The spatial organisation of macromolecular metal chelates

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Inorganic Chemistry , 47 13 , Chemistry of Materials , 20 13 , Chemistry of Materials , 20 10 , Chemistry of Materials , 19 25 , Journal of the American Chemical Society , 27 , Inorganic Chemistry , 46 4 , A unique non-interpenetrated open-framework chalcogenide with a large cavity. Dalton Transactions , 47 1 , Dalton Transactions , 47 12 , From ethylzinc guanidinate to [Zn 10 O 4 ]-supertetrahedron.

Dalton Transactions , 46 37 , Qin-Yu Zhu, Jie Dai. Coordination Chemistry Reviews , , Systems Based on CdS. European Journal of Inorganic Chemistry , Sonochemical syntheses of binuclear lead II -azido supramolecule with ligand 3,4,7,8-tetramethyl-1,phenanthroline as precursor for preparation of lead II oxide nanoparticles.

Ultrasonics Sonochemistry , 23 , Sonochemical syntheses of two new flower-like nano-scale high coordinated lead II supramolecular coordination polymers. A hybrid linkage mode between T2,2 and T3 selenide clusters. Chemical Communications , 51 18 , Dye-sensitized polyoxometalate for visible-light-driven photoelectrochemical cells.

Dalton Transactions , 44 32 , Tuning the efficiency of multi-step energy transfer in a host—guest antenna system based on a chalcogenide semiconductor zeolite through acidification and solvation of guests.

Publication details

Journal of Materials Chemistry C , 3 44 , Sonochemical synthesis of tri-nuclear lead II -azido nano rods coordination polymer with 3,4,7,8-tetramethyl-1,phenanthroline tmph : Crystal structure determination and preparation of nano lead II oxide. Journal of Molecular Structure , , Syntheses, crystal and band structures, and optical properties of a selenidoantimonate and an iron polyselenide.

Journal of Solid State Chemistry , , Dyes and Pigments , , Inorganic Chemistry Communications , 46 , Chemistry - A European Journal , 20 27 , Dalton Transactions , 43 10 , Dalton Transactions , DOI: Dalton Transactions , 43 33 , Dalton Trans. Dalton Transactions , 42 23 , This estimation indicated that the interfaces between each pair of monomers were hydrophobic and interlocked, without unmatched electron donor or acceptor, suggesting that stable macromolecular complexes reinforced by metal chelation existed in solution.

Molecular weights were estimated using Guinier analysis, pair function analysis, BSA calibration and the method of Fischer [ 21 ] Table 2. Consequently, we imposed a P 2 symmetry in the calculation of additional ab initio shapes. This relatively low NSD indicated that the shapes converged toward similar results. However, some of these shapes were composed of a globular shape with a thin extension, for which the spatial orientation differs from one shape to the other Fig 3B.

All together, these results may correspond to a mixture of monomers with a minority of dimers and suggested that, even in the absence of divalent metals, a minor fraction of hVEGFR1d2 exhibited a weak propensity to dimerize in solution. In conclusion, the SAXS results were consistent with the determined homodimer crystal structures. The cobalt ion is shown as a black sphere on D. In principle, these nuclei are observable by NMR, but the existence of a quadrupole moment causes a significant broadening of the signal that renders impossible their observation.

The Cd chemical shifts depend on the nature and on the space organization of the metal ligands [ 25 , 27 ]. However, attempts to observe a signal of the Cd in interaction with the unlabeled hVEGFR1d2 were unsuccessful due to an intermediate exchange between the free form of the metal and its bound state to the protein. In the absence of significant conformational modifications, this method allows the detection of variations in the electronic environment of the protein backbone amides that occur upon binding of the metal ion and upon dimerization.

The full spectra are shown except for residues Phe and Trp , with resonances at 5.

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A general line broadening effect is observed following the addition of the divalent cation due to the dimerization of the hVEGFR1d2 and peaks of residues at the interface completely disappear due to the conformational exchange on an intermediate NMR timescale. B EDTA has been added 1. EDTA chelates cadmium ions, leading to the disruption of the dimer and the reemergence of the previously missing resonances characterizing the interface.

Metal Complexes with Polymer Chelating Ligands | SpringerLink

Chemical shift perturbations were directly observed in the 1 H- 15 N TROSY NMR spectra and several resonances of the protein exhibited a drastic line width broadening or a disappearance of the resonance associated with the addition of cadmium Fig 4A. The broadening of the signal was so extreme that several resonances could not be detected any more in the spectrum in particular those of amino acids involved at the dimer interface. This line broadening is associated with the increase of the molecular weight of the observed system and not to the intermediate exchange phenomenon that impacts the residues at the interface.

The residues involved in the dimer formation in solution were identified by following the decrease or the disappearance of the peaks at different concentrations of cadmium from 0 to 1. Fig 5 and three main areas were highlighted. The first one in the N-terminal region contained residues Tyr -Ile , Glu , Ile , His , Thr , and Gly , a second region included residues Glu -Leu , and a third one in the C-terminal region encompassed residues Thr -Thr Fig 5.

The variation of the peaks volumes was almost completed at around 0. The cadmium concentration was increased from 0 to 1. The peak volumes are normalized against the highest peak volume in the TROSY experiment without cadmium. No bar indicates either the presence of proline or a residue Asn that could not be unambiguously identified on the spectrum.

