Biomedical subjects

Paola D'Angelo

Publications and source records attributed to Paola D'Angelo.

13 recordsLinked to original sources

PubMed2006

A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).

We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.

Cations, Divalent↗

PubMed2006

Detection of second hydration shells in ionic solutions by XANES: computed spectra for Ni2+ in water based on molecular dynamics.

A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space. A very good reproduction of the experimental data was obtained including the second-shell water molecules in the calculation, thus showing that the second hydration shell provides a detectable contribution to the XANES spectra of ionic solutions. The analysis including the first-shell cluster only permitted us to quantitatively determine the effect of disorder on the amplitude of the XANES spectra for molecular complexes. These results simultaneously confirm the reliability of the procedure and the structural results obtained from MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

Journal Article↗

PubMed2005

X-ray absorption investigation of a unique protein domain able to bind both copper(I) and copper(II) at adjacent sites of the N-terminus of Haemophilus ducreyi Cu,Zn superoxide dismutase.

The N-terminal metal binding extension of the Cu,Zn superoxide dismutase from Haemophilus ducreyi is constituted by a histidine-rich region followed by a methione-rich sequence which shows high similarity with protein motifs involved in the binding of Cu(I). X-ray absorption spectroscopy experiments selectively carried out with peptides corresponding to the two metal binding regions indicate that both sequences can bind either Cu(II) or Cu(I). However, competition experiments demonstrate that Cu(II) is preferred by histidine residues belonging to the first half of the motif, while the methionine-rich region preferentially binds Cu(I) via the interaction with three methionine sulfur atoms. Moreover, we have observed that the rate of copper transfer from the peptides to the active site of a copper-free form of the Cu,Zn superoxide dismutase mutant lacking the N-terminal extension depends on the copper oxidation state and on the residues involved in metal binding, histidine residues being critically important for the efficient transfer. Differences in the enzyme reactivation rates in the presence of mixtures of the two peptides when compared to those obtained with the single peptides suggest that the two halves of the N-terminal domain functionally interact during the process of copper transfer, possibly through subtle modifications of the copper coordination environment.

Binding Sites↗

PubMed2005

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution.

A combined extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS) investigation has been performed to evaluate the coordination structure of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea (dmpu) solutions. This approach has singled out the existence of a flexible coordination shell around the cadmium(II) ion in aqueous and dimethyl sulfoxide solutions, whereas a regular octahedral complex is detected in dmpu. The EXAFS and LAXS techniques provide different values of the Cd-O first shell distance (2.27(1) A and 2.302(5) A, respectively) for the hydrated and dimethyl sulfoxide solvated complexes, and this discrepancy is originated by the simultaneous presence of hexa- and heptacoordinated complexes in solution, giving rise to a broad distribution of distances around the ion. These findings demonstrate that, in solution, the cadmium(II) ion forms quite flexible hydration and dimethyl sulfoxide solvate complexes undergoing a solvent exchange with unusually stable seven-coordinated intermediate complexes, and therefore the mean ion-solvent distance is longer in solution than in the solid state. In the dmpu solution, due to the bulkiness of the solvent molecules, the octahedral cadmium(II) solvate is extremely crowded and it is not possible for a seventh ligand to enter the inner-coordination shell. This investigation shows that the combined analysis of the EXAFS and LAXS data allows a reliable determination of the structural properties of electrolyte solutions, also in the presence of flexible coordination shell with a variable number of coordinating molecules.

Cadmium↗

PubMed2005

Computational evidence for a variable first shell coordination of the cadmium(II) ion in aqueous solution.

In this paper, we present a state-of-the-art 100 ns molecular dynamics simulation of a cadmium(II) aqueous solution that highlights a very flexible ion first coordination shell which transits between hexa- and heptahydrated complexes. From this investigation, a dynamical picture of the water exchange process emerges that takes place through an associative mechanism for the solvent substitution reaction. Our procedure starts from the generation of an effective two-body potential from quantum mechanical ab initio calculations in which the many-body ion-water terms are accounted for by the polarizable continuum method (PCM). This approach is computationally very efficient and has allowed us to carry out extremely long molecular dynamics simulations, indispensable to reproduce the dynamic properties of the cadmium(II) aqueous solution. Quantum mechanical ab initio calculations of the hexa- and heptahydrated complexes extracted from MD configurations have revealed stable minima for both clusters with the water molecules arranged in T(h)() and C(2) symmetries in the hexa- and heptahydrated complexes, respectively, with a slight energetic preference for the heptahydrated one. Finally, a comparison of the calculated hexa- and heptahydrated cluster IR and Raman spectra with the experimental data in the literature, has demonstrated that the IR spectroscopy is not able to distinguish between the two species, whereas the Raman spectrum of the Cd(2+)-(H(2)O)(7) cluster provides a better agreement with the experimental data.

