Giordano Mancini

A Coupled Molecular Dynamics and XANES Data Analysis Investigation of Aqueous Cadmium(II)

The flexible nature of the first hydration shell of the cadmium(II) ion has been definitively assessed through an extensive study, combining X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations. The structural and dynamic properties of the cadmium(II) hydration shell have been determined from long-time MD simulations, and the influence of water-water interactions has been evaluated using the SPC/E and TIP5P water models. Comparison of the theoretical results with EXAFS data suggests that the TIP5P simulation provides a better description of the cadmium(II) hydration properties. XANES spectra have been computed starting from MD trajectories, without carrying out any minimization in the structural parameter space. The octahedral solvation of cadmium(II) in aqueous solution cannot be reconciled with the XANES results, while a flexible hydration shell is fully consistent with the experimental data, which unambiguously show the presence of a dominant percentage of heptahydrated species.

Structural and Dynamical Properties of the Hg2+ Aqua Ion: A Molecular Dynamics Study

Molecular dynamics simulations of the Hg2+ ion in aqueous solution have been carried out using an effective two-body potential derived from quantum mechanical calculations. A stable heptacoordinated structure of the Hg2+ first hydration shell has been observed and confirmed by extended X-ray absorption fine structure (EXAFS) experimental data. The structural properties of the Hg2+ hydration shells have been investigated using radial and angular distribution functions, while the dynamical behavior has been discussed in terms of reorientational correlation functions, mean residence times of water molecules in the first and second hydration shells, and self-diffusion coefficients. The effect of water-water interactions on the Hg2+ hydration properties has been evaluated using the SPC/E and TIP5P water models.

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions.

The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the 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.

Structural Investigation of Lanthanoid Coordination: a Combined XANES and Molecular Dynamics Study

This is the first systematic study exploring the potentiality of the X-ray absorption near edge structure (XANES) technique as a structural tool for systems containing lanthanoid(III) ions. A quantitative analysis of the XANES spectra at the K- and L(3)-edges has been carried out for three hydrated lanthanoid(III) ions, namely, Yb, Nd, and Gd, in aqueous solution and in the isostructural trifluoromethanesulfonate salts. The structural and dynamic properties of the hydrated lanthanoid(III) ions in aqueous solution have been investigated by a combined experimental-theoretical approach employing X-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the XANES spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. A comparative K- and L(3)-edge XANES data analysis is presented, demonstrating the clear advantages of the L(3)-edge XANES analysis over the K-edge studies for structural investigations of lanthanoid compounds. The second hydration shells provide a detectable contribution to the L(3)-edge spectra while the K-edge data are insensitive to the more distant coordination spheres because of the strong damping and broadening of the signal caused by the extremely large core hole widths. The XANES technique has been found to be a new valuable tool for the structural characterization of metal complexes both in the solid and in the liquid state, especially in the presence of low symmetry.

An X-Ray Diffraction and X-Ray Absorption Spectroscopy Joint Study of Neuroglobin.

Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in neuroprotection. A combined approach of X-ray diffraction (XRD) on single crystal and X-ray absorption spectroscopy (XAS) in solution, allows to determine the oxidation state and the structure of the Fe-heme both in the bis-histidine and the CO-bound (NgbCO) states. The overall data demonstrate that under X-ray the iron is photoreduced fairly rapidly, and that the previously reported X-ray structure of ferric Ngb [B. Vallone, K. Nienhaus, M. Brunori, G.U. Nienhaus, Proteins 56 (2004) 85-92] very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal. However prolonged X-ray exposure at 15K determines CO release. This preliminary result paves the way to experiments aimed at the characterization of pentacoordinate ferrous Ngb, the only species competent in binding external ligands such as O2, CO or NO.

Effect of the Zn2+ and Hg2+ ions on the structure of liquid water.

The effect of ions on the structure of liquid water is still not completely understood, despite extensive experimental and theoretical studies. A combined XANES and molecular dynamics investigation on diluted Zn(2+) and Hg(2+) aqueous solutions reveals that the influence of a single ion on the bonding pattern of water molecules is strongly dependent on the nature of the ion. While the structure of water is not altered by the presence of the Zn(2+) ion, the Hg(2+) cation has a strong impact on the hydrogen-bond network of water that extends beyond the first coordination shell.

