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: We study the intermittency properties of the energy and helicity cascades in two 15363 direct numerical simulations of helical rotating turbulence. Symmetric and antisymmetric velocity increments are examinedas well as probability density functions of the velocity field and of the helicity density. It is found that the direct cascade of energy to small scales is scale invariant and nonintermittentwhereas the direct cascade of helicity is highly intermittent. Furthermorethe study of structure functions of different orders allows us to identify a recovery of isotropy of strong events at very small scales in the flow. Finallywe observe the juxtaposition in space of strong laminar and persistent helical columns next to time-varying vortex tanglesthe former being associated with the self-similarity of energy and the latter with the intermittency of helicity. © 2010 American Institute of Physics.

Descripción: This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.

Descripción: The factorization theorems are a generalization for J-biexpansive meromorphic operator-valued functions on an infinite-dimensional Hilbert space of the theorems on decomposition of J-expansive matrix functions on a finite-dimensional Hilbert space due to A. V. Efimov and V. P. Potapov [Uspekhi Mat. Nauk 28 (1973), 65-130; Trudy Moskov. Mat. Obšč. 4 (1955), 125-236]. They also generalize theorems on factorization of J-expansive meromorphic operator functions due to Ju. P. Ginzburg [Izv. Vysš. Učebn. Zaved. Matematika 32 (1963), 45-53]. Within the framework of generalized network theory, the results can be applied to the J-biexpansive real operators that characterize a Hilbert port. Application of the extraction procedure to a given real operator leads to its splitting into a product of real factors, corresponding to Hilbert ports of a simpler structure. This can be interpreted as an extension of the classical method of synthesis of passive n-ports by factor decomposition. © 1981.

Descripción: The first direct determination of the inertial range energy cascade rate, using an anisotropic form of Yaglom's law for magnetohydrodynamic turbulence, is obtained in the solar wind with multispacecraft measurements. The two-point mixed third-order structure functions of Elsässer fluctuations are integrated over a sphere in magnetic field-aligned coordinates, and the result is consistent with a linear scaling. Therefore, volume integrated heating and cascade rates are obtained that, unlike previous studies, make only limited assumptions about the underlying spectral geometry of solar wind turbulence. These results confirm the turbulent nature of magnetic and velocity field fluctuations in the low frequency limit, and could supply the energy necessary to account for the nonadiabatic heating of the solar wind. © 2011 American Physical Society.

Descripción: We show that several spaces of holomorphic functions on a Riemann domain over a Banach space, including the nuclear and Hilbert-Schmidt bounded type, are locally m-convex Fréchet algebras. We prove that the spectrum of these algebras has a natural analytic structure, which we use to characterize the envelope of holomorphy. We also show a Cartan-Thullen type theorem. © 2011 Elsevier Inc.

Descripción: The purpose of this review is to examine and discuss the ways in which water is organized at the interface of a biological membrane. The relevance of this structure to the surface properties and to the adsorption of proteins in membranes is also analized. The approach is based on the idea that cell functions are confined to a restricted water media, the cell interior, in which the proximity of the membrane may be key to regulating the enzyme activity and the cell membrane permeability. As the lipid bilayer is the structural base of cell membranes, the distribution of water in the surface sites of a phospholipid membrane is analyzed by means of Fourier Transform spectrometry. The polarization of water at the surface was looked into through the measure of surface potentials and the dynamics of the surface hydration by cyclic voltammetry. Modification of these properties by the replacement of water by polyol molecules such as trehalose and phloretin and by the insertion of aqueous soluble enzymes, has also been investigated.

Descripción: The partition function of two hard spheres in a hard-wall pore is studied, appealing to a graph representation. The exact evaluation of the canonical partition function and the one-body distribution function in three different shaped pores are achieved. The analyzed simple geometries are the cuboidal, cylindrical, and ellipsoidal cavities. Results have been compared with two previously studied geometries; the spherical pore and the spherical pore with a hard core. The search of common features in the analytic structure of the partition functions in terms of their length parameters and their volumes, surface area, edges length, and curvatures is addressed too. A general framework for the exact thermodynamic analysis of systems with few and many particles in terms of a set of thermodynamic measures is discussed. We found that an exact thermodynamic description is feasible based on the adoption of an adequate set of measures and the search of the free energy dependence on the adopted measure set. A relation similar to the Laplace equation for the fluid-vapor interface is obtained, which expresses the equilibrium between magnitudes that in extended systems are intensive variables. This exact description is applied to study the thermodynamic behavior of the two hard spheres in a hard-wall pore for the analyzed different geometries. We obtain analytically the external reversible work, the pressure on the wall, the pressure in the homogeneous region, the wall-fluid surface tension, the line tension, and other similar properties. © 2010 American Institute of Physics.