Extremely perturbed peaks following cadmium addition identify three principal regions potentially involved in dimerization: Tyr -Gly , Ala -Leu and Leu -Thr Among the different identified regions, Tyr -Gly and Thr -Thr contain His and His respectively, involved in both metal ion recognition and dimerization. The obtained spectra Fig 4B indicated that the divalent metal cation was neutralized upon the addition of EDTA, and the spectra recovered the original resonances that were present in the absence of cadmium.

Consequently, the dimer interface identified in solution was very close to that identified in the crystal structure, and dimerization was clearly due to coordination of the metal ion by these two histidines from both monomers. After demonstrating the metal induced dimerization of domain d2 in solution, the question occurring was the capacity of the full VEGF binding site, i.

MD simulation was performed on the resulting monomer using the Gromacs 4. Calculation of the RMS displacements on all atoms showed that the main fluctuations were equally distributed in the loops of both domains, and that the core of each domain was stable.

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The regions presenting a slightly poorer geometrical quality were the — and — segment of d2, and the C-terminus — of d3 oriented toward the fourth domain in the full receptor context. The MD procedures were identical to the previous one, but continued during a total of 2 ns.

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  • All along MD simulations, the d2 domains remained bound via the hydrophobic interface previously described in the crystal structures. Despite this supplementary constraint on Gln , residues — still formed a hinge between the two domains, as in the MD simulation performed on the monomeric d2d3 model. Equivalent orientations of domain 3 are shown in identical colors red or green.

    It suggested, on a structural point of view, that a metal-induced dimer of the full-length receptor could be anchored in the membrane, but that the relative positions of domains 3—7 were completely different than in the dimer induced by VEGF binding, probably precluding activation.

    3. Metal Complexes with Polymer Chelating Ligands

    These various effects suggested that the binding site was flexible and able to adapt to different cation size and coordination, which was consistent with the structural results. For cations of similar size, the observed differences may be due to different preferred coordination geometry [ 35 ] and ligands. B SDS page of loaded samples and eluted peaks. The His and His are conserved in the primate order.

    Consequently, the metal site that we identified in VEGFR1 is not ubiquitous, though Tyr and Asn may frequently act as metal-binder residues. A zinc contamination arising from laboratory items cannot be excluded [ 36 ] or from the putative ligand Laxaphycin B. It might also be the case for Laxaphycin B. The three structures are similar and reveal a homodimer with interlocked hydrophobic surfaces buried at the interface and a divalent cation chelated by four histidine residues two from each monomer. However, as they were not defined as covalently linked in the X-Ray refinement software, the slightly higher distances may result from the repulsive part of the Van der Waals forces.

    All dimers are analyzed as stable in solution by PISA.

    The SAXS shapes are consistent with the determined crystal structures for both monomer and homodimer. We observe a movement of d3 relative to d2 that suggests that a metal-induced dimer of the full-length receptor can be anchored in the membrane, but with a modified relative position of domains 3—7, that probably precludes the tyrosine kinase domains activation Fig 6B.

    However, it constitutes an interesting point, considering the numerous studies that focused on the role of metals in angiogenesis and the lack of mechanistic evidence at the molecular level. Two metals ions, copper and zinc, have been evidenced to regulate angiogenesis in physiological conditions [ 6 ]. They are the second and the third most abundant trace metals in plasma Plasmatic zinc is bound to and transported by albumin and transferrin, and the stock is rapidly exchangeable [ 43 ], while the major part of plasmatic copper is tightly bound to ceruloplasmin, with a low exchangeable fraction 0.

    However Li et al. The role of zinc in a wide range of cellular processes has been well established. It plays an important role in transcription factors function, DNA repair and as antioxidant. More specifically zinc has an anti-angiogenic activity through the Zn-bound endostatin. It may also reverse gene expression of most genes modulated by hypoxia.

    Indeed, numerous compound libraries are synthetized using copper, palladium, and other transition metals as catalysts. Transition metals must be rigorously discarded in the purification steps. The metal site can also be exploited to design new therapeutic compounds that target specifically the hVEGFR1.

    The human hVEGFR1d2 protein residues — was expressed and purified as previously described [ 13 ]. For SAXS analysis, all divalent metal ions were thoroughly removed with 0. Louis, USA. For this study, the divalent metal salts described in Table 3 were used, and Na 2 SO 4 was used as the control. The divalent metal ions were evaluated from 30 to 0. First crystals containing Zn were serendipitously obtained in the presence of a putative VEGFR ligand, the Laxaphycin B [ 13 , 57 ] that revealed to be absent from the electron density. Other divalent metal cations were intentionally introduced. Diffraction-quality crystals were optimized for three crystal forms: the first crystallized in the space group C 1 , from a drop containing 1 mM hVEGFR1d2, 0. The third crystal form crystallized in I space group from a drop containing 1.

    After initial rounds of refinement, two major peaks remained for each molecule in the 2F o -F c and F o -F c difference maps. The first peak corresponded to the cobalt ion, and the second peak corresponded to a distortion of the main chain between residues and An iterative omit map was calculated [ 63 ] to rebuilt this segment in the four molecules of the asymmetric unit.

    The second crystal structure was solved in the C 1 space group, with one molecule per asymmetric unit. An identical procedure was performed using the previously refined model as the search model. Signal amplitude of the multichannel analyzer: 80 counts at 9. The electronic density was consequently interpreted as a Zn atom, although no Zn was intentionally introduced in the crystallization drop. Signal amplitude of the multichannel analyzer: 50 counts at 7. The third crystal structure was solved in the I space group, with three molecules per asymmetric unit.

    The final refinement statistics for the three refined structures are summarized in Table 1. The absence of a concentration dependence of the scattering data was verified using three concentrations ranging from 1.