Descripción: Organic solvents miscible in water (cosolvents) exerted a dual effect on the activation stage of two thioredoxin-linked enzymes of the reductive pentose phosphate cycle, phosphoribulokinase and NADP-glyceraldehyde-3-P dehydrogenase, both from spinach chloroplast; the enzyme specific activity was stimulated and inhibited by low and high concentrations of alcohols, respectively. On the contrary, cosolvents inhibited the catalytic process. In the stimulation of phosphoribulokinase activation, organic solvents reduced the requirement for thioredoxin-f and changed the thiol specificity, so that monothiols became functional. The cosolvent-mediated enhancement of NADP-glyceraldehyde-3-P dehydrogenase was obtained in the absence of modulators. With both enzymes, the concentration of the organic solvents required for activation was inversely proportional to its hydrophobicity (1-butanol < 1-propanol < 2-propanol < ethanol). The present results demonstrate the participation of a new component, the enzyme microenvironment, in the regulation of thioredoxin-linked chloroplast enzymes. © 1985.

Descripción: The stacking of positively charged (or doped) terthiophene oligomers and quaterthiophene polymers in solution is investigated applying a recently developed unified electrostatic and cavitation model for first-principles calculations in a continuum solvent. The thermodynamic and structural patterns of the dimerization are explored in different solvents, and the distinctive roles of polarity and surface tension are characterized and analyzed. Interestingly, we discover a saturation in the stabilization effect of the dielectric screening that takes place at rather small values of ε0. Moreover, we address the interactions in trimers of terthiophene cations, with the aim of generalizing the results obtained for the dimers to the case of higher-order stacks and nanoaggregates. © 2006 American Institute of Physics.

Descripción: A simple model is used for dilute polar/nonpolar systems, based on the additivity of electric susceptibilities of a solute/solvent interaction species and a nonpolar solvent. A spherical cavity is considered. Permittivity values, calculated as a function of concentration, are in good agreement with experimental results when the model is applied to systems containing water or lower alcohols in nine nonpolar solvents. © 1982 American Chemical Society.

Descripción: Lipases from different sources catalyze the polyesterification of glycerol and several dicarboxylic acids in presence or organic solvents.

Descripción: An equation proposed by H. Mechetti to describe the permittivity of very dilute polar/nonpolar solutions as a function of concentration was used to calculate the molecular dipole moment of the solutes. The procedure is very simple, and the results are in good agreement with those obtained through more elaborate known methods. Furthermore, an adequate choice of solvents leads to results that are in very good agreement with the corresponding vapor-phase values. © 1985 American Chemical Society.

Descripción: We present results from molecular dynamics simulations performed on reverse micelles immersed in cyclohexane. Three different inner polar phases are considered: water (W), formamide (FM), and an equimolar mixture of the two solvents. In all cases, the surfactant was sodium bis(2-ethylhexyl) sulfosuccinate (usually known as AOT). The initial radii of the micelles were R∼15 Å, while the corresponding polar solvent-to-surfactant molar ratios were intermediate between w0 =4.3 for FM and w0 =7 for W. The resulting overall shapes of the micelles resemble distorted ellipsoids, with average eccentricities of the order of ∼0.75. Moreover, the pattern of the surfactant layer separating the inner pool from the non-polar phase looks highly irregular, with a roughness characterized by length scales comparable to the micelle radii. Solvent dipole orientation polarization along radial directions exhibit steady growths as one moves from central positions toward head group locations. Local density correlations within the micelles indicate preferential solvation of sodium ionic species by water, in contrast to the behavior found in bulk equimolar mixtures. Still, a sizable fraction of ∼90% of Na+ remains associated with the head groups. Compared to bulk results, the translational and rotational modes of the confined solvents exhibit important retardations, most notably those operated in rotational motions where the characteristic time scales may be up to 50 times larger. Modifications of the intramolecular connectivity expressed in terms of the average number of hydrogen bonds and their lifetimes are also discussed. © 2008 American Institute of Physics.

Descripción: A strain isolated from Argentinean regional fermented sausages was found to produce and secrete a compound that inhibited growth of Lactobacillus strains used as indicators. It was characterized as Paenibacillus polymyxa (P13). The antimicrobial activity, named polyxin, was obtained from culture supernatant fluid of late stationary phase and was inhibitory to actively growing cells. It was effective against a wide range of Gram-positive and Gram-negative bacterial species tested including food-borne pathogens. Bacteriocin-like properties such as proteinaceous nature (sensitive to proteases), insensitivity to organic solvents and chelators, stability to heat (up to 10 min at 90°C), and acidic pH but instability in alkaline conditions, were determined. A molecular mass of 10 kDa was estimated by molecular gel filtration.

Descripción: We have studied the hydration and diffusion of the hydroxyl radical O H0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the O H0 has one water molecule bound to the O H0 oxygen (57% of the time), and one water molecule bound to the O H0 hydrogen (88% of the time). In the hydrogen bonds between the O H0 and the water that surrounds it the O H0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the O H0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the O H0 obtained from the simulation was 7.1× 10-9 m2 s-1, which is higher than those of the water and the O H-. © 2005 American Institute of Physics.

Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: Two copper complex solvatomorphs, namely (3,10-C-meso-3,5,7,7,10,12,14,14- octamethyl-1,4,8,11-tetraazacyclotetradecane)bis(perchlorato-κO)copper(II) 1.2-hydrate, [Cu(ClO4)2(C18H 40N4)]·1.2H2O, (I), and (3,10-C-meso-3,5,7,7,10,12,14,14-octamethyl-1,4,8,11-tetraazacyclotetradecane) bis(perchlorato-κO)copper(II), [Cu(ClO4)2(C 18H40N4)], (II), are described and compared with each other and with a third, already reported, anhydrous diastereomer, denoted (III). Both compounds present very similar centrosymmetic coordination environments, with the CuII cation lying on an inversion centre in a distorted 4+2 octahedral environment, defined by the macrocyclic N4 group in the equatorial sites and two perchlorate groups in trans-axial positions [one of the perchlorate ligands in (I) is partially disordered]. The most significant difference in molecular shape is seen in the orientation of the perchlorate anions, and the influence of this on the intramolecular hydrogen bonding is discussed. The (partially) hydrated state of (I) favours the formation of chains along [011], while the anhydrous character of (II) and (III) promotes loosely bound structures with low packing indices. © 2013 International Union of Crystallography.

Descripción: A model for the dependence of the electrical conductance, G, with the strain induced by external mechanical stress in conducting particles-polymer composites is presented. The model assumes that the percolation probability between neighboring particles must depart from a scale-invariant behavior but saturate at moderated-high strains, reaching percolation path's saturation, with sigmoid dependence. This dependence is obtained by proposing a dynamic picture where contacts or bonds between neighboring particles are created but also destructed when a stress is applied and relatively moderated or high strains, ε, are produced in the composite. The electrical conductance of prepared graphite-polydimethylsiloxane composites were measured as function of the applied pressure and fitted by the presented model. The elastic response to the uniaxial compression was studied using a texture analyzer. The possibility of nonuniversal effects in the conduction critical exponent, t, was taken into account. It is concluded that the saturation of the response in the G versus ε plots cannot be assigned to nonuniversal behavior of the exponent t, or to saturation of the elastic response. On the other hand, the presented model accounts for all the main experimental features observed in these systems and for previously reported data of elastomer composites. The simulated behavior of the piezoresistivity coefficient is also in qualitative agreement with previous reports. © 2010 American Institute of Physics.

Descripción: Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function. © 2012 Roman et al.

Descripción: Using molecular dynamics experiments, we analyze equilibrium and dynamical characteristics related to the solvation of excess protons in water-acetone mixtures. Our approach is based on the implementation of an extended valence-bond Hamiltonian, which incorporates translocation of the excess charge between neighboring water molecules. Different mixtures have been analyzed, starting from the pure water case down to solutions with a water molar fraction x w 0.25. In all cases, we have verified that the structure of the first solvation shell of the H 3 O moiety remains practically unchanged, compared to the one observed in pure water. This shell is composed by three water molecules acting as hydrogen bond acceptors, with no evidence of hydrogen bond donor-like connectivity. Moreover, the increment in the acetone concentration leads to a gradual stabilization of Eigen-like [H 3O·(H 2O) 3] configurations, in detriment of Zundel-like [H·(H 2O) 2] ones. Rates of proton transfer and proton diffusion coefficients have been recorded at various water-acetone relative concentrations. In both cases, we have found a transition region, in the vicinity of x w ∼ 0.8, where the concentration dependences of the two magnitudes change at a quantitative level. A crude estimate shows that, at this tagged concentration, the volumes occupied by the two solvents become comparable. The origins of this transition separating water-rich from acetone-rich realms is rationalized in terms of modifications operated in the nearby, second solvation shell, which in the latter solutions, normally includes at least, one acetone molecule. Our results would suggest that one possible mechanism controlling the proton transfer in acetone-rich solutions is the exchange of one of these tagged acetone molecules, by nearby water ones. This exchange would give rise to Zundel-like structures, exhibiting a symmetric, first solvation shell composed exclusively by water molecules, and would facilitate the transfer between neighboring water molecules along the resonant complex. © 2012 American Institute of Physics.

