Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study.

The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.

Disentangling time-focusing from beam divergence: A novel approach for high-flux thermal neutron spectroscopy at continuous and long-pulse sources.

We present the concept of a novel time-focusing technique for neutron spectrometers, which allows us to disentangle time-focusing from beam divergence. The core of this approach is a double rotating-crystal monochromator that can be used to extract a larger wavelength band from a white beam, thus providing a higher flux at the sample compared to standard time-of-flight instruments, yet preserving energy resolution and beam collimation. The performances of a spectrometer based on this approach are quantitatively discussed in terms of possible incident wavelengths, flux at the sample, and (Q, E)-resolution. Analytical estimates suggest flux gains of about one order of magnitude at comparable resolutions in comparison to conventional time-of-flight spectrometers. Moreover, the double monochromator configuration natively shifts the sample away from the source line-of-sight, thus significantly improving the signal-to-noise ratio. The latter, in combination with a system that does not increase the beam divergence, brings the further advantage of a cleaner access to the low-Q region, which is recognized to be of fundamental interest for magnetism and for disordered materials, from glasses to biological systems.

Protein-Polymer Dynamics as Affected by Polymer Coating and Interactions.

We investigate the relaxation dynamics of protein-polymer conjugates by neutron scattering spectroscopy to understand to which extent the coating of a protein by a polymer can replace water in promoting thermal structural fluctuations. For this purpose, we compare the dynamics of protein-polymer mixtures to that of conjugates with a variable number of polymers covalently attached to the protein. Results show that the flexibility of the protein is larger in protein-polymer mixtures than in native protein or in conjugates, even in the dry state. Upon hydration, both the native protein and the conjugate show equivalent dynamics, suggesting that the polymer grafted on the protein surface adsorbs all water molecules.

All-DNA System Close to the Percolation Threshold.

We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.

A high-flux upgrade for the BRISP spectrometer at ILL.

To date, the BRISP spectrometer represents the state-of-the-art for every instrument aiming to perform Brillouin neutron scattering. Exploiting accurate ray-tracing McStas simulations, we investigate an improved configuration of the BRISP primary spectrometer to provide a higher flux at the sample position, while preserving all the present capabilities of the instrument. This configuration is based on a neutron guide system and is designed to fit the instrument platform with no modifications of the secondary spectrometer. These evaluations show that this setup can achieve a flux gain factor ranging from 3 to 6, depending on the wavelength. This can expand the experimental possibilities of BRISP towards smaller samples, possibly using also complex sample environments.

SANS investigation of water adsorption in tunable cyclodextrin-based polymeric hydrogels.

The focus of this work is on addressing how the adsorption properties of cyclodextrin (CD) based polymeric hydrogels (cyclodextrin nanosponges, CDNS) can be regulated by a precise control of a crucial parameter such as the characteristic pore size of the polymer network. With this aim, Small Angle Neutron Scattering (SANS) experiments are performed on different CDNS polymer formulations, differing by (i) the chemical structure of the cross-linking agent used for the polymerization of CD, which affects the flexibility of the strands between two crosslinking junctions, (ii) the relative molar ratio of cross-linker to monomer, affecting the cross-linking density, and (iii) the dimension of the CD macrocycle, regulating the steric hindrance and number of available reactive sites on the monomer. The analysis of the experimental data in terms of a two-correlation-length model allows one to extract a correlation length ζ that is interpreted as an experimental assessment of the average mesh-size of the cross-linked polymer, confirming the effective nano-size of the cavities formed in the network of CDNS. The hydration-dependence of ζ is modelled by an empirical functional form, that provides as key parameters the swelling rate of the polymeric network and the upper limit for the mesh size of the material. These parameters are useful for the characterization of the dynamic response of the hydrogel to swelling and the maximum mesh size compatible with the chemical structure of the polymer.

Dynamics of hydrated proteins and bio-protectants: Caged dynamics, ß-relaxation, and α-relaxation.