Descripción: Background: Self-assembly is a common theme in proteins of unrelated sequences or functions. The human papillomavirus E7 oncoprotein is an extended dimer with an intrinsically disordered domain, that can form large spherical oligomers. These are the major species in the cytosol of HPV transformed and cancerous cells. E7 binds to a large number of targets, some of which lead to cell transformation. Thus, the assembly process not only is of biological relevance, but represents a model system to investigate a widely distributed mechanism. Methodology/Principal Findings: Using various techniques, we monitored changes in secondary, tertiary and quaternary structure in a time course manner. By applying a robust kinetic model developed by Zlotnik, we determined the slow formation of a monomeric "Z-nucleus" after zinc removal, followed by an elongation phase consisting of sequential second-order events whereby one monomer is added at a time. This elongation process takes place at a strikingly slow overall average rate of one monomer added every 28 seconds at 20 μM protein concentration, strongly suggesting either a rearrangement of the growing complex after binding of each monomer or the existence of a "conformation editing" mechanism through which the monomer binds and releases until the appropriate conformation is adopted. The oligomerization determinant lies within its small 5 kDa C-terminal globular domain and, remarkably, the E7 N-terminal intrinsically disordered domain stabilizes the oligomer, preventing an insoluble amyloid route. Conclusion: We described a controlled ordered mechanism with features in common with soluble amyloid precursors, chaperones, and other spherical oligomers, thus sharing determining factors for symmetry, size and shape. In addition, such a controlled and discrete polymerization reaction provides a valuable tool for nanotechnological applications. Finally, its increased immunogenicity related to its supramolecular structure is the basis for the development of a promising therapeutic vaccine candidate for treating HPV cancerous lesions. © 2012 Smal et al.

Descripción: 2-Cys peroxiredoxins (2-Cys Prxs) are ubiquitous peroxidases with important roles in cellular antioxidant defense and hydrogen peroxide-mediated signaling. Post-translational modifications of conserved cysteines cause the transition from low to high molecular weight oligomers, triggering the functional change from peroxidase to molecular chaperone. However, it remains unclear how non-covalent interactions of 2-Cys Prx with metabolites modulate the quaternary structure. Here, we disclose that ATP and Mg2+ (ATP/Mg) promote the self-polymerization of chloroplast 2-Cys Prx (polypeptide 23.5 kDa) into soluble higher order assemblies (>2 MDa) that proceed to insoluble aggregates beyond 5mMATP. Remarkably, the withdrawal of ATP or Mg2+ brings soluble oligomers and insoluble aggregates back to the native conformation without compromising the associated functions. As confirmed by transmission electron microscopy, ATP/Mg drive the toroid-like decamers (diameter 13 nm) to the formation of large sphere-like particles (diameter ∼30 nm). Circular dichroism studies on ATP-labeled 2-Cys Prx reveal that ATP/Mg enhance the proportion of β-sheets with the concurrent decrease in the content of α-helices. In line with this observation, the formation of insoluble aggregates is strongly prevented by 2,2,2-trifluoroethanol, a cosolvent employed to induce α-helical conformations. We further find that the response of self-polymerization to ATP/Mg departs abruptly from that of the associated peroxidase and chaperone activities when two highly conserved residues, Arg129 and Arg152, are mutated. Collectively, our data uncover that non-covalent interactions of ATP/Mg with 2-Cys Prx modulate dynamically the quaternary structure, thereby coupling the non-redox chemistry of cell energy with redox transformations at cysteine residues. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: Recently, exact agreement has been found between bulk and boundary three-point functions in Ad S3 × S3 × T4 with Neveu-Schwarz-Neveu- Schwarz (NSNS) fluxes. This represents a nontrivial check of AdS/CFT correspondence beyond the supergravity approximation as it corresponds to an exact worldsheet computation. When taking a closer look at this computation, one notices that a crucial point for the bulk-boundary agreement to hold is an intriguing mutual cancellation between worldsheet contributions corresponding to the Ad S3 and to the S3 pieces of the geometry, that results in a simple factorized form for the final three-point function. In this note we review this cancellation and clarify some points about the analytic relation between the SU (2) and the SL (2,R) structure constants. In particular, we dicuss the connection to the Coulomb gas representation. We also make some comments on the four-point function. © 2009 American Institute of Physics.

Descripción: We study the effect of translational-rotational hydrodynamic coupling on the transient electric linear dichroism of DNA fragments in aqueous solution. As opposed to previous theoretical works, where analytic solutions valid in the limit of low electric field were reported, we present here a numerical approach which allows to obtain numerical results valid independently from the applied electric field strength. Numerical procedures here used are an extension to the transient-state of those developed in a previous work for the study of the problem in the steady-state. The molecular orientational processes induced by an electric field is characterized with statistical arguments solving the Fokker-Planck equation by means of the finite difference method to know the orientational distribution function of molecules. © 2013 American Institute of Physics.

Descripción: In the present work, we study the effect of translational-rotational hydrodynamic coupling on the stationary electric linear dichroism of DNA fragments. The theoretical resolution of the problem has, so far, been dealt with analytic methods valid only in the limit of low electric fields. In this work, we apply numerical methods that allow us to study the problem and also consider electric fields of arbitrary strength. We use the bent rod molecules model to describe DNA fragments with physical properties characterized by their electric charge, electric polarizability tensor, rotational diffusion tensor, and translation-rotation coupling diffusion tensor. The necessary orientational distribution function to calculate electric dichroism is obtained by solving the Fokker-Planck equation through the finite difference method. We analyze the different contributions due to electric polarizability and translational- rotational coupling to the electric dichroism. © 2011 American Institute of Physics.

