Polaron formation at impurity-endowed lattices.

In semiconducting materials, lattice deformities can play the role of localizing the charge carriers. Polarons are understood as attractive interactions between charge and lattice deformations that result in a single structure composed by a charged particle surrounded by a cloud of phonons. These composite quasi-particles are vital structures when it comes to charge transport mechanism in a wide range of semiconducting materials. In the present work, we investigated the drift of an electron and the subsequent polaron formation in impurity-endowed lattices in the framework of a one-dimensional tight-binding model. Primarily, we scrutinized electronic dynamics in lattices containing two sources of disorders: a barrier and a well. The dispersion of the gamma distribution gives an idea of the extension of the disorder region in the lattice. We studied the dynamics of an injected electron interacting with the lattice vibrations where we consider, for a given degree of disorder, different velocities of the incoming particle. Our results show that there are different kinds of propagation/localization for the electron according to the assumed initial velocity. Importantly, we obtained the critical values for the impurity strength to promote the quenching of Bloch oscillations and the localization of polarons.

Bloch Oscillations in Fibonacci lattices: polaron formation.

We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical picture, we obtained a novel dynamical process with no counterpart in ordered lattices. Our findings showed that in low-disorder limit, the electron performs spatial Bloch oscillations, generating, in the turning points of its trajectory, composite quasi-particles-namely, polarons. When it comes to highly disordered systems, two strongly localized polarons are formed in the region where the oscillating charge is confined, thus propagating excitations that are present in the lattice.

The N-terminal domains of TRF1 and TRF2 regulate their ability to condense telomeric DNA.

TRF1 and TRF2 are key proteins in human telomeres, which, despite their similarities, have different behaviors upon DNA binding. Previous work has shown that unlike TRF1, TRF2 condenses telomeric, thus creating consequential negative torsion on the adjacent DNA, a property that is thought to lead to the stimulation of single-strand invasion and was proposed to favor telomeric DNA looping. In this report, we show that these activities, originating from the central TRFH domain of TRF2, are also displayed by the TRFH domain of TRF1 but are repressed in the full-length protein by the presence of an acidic domain at the N-terminus. Strikingly, a similar repression is observed on TRF2 through the binding of a TERRA-like RNA molecule to the N-terminus of TRF2. Phylogenetic and biochemical studies suggest that the N-terminal domains of TRF proteins originate from a gradual extension of the coding sequences of a duplicated ancestral gene with a consequential progressive alteration of the biochemical properties of these proteins. Overall, these data suggest that the N-termini of TRF1 and TRF2 have evolved to finely regulate their ability to condense DNA.

A RasGAP SH3 peptide aptamer inhibits RasGAP-Aurora interaction and induces caspase-independent tumor cell death.

The Ras GTPase-activating protein RasGAP catalyzes the conversion of active GTP-bound Ras into inactive GDP-bound Ras. However, RasGAP also acts as a positive effector of Ras and exerts an anti-apoptotic activity that is independent of its GAP function and that involves its SH3 (Src homology) domain. We used a combinatorial peptide aptamer approach to select a collection of RasGAP SH3 specific ligands. We mapped the peptide aptamer binding sites by performing yeast two-hybrid mating assays against a panel of RasGAP SH3 mutants. We examined the biological activity of a peptide aptamer targeting a pocket delineated by residues D295/7, L313 and W317. This aptamer shows a caspase-independent cytotoxic activity on tumor cell lines. It disrupts the interaction between RasGAP and Aurora B kinase. This work identifies the above-mentioned pocket as an interesting therapeutic target to pursue and points its cognate peptide aptamer as a promising guide to discover RasGAP small-molecule drug candidates.

[Assembly of ribonucleoparticle complexes]. / Assemblage des complexes ribonucléoprotéiques.

RNA-proteins interactions are involved in numerous cellular functions. These interactions are found in most cases within complex macromolecular assemblies. The recent development of tools and techniques to study RNA-protein complexes has significantly increased our knowledge in the nature of these specific interactions. The aim of this article is to present the different techniques used to study RNA-protein complexes, as well as recent data concerning the application of RNA as therapeutic molecules.

Functional aspects of co-variant surface charges in an antibody fragment.