Journal Article↗

PubMed2005

The solution structure of [Cu(aq)]2+ and its implications for rack-induced bonding in blue copper protein active sites.

The structure of [Cu(aq)]2+ has been investigated by using full multiple-scattering theoretical (MXAN) analysis of the copper K-edge X-ray absorption (XAS) spectrum and density functional theory (DFT) to test both ideal Td and square-planar four-coordinate, five-coordinate square-pyramidal, and six-coordinate octahedral [Cu(aq)]2+ models. The best fit was an elongated five-coordinate square pyramid with four Cu-O(eq) bonds (2 x 1.98 +/- 0.03 A and 2 x 1.95 +/- 0.03 A) and a long Cu-O(ax) bond (2.35 +/- 0.05 A). The four equatorial ligands were D2d-distorted from the mean equatorial plane by +/-(17 +/- 4) degrees, so that the overall symmetry of [Cu(H2O)5]2+ is C2v. The four-coordinate MXAN fit was nearly as good, but the water ligands (4 x 1.96 +/- 0.02 A) migrated +/-(13 +/- 4) degrees from the mean equatorial plane, making the [Cu(H2O)4]2+ model again D2d-distorted. Spectroscopically calibrated DFT calculations were carried out on the C2v elongate square-pyramidal and D2d-distorted four-coordinate MXAN copper models, providing comparative electronic structures of the experimentally observed geometries. These calculations showed 0.85e spin on Cu(II) and 0.03e electron spin on each of the four equatorial water oxygens. All covalent bonding was restricted to the equatorial plane. In the square-pyramidal model, the electrostatic Cu-O(ax) bond was worth only 96.8 kJ mol(-1), compared to 304.6 kJ mol(-1) for each Cu-O(eq) bond. Both MXAN and DFT showed the potential well of the axial bond to be broad and flat, allowing large low-energy excursions. The irregular geometry and D2d-distorted equatorial ligand set sustained by unconstrained [Cu(H2O)5]2+ warrants caution in drawing conclusions regarding structural preferences from small molecule crystal structures and raises questions about the site-structural basis of the rack-induced bonding hypothesis of blue copper proteins. Further, previously neglected protein folding thermodynamic consequences of the rack-bonding hypothesis indicate an experimental disconfirmation.

Algorithms↗

PubMed2004

Quantitative analysis of XANES spectra of disordered systems based on molecular dynamics.

A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting from the individual configurations obtained from molecular dynamics (MD) simulations has been developed. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems and to estimate the effect of disorder on the low-energy region of the X-ray absorption spectra. As a test case, a Ni2+ aqueous solution has been investigated. The configurational averaged XANES theoretical spectrum obtained from the MD configurations compares well with the experimental data. This confirms simultaneously the reliability of the procedure and of the structural results obtained from the MD simulation.

Metalloproteins↗

PubMed2004

Full quantitative multiple-scattering analysis of X-ray absorption spectra: application to potassium hexacyanoferrat(II) and -(III) complexes.

A recently developed method to the full quantitative analysis of the XAS spectra extending from the absorption edge to the high-energy region is presented. This method is based on the use of two independent approaches to the analysis of the EXAFS and XANES data, the well-known GNXAS and the newly developed MXAN procedures. Herein, we report the application of this technique to two iron complexes of known structure where multiple-scattering effects are prominent, the potassium hexacyanoferrat(II) and -(III) crystals and aqueous solutions. The structural parameters obtained from refinements using the two methods are equal and compare quite well with crystallographic values. Small discrepancies between the experimental and calculated XANES spectra have been observed, and their origin has been investigated in the framework of non-muffin-tin correction. The ligand dependence of the theoretical spectra has been also examined. Analysis of the whole energy range of the XAS spectra has been found to be useful in elucidating both the type of ligands and the geometry of iron sites. These results are of particular use in studying the geometrical environment of metallic sites in proteins and complexes of chemical interest.