Descripción: Chagas' disease, caused by Trypanosoma cruzi, affects about 18 million people in Latin America, and no effective treatment is available to date. To acquire sialic acid from the host glycoconjugates, T. cruzi expresses an unusual surface sialidase with trans-sialidase activity (TcTS) that transfers the sugar to parasite mucins. Surface sialic acid was shown to have relevant functions in protection of the parasite against the lysis by complement and in mammalian host cell invasion. The recently determined 3D structure of TcTS allowed a detailed analysis of its catalytic site and showed the presence of a lactose-binding site where the β-linked galactose accepting the sialic acid is placed. In this article, the acceptor substrate specificity of lactose derivatives was studied by high pH anion-exchange chromatography with pulse amperometric detection. The lactose open chain derivatives lactitol and lactobionic acid, as well as other derivatives, were found to be good acceptors of sialic acid. Lactitol, which was the best of the ones tested, effectively inhibited the transfer of sialic acid to N-acetyllactosamine. Furthermore, lactitol inhibited parasite mucins re-sialylation when incubated with live trypanosomes and TcTS. Lactitol also diminished the T. cruzi infection in cultured Vero cells by 20-27%. These results indicate that compounds directed to the lactose binding site might be good inhibitors of TcTS. © Oxford University Press 2004; all rights reserved.

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: Mucins are highly O-glycosylated molecules which in mammalian cells accomplish essential functions, like cytoprotection and cell-cell interactions. In the protozoan parasite Trypanosoma cruzi, mucin-related glycoproteins have been shown to play a relevant role in the interaction with and invasion of host cells. We have previously reported a family of mucin- like genes in T. cruzi whose overall structure resembled that of mammalian mucin genes. We have now analyzed the relationship between these genes and mucin proteins. A monoclonal antibody specific for a mucin sugar epitope and a polyclonal serum directed to peptide epitopes in a MUC gene-encoded recombinant protein, detected identical bands in three out of seven strains of T. cruzi. Immunoprecipitation experiments confirmed these results. When expressed in eukaryotic cells, the MUC gene product is post-translationally modified, most likely, through extensive O-glycosylation. Gene sequencing showed that the central domains encoding the repeated sequences with the consensus T 8KP 2, varies in number from 1 to 10, and the number of Thr residues in each repeat could be 7, 8, or 10. A run of 16 to 18 Thr residues was present in some, but not all, MUC gene-derived sequences. Direct compositional analysis of mucin core proteins showed that Thr residues are much more frequent than Ser residues. The same fact occurs in MUC gene- derived protein sequences. Molecular mass determinations of the 35-kDa glycoproteins further extend the heterogeneity of the family to the natural mucin molecules. Difficulties in assigning each of the several MUC genes identified to a mucin product arise from the high diversity and partial sequence conservation of the members of this family.

Descripción: SUMO conjugation to proteins is involved in the regulation of diverse cellular functions. We have identified a protein, RWD-containing sumoylation enhancer (RSUME), that enhances overall SUMO-1, -2, and -3 conjugation by interacting with the SUMO conjugase Ubc9. RSUME increases noncovalent binding of SUMO-1 to Ubc9 and enhances Ubc9 thioester formation and SUMO polymerization. RSUME enhances the sumoylation of IkB in vitro and in cultured cells, leading to an inhibition of NF-kB transcriptional activity. RSUME is induced by hypoxia and enhances the sumoylation of HIF-1α, promoting its stabilization and transcriptional activity during hypoxia. Disruption of the RWD domain structure of RSUME demonstrates that this domain is critical for RSUME action. Together, these findings point to a central role of RSUME in the regulation of sumoylation and, hence, several critical regulatory pathways in mammalian cells. © 2007 Elsevier Inc. All rights reserved.

Descripción: We continue the study of hidden Z2 symmetries of the four-point sl (2) k Knizhnik-Zamolodchikov equation initiated by Giribet [Phys. Lett. B 628, 148 (2005)]. Here, we focus our attention on the four-point correlation function in those cases where one spectral flowed state of the sector ω=1 is involved. We give a formula that shows how this observable can be expressed in terms of the four-point function of non spectral flowed states. This means that the formula holding for the winding violating four-string scattering processes in AdS3 has a simple expression in terms of the one for the conservative case, generalizing what is known for the case of three-point functions, where the violating and the nonviolating structure constants turn out to be connected one to each other in a similar way. What makes this connection particularly simple is the fact that, unlike what one would naively expect, it is not necessary to explicitly solve the five-point function containing a single spectral flow operator to this end. Instead, nondiagonal functional relations between different solutions of the Knizhnik-Zamolodchikov equation turn out to be the key point for this short path to exist. Considering such functional relation is necessary but it is not sufficient; besides, the formula also follows from the relation existing between correlators in both Wess-Zumino-Novikov-Witten (WZNW) and Liouville conformal theories. © 2007 American Institute of Physics.

Descripción: It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or "species" of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or "species" populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes. © 2013 Serra et al.