Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations

Epigenetic therapy is an important focus of research for drug development in the treatment of cancer. Valproic acid (VPA) is an HDAC inhibitor that has been evaluated in clinical studies. Despite its success in treating cancer, the mechanism of inhibition of VPA in HDAC is unknown. To this end, we have used docking and molecular dynamic simulations to investigate VPA binding to HDAC, employing both native and rebuilt 3-D structures. The results showed that VPA, via its carboxyl group, coordinates the Zn atom and other local residues (H141-142 and Y360) located at the catalytic site (CS) of HDAC. This causes electrostatic and hydrogen bonding interactions while having little interaction with the hydrophobic side chains, resulting in a low affinity. However, after several docking studies on different native HDAC 3-D structures and after using several snapshots from MD simulations, it became apparent that VPA bound with highest affinity at a site located at the acetyl-releasing channel, termed the hydrophobic active site channel (HASC). The affinity of VPA for HASC was due to its highly hydrophobic properties that allow VPA to take part in van der Waals interactions with Y18, I19, Y20, V25, R37, A38, V41, H42, I135 and W137, while VPA's carboxylate group has several hydrogen bonding interactions with the backbones of S138, I19, N136 and W137. MD simulations showed that the HASC door continuously opened and closed, which affected the affinity of VPA to the HASC, but the affinity toward the HASC was consistently higher than that obtained for the CS, suggesting that the HASC could be involved in the mechanism of inhibition.     

Differential modulation of Kv4.2 and Kv4.3 channels by calmodulin-dependent protein kinase II in rat cardiac myocytes

In this work we have combined biochemical and electrophysiological approaches to explore the modulation of rat ventricular transient outward K(+) current (I(to)) by calmodulin kinase II (CaMKII). Intracellular application of CaMKII inhibitors KN93, calmidazolium, and autocamtide-2-related inhibitory peptide II (ARIP-II) accelerated the inactivation of I(to), even at low [Ca(2+)]. In the same conditions, CaMKII coimmunoprecipitated with Kv4.3 channels, suggesting that phosphorylation of Kv4.3 channels modulate inactivation of I(to). Because channels underlying I(to) are heteromultimers of Kv4.2 and Kv4.3, we have explored the effect of CaMKII on human embryonic kidney (HEK) cells transfected with either of those Kvalpha-subunits. Whereas Kv4.3 inactivated faster upon inhibition of CaMKII, Kv4.2 inactivation was insensitive to CaMKII inhibitors. However, Kv4.2 inactivation became slower when high Ca(2+) was used in the pipette or when intracellular [Ca(2+)] ([Ca(2+)](i)) was transiently increased. This effect was inhibited by KN93, and Western blot analysis demonstrated Ca(2+)-dependent phosphorylation of Kv4.2 channels. On the contrary, CaMKII coimmunoprecipitated with Kv4.3 channels without a previous Ca(2+) increase, and the association was inhibited by KN93. These results suggest that both channels underlying I(to) are substrates of CaMKII, although with different sensitivities; Kv4.2 remain unphosphorylated unless [Ca(2+)](i) increases, whereas Kv4.3 are phosphorylated at rest. In addition to the functional impact that phosphorylation of Kv4 channels could cause on the shape of action potential, association of CaMKII with Kv4.3 provides a new role of Kv4.3 subunits as molecular scaffolds for concentrating CaMKII in the membrane, allowing Ca(2+)-dependent modulation by this enzyme of the associated Kv4.2 channels.     

The volume and hydration of the Cryptococcus neoformans polysaccharide capsule

We present a new method to measure capsule size in the human fungal pathogen Cryptococcus neoformans that avoids the limitations and biases inherent in India ink measurements. The method is based on the use of gamma-radiation, which efficiently releases the capsule from the cell. By comparing the volume of irradiated and non-irradiated cells, one can accurately estimate the relative size of the capsule per cell. This method was also used to obtain an estimate of the capsule weight and water content. The C. neoformans capsule is a highly hydrated structure in all the conditions measured. However, after capsule enlargement, the amount of capsular polysaccharide significantly increases, suggesting a that capsule growth has a high energy cost for the cell.     

