and summarizes results from spectroscopic and other approaches that provide insights into the chemical mechanisms.     

Isolation and chemical modification of clerodane diterpenoids from Salvia species as potential agonists at the kappa-opioid receptor

The clerodane diterpenoid salvinorin A (1), the main active component of the psychotropic herb Salvia divinorum, has been reported to be a potent agonist at the kappa-opioid receptor. Computer modeling suggested that splendidin (2) from S. splendens, as well as related compounds, might possess similar activities. In the present study, this hypothesis was tested by determination of the binding properties of a series of structural congeners, compounds 2-8, at the mu-, delta-, and kappa-opioid receptors. However, none of these compounds showed significant binding to any of the opioid-receptor subtypes, thus disproving the above hypothesis. The novel compounds 7 and 8 were obtained semi-synthetically by selective modification of salvifarin (5), isolated from Salvia farinacea, upon epoxide-ring opening with AcOH in the presence of indium(III) triflate. Also, the X-ray crystal structure of salvifaricin (6; Fig.), obtained from S. farinacea, was determined for the first time and used, in combination with in-depth NMR experiments, to elucidate the absolute configurations of the new products. Our experiments demonstrate that the relatively well-accessible diterpenoid 6 could be used as starting material for future studies into the structure-activity relationship at the kappa-opioid receptor.     

Intermediate states in ligand photodissociation of carboxymyoglobin studied by dispersive X-ray absorption

The ligand photodissociation of sperm whale carboxymyoglobin (MbCO) at low temperature (15 K-100 K) under extended illumination has been studied by X-ray Absorption Near Edge Structure (XANES) spectroscopy using the dispersive technique. XANES simulations through the multiple scattering (MS) approach allow one to interpret the spectroscopic data in structural terms, and to investigate the Fe site structure configurations of the states that follow the CO photodissociation as a function of temperature. The Fe site in the photoproduct is unbound, with an overall structure similar to the deoxy-form (Mb) of the protein. The Fe site structure changes from T < 30 K (Mb^*) to T>50 K (Mb^**), revealing the existence of a slower unbound state Mb^**. A model is proposed which includes the faster state (Mb^*) as a planar porphyrin ring with a displacement of Fe from the heme plane of less than 0.3 Å, and the slower state (Mb**) with a domed heme. Correspondence to: S. Della Longa     

Determination of the nature of the heme environment in nitrosyl indoleamine 2,3-dioxygenase using Multiple-scattering analyses of X-ray absorption fine structure

Multiple-scattering analysis of X-ray absorption fine structure data on the NO adducts of indoleamine 2,3-dioxygenase (IDO) and analysis of X-ray absorption near-edge structure (XANES) have provided the first direct structural information about the iron center for this ubiquitous mammalian metalloprotein. The IDO(II)NO adduct, which is likely to play a physiological role in the immune system, differs from similar adducts such as Mb(II)NO and Lb(II)NO in that the Fe-His bond is essentially broken. At 10 K, the Fe-N(p)(av) bond length = 2.00(2) A, Fe-NO bond length = 1.75 A, and angle = 140 degrees, which are typical of five-coordinate Fe(II)NO species. The XANES is also closer to that of five-coordinate model complexes than six-coordinate species. In addition to the Fe(II)NO species, there was a minor component of the Fe(III)NO adduct because of incomplete reduction of the Fe(II) species. This was also a five-coordinate center and consists of a linear Fe(II)NO(+) moiety with the Fe-N(p)(av) bond length = 2.00(2) A, Fe-NO bond length = 1.63(3) A, and angle = 179 degrees. The results indicate that both the blocking of the heme site to O(2) binding and conformational changes induced by breaking the Fe-N(epsilon) bond may be important mechanisms by which NO inhibits IDO in vitro and in vivo.