Journal Article↗

PubMed2004

Structure of the hydrated and dimethyl sulfoxide solvated rubidium ions in solution.

The structure of the hydrated and the dimethyl sulfoxide solvated rubidium ions in solution has been determined by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) studies. The models of the hydrated and dimethyl sulfoxide solvated rubidium ions fitting the experimental data best are square antiprisms with Rb-O bond distances of 2.98(2) and 2.98(3) A, respectively. The EXAFS data show a significant asymmetry in the Rb-O bond distance distribution with C(3) values of 0.0076 and 0.015 A(3), respectively. No second hydration sphere is observed around the hydrated rubidium ion. The dimethyl sulfoxide solvated rubidium ion displays a Rb-O-S bond angle of ca. 130 degrees, which is typical for a medium hard electron acceptor such as rubidium.

Cations↗

PubMed2004

Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin.

Escherichia coli flavohemoglobin is endowed with the notable property of binding specifically unsaturated and/or cyclopropanated fatty acids both as free acids or incorporated into a phospholipid molecule. Unsaturated or cyclopropanated fatty acid binding to the ferric heme results in a spectral change observed in the visible absorption, resonance Raman, extended x-ray absorption fine spectroscopy (EXAFS), and x-ray absorption near edge spectroscopy (XANES) spectra. Resonance Raman spectra, measured on the flavohemoglobin heme domain, demonstrate that the lipid (linoleic acid or total lipid extracts)-induced spectral signals correspond to a transition from a five-coordinated (typical of the ligand-free protein) to a hexacoordinated, high spin heme iron. EXAFS and XANES measurements have been carried out both on the lipid-free and on the lipid-bound protein to assign the nature of ligand in the sixth coordination position of the ferric heme iron. EXAFS data analysis is consistent with the presence of a couple of atoms in the sixth coordination position at 2.7 A in the lipid-bound derivative (bonding interaction), whereas a contribution at 3.54 A (nonbonding interaction) can be singled out in the lipid-free protein. This last contribution is assigned to the CD1 carbon atoms of the distal LeuE11, in full agreement with crystallographic data on the lipid-free protein at 1.6 A resolution obtained in the present work. Thus, the contributions at 2.7 A distance from the heme iron are assigned to a couple of carbon atoms of the lipid acyl chain, possibly corresponding to the unsaturated carbons of the linoleic acid.

Cloning, Molecular↗

PubMed2003

Ion hydration under pressure.

The pressure dependence of the radial distribution of water oxygen atoms around Rb+ and Br- ions in a diluted RbBr aqueous solution has been investigated by means of x-ray absorption spectroscopy at the Br and Rb K edges up to 2.8 GPa, using a large-volume high-pressure setup developed at a third generation synchrotron radiation facility. Dramatic effects in the anion hydration structure, in particular, are observed, indicating that upon increasing pressure water undergoes a structural transformation which involves considerable molecular reorientation.

Journal Article↗

PubMed2002

Hydrogen and higher shell contributions in Zn2+, Ni2+, and Co2+ aqueous solutions: an X-ray absorption fine structure and molecular dynamics study.

A detailed investigation of the hydration structure of Zn2+, Ni2+, and Co2+ in water solutions has been carried out combining X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. The first quantitative analysis of EXAFS from hydrogen atoms in 3d transition metal ions in aqueous solutions has been carried out and the ion-hydrogen interactions have been found to provide a detectable contribution to the EXAFS spectra. An accurate determination of the structural parameters associated with the first hydration shell has been performed and compared with previous experimental results. No evidence of significant contributions from the second hydration shell to the EXAFS signal has been found for these solutions, while the inclusion of the hydrogen signal has been found to be important in performing a quantitative analysis of the experimental data. The high-frequency contribution present in the EXAFS spectra has been found to be due to multiple scattering (MS) effects inside the ion-oxygen first coordination shell. MD has been used to generate three-body distribution functions from which a reliable analysis of the MS contributions to the EXAFS spectra of these systems has been carried out.

Journal Article↗

PubMed2002

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions.

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.

Journal Article↗