Guiding Neuronal Cell Migrations

Neuronal migration is, along with axon guidance, one of the fundamental mechanisms underlying the wiring of the brain. As other organs, the nervous system has acquired the ability to grow both in size and complexity by using migration as a strategy to position cell types from different origins into specific coordinates, allowing for the generation of brain circuitries. Guidance of migrating neurons shares many features with axon guidance, from the use of substrates to the specific cues regulating chemotaxis. There are, however, important differences in the cell biology of these two processes. The most evident case is nucleokinesis, which is an essential component of migration that needs to be integrated within the guidance of the cell. Perhaps more surprisingly, the cellular mechanisms underlying the response of the leading process of migrating cells to guidance cues might be different to those involved in growth cone steering, at least for some neuronal populations.The migration of newly born neurons is a precisely regulated process that is critical for the development of brain architecture. Neurons arise from the proliferative epithelium that covers the ventricular space throughout the neural tube, an area named the ventricular zone (VZ). From there, newly born neurons adopt two main strategies to disperse throughout the central nervous system (CNS), designated as radial and tangential migration (Hatten 1999; Marín and Rubenstein 2003). During radial migration, neurons follow a trajectory that is perpendicular to the ventricular surface, moving alongside radial glial fibers expanding the thickness of the neural tube. In contrast, tangentially migrating neurons move in trajectories that are parallel to the ventricular surface and orthogonal to the radial glia palisade (Fig. 1). Besides their relative orientation, some of the basic mechanisms underlying the movement of cells using each of these two modes of migration are also different. For example, radially migrating neurons often use radial glial fibers as substrate, whereas tangentially migrating neurons do not seem to require their support to migrate. Even so, neurons may alternate from radial to tangential movement and vice versa during the course of their migration. This suggests that both types of migrations share common principles, in particular those directly related to the cell biology of movement (Marín et al. 2006).Open in a separate windowFigure 1.Representative migrations in the developing CNS. Multiple migrations coexist during embryonic development at different areas of the central nervous system. This schema summarizes some of these migrations during the second week of the embryonic period in the mouse. Neurons use tangential and radial migration to reach their final destination; both strategies are used by the same neurons at different stages of development (i.e., cortical interneurons in the forebrain and precerebellar neurons in the hindbrain). (IML) intermediolateral region of the spinal cord; (IO) inferior olive nucleus; (LGE) lateral ganglionic eminence; (LRN) lateral reticular nucleus; (MGE) medial ganglionic eminence; (NCx) neocortex; (OB) olfactory bulb.One of the structures that better illustrates how both types of migrations are integrated during brain development is the cerebral cortex, and so we will primarily refer to studies performed on cortical neurons for this review. The adult cerebral cortex contains two main classes of neurons: glutamatergic cortical projection neurons (also known as pyramidal cells) and GABAergic interneurons. Pyramidal cells are generated in the ventricular zone (VZ) of the embryonic pallium—the roof of the telencephalon—and reach their final position by radial migration (Rakic 2007). In contrast, cortical interneurons are born in the subpallium—the base of telencephalon—and reach the cerebral cortex through a long tangential migration (Corbin et al. 2001; Marín and Rubenstein 2001).The earliest cortical neurons form a transient structure known as the preplate, around embryonic day 10 (E10) of gestation age in the mouse. This primordial layer consists of Cajal-Retzius cells and the first cohort of pyramidal neurons, which will eventually populate the subplate. Cajal-Retzius cells, which play important roles during neuronal migration, arise from discrete pallial sources and colonize the entire surface of the cortex through tangential migration (Bielle et al. 2005; Takiguchi-Hayashi et al. 2004; Yoshida et al. 2006). The next cohort of pyramidal cells forms the cortical plate (CP) by intercalating in the preplate and splitting this primitive structure in a superficial layer, the marginal zone (MZ or layer I), and a deep layer, the subplate. The development of the neocortex progresses with new waves of neurons that occupy progressively more superficial positions within the CP (Gupta et al. 2002; Marín and Rubenstein 2003). Birth dating studies have shown that layers II–VI of the cerebral cortex are generated in an “inside-out” sequence. Neurons generated earlier reside in deeper layers, whereas later-born neurons migrate past existing layers to form superficial layers (Angevine and Sidman 1961; Rakic 1974). In parallel to this process, GABAergic interneurons migrate to the cortex, where they disperse tangentially via highly stereotyped routes in the MZ, SP, and lower intermediate zone/subventricular zone (IZ/SVZ) (Lavdas et al. 1999). Interneurons then switch from tangential to radial migration to adopt their final laminar position in the cerebral cortex (Ang et al. 2003; Polleux et al. 2002; Tanaka et al. 2003).     

Stability and kinetic behavior of immobilized laccase from Myceliophthora thermophila in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium ethylsulfate

