Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

Spin-crossover in metallomesogens of iron(II)

Covalent grafting mesogenic groups to the coordination cores of the parent mononuclear low-spin and spin-crossover compounds afforded metallomesogenic complexes of iron(II). In comparison with the parent complexes the spin-crossover properties of the alkylated derivatives are substantially modified. The type of the modification was found to be dependent on the properties of the parent system and the nature of the used anion, however, the general tendency is the destabilization of the low-spin state at the favor of spin-crossover or high-spin behavior below 400 K. The structural insight revealed the micro-segregated layered organization. The effect of the alkylation of the parent compounds consists first of all in the change of the lattice to a two-dimensional lamellar one retaining significant intermolecular contacts only within the ionic bilayers. The comprehensive analysis of the structural and thermodynamic data in the homologous series pointed at the mechanism of the interplay between the structural modification on melting and the induced anomalous change of the magnetic properties. A family of one-dimensional spin-crossover polymers was synthesized and characterized using a series of spectroscopic methods, X-ray powder diffraction, magnetic susceptibility measurements and differential scanning calorimetry. The copper analogue of was also synthesized and its crystal structure solved. In comparison with the mononuclear systems, the polymeric mesogens of iron(II) are less sensitive to the glass transition, which was attributed to the moderate concomitant variation of the structure. Nevertheless, the observed increase of the magnetic hysteresis with lengthening of the alkyl substituents was ascribed to the interplay of the structural reorganization of the coordination core due to spin-crossover with the structural delay in the spatial reorganization of the mesogenic substituents. The classification of mononuclear and polymeric metallomesogens according to the interactions between the structural- and the spin-transition and analysis of the data on the reported spin-crossover metallomesogens led to the separation of three types, namely: Type i: systems with coupling between the electronic structure of the iron(II) ions and the mesomorphic behavior of the substance; Type ii: systems where both transitions coexist in the same temperature region but are not coupled due to competition with the dehydration or due to negligible structural transformation; Type iii: systems where both transitions occur in different temperature regions and therefore are uncoupled. Fine-tuning, in particular regarding the temperature at which the spin-transition occurs with hysteresis properties responsible for the memory effect, are still a major challenge towards practical implementation of spin-crossover materials. A possible answer to the problem could be materials in which the spin-crossover transition is coupled with another transition easily controllable by external stimuli. In the present thesis we have shown the viability of the approach realized in the mesogenic systems with coupled phase- and spin-transitions.

Petrogenetic evolution of Uralian-Alaskan-type mafic-ultramafic complexes in the southern and middle Urals, Russia

