Thermodynamics of Cooperative DNA Recognition at a Replication Origin and Transcription Regulatory Site

Binding cooperativity guides the formation of protein-nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic-entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.Fil: Dellarole, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: Sánchez Miguel, Ignacio Enrique. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: de Prat Gay, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; Argentin

The influence of lipids on the fate of nitrogen during hydrothermal liquefaction of protein-containing biomass

Nitrogen (N) in the bio-crude obtained from hydrothermal liquefaction (HTL) of protein-containing biomass not only reduces the heating value of fuels, but also increases cost for upgrading to meet the existing fuel standards. Considerable work so far had been focused on N-containing heterocycles formed via Maillard reactions. However, limited information is available on the influence of lipids, as the amides formation could compete with the Maillard reactions, further affecting the fate of N. The objective of this work is therefore to identify the influence of lipids on the nitrogen distribution in the different product phases, with a particular focus on the reaction of N-containing compounds, trying to achieve deeper understanding about reaction mechanism of HTL. In this study, we tested a set of model compounds (lactose as model carbohydrate, lysine as model protein, palmitic acid as model component of a lipid) to conduct HTL. The model compounds were treated individually and in mixtures at 250 - 350 °C for batch reaction times of 20 min. We investigated the N-distribution in the different HTL-products, mainly focusing on the bio-crude. At 300 °C, only 4.9 wt.% of N distribution (defined as the amount of N in the product relative to that in the feedstocks) is found from HTL of single lysine, while 43.6 wt.% of that is obtained from HTL of the ternary mixture. This is most likely because the higher yield (54.1wt.%) of bio-crude produced from mixture. Specific N-containing compounds in the bio-crude were quantified. With addition of lipids, less yields of typical Maillard reaction products like pyrazines and caprolactam, generated from HTL of carbohydrates and proteins, were obtained, while amides are revealed with significant yield of 2.1 wt.%, indicating that in the presence of lipids, amide formation competes with the generation of Maillard reaction products. These results provide valuable insights for the transformation of nitrogen as well as the reaction pathways of complex systems such as sewage sludge, micro algae, food waste and on the like

Effective Action Method for Computing Next to Leading Corrections of O(N)O(N) Models

We compute the corrections of next to leading order in the ${1 \over N}$ expansion to the effective potential of a system described by a Ginzburg-Landau model with $N$ components and quartic interaction, in the case of spontaneous symmetry breaking. The method we apply allows to generalize in a simple way the so-called Self-Consistent Screened Approximation (SCSA).Comment: p. 8, LATEX, DFF 193/9/199

Lifetime of magnetic excitations in supported ferromagnetic and antiferromagnetic spin-1/2 Heisenberg chains

The lifetime of magnetic excitations in finite 1D-supported Heisenberg chains of magnetic atoms is studied theoretically for a model system formed of S = 1/2 spins. Both ferromagnetic and antiferromagnetic cases are considered as well as open chains and rings of atoms. Different chain lengths are considered allowing extrapolation to infinite chains. All the excited magnetic states in the finite chains and rings are studied, not only the spin-wave mode. The magnetic excitations decay by electron-hole pair creation in the substrate. As the main result, for all the systems considered, the decay rate appears to vary approximately proportionally to the excitation energy of the state, with a proportionality constant independent of the strength of the Heisenberg exchange term. In certain finite systems, a stable state is evidenced at low energy, associated with a special spin coupling structure. © 2012 American Physical Society.Peer Reviewe

Recent TEM studies of precipitate growth mechanisms

In this review recent results of transmission electron microscopy studies of precipitation in a number of model binary alloy systems are presented. Emphasis is placed on identifying (i) the nature of the structural change occurring during the transformations, and (ii) the crystal lattice defects and deformation modes required to accommodate the growing precipitate in the parent phase. Precipitation reactions are classified in terms of their transformation strains, and simple predictive models for the precipitate morphology are developed for each case. Brief discussions are also given on the nature of a general plate precipitate interface and the effect of crystal symmetry on morphological distributions.Des exemples récents d'étude par microscopie électronique en transmission sont analysés dans cette revue. L'accent est mis sur l'identification (i) de la nature des modifications de structure intervenant lors des transformations, (ii) des défauts cristallins et des modes de déformation nécessaires à la croissance du précipité dans la phase mère. Un classement des réactions de précipitation est effectué selon les mécanismes de déformation mis en jeu. Des modèles simples permettant de prévoir la morphologie des précipités sont précisés dans chaque cas. Des éléments de discussion concernant la nature de l'interface entre la matrice et un précipité quelconque en plaquette sont également fournis. Les effets de la symétrie cristalline sur les distributions de forme sont brièvement abordés