A new set of ionic radii in aqueous solution has been derived for lanthanoid(III) cations starting from a very accurate experimental determination of the ion-water distances obtained from extended X-ray absorption fine structure (EXAFS) data. At variance with previous results, a very regular trend has been obtained, as expected for this series of elements. A general procedure to compute ionic radii in solution by combining the EXAFS technique and molecular dynamics (MD) structural data has been developed. This method can be applied to other ions allowing one to determine ionic radii in solution with an accuracy comparable to that of the Shannon crystal ionic radii.

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.

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C2 symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species. This picture is fully consistent with X-ray absorption near-edge structure experimental data which unambiguously show the preference for a sevenfold instead of a sixfold coordination.

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.

From a specific definition of the roto-translational ͑external͒ and intramolecular ͑internal͒ coordinates, a constrained dynamics algorithm is derived for removing the roto-translational motions during molecular dynamics simulations, within the leap-frog integration scheme. In the paper the theoretical basis of this new method and its statistical mechanical consistency are reported, together with two applications.

Background: Virus-associated cell membrane proteins acquired by HIV-1 during budding may give information on the cellular source of circulating virions. In the present study, by applying immunosorting of the virus and of the cells with antibodies targeting monocyte (CD36) and lymphocyte (CD26) markers, it was possible to directly compare HIV-1 quasispecies archived in circulating monocytes and T lymphocytes with that present in plasma virions originated from the same cell types. Five chronically HIV-1 infected patients who underwent therapy interruption after prolonged HAART were enrolled in the study. The analysis was performed by the powerful technology of ultra-deep pyrosequencing after PCR amplification of part of the env gene, coding for the viral glycoprotein (gp) 120, encompassing the tropism-related V3 loop region. V3 amino acid sequences were used to establish heterogeneity parameters, to build phylogenetic trees and to predict co-receptor usage.

DNA topoisomerase I relaxes supercoiled DNA by the formation of a covalent intermediate in which the active-site tyrosine is transiently bound to the cleaved DNA strand. The antineoplastic agent camptothecin specifically targets DNA topoisomerase I, and several mutations have been isolated that render the enzyme camptothecin-resistant. The catalytic and structural dynamical properties of a human DNA topoisomerase I mutant in which Ala-653 in the linker domain was mutated into Pro have been investigated. The mutant is resistant to camptothecin and in the absence of the drug displays a cleavage-religation equilibrium strongly shifted toward religation. The shift is mainly because of an increase in the religation rate relative to the wild type enzyme, indicating that the unperturbed linker is involved in slowing religation. Molecular dynamics simulation indicates that the Ala to Pro mutation increases the linker flexibility allowing it to sample a wider conformational space. The increase in religation rate of the mutant, explained by means of the enhanced linker flexibility, provides an explanation for the mutant camptothecin resistance. DNA topoisomerase I (Top1p)1 catalyzes the relaxation of supercoiled DNA through the transient cleavage of one strand of a DNA duplex and is fundamental to processes such as replication, recombination, and transcription (1-4). The threedimensional structure of reconstituted and N-terminal truncated versions of human topoisomerase I (hTop1p) in complex with a 22-bp DNA molecule have shown that the enzyme is organized in multiple domains that "clamp" around the DNA molecule (5, 6). Changes in DNA topology are achieved by introducing a transient break in the phosphodiester bond of one strand in the duplex DNA. The phosphodiester bond energy is preserved during catalysis through the formation of a transient covalent phosphotyrosine bond between the catalytic Tyr-723 and the 3Ј end of the broken DNA strand. DNA relaxation has been proposed to proceed via "controlled rotation" in which the covalently bound enzyme holds one end of the DNA duplex and allows the end downstream of the cleavage site to rotate around the remaining phosphodiester bond (6). Eukaryotic Top1p is the cellular target of the anti-tumor drug camptothecin (CPT), which reversibly stabilizes the cleavable intermediate complex formed in the catalytic cycle of the enzyme (1, 2, 7).Recently Staker et al. (8) have solved the x-ray crystal structure of hTop1p covalently joined to double-stranded DNA and bound to the CPT analog Topotecan (8). This structure revealed that the drug molecule intercalates between upstream (Ϫ1) and downstream (ϩ1) bp, displacing the downstream DNA and thus preventing the religation of the cleaved strand. The structure helps to clarify the role of several, but not all, mutant residues that produce a CPT-resistant enzyme. In particular the structure permits to explain the CPT resistance for mutations involving residues that interact directly with the drug or that would alter the interaction with DNA...

Microtubules are dynamic cytoskeletal elements coordinating and supporting a variety of neuronal processes, including cell division, migration, polarity, intracellular trafficking, and signal transduction. Mutations in genes encoding tubulins and microtubule-associated proteins are known to cause neurodevelopmental and neurodegenerative disorders. Growing evidence suggests that altered microtubule dynamics may also underlie or contribute to neurodevelopmental disorders and neurodegeneration. We report that biallelic mutations in TBCD, encoding one of the five co-chaperones required for assembly and disassembly of the αβ-tubulin heterodimer, the structural unit of microtubules, cause a disease with neurodevelopmental and neurodegenerative features characterized by early-onset cortical atrophy, secondary hypomyelination, microcephaly, thin corpus callosum, developmental delay, intellectual disability, seizures, optic atrophy, and spastic quadriplegia. Molecular dynamics simulations predicted long-range and/or local structural perturbations associated with the disease-causing mutations. Biochemical analyses documented variably reduced levels of TBCD, indicating relative instability of mutant proteins, and defective β-tubulin binding in a subset of the tested mutants. Reduced or defective TBCD function resulted in decreased soluble α/β-tubulin levels and accelerated microtubule polymerization in fibroblasts from affected subjects, demonstrating an overall shift toward a more rapidly growing and stable microtubule population. These cells displayed an aberrant mitotic spindle with disorganized, tangle-shaped microtubules and reduced aster formation, which however did not alter appreciably the rate of cell proliferation. Our findings establish that defective TBCD function underlies a recognizable encephalopathy and drives accelerated microtubule polymerization and enhanced microtubule stability, underscoring an additional cause of altered microtubule dynamics with impact on neuronal function and survival in the developing brain.