BACKGROUND: The properties of the three dynamic processes, α-relaxation, ν-relaxation, and caged dynamics in aqueous mixtures and hydrated proteins are analogous to corresponding processes found in van der Waals and polymeric glass-formers apart from minor differences. METHODS: Collection of various experimental data enables us to characterize the structural α-relaxation of the protein coupled to hydration water (HW), the secondary or ν-relaxation of HW, and the caged HW process. RESULTS: From the T-dependence of the ν-relaxation time of hydrated myoglobin, lysozyme, and bovine serum albumin, we obtain Ton at which it enters the experimental time windows of Mössbauer and neutron scattering spectroscopies, coinciding with protein dynamical transition (PDT) temperature Td. However, for all systems considered, the α-relaxation time at Ton or Td is many orders of magnitude longer. The other step change of the mean-square-displacement (MSD) at Tg_alpha originates from the coupling of the nearly constant loss (NCL) of caged HW to density. The coupling of the NCL to density is further demonstrated by another step change at the secondary glass temperature Tg_beta in two bio-protectants, trehalose and sucrose. CONCLUSIONS: The structural α-relaxation plays no role in PDT. Since PDT is simply due to the ν-relaxation of HW, the term PDT is a misnomer. NCL of caged dynamics is coupled to density and show transitions at lower temperature, Tg_beta and Tg_alpha. GENERAL SIGNIFICANCE: The so-called protein dynamical transition (PDT) of hydrated proteins is not caused by the structural α-relaxation of the protein but by the secondary ν-relaxation of hydration water. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars.

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: a neutron scattering study.

The dynamics of the human oligonucleotide AG3(T2AG3)3 has been investigated by incoherent neutron scattering in the sub-nanosecond timescale. A hydration-dependent dynamical activation of thermal fluctuations in weakly hydrated samples was found, similar to that of protein powders. The amplitudes of such thermal fluctuations were evaluated in two different exchanged wave-vector ranges, so as to single out the different contributions from intra- and inter-nucleotide dynamics. The activation energy was calculated from the temperature-dependent characteristic times of the corresponding dynamical processes. The trends of both amplitudes and activation energies support a picture where oligonucleotides possess a larger conformational flexibility than long DNA sequences. This additional flexibility, which likely results from a significant relative chain-end contribution to the average chain dynamics, could be related to the strong structural polymorphism of the investigated oligonucleotides.

Collective ion dynamics in liquid zinc: evidence for complex dynamics in a non-free-electron liquid metal.

A detailed inelastic neutron scattering investigation of the THz dynamics of liquid zinc is presented. The observed Q dependence clearly reveals the existence of a complex dynamics made up of two distinct excitations. The highest energy mode is the prolongation of the longitudinal acoustic density fluctuations whereas the comparison with the phonon dynamics of crystalline hcp zinc suggests a transverse acousticlike nature for the second one. This mode seems related to peculiar anisotropic interactions, possibly connected to the behavior of the crystalline phase.

Terahertz Dynamics in Human Cells and Their Chromatin.

The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.

Change of caged dynamics at T(g) in hydrated proteins: trend of mean squared displacements after correcting for the methyl-group rotation contribution.

The question whether the dynamics of hydrated proteins changes with temperature on crossing the glass transition temperature like that found in conventional glassformers is an interesting one. Recently, we have shown that a change of temperature dependence of the mean square displacement (MSD) at Tg is present in proteins solvated with bioprotectants, such as sugars or glycerol with or without the addition of water, coexisting with the dynamic transition at a higher temperature Td. The dynamical change at Tg is similar to that in conventional glassformers at sufficiently short times and low enough temperatures, where molecules are mutually caged by the intermolecular potential. This is a general and fundamental property of glassformers which is always observed at or near Tg independent of the energy resolution of the spectrometer, and is also the basis of the dynamical change of solvated proteins at Tg. When proteins are solvated with bioprotectants they show higher Tg and Td than the proteins hydrated by water alone, due to the stabilizing action of excipients, thus the observation of the change of T-dependence of the MSD at Tg is unobstructed by the methyl-group rotation contribution at lower temperatures [S. Capaccioli, K. L. Ngai, S. Ancherbak, and A. Paciaroni, J. Phys. Chem. B 116, 1745 (2012)]. On the other hand, in the case of proteins hydrated by water alone unambiguous evidence of the break at Tg is hard to find, because of their lower Tg and Td. Notwithstanding, in this paper, we provide evidence for the change at Tg of the T-dependence of proteins hydrated by pure water. This evidence turns out from (i) neutron scattering experimental investigations where the sample has been manipulated by either full or partial deuteration to suppress the methyl-group rotation contribution, and (ii) neutron scattering experimental investigations where the energy resolution is such that only motions with characteristic times shorter than 15 ps can be sensed, thus shifting the onset of both the methyl-group rotation and the dynamic transition contribution to higher temperatures. We propose that, in general, coexistence of the break of the elastic intensity or the MSD at Tg with the dynamic transition at Td in hydrated and solvated proteins. Recognition of this fact helps to remove inconsistency and conundrum encountered in interpreting data of hydrated proteins that thwart progress in understanding the origin of the dynamic transition.

