Interaction between the elastin peptide VGVAPG and human elastin binding protein
The elastin binding protein (EBP), a spliced variant of lysosomal β-galactosidase, is the primary receptor of elastin peptides that have been linked to emphysema, aneurysm and cancer progression. The sequences recognized by EBP share the XGXXPG consensus pattern found in numerous matrix proteins, notably in elastin where the VGVAPG motif is repeated. To delineate the elastin binding site of human EBP, we built a homology model of this protein and docked VGVAPG on its surface. Analysis of this model suggested that Gln-97 and Asp-98 were required for interaction with VGVAPG because they contribute to the definition of a pocket thought to represent the elastin binding site of EBP. Additionally, we proposed that Leu-103, Arg-107, and Glu-137 were essential residues because they could interact with VGVAPG itself. Site-directed mutagenesis experiments at these key positions validated our model. This work therefore provides the first structural data concerning the interaction of the VGVAPG with its cognate receptor. The present structural data should now allow the development of EBP-specific antagonists.
Many environmental stimuli present a quasi-rhythmic structure at different timescales that the brain needs to decompose and integrate. Cortical oscillations have been proposed as instruments of sensory de-multiplexing, i.e., the parallel processing of different frequency streams in sensory signals. Yet their causal role in such a process has never been demonstrated. Here, we used a neural microcircuit model to address whether coupled theta–gamma oscillations, as observed in human auditory cortex, could underpin the multiscale sensory analysis of speech. We show that, in continuous speech, theta oscillations can flexibly track the syllabic rhythm and temporally organize the phoneme-level response of gamma neurons into a code that enables syllable identification. The tracking of slow speech fluctuations by theta oscillations, and its coupling to gamma-spiking activity both appeared as critical features for accurate speech encoding. These results demonstrate that cortical oscillations can be a key instrument of speech de-multiplexing, parsing, and encoding.
Elastin is an essential component of numerous human tissues and plays a critical role in elasticity of skin, lungs and arteries. During vascular aging, the elastin network is degraded generating elastin-derived peptides (EDP). The ERC (Elastin Receptor Complex) is a membrane heterotrimeric receptor composed, amongst others, of a membrane-bound neuraminidase, NEU-1. Binding of EDP to the ERC induces the activation of signaling pathways associated with biological effects notably the development of diseases such as atherosclerosis, cancer and diabetes. Previous studies of our laboratory have shown that NEU-1 catalytic activity is linked to its ability to homodimerize. Thus, NEU-1 constitutes a key pharmacological target to fight against deleterious effects of EDP. The aim of this work is to develop by biological/biochemical experiments and molecular dynamic (MD) simulations a transmembrane interfering peptide (pI) able to inhibit specifically NEU-1 dimerization. Peptides are delivered into cells using two strategies, TAT peptides, which are cell-penetrating peptides, or lithium dodecyl sulfate micelles. No cellular toxicity was observed in both approaches. Confocal microscopy underlines a colocalization between pI and NEU-1 at the plasma membrane and coimmunoprecipitation experiments show an interaction between pI and NEU-1. Furthermore, sialidase activity assays point out the ability of pI to inhibit NEU-1 homodimerization (47%; 51%) and its associated sialidase activity (21%; 47%). Preliminary MD simulation studies emphasize that both pI and the transmembrane domain of NEU-1 are stable and helix integrity is conserved in lipid bilayer environments. Moreover, the formation of a spontaneous dimer between NEU-1 and pI was identified. Further MD analyses underline the bio- logical relevance of our membrane model. These results reveal the ability of pI to bind to NEU-1, inhibit its dimerization and sialidase activity.
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.