Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport

Comparative homology modelling techniques have been used to model the protein ZnuA from Salmonella enterica serovar Typhimurium using the 3D structure of the homologous protein from Escherichia coli. These two-domain proteins bind one Zn²⁺ atom, with high affinity, in the inter-domain cleft and possess a histidine-rich loop in the N-terminal domain. Alternative structures of the ZnuA histidine-rich loop, never resolved by the X-ray diffraction method, have been modelled. A model of the apo form, one with the histidine-rich loop deleted and two alternative structures with a second zinc ion bound to the histidine-rich loop, have been generated. In all the modelled proteins, investigated through molecular dynamics simulation, the histidine-rich loop is highly mobile and its fluctuations are correlated to the ligand stability observed in the zinc sites. Based on the plasticity of the histidine-rich loop and its significant effects on protein mobility a possible role in the capture and/or transfer of the zinc ions has been suggested.     

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600?K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation.     

A Chaotic Circuit with Ferroelectric Nonlinearity

In this paper, the possibility of observing strange attractors in an electronic circuit including a nonlinear ferroelectric component has been investigated. The ferroelectric constitutes the medium interposed between the two plates of a capacitor. A circuit including the nonlinearity of the ferroelectric has been designed, while the parameters have been found by performing numerical integration with respect to different values of them. The circuit has been realized on a discrete components board. Experimental results, showing that for a suitable range of parameters a chaotic attractor emerges, are reported.     

Stacking interactions in the acridine dyes: spectrophotometric data and crystal structure of acridine orange hydroiodide and acridine orange hydrochloride monohydrate

The crystal structure of acridine orange hydroiodide and that of acridine orange hydrochloride monohydrate have been solved by X-ray diffraction analysis. The absorption spectra of both derivatives in the solid state have also been reported and compared with those of the acridinium ion in solution. The stacking interactions of the acridine orange molecule in both derivatives is discussed in the light of the visible absorption spectra in the solid state and in solution.     

Separation of human fibrinopeptides by capillary zone electrophoresis

We describe a method for the simultaneous determination of the five fibrinopeptide forms derived from the thrombin-promoted activation of human fibrinogen by capillary zone electrophoresis (CZE). The fibrinopeptide mixture was first desalted by a solid-phase extraction (SPE) step. The analysis was performed in reversed polarity in a highly cross-linked polyethylene glycol (PEG)-coated capillary with UV-light absorption detection at 200 nm. Several parameters including buffer concentration and pH, presence of an organic modifier, temperature, and applied voltage, have been tested. The best separations were obtained within 20 min, utilizing a 20 mM sodium phosphate buffer without organic modifier, in the narrow 6.1-6.2 pH range, at 25 degrees C, with an applied voltage of 20 kV. Quantitative analysis is made possible by the use of sheep fibrinopeptide A as an internal standard to correct for both extraction and injection errors.     

Controlling unpredictability in the randomly driven Hénon–Heiles system

Noisy scattering dynamics in the randomly driven Hénon–Heiles system is investigated in the range of initial energies where the motion is unbounded. In this paper we study, with the help of the exit basins and the escape time distributions, how an external perturbation, be it dissipation or periodic forcing with a random phase, can enhance or mitigate the unpredictability of a system that exhibit chaotic scattering. In fact, if basin boundaries have the Wada property, predictability becomes very complicated, since the basin boundaries start to intermingle, what means that there are points of different basins close to each other. The main responsible of this unpredictability is the external forcing with random phase, while the dissipation can recompose the basin boundaries and turn the system more predictable. Therefore, we do the necessary simulations to find out the values of dissipation and external forcing for which the exit basins present the Wada property. Through these numerical simulations, we show that the presence of the Wada basins have a specific relation with the damping, the forcing amplitude and the energy value. Our approach consists on investigating the dynamics of the system in order to gain knowledge able to control the unpredictability due to the Wada basins.     

Excited-State Dynamics of Thienoguanosine,an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^thG) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^thG exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto–amino tautomers. We herein investigate the photophysics of ^thG in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5–20.5 and 7–13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^thG, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.     

Molecular dynamics characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization

Aicardi–Goutières syndrome, a rare genetic disorder characterized by calcification of basal ganglia, results in psychomotor delays and epilepsy states from the early months of children life. This disease is caused by mutations in seven different genes encoding proteins implicated in the metabolism of nucleic acids, including SAMHD1. Twenty SAMHD1 gene variants have been discovered and in this work, a structural characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant is reported by classical molecular dynamics simulation. Four simulations have been carried out and compared. Two concerning the wild-type SAMHD1 form in presence and absence of cofactors, in order to explain the role of cofactors in the SAMHD1 assembly/disassembly process and, two concerning the Arg145Gln mutant, also in presence and absence of cofactors, in order to have an accurate comparison with the corresponding native forms. Results show the importance of native residue Arg145 in maintaining the tetramer, interacting with GTP cofactor inside allosteric sites. Replacement of arginine in glutamine gives rise to a loosening of GTP–protein interactions, when cofactors are present in allosteric sites, whilst in absence of cofactors, the occurrence of intra and inter-chain interactions is observed in the mutant, not seen in the native enzyme, making energetically unfavourable the tetramerization process.