Identification of a Short Region on Chromosome 6 Affecting Direct Calving Ease in Piedmontese Cattle Breed

Calving in cattle is affected by calf morphology and by dam characteristics. It is described by two different traits: maternal calving ease, which is the ability to generate dams with good physiological predisposition to calving, and direct calving ease, which is the ability to generate calves that are easily born. The aim of this study was to identify regions of cattle genome harboring genes possibly affecting direct calving ease in the Piedmontese cattle breed. A population of 323 bulls scored for direct calving ease (EBV) was analyzed by a medium-density SNP marker panel (54,001 SNPs) to perform a genome-wide scan. The strongest signal was detected on chromosome 6 between 37.8 and 38.7 Mb where 13 SNPs associated to direct calving ease were found. Three genes are located in this region: LAP3, encoding for a leucine aminopeptidase involved in the oxytocin hydrolysis; NCAPG, encoding for a non-SMC condensin I complex, which has been associated in cattle with fetal growth and carcass size; and LCORL, which has been associated to height in humans and cattle. To further confirm the results of the genome-wide scan we genotyped additional SNPs within these genes and analyzed their association with direct calving ease. The results of this additional analysis fully confirmed the findings of the GWAS and particularly indicated LAP3 as the most probable gene involved. Linkage Disequilibrium (LD) analysis showed high correlation between SNPs located within LAP3 and LCORL indicating a possible selection signature due either to increased fitness or breeders’ selection for the trait.

UV-Vis Spectra of the Anticancer Campothecin Family Drugs in Aqueous Solution: Specific Spectroscopic Signatures Unraveled by a Combined Computational and Experimental Study

The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.

Structural and dynamical effects induced by the anticancer drug topotecan on the human topoisomerase I - DNA complex

Background Human topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation. It is the only target of the camptothecin family of anticancer drugs. Among these, topotecan has been used to treat lung and ovarian carcinoma for several years. Camptothecins reversibly binds to the covalent intermediate DNA-enzyme, stabilizing the cleavable complex and reducing the religation rate. The stalled complex then collides with the progression of the replication fork, producing lethal double strand DNA breaks and eventually cell death. Methodology/Principal Findings Long lasting molecular dynamics simulations of the DNA-topoisomerase I binary complex and of the DNA-topoisomerase-topotecan ternary complex have been performed and compared. The conformational space sampled by the binary complex is reduced by the presence of the drug, as observed by principal component and cluster analyses. This conformational restraint is mainly due to the reduced flexibility of residues 633–643 (the region connecting the linker to the core domain) that causes an overall mobility loss in the ternary complex linker domain. During the simulation, DNA/drug stacking interactions are fully maintained, and hydrogen bonds are maintained with the enzyme. Topotecan keeps the catalytic residue Lys532 far from the DNA, making it unable to participate to the religation reaction. Arg364 is observed to interact with both the B and E rings of topotecan with two stable direct hydrogen bonds. An interesting constrain exerted by the protein on the geometrical arrangement of topotecan is also observed. Conclusions/Significance Atomistic-scale understanding of topotecan interactions with the DNA-enzyme complex is fundamental to the explaining of its poisonous effect and of the drug resistance observed in several single residue topoisomerase mutants. We observed significant alterations due to topotecan in both short-range interactions and long-range protein domain communications.

Hydration Properties of the Zn2+ Ion in Water at High Pressure

The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. Modification of the hydration properties of the Zn(2+) ion induced by a pressure increase from ambient condition up to ∼6.4 GPa has been revealed and accurately analyzed. With increasing pressure the first hydration shell of the Zn(2+) ion has been found to retain an octahedral symmetry with a shortening of the Zn-O distance up to 0.09 Å and an increased width associated with thermal motion, as compared to the ambient condition hydration complex. A very interesting picture of the dynamic behavior of the first hydration shell has emerged from the analysis of the simulations: up to 2.5 GPa no exchange events between first and second shell water molecules occurred, while above this pressure value several exchange events take place in the solution following an associative interchange mechanism. This result can be explained by the very high compression and packing of the solvent which force second shell water molecules to enter the Zn(2+) first hydration shell. MD simulations indicate a strong pressure effect also on the structure of the second coordination shell which is compressed and becomes more disordered and less structured with increasing pressure. The water mobility and the ion diffusion coefficient have been found to increase in the high density conditions, as a consequence of the rupture of the hydrogen bond network caused by pressure.