The use of ionic liquids (ILs) as reaction media for enzymatic reactions has increased their potential because they can improve enzyme activity and stability. Kinetic and stability properties of immobilized commercial laccase from Myceliophthora thermophila in the water‐soluble IL 1‐ethyl‐3‐methylimidazolium ethylsulfate ([emim][EtSO₄]) have been studied and compared with free laccase. Laccase immobilization was carried out by covalent binding on glyoxyl–agarose beads. The immobilization yield was 100%, and the activity was totally recovered. The Michaelis‐Menten model fitted well to the kinetic data of enzymatic oxidation of a model substrate in the presence of the IL [emim][EtSO₄]. When concentration of the IL was augmented, the values of V_max for free and immobilized laccases showed an increase and slight decrease, respectively. The laccase–glyoxyl–agarose derivative improved the laccase stability in comparison with the free laccase regarding the enzymatic inactivation in [emim][EtSO₄]. The stability of both free and immobilized laccase was slightly affected by small amounts of IL (<50%). A high concentration of the IL (75%) produced a large inactivation of free laccase. However, immobilization prevented deactivation beyond 50%. Free and immobilized laccase showed a first‐order thermal inactivation profile between 55 and 70°C in the presence of the IL [emim][EtSO₄]. Finally, thermal stability was scarcely affected by the presence of the IL. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:790–796, 2014     

N-glycans on Nipah virus fusion protein protect against neutralization but reduce membrane fusion and viral entry

Nipah virus (NiV) is a deadly emerging paramyxovirus. The NiV attachment (NiV-G) and fusion (NiV-F) envelope glycoproteins mediate both syncytium formation and viral entry. Specific N-glycans on paramyxovirus fusion proteins are generally required for proper conformational integrity and biological function. However, removal of individual N-glycans on NiV-F had little negative effect on processing or fusogenicity and has even resulted in slightly increased fusogenicity. Here, we report that in both syncytium formation and viral entry assays, removal of multiple N-glycans on NiV-F resulted in marked increases in fusogenicity (>5-fold) but also resulted in increased sensitivity to neutralization by NiV-F-specific antisera. The mechanism underlying the hyperfusogenicity of these NiV-F N-glycan mutants is likely due to more-robust six-helix bundle formation, as these mutants showed increased fusion kinetics and were more resistant to neutralization by a fusion-inhibitory reagent based on the C-terminal heptad repeat region of NiV-F. Finally, we demonstrate that the fusogenicities of the NiV-F N-glycan mutants were inversely correlated with the relative avidities of NiV-F's interactions with NiV-G, providing support for the attachment protein "displacement" model of paramyxovirus fusion. Our results indicate that N-glycans on NiV-F protect NiV from antibody neutralization, suggest that this "shielding" role comes together with limiting cell-cell fusion and viral entry efficiencies, and point to the mechanisms underlying the hyperfusogenicity of these N-glycan mutants. These features underscore the varied roles that N-glycans on NiV-F play in the pathobiology of NiV entry but also shed light on the general mechanisms of paramyxovirus fusion with host cells.     

Phenomorphology and ecomorphological characters of Maytenus senegalensis L. Shrublands in the Iberian Peninsula: A comparison with other Mediterranean plant communities

This work sets out to establish ecomorphological and phenomorphological patterns in the constituent flora of an Iberian Maytenus senegalensis plant community in order to relate it with or separate it from other types of Mediterranean vegetation. This plant community contains tall shrubs, scrubs, palms and vines of a variety of families. Typical ecomorphological adaptations to the Mediterranean climate were observed in the community studied: an abundance of thorny species or species with tomentose leaves and photosynthetic stems, small leaves and a high presence of species with organs capable of post-fire regeneration. However, the community also showed hybrid characteristics between scrubland (predominantly malacophyllous leaves lasting 9 months on average and low biomass) and tall shrubland communities (predominance of phanerophytes up to 3 m in height, predominantly smooth bark, periodical reposition of leaves, mean lifespan of plants 25 years and mainly fleshy fruit). The community also presents an outstanding quantity of amphiphytes (29%). From a phenological point of view, the formation of buds in winter, flowering in spring, summer–autumn seed dispersal and leaf shedding in summer are typical of other Mediterranean communities, while fructification and growth lasting three seasons, as in the case of Maytenus shrubland, is not. The RVA phenophasic index (balance between reproductive and vegetative phenophases) with values of 0.4–2 shows an intermediate value between typical shrubland (0.3–1) and forest community (1–2) values. The APC index (period of phenophasic activity of the community) differentiates it from others, since it remains at 100% for seven months, three of which are winter months. Phenophasic patterns (overlapping, or not, of flower bud formation, flowering and growth) show how similar M. senegalensis shrubland is to forests because of the absence of phenophase pattern type A (characteristic in open-scrublands); in addition, we have detected a new pattern (type G), still regarded as exclusive to M. senegalensis. As regards the existence of coenomorphs (group of species with similar morpho-functional strategies), the studied community showed much greater diversity than other communities studied to date, with an Strategies Richness index (SRi) of 0.79 (11 groups covering the 14 species existing), pointing to the co-existence of a great variety of eco-phenomorphological strategies, each with a successful response to the same ecological conditions. Finally, some of the species in the community, e.g. Asparagus horridus, Chamaerops humilis and M. senegalensis, stand out because of their unique ecomorphological and phenological characteristics.