The PhD thesis at hand consists of three parts and describes the petrogenetic evolution of Uralian-Alaskan-type mafic ultramafic complexes in the Ural Mountains, Russia. Uralian-Alaskan-type mafic-ultramafic complexes are recognized as a distinct class of intrusions. Characteristic petrologic features are the concentric zonation of a central dunite body grading outward into wehrlite, clinopyroxenite and gabbro, the absence of orthopyroxene and frequently occurring platinum group element (PGE) mineralization. In addition, the presence of ferric iron-rich spinel discriminates Uralian-Alaskan-type complexes from most other mafic ultramafic rock assemblages. The studied Uralian-Alaskan-type complexes (Nizhnii Tagil, Kytlym and Svetley Bor) belong to the southern part of a 900 km long, N–S-trending chain of similar intrusions between the Main Uralian Fault to the west and the Serov-Mauk Fault to the east. The first chapter of this thesis studies the evolution of the ultramafic rocks tracing the compositional variations of rock forming and accessory minerals. The comparison of the chemical composition of olivine, clinopyroxene and chromian spinel from the Urals with data from other localities indicates that they are unique intrusions having a characteristic spinel and clinopyroxene chemistry. Laser ablation-ICPMS (LA-ICPMS ) analyses of trace element concentrations in clinopyroxene are used to calculate the composition of their parental melt which is characterized by enriched LREE (0.5-5.2 prim. mantle) and other highly incompatible elements (U, Th, Ba, Rb) relative to the HREE (0.25-2.0 prim. mantle). A subduction-related geotectonic setting is indicated by a positive anomaly for Sr and negative anomalies for Ti, Zr and Hf. The mineral compositions monitor the evolution of the parental magmas and decipher differences between the studied complexes. In addition, the observed variation in LREE/HREE (for example La/Lu = 2-24) can be best explained with the model of an episodically replenished and erupted open magma chamber system with the extensive fractionation of olivine, spinel and clinopyroxene. The data also show that ankaramites in a subduction-related geotectonic setting could represent parental magmas of Uralian-Alaskan-type complexes. The second chapter of the thesis discusses the chemical variation of major and trace elements in rock-forming minerals of the mafic rocks. Electron microprobe and LA-ICPMS analyses are used to quantitatively describe the petrogenetic relationship between the different gabbroic lithologies and their genetic link to the ultramafic rocks. The composition of clinopyroxene identifies the presence of melts with different trace element abundances on the scale of a thin section and suggests the presence of open system crustal magma chambers. Even on a regional scale the large variation of trace element concentrations and ratios in clinopyroxene (e.g. La/Lu = 3-55) is best explained by the interaction of at least two fundamentally different magma types at various stages of fractionation. This requires the existence of a complex magma chamber system fed with multiple pulses of magmas from at least two different coeval sources in a subduction-related environment. One source produces silica saturated Island arc tholeiitic melts. The second source produces silica undersaturated, ultra-calcic, alkaline melts. Taken these data collectively, the mixing of the two different parental magmas is the dominant petrogenetic process explaining the observed chemical variations. The results further imply that this is an intrinsic feature of Uralian-Alaskan-type complexes and probably of many similar mafic-ultramafic complexes world-wide. In the third chapter of this thesis the major element composition of homogeneous and exsolved spinel is used as a petrogenetic indicator. Homogeneous chromian spinel in dunites and wehrlites monitors the fractionation during the early stages of the magma chamber and the onset of clinopyroxene fractionation as well as the reaction of spinel with interstitial liquid. Exsolved spinel is present in mafic and ultramafic rocks from all three studied complexes. Its composition lies along a solvus curve which defines an equilibrium temperature of 600°C, given that spinel coexists with olivine. This temperature is considered to be close to the temperature of the host rocks into which the studied Uralian-Alaskan-type complexes intruded. The similarity of the exsolution temperatures in the different complexes over a distance of several hundred kilometres implies a regional tectonic event that terminated the exsolution process. This event is potentially associated with the final exhumation of the Uralian-Alaskan-type complexes along the Main Uralian Fault and the Serov-Mauk Fault in the Uralian fold belt.

N-Heterocyclic carbene complexes of rhodium: structures, dynamics and catalysis

A series of imidazolium salts of the type [BocNHCH2CH2ImR]X (Boc = t-Bu carbamates; Im = imidazole) (R = Me, X = I, 1a; R = Bn, X = Br, 1b; R = Trityl, X = Cl, 1c) and [BnImR’]X (R’ = Me, X = Br, 1d; R’ = Bn, X = Br, 1e; R’ = Trityl, X = Cl, 1g; R’ = tBu, X = Br, 1h) bearing increasingly bulky substituents were synthetized and characterized. Subsequently, these precursors were employed in the synthesis of silver(I)-N-heterocyclic (NHC) complexes as transmetallating reagents for the preparation of rhodium(I) complexes [RhX(NBD)(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl; R = Me, 4a; R = Bn, 4b; R = Trityl, 4c; X = I, R = Me, 5a; NHC = 1-Bn-3-R’-imidazolin-2-ylidene; X = Cl; R’ = Me, 4d, R’ = Bn, 4e, R’ = Trityl, 4g; R’ = tBu, 4h). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. While the rotation barriers calculated for the complexes in which R = Me, Bn (4a,b,d,e and 5a) matched the experimental values, this was not true for the complexes 4c,g, bearing a trityl group for which the values are much smaller than the calculated ones. Energy barriers for 4c,g, derived from a line shape simulation, showed a strong dependence on the temperature while for 4h the rotational energy barrier is stopped at room temperature. The catalytic activity of the new rhodium compounds was investigated in the hydrosilylation of terminal alkynes and in the addition of phenylboronic acid to benzaldehyde. The imidazolium salts 1d,e were also employed in the synthesis of new iron(II)-NHC complexes. Finally, during a six-months stay at the University of York a new ligand derived from Norharman was prepared and employed in palladium-mediated cross-coupling.

