Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

The in vitro antioxidant properties of the Al-quercetin/beta CD and Al-catechin/beta CD inclusion compounds, rationalized in terms of their electrochemical behaviour

Inclusion compounds of Al-quercetin and Al-catechin complexes with beta-cyclodextrin (beta CD) were investigated. The complex and the inclusion compound of quercetin are more effective DPPHaEuro cent scavengers than the corresponding catechin compounds and the inclusion does not compromise their scavenging abilities, with only a slight decrease in the EC50 values. This is in accordance with the electrochemical data, which revealed that the inclusion compounds have lower diffusion coefficients in aqueous solution than the non-included compounds. For the quercetin compounds, some spectroscopic properties were also addressed by means of UV-visible and NMR measurements in aqueous media.

Solvation in aqueous binary mixtures: consequences of the hydrophobic character of the ionic liquids and the solvatochromic probes

Information on the solvation in mixtures of water, W, and the ionic liquids, ILs, 1-allyl-3-R-imidazolium chlorides; R = methyl, 1-butyl, and 1-hexyl, has been obtained from the responses of the following solvatochromic probes: 2,6-dibromo-4-[(E)-2-(1-R-pyridinium-4-yl)ethenyl] phenolate, R = methyl, MePMBr2; 1-octyl, OcPMBr(2), and the corresponding quinolinium derivative, MeQMBr(2). A model developed for solvation in binary mixtures of W and molecular solvents has been extended to the present mixtures. Our objective is to assess the relevance to solvation of hydrogen-bonding and the hydrophobic character of the IL and the solvatochromic probe. Plots of the medium empirical polarity, E-T(probe) versus its composition revealed non-ideal behavior, attributed to preferential solvation by the IL and, more efficiently, by the IL-W hydrogen-bonded complex. The deviation from linearity increases as a function of increasing number of carbon atoms in the alkyl group of the IL, and is larger than that observed for solvation by W plus molecular solvents (1-propanol and 2-(1-butoxy)ethanol) that are more hydrophobic than the ILs investigated. This enhanced deviation is attributed to the more organized structure of the ILs proper, which persists in their aqueous solutions. MeQMBr(2) is more susceptible to solvent lipophilicity than OcPMBr(2), although the former probe is less lipophilic. This enhanced susceptibility agrees with the important effect of annelation on the contributions of the quinonoid and zwitterionic limiting structures to the ground and excited states of the probe, hence on its response to both medium composition and lipophilicity of the IL.

OPTIMUM RATIO OF CALCIUM AND BORON IN THE NUTRIENT SOLUTION OR IN CASTOR BEAN SHOOT FOR FRUIT YIELD AND SEED OIL CONTENT

Calcium (Ca) and boron (B) have been reported as the major macro-and micronutrient required for castor bean plant yield. The objective of this study was to determine the Ca: B ratios (in the growth media and plant tissue) for fruit yield and shoot dry weight of the castor bean (Ricinus communis L.), grown in a nutrient solution, and to evaluate Ca and B supply on concentration and total uptake of Ca, potassium (K), magnesium (Mg), and B, as well on the seed oil content. The treatments were arranged in a 3 x 3 factorial fashion, consisting of three rates of Ca (40, 80, and 160 mg L-1) and three of B (0.32, 0.96, and 1.60 mg L-1). Calcium and B rates increased the shoot and root dry weight and fruit yield at a Ca: B ratio in the nutrient solution of 166 and 100, respectively. Symptoms of B deficiency were observed in plants supplied with 0.32 mg B L-1, regardless of the Ca concentration in the nutrient solution. Plants which showed visual symptoms of Ca deficiency cultivated with 40 mg Ca L-1 presented concentration of Ca in plant tissue up to 10 g kg(-1). The concentration and total Ca and B uptake increased with the rates of them. Notwithstanding, the shoot Ca accumulation was improved by B rates. In addition, there were no decreases in K and Mg uptake due to Ca rates. Furthermore, addition of 80 mg L-1 of Ca and 1.60 mg L-1 of B in the growth media increased the seed oil content. The Ca: B ratio in the diagnostic leaf associated with the highest plant dry weight (shoot and root) and fruit yield, was 500 (16 to 20 g kg(-1) of Ca, and for 30 to 40 mg kg(-1) of B).

