Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins

Ferritin-like molecules show a remarkable combination of the evolutionary conserved activity of iron uptake and release that engage different pores in the conserved ferritin shell. It was hypothesized that pore selection and iron traffic depend on dynamic allostery with no conformational changes in the backbone. In this study, we detect the allosteric networks in Pseudomonas aeruginosa bacterioferritin (BfrB), bacterial ferritin (FtnA), and bullfrog M and L ferritins (Ftns) by a network-weaving algorithm (NWA) that passes threads of an allosteric network through highly correlated residues using hierarchical clustering. The residue-residue correlations are calculated in the packing-on elastic network model that introduces atom packing into the common packing-off model. Applying NWA revealed that each of the molecules has an extended allosteric network mostly buried inside the ferritin shell. The structure of the networks is consistent with experimental observations of iron transport: The allosteric networks in BfrB and FtnA connect the ferroxidase center with the 4-fold pores and B-pores, leaving the 3-fold pores unengaged. In contrast, the allosteric network directly links the 3-fold pores with the 4-fold pores in M and L Ftns. The majority of the network residues are either on the inner surface or buried inside the subunit fold or at the subunit interfaces. We hypothesize that the ferritin structures evolved in a way to limit the influence of functionally unrelated events in the cytoplasm on the allosteric network to maintain stability of the translocation mechanisms. We showed that the residue-residue correlations and the resultant long-range cooperativity depend on the ferritin shell packing, which, in turn, depends on protein sequence composition. Switching from the packing-on to the packing-off model reduces correlations by 35%-38% so that no allosteric network can be found. The influence of the side-chain packing on the allosteric networks explains the diversity in mechanisms of iron traffic suggested by experimental approaches. © 2014 AIP Publishing LLC

Protein Dynamics and Ion Traffic in Bacterioferritin

Bacterioferritin (Bfr) is a spherical protein composed of 24 subunits and 12 heme molecules. Bfrs contribute to regulate iron homeostasis in bacteria by capturing soluble but potentially toxic Fe2+ and by compartmentalizing it in the form of a bioavailable ferric mineral inside the protein’s hollow cavity. When iron is needed, Fe3+ is reduced and mobilized into the cytosol as Fe2+. Hence, key to the function of Bfr is its ability to permeate iron ions in and out of its interior cavity, which is likely imparted by a flexible protein shell. To examine the conformational flexibility of Bfrs in a native-like environment and the way in which the protein shell interacts with monovalent cations, we have performed molecular dynamics (MD) simulations of BfrB from Pseudomonas aeruginosa (Pa BfrB) in K2HPO4 solutions at different ionic strengths. The results indicate the presence of coupled thermal fluctuations (dynamics) in the 4-fold and B-pores of the protein, which is key to enable passage of monovalent cations through the protein shell using B-pores as conduits. The MD simulations also show that Pa BfrB ferroxidase centers are highly dynamic and permanently populated by transient cations exchanging with other cations in the interior cavity, as well as the solution bathing the protein. Taken together, the findings suggest that Fe2+ traffic across the Pa BfrB shell via B-pores and that the ferroxidase pores enable capture and oxidation of Fe2+, followed by translocation of Fe3+ to the interior cavity, aided by the conformationally active H130

Hydrodynamical simulations of protoplanetary disks including irradiation of stellar photons. I. Resolution study for Vertical Shear Instability (VSI)

In recent years hydrodynamical (HD) models have become important to describe the gas kinematics in protoplanetary disks, especially in combination with models of photoevaporation and/or magnetic-driven winds. We focus on diagnosing the the vertical extent of the VSI at 203 cells per scale height and allude at what resolution per scale height we obtain convergence. Finally, we determine the regions where EUV, FUV and X-Rays are dominant in the disk. We perform global HD simulations using the PLUTO code. We adopt a global isothermal accretion disk setup, 2.5D (2 dimensions, 3 components) which covers a radial domain from 0.5 to 5.0 and an approximately full meridional extension. We determine the 50 cells per scale height to be the lower limit to resolve the VSI. For higher resolutions, greater than 50 cells per scale height, we observe the convergence for the saturation level of the kinetic energy. We are also able to identify the growth of the `body' modes, with higher growth rate for higher resolution. Full energy saturation and a turbulent steady state is reached after 70 local orbits. We determine the location of the EUV-heated region defined by the radial column density to be 10$^{19}$ cm$^{-2}$ located at $H_\mathrm{R}\sim9.7$, and the FUV/X-Rays-heated boundary layer defined by 10$^{22}$ cm$^{-2}$ located at $H_\mathrm{R}\sim6.2$, making it necessary to introduce the need of a hot atmosphere. For the first time, we report the presence of small scale vortices in the r-Z plane, between the characteristic layers of large scale vertical velocity motions. Such vortices could lead to dust concentration, promoting grain growth. Our results highlight the importance to combine photoevaporation processes in the future high-resolution studies of the turbulence and accretion processes in disks