Nanoparticular iron complex drugs for parenteral administration - physicochemical characterization, biological distribution and pharmacological safety

Iron deficiency is the most common deficiency disease worldwide with many patients who require intravenous iron. Within the last years new kind of parenteral iron complexes as well as generic preparations entered the market. There is a high demand for methods clarifying benefit to risk profiles of old and new iron complexes. It is also necessary to disclose interchangeability between originator and intended copies to avoid severe anaphylactic and anaphylactoid side reaction and assure equivalence of therapeutic effect.rnrnThe investigations presented in this work include physicochemical characterization of nine different parenteral iron containing non-biological complex drugs. rnWe developed an in-vitro assay, which allows the quantification of labile iron in the different complexes and thus it is a useful tool to estimate the pharmaclogical safety regarding iron related adverse drug events. This assay additionally allowed the estimation of complex stability by evaluation of degradation kinetics at the applied conditions.rnrnAn in-ovo study was performed to additionally compare different complexes in respect to body distribution. This in combination with complex stability information allowed the risk estimation of potential local acute and chronic reactions to iron overload.rnrnInformation obtained by the combination of the methods within this work are helpful to estimate the safety and efficacy profile of different iron containing non-biological complex drugs. rnrnPhysicochemical differences between the complexes were demonstrated in respect to size of the inorganic fraction, size and size distribution of the complete particles, structure of the inorganic iron fraction, morphology of the complexes and charge of the complexes. And furthermore significant differences in the biological behavior of different complexes were demonstrated. rnrnThe combination of complex stability and biodistribution as well as the combination of structure, size and stability represent helpful tools for the physicochemical characterization of iron containing non-biological complex drugs and for the estimation of pharmacological safety. This work thus represents an up to date summary of some relevant methods for the characterization of intravenous iron complex drugs in respect to pharmaceutical quality, pharmacological safety and aspects of efficacy. rnrnProspectively, it is worthwhile that the methods within this work will contribute to the development and/or characterization of iron containing nanoparticular formulations with beneficial efficacy and safety profiles.rn

Iron-Promoted Nucleophilic Additions to Diimine-Type Ligands: A Synthetic and Structural Study

We report here three examples of the reactivity of protic nucleophiles with diimine-type ligands in the presence of FeII salts. In the first case, the iron-promoted alcoholysis reaction of one nitrile group of the ligand 2,3-dicyano-5,6-bis(2-pyridyl)-pyrazine (L1) permitted the isolation of an stable E-imido−ester, [Fe(L1‘)2](CF3SO3)2 (1), which has been characterized by spectroscopic studies (IR, ES-MS, Mössbauer), elemental analysis, and crystallographically. Compound 1 consists of mononuclear octahedrally coordinated FeII complexes where the FeII ion is in its low-spin state. The iron-mediated nucleophilic attack of water to the asymmetric ligand 2,3-bis(2-pyridyl)pyrido[3,4-b]pyrazine (L2) has also been studied. In this context, the crystal structures of two hydration−oxidation FeIII products, [Fe(L2‘)2](ClO4)3·3CH3CN (2) and trans-[FeL2‘‘Cl2] (3), are described. Compounds 2 and 3 are both mononuclear FeIII complexes where the metals occupy octahedral positions. In principle, L2 is expected to coordinate to metal ions through its bipyridine-type units to form a five-membered ring; however, this is not the case in compounds 2 and 3. In 2, the ligand coordinates through its pyridines and through the hydroxyl group attached to the pyrazine imino carbon after hydration, that is, in an N,O,N tridentate manner. In compound 3, the ligand has suffered further transformations leading to a very stable diamido complex. In this case, the metal ion achieves its octahedral geometry by means of two pyridines, two amido N atoms, and two axial chlorine atoms. Magnetic susceptibility measurements confirmed the spin state of these two FeIII species:  compounds 2 and 3 are low-spin and high-spin, respectively.