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

The peroxisome proliferator-activated receptors (PPARs) regulate genes involved in lipid and carbohydrate metabolism, and are targets of drugs approved for human use. Whereas the crystallographic structure of the complex of full length PPAR gamma and RXR alpha is known, structural alterations induced by heterodimer formation and DNA contacts are not well understood. Herein, we report a small-angle X-ray scattering analysis of the oligomeric state of hPPAR gamma alone and in the presence of retinoid X receptor (RXR). The results reveal that, in contrast with other studied nuclear receptors, which predominantly form dimers in solution, hPPAR gamma remains in the monomeric form by itself but forms heterodimers with hRXR alpha. The low-resolution models of hPPAR gamma/RXR alpha complexes predict significant changes in opening angle between heterodimerization partners (LBD) and extended and asymmetric shape of the dimer (LBD-DBD) as compared with X-ray structure of the full-length receptor bound to DNA. These differences between our SAXS models and the high-resolution crystallographic structure might suggest that there are different conformations of functional heterodimer complex in solution. Accordingly, hydrogen/deuterium exchange experiments reveal that the heterodimer binding to DNA promotes more compact and less solvent-accessible conformation of the receptor complex.

STRUCTURE OF THE ELECTROMAGNETIC FIELD ALLOWING EXACT SOLUTION OF THE SCHRODINGER EQUATION IN SUPERPOSITION WITH AN AHARONOV-BOHM FIELD

A charged particle is considered in a complex external electromagnetic field. The field is a superposition of an Aharonov-Bohm field and some additional field. Here we describe all additional fields known up to the present time that allow exact solution of the Schrodinger equation in a complex field.

Influence of the Bilayer Composition on the Binding and Membrane Disrupting Effect of Polybia-MP1, an Antimicrobial Mastoparan Peptide with Leukemic T-Lymphocyte Cell Selectivity

This study shows that MP-1, a peptide from the venom of the Polybia paulista wasp, is more toxic to human leukemic T-lymphocytes than to human primary lymphocytes. By using model membranes and electrophysiology measurements to investigate the molecular mechanisms underlying this selective action, the porelike activity of MP-1 was identified with several bilayer compositions. The highest average conductance was found in bilayers formed by phosphatidylcholine or a mixture of phosphatidylcholine and phosphatidylserine (70:30). The presence of cholesterol or cardiolipin substantially decreases the MP-1 pore activity, suggesting that the membrane fluidity influences the mechanism of selective toxicity. The determination of partition coefficients from the anisotropy of Tip indicated higher coefficients for the anionic bilayers. The partition coefficients were found to be 1 order of magnitude smaller when the bilayers contain cholesterol or a mixture of cholesterol and sphingomyelin. The blue shift fluorescence, anisotropy values, and Stern-Volmer constants are indications of a deeper penetration of MP-1 into anionic bilayers than into zwitterionic bilayers. Our results indicate that MP-1 prefers to target leukemic cell membranes, and its toxicity is probably related to the induction of necrosis and not to DNA fragmentation. This mode of action can be interpreted considering a number of bilayer properties like fluidity, lipid charge, and domain formation. Cholesterol-containing bilayers are less fluid and less charged and have a tendency to form domains. In comparison to healthy cells, leukemic T-lymphocyte membranes are deprived of this lipid, resulting in decreased peptide binding and lower conductance. We showed that the higher content of anionic lipids increases the level of binding of the peptide to bilayers. Additionally, the absence of cholesterol resulted in enhanced pore activity. These findings may drive the selective toxicity of MP-1 to Jurkat cells.

On the optical properties of copper nanocubes as a function of the edge length as modeled by the discrete dipole approximation

This Letter reports an investigation on the optical properties of copper nanocubes as a function of size as modeled by the discrete dipole approximation. In the far-field, our results showed that the extinction resonances shifted from 595 to 670 nm as the size increased from 20 to 100 nm. Also, the highest optical efficiencies for absorption and scattering were obtained for nanocubes that were 60 and 100 nm in size, respectively. In the near-field, the electric-field amplitudes were investigated considering 514, 633 and 785 nm as the excitation wavelengths. The E-fields increased with size, being the highest at 633 nm. (c) 2012 Elsevier B.V. All rights reserved.