How productive are academic researchers in agriculture-related sciences? The Mexican case

This paper explores the effect of commercial farmers-academic researchers linkages on research productivity in fields related to agriculture. Using original data and econometric analysis, our findings show a positive and significant relationship between intensive linkages with a small number of commercial farmers and research productivity, when this is defined as publications in ISI journals. This evidence seems contrary to other contributions that argue that strong ties with the business sector reduce research productivity and distort the original purposes of university, i.e., conducting basic research and preparing highly-trained professionals. When research productivity is defined more broadly adding other types of research outputs, the relationship is also positive and significant confirming the argument that close ties between public research institutions and businesses foster the emergence of new ideas that can be translated into innovations with commercial and/or social value. Another important finding is that researchers in public institutions produce several types of research outputs; therefore, measuring research productivity only by published ISI papers misses important dimensions of research activities.agriculture sector, research productivity, university-business sector interaction, university-industry collaboration

Medida de áreas en contextos auténticos: un enfoque desde la modelación matemática

Este artículo muestra algunos avances de la investigación llevada a cabo en el marco de la Maestría en Educación de la Universidad de Antioquia; usa el entorno de las inundaciones presentadas en una institución educativa por causa del desbordamiento del Río Cauca. El estudio tiene que ver con la construcción de modelos que hacen estudiantes de grado décimo a partir de relaciones de dependencia establecidas entre las áreas inundadas en su institución educativa y la altura del nivel del agua en un punto de referencia, lo que les ha permitido lograr no solo una forma alternativa de asociar las operaciones al medio, sino también reflexionar sobre cómo estas emergen en el fenómeno en cuestión y la proposición de alternativas de solución que contribuyan a minimizar el impacto social y ambiental de dicho fenómeno. Para el desarrollo del estudio, se tienen en cuenta el ambiente cotidiano, la comunicación, las experiencias de cada individuo y su interacción con el grupo, aspectos propios de la investigación cualitativa. En este sentido, el estudio de casos pretende explorar, indagar y analizar las diversas formas en que el alumno construye y otorga significado a elementos matemáticos en un contexto auténtico

Medida de área y el volumen en contextos auténticos: una alternativa de aprendizaje a través de la modelación matemática

Este proyecto de investigación se desarrolla en el contexto de las inundaciones presentadas en una Institución Educativa por causa del desbordamiento del río Cauca. Esta situación adversa funciona como una oportunidad para construir relaciones matemáticas referidas a la medida del área y el volumen mediante procesos de modelación matemática. Estos, obtenidos desde situaciones en el contexto de los estudiantes, permiten una resignificación de conceptos matemáticos. Para el desarrollo del proyecto, se tiene en cuenta el entorno cotidiano, la comunicación y las experiencias de cada individuo, aspectos propios de la investigación cualitativa; en este sentido se realiza un estudio de casos donde se pretende explorar, indagar y analizar las diversas formas como el estudiante construye y da significado a elementos matemáticos que emergen de una situación en contexto

Una facultad llena de posibilidades

Con cierta frecuencia, los estudiantes acostumbramos a quejarnos (muchas veces con razón) acerca de lo que necesitamos, lo que nos falta y que la universidad no es capaz de ofrecernos. Sin embargo, muchas veces desconocemos la gran cantidad de actividades y posibilidades que emanan de ésta, y no somos capaces de aprovecharlas por falta de información. El caso de la Facultad de Medicina de la Universidad de Granada es un perfecto ejemplo de ello, y fruto del intenso trabajo y preclaras ideas que proceden de la motivación y ganas de mejoría del colectivo estudiantil, nuestra facultad goza de una incuestionable “red” de asociaciones, actividades y, por tanto, posibilidades