Descripción: In silico analyses have revealed a conserved protein domain (CHDL) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. A CHDL domain was shown to be present in RapA, a protein that is involved in autoaggregation of Rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. Structural similarity to cadherins suggested calcium-dependent oligomerization of CHDL domains as a mechanistic basis for RapA action. Here we show by circular dichroism spectroscopy, light scattering, isothermal titration calorimetry, and other methods that RapA2 from Rhizobium leguminosarum indeed exhibits a cadherin-like β-sheet conformation and that its proper folding and stability are dependent on the binding of one calcium ion per protein molecule. By further in silico analysis we also reveal that RapA2 consists of two CHDL domains and expand the range of CHDLcontaining proteins in bacteria and archaea. However, light scattering assays at various concentrations of added calcium revealed that RapA2 formed neither homo-oligomers nor hetero-oligomers with RapB (a distinct CHDL protein), indicating that RapA2 does not mediate cellular interactions through a cadherin-like mechanism. Instead, we demonstrate that RapA2 interacts specifically with the acidic exopolysaccharides (EPSs) produced by R. leguminosarum in a calcium-dependent manner, sustaining a role of these proteins in the development of the biofilm matrix made of EPS. Because EPS binding by RapA2 can only be attributed to its two CHDL domains, we propose that RapA2 is a calcium-dependent lectin and thatCHDLdomains in various bacterial and archaeal proteins confer carbohydrate binding activity to these proteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: The trypanocidal action of green tea catechins against two different developmental stages of Trypanosoma cruzi is reported for the first time. This activity was assayed with the nonproliferative bloodstream trypomastigote and with the intracellular replicative amastigote parasite forms. An ethyl acetate fraction from Camellia sinensis green tea leaves, which contains most of the polyphenolic compounds and the maximal trypanocidal activity, was obtained by fractionation of the aqueous extract with organic solvents. The active compounds present in this extract were further purified by LH-20 column chromatography and were identified by high-performance liquid chromatography analysis with a photo diode array detector and gas chromatography coupled to mass spectroscopy. The following flavan-3-ols derivatives, known as catechins, were identified: catechin, epicatechin, gallocatechin, epigallocatechin, catechin gallate, epicatechin gallate, gallocatechin gallate, and epigallocatechin gallate. The purified compounds lysed more than 50% of the parasites present in the blood of infected BALB/c mice at concentrations as low as 0.12 to 85 pM. The most active compounds were gallocatechin gallate and epigallocatechin gallate, with minimal bactericidal concentrations that inhibited 50% of isolates tested of 0.12 and 0.53 pM, respectively. The number of amastigotes in infected Vero cells decreased by 50% in the presence of each of these compounds at 100 nM. The effects of the catechins on the recombinant T. cruzi arginine kinase, a key enzyme in the energy metabolism of the parasite, were assayed. The activity of this enzyme was inhibited by about 50% by nanomolar concentrations of catechin gallate or gallocatechin gallate, whereas the other members of the group were less effective. On the basis of these results, we suggest that these compounds could be used to sterilize blood and, eventually, as therapeutic agents for Chagas' disease.

Descripción: Vertical excitation and electron detachment energies associated with the optical absorption of iodide ions dissolved in supercritical ammonia at 420 K have been calculated in two limiting scenarios: as a solvated free I- ion and forming a K+ I- contact ion pair (CIP). The evolution of the transition energies as a result of the gradual building up of the solvation structure was studied for each absorbing species as the solvent's density increased, i.e., changing the N H3 supercritical thermodynamic state. In both cases, if the solvent density is sufficiently high, photon absorption produces a spatially extended electron charge beyond the volume occupied by the solvated solute core; this excited state resembles a typical charge-transfer-to-solvent (CTTS) state. A combination of classical molecular dynamics simulations followed by quantum mechanical calculations for the ground, first-excited, and electron-detached electronic states have been carried out for the system consisting of one donor species (free I- ion or K+ I- CIP) surrounded by ammonia molecules. Vertical excitation and electron detachment energies were obtained by averaging 100 randomly chosen microconfigurations along the molecular dynamics trajectory computed for each thermodynamic condition (fluid density). Short- and long-range contributions of the solvent-donor interaction upon the CTTS states of I- and K+ I- were identified by performing additional electronic structure calculations where only the solvent interaction due to the first neighbor molecules was taken into account. These computations, together with previous experimental evidence that we collected for the system, have been used to analyze the solvent effects on the CTTS transition. In this paper we have established the following: (i) the CTTS electron of free I- ion or K+ I- CIP presents similar features, and it gradually localizes in close proximity of the iodine parent atom when the ammonia density is increased; (ii) for the free I- ion, the short-range solvent interaction contributes to the stabilization of the ground state more than it does for the CTTS excited state, which is evidenced experimentally as a blueshift in the maximum absorption of the CTTS transition when the density is increased; (iii) this effect is less noticeable for the K+ I- ion pair, because in this case a tight solvation structure, formed by four N H3 molecules wedged between the ions, appears at very low density and is very little affected by changes in the density; (iv) the long-range contribution to the solvent stabilization can be neglected for the K+ I- CIP, since the main features of its electronic transition can be explained on the basis of the vicinity of the cation; (v) however, the long-range solvent field contribution is essential for the free I- ion to become an efficient CTTS donor upon photoexcitation, and this establishes a difference in the CTTS behavior of I- in bulk and in clusters. © 2007 American Institute of Physics.