Iron accumulation in Alzheimer disease is a source of redox-generated free radicals

Damage from free radicals has been demonstrated in susceptible neuronal populations in cases of Alzheimer disease. In this study, we investigated whether iron, a potent source of the highly reactive hydroxyl radical that is generated by the Fenton reaction with H2O2, might contribute to the source of radicals in Alzheimer disease. We found, using a modified histochemical technique that relies on the formation of mixed valence iron complexes, that redox-active iron is associated with the senile plaques and neurofibrillary tangles—the pathological hallmark lesions of this disease. This lesion-associated iron is able to participate in in situ oxidation and readily catalyzes an H2O2-dependent oxidation. Furthermore, removal of iron was completely effected using deferoxamine, after which iron could be rebound to the lesions. Characterization of the iron-binding site suggests that binding is dependent on available histidine residues and on protein conformation. Taken together, these findings indicate that iron accumulation could be an important contributor toward the oxidative damage of Alzheimer disease.

Iron chelates bind nitric oxide and decrease mortality in an experimental model of septic shock.

The hydroxamic acid siderophore ferrioxamine B [FeIII(HDFB)+] and the iron complex of diethylenetri-aminepentaacetic acid [FeIII(DTPA)2-] protected mice against death by septic shock induced by Corynebacterium parvum + lipopolysaccharide. Although FeIII(DTPA)2- was somewhat more effective than FeIII(HDFB)+, the iron-free ligand H4DFB+ was significantly more effective than DTPA. The hydroxamic acid chelator has a much higher iron affinity than the amine carboxylate, allowing for more efficient formation of the FeIII(HDFB)+ complex upon administration of the iron-free ligand. Electrochemical studies show that FeIII(DTPA)2- binds NO stoichiometrically upon reduction to iron(II) at biologically relevant potentials to form a stable NO adduct. In contrast, FeIII(HDFB)+ is a stable and efficient electrocatalyst for the reduction of NO to N2O at biologically relevant potentials. These results suggest that the mechanism of protection against death by septic shock involves NO scavenging and that particularly effective drugs that operate a low dosages may be designed based on the principle of redox catalysis. These complexes constitute a new family of drugs that rely on the special ability of transition metals to activate small molecules. In addition, the wealth of information available on siderophore chemistry and biology provides an intellectual platform for further development.

Conformational changes of dissolved humic and fulvic superstructures with progressive iron complexation

Conformational changes of a humic acid (HA) and a fulvic acid (FA) induced by iron complexation were followed by high-performance size exclusion chromatography (HPSEC) with both UV–vis and refractive index (RI) detectors. Molecular size distribution was reduced for HA and increased for FA with progressive iron complexation. Since interactions of Fe with humic components are electrostatic, it is likely that the triple-charged Fe ions formed stronger complexes with the more acidic hydrophilic and hydrated FA than with the less acidic and more hydrophobic HA. The large content of ionized carboxyl groups in FA, thus favored the formation of intra- or intermolecular bridges between the negatively charged fulvic acid molecules, and led to more compact and larger size network than for HA. Conversely, iron complexation with HA disrupted the humic conformational arrangements stabilized by only weak hydrophobic bonds into smaller-size aggregates of greater conformational stability due to formation of strong metal complexes. These results confirmed that humic molecules in solution were organized in supramolecular associations of relatively small molecules loosely bound together by dispersive interactions and hydrogen bonds, and they specifically responded to chemical changes brought about by metal additions. The present study revealed the molecular changes occurring in superstructures of natural organic matter when in metal complexes and contributed to understand and predict the environmental behavior in waters and soil of metal complexes with natural organic matter.

Chemical and mineral compositions of cherty and siliceous-clayey rocks from accretionary complexes in Sikhote Alin

The paper reports results of a study of clastic heavy mineral assemblages and geochemical features of some assemblages in several Permian-Mesozoic cherty and siliceous-clayey sequences of the Sikhote Alin Region. They are composed of pelagic and hemipelagic sediments of the Panthalassa (Paleopacific) Ocean. Four typical mineral assemblages and their environments are established. In one of the ocean segments, where the sedimentary cover formed during Late Paleozoic - Early Cretaceous, the Permian pelagic domain was characterized by the amphibole-pyroxene assemblage with heavy minerals derived from ophiolites. The Triassic-Jurassic stage was marked by development of the clinopyroxene assemblage with heavy minerals derived from intraplate alkaline volcanic complexes. Middle-Late Jurassic hemipelagic sediments host the zircon-clinopyroxene assemblage with greater role of continental environments and presence of volcanic products of the convergence zone. Another segment of the ocean accumulated red cherts and siliceous-clayey sediments during Jurassic - Early Cretaceous under influence of island-arc volcanism.