Influence of the Sol-Gel pH Process and Compact Film on the Efficiency of TiO2-Based Dye-Sensitized Solar Cells

The influence of pH during hydrolysis of titanium(IV) isopropoxide on the morphological and electronic properties of TiO2 nanoparticles prepared by the sol-gel method is investigated and correlated to the photoelectrochemical parameters of dye-sensitized solar cells (DSCs) based on TiO2 films. Nanoparticles prepared under acid pH exhibit smaller particle size and higher surface area, which result in higher dye loadings and better short-circuit current densities than DSCs based on alkaline TiO2-processed films. On the other hand, the product of charge collection and separation quantum yields in films with TiO2 obtained by alkaline hydrolysis is c. a. 27% higher than for the acid TiO2 films. The combination of acid and alkaline TiO2 nanoparticles as mesoporous layer in DSCs results in a synergic effect with overall efficiencies up to 6.3%, which is better than the results found for devices employing one of the nanoparticles separately. These distinct nanoparticles can be also combined by using the layer-by-layer technique (LbL) to prepare compact TiO2 films applied before the mesoporous layer. DSCs employing photoanodes with 30 TiO2 bilayers have shown efficiencies up to 12% higher than the nontreated photoanode ones. These results can be conveniently used to develop optimized synthetic procedures of TiO2 nanoparticles for several dye-sensitized solar cell applications.

Theoretical Study of the Molecules in Solution and Phospholipid Bilayers

Using Molecular Dynamics simulations and Quantum Mechanical calculations, we study the behavior of molecules with biophysical and pharmacological interest in solution and in phospholipid bilayer.

Influence of the network modifier on the characteristics of MSnO3 (M=Sr and Ca) thin films synthesized by chemical solution deposition

CaSnO3 and SrSnO3 alkaline earth stannate thin films were prepared by chemical solution deposition using the polymeric precursor method on various single crystal substrates (R- and C-sapphire and 100-SrTiO3) at different temperatures. The films were characterized by X-ray diffraction (θ-2θ, ω- and φ-scans), field emission scanning electron microscopy, atomic force microscopy, micro-Raman spectroscopy and photoluminescence. Epitaxial SrSnO3 and CaSnO3 thin films were obtained on SrTiO3 with a high crystalline quality. The long-range symmetry promoted a short-range disorder which led to photoluminescence in the epitaxial films. In contrast, the films deposited on sapphire exhibited a random polycrystalline growth with no meaningful emission regardless of the substrate orientation. The network modifier (Ca or Sr) and the substrate (sapphire or SrTiO3) influenced the crystallization process and/or the microstructure. Higher is the tilts of the SnO6 octahedra, as in CaSnO3, higher is the crystallization temperature, which changed also the nucleation/grain growth process.

Light energy management in peach: utilization, photoprotection , photodamage and recovery. Maximizing light absorption in orchard is not always the best solution

