Divalent Metal Binding Properties of the Methionyl Aminopeptidase from \u3cem\u3eEscherichia coli\u3c/em\u3e

The metal-binding properties of the methionyl aminopeptidase from Escherichia coli (MetAP) were investigated. Measurements of catalytic activity as a function of added Co(II) and Fe(II) revealed that maximal enzymatic activity is observed after the addition of only 1 equiv of divalent metal ion. Based on these studies, metal binding constants for the first metal binding event were found to be 0.3 ± 0.2 μM and 0.2 ± 0.2 μM for Co(II)- and Fe(II)-substituted MetAP, respectively. Binding of excess metal ions (\u3e50 equiv) resulted in the loss of ∼50% of the catalytic activity. Electronic absorption spectral titration of a 1 mM sample of MetAP with Co(II) provided a binding constant of 2.5 ± 0.5 mM for the second metal binding site. Furthermore, the electronic absorption spectra of Co(II)-loaded MetAP indicated that both metal ions reside in a pentacoordinate geometry. Consistent with the absorption data, electron paramagnetic resonance (EPR) spectra of [CoCo(MetAP)] also indicated that the Co(II) geometries are not highly constrained, suggesting that each Co(II) ion in MetAP resides in a pentacoordinate geometry. EPR studies on [CoCo(MetAP)] also revealed that at pH 7.5 there is no significant spin-coupling between the two Co(II) ions, though a small proportion (∼5%) of the sample exhibited detectable spin−spin interactions at pH values \u3e 9.6. EPR studies on [Fe(III)_(MetAP)] and [Fe(III)Fe(III)(MetAP)] also suggested no spin-coupling between the two metal ions. 1H nuclear magnetic resonance (NMR) spectra of [Co(II)_(MetAP)] in both H2O and D2O buffer indicated that the first metal binding site contains the only active-site histidine residue, His171. Mechanistic implications of the observed binding properties of divalent metal ions to the MetAP from E. coli are discussed

Structure and Metal Binding Properties of ZnuA, a Periplasmic Zinc Transporter from \u3cem\u3eEscherichia coli\u3c/em\u3e

ZnuA is the periplasmic Zn2+-binding protein associated with the high-affinity ATP-binding cassette ZnuABC transporter from Escherichia coli. Although several structures of ZnuA and its homologs have been determined, details regarding metal ion stoichiometry, affinity, and specificity as well as the mechanism of metal uptake and transfer remain unclear. The crystal structures of E. coli ZnuA (Eco-ZnuA) in the apo, Zn2+-bound, and Co2+-bound forms have been determined. ZnZnuA binds at least two metal ions. The first, observed previously in other structures, is coordinated tetrahedrally by Glu59, His60, His143, and His207. Replacement of Zn2+ with Co2+ results in almost identical coordination geometry at this site. The second metal binding site involves His224 and several yet to be identified residues from the His-rich loop that is unique to Zn2+ periplasmic metal binding receptors. Electron paramagnetic resonance and X-ray absorption spectroscopic data on CoZnuA provide additional insight into possible residues involved in this second site. The second site is also detected by metal analysis and circular dichroism (CD) titrations. Eco-ZnuA binds Zn2+ (estimated K d \u3c 20 nM), Co2+, Ni2+, Cu2+, Cu+, and Cd2+, but not Mn2+. Finally, conformational changes upon metal binding observed in the crystal structures together with fluorescence and CD data indicate that only Zn2+ substantially stabilizes ZnuA and might facilitate recognition of ZnuB and subsequent metal transfer

A tight-binding potential for atomistic simulations of carbon interacting with transition metals: Application to the Ni-C system

We present a tight-binding potential for transition metals, carbon, and transition metal carbides, which has been optimized through a systematic fitting procedure. A minimal basis, including the s, p electrons of carbon and the d electrons of the transition metal, is used to obtain a transferable tight-binding model of the carbon-carbon, metal-metal and metal-carbon interactions applicable to binary systems. The Ni-C system is more specifically discussed. The successful validation of the potential for different atomic configurations indicates a good transferability of the model and makes it a good choice for atomistic simulations sampling a large configuration space. This approach appears to be very efficient to describe interactions in systems containing carbon and transition metal elements

Synthesis and inclusion behavior of a heterotritopic receptor based on hexahomotrioxacalix[3]arene

A heterotritopic hexahomotrioxacalix[3]arene receptor with the capability of binding two alkali metals and a transition metal in a cooperative fashion was synthesized. The binding model was investigated by using ¹H NMR titration experiments in CDCl₃–CD₃CN (10:1, v/v), and the results revealed that the transition metal was bound at the upper rim and the alkali metals at the lower and upper rims. Interestingly, the alkali metal ions Li⁺ and Na⁺ bind at the lower and upper rim respectively depending on the dimensions of the alkali metal ions versus the size of the cavities formed by the calix[3]arene derivative. The hexahomotrioxacalix[3]arene receptor acts as a heterotritopic receptor, binding with the transition metal ion Ag⁺ and the alkali metals ions Li⁺ and Na⁺. These findings were not applicable to other different sized alkali metals, such as K⁺ and Cs⁺