Mediastinal parathyroid adenoma: a case report.

Ectopic parathyroid adenomas represent a diagnostic challenge, since they are quite rare in clinical practice. We present a case of a 61 years old man with symptomatic hypercalcemia due to an ectopic parathyroid adenoma in the upper-anterior mediastinum that was not localized by the scintigraphy. Ultrasonography identified a nodule on the left upper-superior lobe of the thyroid gland, consistent with a parathyroid adenoma; scintigraphy showed two focuses of abnormal tracer uptake, one on the left upper-superior lobe of the gland and the other on the right inferior lobe of the gland. Patient underwent surgery to remove the adenoma on the left side, but postoperatively PTH and serum calcium level were still elevated. CT scan showed a mass of 27 x 22 mm in the upper anterior mediastinum, in front of the right emisoma of D2. The final surgery allowed us to remove the adenoma with a laterocervical approach. The histopathology was consistent with parathyroid adenoma.

[Effect of treatment with selective serotonin reuptake inhibitors on lipid profile: state of the art]. / Effetto del trattamento con inibitori selettivi del reuptake della serotonina sul profilo lipidico: stato dell'arte.

Selective Serotonin Reuptake Inhibitors (SSRI) are an effective treatment for depressive disorder. Nevertheless, there is evidence suggesting a negative effect of these drugs on the lipid profile of the patients. We carried out a systematic review of the literature evaluating the influence of therapy with SSRI on lipid profile. Data source was MEDLINE. Clinical trials, prospective studies, retrospective studies and reviews published until November 2011 were considered. We identified twelve studies published from 1994 to 2011, of which four were randomized clinical trials, six were prospective studies and two were retrospective studies. Sertraline and Paroxetine seemed to have negative effects on the serum levels of Total and LDL Cholesterol. Citalopram did not demonstrate any influence on Total and LDL Cholesterol blood levels, being conversely associated with a slight increase of the HDL Cholesterol levels. Few data were found about the effects of Fluoxetina e Fluvoxamina on lipid profile and no data were found about Escitalopram. Sertaline and Paroxetine, two effective and widely used drugs for the treatment of major depression, seem to have a negative effect on the lipid profile; Citalopram, with its neutral or positive effect on lipid profile, should be considered the treatment of choice for depressive patients affected by dyslipidemia.

Water dynamics as affected by interaction with biomolecules and change of thermodynamic state: a neutron scattering study.

The dynamics of water as subtly perturbed by both the interaction with biomolecules and the variation of temperature and pressure has been investigated via neutron scattering spectroscopy. A measurement of inelastic neutron scattering devoted to the study of the coherent THz dynamics of water in a water-rich mixture with DNA (hydration level of 1 g DNA/15 g D(2)O) at room temperature is reported. The DNA hydration water coherent dynamics is characterised by the presence of collective modes, whose dispersion relations are similar to those observed in bulk water. These dispersion relations are well described by the interaction model developed in the case of bulk water, and the existence of a fast sound is experimentally demonstrated. The behaviour of the collective water dynamics was complemented by studying the single-particle dynamics of bulk water along the isotherm T = 298 K in the pressure range 0.1-350 MPa by means of incoherent scattering. This experiment is an attempt to simulate the change of the water molecular arrangement due to the interaction with DNA, by increasing the pressure as the presence of the biomolecule produces an increase in the density. An anomaly is found in the behaviour of the relaxation time derived from the quasi-elastic scattering signal, which can be related to the hypothetical second critical point in water. This anomaly and the transition from slow to fast sound take place in the same Q range, thus suggesting that the two phenomena could be related at some microscopic level.