The relation between the intercepted light and orchard productivity was considered linear, although this dependence seems to be more subordinate to planting system rather than light intensity. At whole plant level not always the increase of irradiance determines productivity improvement. One of the reasons can be the plant intrinsic un-efficiency in using energy. Generally in full light only the 5 – 10% of the total incoming energy is allocated to net photosynthesis. Therefore preserving or improving this efficiency becomes pivotal for scientist and fruit growers. Even tough a conspicuous energy amount is reflected or transmitted, plants can not avoid to absorb photons in excess. The chlorophyll over-excitation promotes the reactive species production increasing the photoinhibition risks. The dangerous consequences of photoinhibition forced plants to evolve a complex and multilevel machine able to dissipate the energy excess quenching heat (Non Photochemical Quenching), moving electrons (water-water cycle , cyclic transport around PSI, glutathione-ascorbate cycle and photorespiration) and scavenging the generated reactive species. The price plants must pay for this equipment is the use of CO2 and reducing power with a consequent decrease of the photosynthetic efficiency, both because some photons are not used for carboxylation and an effective CO2 and reducing power loss occurs. Net photosynthesis increases with light until the saturation point, additional PPFD doesn’t improve carboxylation but it rises the efficiency of the alternative pathways in energy dissipation but also ROS production and photoinhibition risks. The wide photo-protective apparatus, although is not able to cope with the excessive incoming energy, therefore photodamage occurs. Each event increasing the photon pressure and/or decreasing the efficiency of the described photo-protective mechanisms (i.e. thermal stress, water and nutritional deficiency) can emphasize the photoinhibition. Likely in nature a small amount of not damaged photosystems is found because of the effective, efficient and energy consuming recovery system. Since the damaged PSII is quickly repaired with energy expense, it would be interesting to investigate how much PSII recovery costs to plant productivity. This PhD. dissertation purposes to improve the knowledge about the several strategies accomplished for managing the incoming energy and the light excess implication on photo-damage in peach. The thesis is organized in three scientific units. In the first section a new rapid, non-intrusive, whole tissue and universal technique for functional PSII determination was implemented and validated on different kinds of plants as C3 and C4 species, woody and herbaceous plants, wild type and Chlorophyll b-less mutant and monocot and dicot plants. In the second unit, using a “singular” experimental orchard named “Asymmetric orchard”, the relation between light environment and photosynthetic performance, water use and photoinhibition was investigated in peach at whole plant level, furthermore the effect of photon pressure variation on energy management was considered on single leaf. In the third section the quenching analysis method suggested by Kornyeyev and Hendrickson (2007) was validate on peach. Afterwards it was applied in the field where the influence of moderate light and water reduction on peach photosynthetic performances, water requirements, energy management and photoinhibition was studied. Using solar energy as fuel for life plant is intrinsically suicidal since the high constant photodamage risk. This dissertation would try to highlight the complex relation existing between plant, in particular peach, and light analysing the principal strategies plants developed to manage the incoming light for deriving the maximal benefits as possible minimizing the risks. In the first instance the new method proposed for functional PSII determination based on P700 redox kinetics seems to be a valid, non intrusive, universal and field-applicable technique, even because it is able to measure in deep the whole leaf tissue rather than the first leaf layers as fluorescence. Fluorescence Fv/Fm parameter gives a good estimate of functional PSII but only when data obtained by ad-axial and ab-axial leaf surface are averaged. In addition to this method the energy quenching analysis proposed by Kornyeyev and Hendrickson (2007), combined with the photosynthesis model proposed by von Caemmerer (2000) is a forceful tool to analyse and study, even in the field, the relation between plant and environmental factors such as water, temperature but first of all light. “Asymmetric” training system is a good way to study light energy, photosynthetic performance and water use relations in the field. At whole plant level net carboxylation increases with PPFD reaching a saturating point. Light excess rather than improve photosynthesis may emphasize water and thermal stress leading to stomatal limitation. Furthermore too much light does not promote net carboxylation improvement but PSII damage, in fact in the most light exposed plants about 50-60% of the total PSII is inactivated. At single leaf level, net carboxylation increases till saturation point (1000 – 1200 μmolm-2s-1) and light excess is dissipated by non photochemical quenching and non net carboxylative transports. The latter follows a quite similar pattern of Pn/PPFD curve reaching the saturation point at almost the same photon flux density. At middle-low irradiance NPQ seems to be lumen pH limited because the incoming photon pressure is not enough to generate the optimum lumen pH for violaxanthin de-epoxidase (VDE) full activation. Peach leaves try to cope with the light excess increasing the non net carboxylative transports. While PPFD rises the xanthophyll cycle is more and more activated and the rate of non net carboxylative transports is reduced. Some of these alternative transports, such as the water-water cycle, the cyclic transport around the PSI and the glutathione-ascorbate cycle are able to generate additional H+ in lumen in order to support the VDE activation when light can be limiting. Moreover the alternative transports seems to be involved as an important dissipative way when high temperature and sub-optimal conductance emphasize the photoinhibition risks. In peach, a moderate water and light reduction does not determine net carboxylation decrease but, diminishing the incoming light and the environmental evapo-transpiration request, stomatal conductance decreases, improving water use efficiency. Therefore lowering light intensity till not limiting levels, water could be saved not compromising net photosynthesis. The quenching analysis is able to partition absorbed energy in the several utilization, photoprotection and photo-oxidation pathways. When recovery is permitted only few PSII remained un-repaired, although more net PSII damage is recorded in plants placed in full light. Even in this experiment, in over saturating light the main dissipation pathway is the non photochemical quenching; at middle-low irradiance it seems to be pH limited and other transports, such as photorespiration and alternative transports, are used to support photoprotection and to contribute for creating the optimal trans-thylakoidal ΔpH for violaxanthin de-epoxidase. These alternative pathways become the main quenching mechanisms at very low light environment. Another aspect pointed out by this study is the role of NPQ as dissipative pathway when conductance becomes severely limiting. The evidence that in nature a small amount of damaged PSII is seen indicates the presence of an effective and efficient recovery mechanism that masks the real photodamage occurring during the day. At single leaf level, when repair is not allowed leaves in full light are two fold more photoinhibited than the shaded ones. Therefore light in excess of the photosynthetic optima does not promote net carboxylation but increases water loss and PSII damage. The more is photoinhibition the more must be the photosystems to be repaired and consequently the energy and dry matter to allocate in this essential activity. Since above the saturation point net photosynthesis is constant while photoinhibition increases it would be interesting to investigate how photodamage costs in terms of tree productivity. An other aspect of pivotal importance to be further widened is the combined influence of light and other environmental parameters, like water status, temperature and nutrition on peach light, water and phtosyntate management.