Root-induced decrease in metal binding capacity of dissolved organic matters in the rhizosphere: evidences from two convergent studies : S10.01b -1

The parallel understanding of dissolved organic matters (DOM) impact on trace metal speciation in soil and root ability to change DOM concentration and composition in the rhizosphere strongly suggests a substantial alteration of metal binding capacity of DOM in the rhizosphere, with consequent impacts on metal phytoavailability. This hypothesis is investigated in the present communication on the basis of two independent set of experiments. Both experiments used the RHIZOtest experimental set-up, which enables an easy and fast recovery of both plants (i.e. shoots and roots) and rhizosphere, to grown either lettuce (Lactuca sativa) or durum wheat (Triticum turgidum durum) on two different soil samples notably varying in pH, organic matter content and geographical origin (tropical vs. temperate area). Usual chemical properties (i.e. pH, concentration of DOM, major cations/anions and metals) and free copper activity were measured in the rhizosphere solution. Copper speciation was then modelled in the rhizosphere solution with the humic ion-binding model VI (Model VI) by adjusting the metal binding capacity of DOM to fit experimental data. Compared with bulk soil measurements, a large increase in both pH and DOM concentration was observed in durum wheat rhizosphere while these two parameters did not change significantly in lettuce rhizosphere. Alternatively, the fraction of DOM involved in copper binding decreased similarly by 40 % in both durum wheat and lettuce rhizosphere. These very convergent pictures of a decrease in metal binding capacity of DOM in both experiments lead to discuss the hypothetical governing mechanisms and the genericity of this finding. (Texte intégral

\u3cem\u3eArabidopsis thaliana\u3c/em\u3e GLX2-1 Contains a Dinuclear Metal Binding Site, but Is Not a Glyoxalase 2

In an effort to probe the structure and function of a predicted mitochondrial glyoxalase 2, GLX2-1, from Arabidopsis thaliana, GLX2-1 was cloned, overexpressed, purified and characterized using metal analyses, kinetics, and UV–visible, EPR, and 1H-NMR spectroscopies. The purified enzyme was purple and contained substoichiometric amounts of iron and zinc; however, metal-binding studies reveal that GLX2-1 can bind nearly two equivalents of either iron or zinc and that the most stable analogue of GLX2-1 is the iron-containing form. UV–visible spectra of the purified enzyme suggest the presence of Fe(II) in the protein, but the Fe(II) can be oxidized over time or by the addition of metal ions to the protein. EPR spectra revealed the presence of an anti-ferromagnetically-coupled Fe(III)Fe(II) centre and the presence of a protein-bound high-spin Fe(III) centre, perhaps as part of a FeZn centre. No paramagnetically shifted peaks were observed in 1H-NMR spectra of the GLX2-1 analogues, suggesting low amounts of the paramagnetic, anti-ferromagnetically coupled centre. Steady-state kinetic studies with several thiolester substrates indicate that GLX2-1 is not a GLX2. In contrast with all of the other GLX2 proteins characterized, GLX2-1 contains an arginine in place of one of the metal-binding histidine residues at position 246. In order to evaluate further whether Arg246 binds metal, the R246L mutant was prepared. The metal binding results are very similar to those of native GLX2-1, suggesting that a different amino acid is recruited as a metal-binding ligand. These results demonstrate that Arabidopsis GLX2-1 is a novel member of the metallo-β-lactamase superfamily

Towards a model of non-equilibrium binding of a metal ion in a biological system

We have used a systems biology approach to address the hitherto insoluble problem of the quantitative analysis of non-equilibrium binding of aqueous metal ions by competitive ligands in heterogeneous media. To-date, the relative proportions of different metal complexes in aqueous media have only been modelled at chemical equilibrium and there are no quantitative analyses of the approach to equilibrium1. While these models have improved our understanding of how metals are used in biological systems they cannot account for the influence of kinetic factors in metal binding, transport and fate2. Here we have modelled the binding of aluminium in blood serum by the iron transport protein transferrin (Tf) as it is widely accepted that the biological fate of this non-essential metal is not adequately described by experiments, in vitro and in silico, which have consistently demonstrated that at equilibrium 90% of serum Al(III) is bound by Tf3-5. We have coined this paradox 'the blood-aluminium problem'6 and herein applied a systems biology approach which utilised well-found assumptions to pare away the complexities of the problem such that it was defined by a comparatively simple set of computational rules and, importantly, its solution assumed significant predictive capabilities. Here we show that our novel computational model successfully described the binding of Al(III) by Tf both at equilibrium and as equilibrium for AlTf was approached. The model provided an explanation of why the distribution of Al(III) in the body cannot be adequately described by its binding and transport by Tf and it highlighted the significance of kinetic in addition to thermodynamic constraints in defining the fate of metal ions in biological systems. This is the first model of non-equilibrium metal binding in a biological system and it should prove to be a valuable predictive tool in furthering our understanding of the bioinorganic chemistry of metals