Evidence of coexistence of change of caged dynamics at T(g) and the dynamic transition at T(d) in solvated proteins.

Mössbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, , commonly referred to as the dynamic transition at some temperature T(d). At low temperatures, increases slowly, but it assumes stronger temperature dependence after crossing T(d), which depends on the time/frequency resolution of the spectrometer. Various authors have made connection of the dynamics of solvated proteins, including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of obtained by quasielastic neutron scattering when crossing the glass transition temperature T(g), generally observed in inorganic, organic, and polymeric glass-formers. Evidences are presented here to show that such a change of the temperature dependence of from neutron scattering at T(g) is present in hydrated or solvated proteins, as well as in the solvent used, unsurprisingly since the latter is just another organic glass-former. If unaware of the existence of such a crossover of at T(g), and if present, it can be mistaken as the dynamic transition at T(d) with the ill consequences of underestimating T(d) by the lower value T(g) and confusing the identification of the origin of the dynamic transition. The obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein ß-relaxation or of the merged α-ß relaxation. The universal change of at T(g) of glass-formers, independent of the spectrometer resolution, had been rationalized by sensitivity to change in volume and entropy of the dissipation of the caged molecules and its contribution to . The same rationalization applies to hydrated and solvated proteins for the observed change of at T(g).

Acoustic dissipation and density of states in liquid, supercooled, and glassy glycerol.

Combined Brillouin spectra collected at visible, ultraviolet, and x-ray frequencies are used to reconstruct the imaginary part of the acoustic compliance J'' over a wide frequency range between 0.5 GHz and 5 THz. For liquid, supercooled, and glassy glycerol, J'' is found to be linearly dependent on the tagged-particle susceptibility measured by incoherent neutron scattering up to ≃1 THz, giving evidence of a clear relation between acoustic power dissipation and density of states. A simple but general formalism is presented to quantitatively explain this relation, thus clarifying the connection between the quasielastic component observed in neutron scattering experiments and the fast relaxation dynamics probed by Brillouin scattering.

Anomalous proton dynamics in ice at low temperatures.

We present incoherent quasielastic neutron scattering measurements on ice Ih (ordinary ice) and Ic (cubic ice) which show the existence of nonharmonic motion of hydrogen at low temperatures, down to 5 K. We show that this dynamics is localized, nonvibrational, and related to the hydrogen disorder since it is absent in ordered ice VIII. A main jump distance of 0.75 A is identified, hence close to the distance between the two possible proton sites along the oxygen-oxygen bond. The dynamics is non-Arrhenius, has a large time rate of 2.7x10(11) s-1, and affects only a few percent of the total number of hydrogen atoms in the crystal. These results give evidence for the existence of concerted proton tunneling in these ice phases.

Coupled relaxations at the protein-water interface in the picosecond time scale.

The spectral behaviour of a protein and its hydration water has been investigated through neutron scattering. The availability of both hydrogenated and perdeuterated samples of maltose-binding protein (MBP) allowed us to directly measure with great accuracy the signal from the protein and the hydration water alone. Both the spectra of the MBP and its hydration water show two distinct relaxations, a behaviour that is reminiscent of glassy systems. The two components have been described using a phenomenological model that includes two Cole-Davidson functions. In MBP and its hydration water, the two relaxations take place with similar average characteristic times of approximately 10 and 0.2 ps. The common time scales of these relaxations suggest that they may be a preferential route to couple the dynamics of the water hydrogen-bond network around the protein surface with that of protein fluctuations.

Fingerprints of amorphous icelike behavior in the vibrational density of states of protein hydration water.

The low-frequency modes of protein hydration water are investigated by inelastic neutron scattering. Experiments on both protonated and fully deuterated maltose binding protein samples allow us to unambiguously single out the contribution from water. The low-energy vibrational density of states of hydration water at 100 K is similar to the density of states of high- and low-density amorphous ice, and quite different from that of simple forms of crystalline ice. This result can be related to the picture of hydration water mass density depending on the protein surface curvature, which supports its glassy behavior.