A mutational analysis of three co-variant pairs of residues, located at the surface of a single-chain fragment, variable (scFv), remote from the antigen-binding site, was performed to investigate the tolerance of these positions to amino acid changes. The replacements consisted of the elimination or addition of charges, or in their replacement by a charge of opposite sign. As measured by Biacore, antigen-binding kinetics and specificity were essentially unaffected by the mutations. The purified scFvs remained mostly 100% active for 14 h, and their sensitivity to guanidinium-chloride denaturation was similar. These observations indicate that the mutations did not affect antigen-binding properties and that protein folding was conserved. However, the various scFvs differed greatly in half-life in periplasmic extracts (<4 h to >16 h at 25 degrees C). The deleterious effect on half-life produced by single mutations could be reversed by introducing a second mutation that restores the natural combination of amino acids in the co-variant pair, indicating that the consequence of charge modifications at these locations depends on the sequence context. We propose that the differences in half-life result from differences in aggregation propensities with other periplasmic proteins, related to the presence of charged patches at the surface of the scFvs. The practical implication is that changes in surface charge may drastically affect the level of active molecules in complex protein mixtures, a potentially important consideration in engineering scFvs for biotechnological or medical purposes.

Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies.

The possibility of obtaining from any antibody a fluorescent conjugate which responds to the binding of the antigen by a variation of its fluorescence, would be of great interest in the analytical sciences and for the construction of protein chips. This possibility was explored with antibody mAbD1.3 directed against hen egg white lysozyme. Rules of design were developed to identify the residues of the antibody to which a fluorophore could be chemically coupled, after changing them to cysteine by mutagenesis. These rules were based on: the target residue belonging to a topological neighbourhood of the antigen in the structure of the complex between antibody and antigen; its absence of functional importance for the interaction with the antigen; and its solvent accessibility in the structure of the free antibody. Seventeen conjugates between the single-chain variable fragment scFv of mAbD1.3 and an environment-sensitive fluorophore were constructed. For six of the ten residues which fully satisfied the design rules, the relative variation of the fluorescence intensity between the free and bound states of the conjugate was comprised between 12 and 75% (in non-optimal buffer), and the affinity of the conjugate for lysozyme remained unchanged relative to the parental scFv. In contrast, such results were true for only one of the seven residues which failed to satisfy one of the rules and were used as controls. One of the conjugates was studied in more detail. Its fluorescence increased proportionally to the concentration of lysozyme in a nanomolar range, up to 90% in a defined buffer, and 40% in serum. This increase was specific for hen egg lysozyme and it was not observed with a closely related protein, turkey egg lysozyme. The residues which gave operational conjugates (six in V(L) and one in V(H)), were located in the immediate vicinity of residues which are functionally important, along the sequence of FvD1.3. The results suggest rules of design for constructing antigen-sensitive fluorescent conjugates from any antibody, in the absence of structural data.

Functional mapping of conserved, surface-exposed charges of antibody variable domains.

Surface-exposed charges can affect protein structure, stability and solubility as well as the kinetics of both the folding process and interaction with binding partners. We have investigated the influence on kinetic interaction parameters of 14 conserved, surface-exposed charges located away from the paratope in the variable domains of two antibodies of different specificity. We found that conserved, surface-exposed, charged framework residues are asymmetrically distributed on opposite faces of both VH and VL domains. Some of the charges play a critical role in protein folding and stability. While electrostatic forces within or close to the binding interface can be used to optimize the association rate, we confirmed the predicted minor effects of charge modifications remote from the binding site. They had no effect on the dissociation rate parameter. Our study demonstrates the role of residues remote from the interaction site in the recognition function as well as the limited effect of surface charge modifications in antibody fragments on kinetic interaction parameters.

Gestion ambiental del sistema nacional de areas protegicas con partcipacion de las FF.AA: estructuras sociales y redes institucionales / sss

El trabajo consiste en una propuesta de gestion ambiental del SNAP con participacion de las FF.AA, tomando en cuenta el historicxo y escaso dominio territorial que el componente ejerce en el oriente boliviano, el mismo que en la actualidad esta revertido por tanto se requiere con urgencia la participacion ampliada de instituciones con presencia nacional que pueden actuar en el cinturon de amortiguamiento conservando y preservando el SNAP mediante el desempeño de funciones sustentadas en estructuras sociales y redes institucionales lideralizadas por las FF:AA. orientando estrategicamente los esfuerzo al desarrollo sostenible y el medio ambiente...