Stéphanie Baud

Elastin-Derived Peptides Are New Regulators of Insulin Resistance Development in Mice

Although it has long been established that the extracellular matrix acts as a mechanical support, its degradation products, which mainly accumulate during aging, have also been demonstrated to play an important role in cell physiology and the development of cardiovascular and metabolic diseases. In the current study, we show that elastin-derived peptides (EDPs) may be involved in the development of insulin resistance (IRES) in mice. In chow-fed mice, acute or chronic intravenous injections of EDPs induced hyperglycemic effects associated with glucose uptake reduction and IRES in skeletal muscle, liver, and adipose tissue. Based on in vivo, in vitro, and in silico approaches, we propose that this IRES is due to interaction between the insulin receptor (IR) and the neuraminidase-1 subunit of the elastin receptor complex triggered by EDPs. This interplay was correlated with decreased sialic acid levels on the β-chain of the IR and reduction of IR signaling. In conclusion, this is the first study to demonstrate that EDPs, which mainly accumulate with aging, may be involved in the insidious development of IRES.

Interaction between the elastin peptide VGVAPG and human elastin binding protein

Background: The interaction of the peptide VGVAPG with the elastin binding protein is critically involved in aneurysm progression. Results: A molecular model of this interaction is proposed and explored using a site-directed mutagenesis strategy. Conclusion: Three residues, Leu-103, Arg-107, and Glu-137, of elastin binding protein are critical players in this interaction. Significance: Our data now allow the design of antagonists of VGVAPG. 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.

Binding of inositol stereoisomers to model amyloidogenic peptides.

The self-aggregation of proteins into amyloid fibrils is a pathological hallmark of numerous incurable diseases such as Alzheimers disease. scyllo-Inositol is a stereochemistry-dependent in vitro inhibitor of amyloid formation. As the first step to elucidate its mechanism of action, we present molecular dynamics simulations of scyllo-inositol and its inactive stereoisomer, chiro-inositol, with simple peptide models, alanine dipeptide (ADP) and (Gly-Ala)(4). We characterize molecular interactions and compute equilibrium binding constants between inositol and ADP as well as, successively, monomers, amorphous aggregates, and fibril-like β-sheet aggregates of (Gly-Ala)(4). Inositol interacts weakly with all peptide systems considered, with millimolar to molar affinities, and displaces the conformational equilibria of ADP but not of the (Gly-Ala)(4) systems. However, scyllo- and chiro-inositol adopt different binding modes on the surface of β-sheet aggregates. These results suggest that inositol does not inhibit amyloid formation by breaking up preformed aggregates but rather by binding to the surface of prefibrillar aggregates.

Molecular-level characterization of elastin-like constructs and human aortic elastin

This study aimed to characterize the structures of two elastin-like constructs, one composed of a cross-linked elastin-like polypeptide and the other one of cross-linked tropoelastin, and native aortic elastin. The structures of the insoluble materials and human aortic elastin were investigated using scanning electron microscopy. Additionally, all samples were digested with enzymes of different specificities, and the resultant peptide mixtures were characterized by ESI mass spectrometry and MALDI mass spectrometry. The MS(2) data was used to sequence linear peptides, and cross-linked species were analyzed with the recently developed software PolyLinX. This enabled the identification of two intramolecularly cross-linked peptides containing allysine aldols in the two constructs. The presence of the tetrafunctional cross-link desmosine was shown for all analyzed materials and its quantification revealed that the cross-linking degree of the two in vitro cross-linked materials was significantly lower than that of native elastin. Molecular dynamics simulations were performed, based on molecular species identified in the samples, to follow the formation of elastin cross-links. The results provide evidence for the significance of the GVGTP hinge region of domain 23 for the formation of elastin cross-links. Overall, this work provides important insight into structural similarities and differences between elastin-like constructs and native elastin. Furthermore, it represents a step toward the elucidation of the complex cross-linking pattern of mature elastin.

Elastin peptides in aging and pathological conditions

Abstract Elastin is the protein responsible for the resilience of vertebrate tissue. It is an extremely stable protein deposited during the early stages of life and experiencing almost no renewal. As a consequence, it can be considered that each individual has an elastin capital for life. Despite its extreme stability, elastin can be degraded by several enzymes termed elastases. Elastases are among the most aggressive proteases, and their presence is increased with age. As a consequence, elastin fragmentation resulting in the generation of elastin peptides is one of the hallmarks of aging. This review will examine their nature and further expose our current understanding of the role played by these peptides in aging and their contribution to tissue homeostasis and several pathologies.

Impact of sialic acids on the molecular dynamic of bi-antennary and tri-antennary glycans

Sialic acids (SA) are monosaccharides that can be located at the terminal position of glycan chains on a wide range of proteins. The post-translational modifications, such as N-glycan chains, are fundamental to protein functions. Indeed, the hydrolysis of SA by specific enzymes such as neuraminidases can lead to drastic modifications of protein behavior. However, the relationship between desialylation of N-glycan chains and possible alterations of receptor function remains unexplored. Thus, the aim of the present study is to establish the impact of SA removal from N-glycan chains on their conformational behavior. We therefore undertook an in silico investigation using molecular dynamics to predict the structure of an isolated glycan chain. We performed, for the first time, 3 independent 500 ns simulations on bi-antennary and tri-antennary glycan chains displaying or lacking SA. We show that desialylation alters both the preferential conformation and the flexibility of the glycan chain. This study suggests that the behavior of glycan chains induced by presence or absence of SA may explain the changes in the protein function.

Inverse docking method for new proteins targets identification

A framework to perform inverse docking was developed.Different strategies to distribute the docking procedure were implemented.Validation with experimental complex have been done.A docking test of one ligand versus 100 proteins was performed.A better conformational sampling is processed than current methods. Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies since it improves the execution of inverse docking.

Small leucine-rich proteoglycans and matrix metalloproteinase-14: Key partners?

Small leucine-rich proteoglycans (SLRPs) are important regulators of extracellular matrix assembly and cell signaling. They are a family of proteoglycans that are present in extracellular matrix and that share in common multiple repeats of a leucine-rich structural motif. SLRPs have been identified as inhibitors of cancer progression by affecting MMPs, especially MMP-14 activity. Lumican, a member of the SLRPs family, and its derived peptides were shown to possess anti-tumor activity. Interestingly, it was demonstrated recently that lumican interacts directly with the catalytic domain of MMP-14 and inhibits its activity. The aim of this review was to summarize the interactions between SLRPs and MMPs with a special interest to lumican.

Parallel strategies for an inverse docking method

Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies as a way to improve the execution of inverse docking.

Conformation-dependent binding of a Tetrastatin peptide to α v β 3 integrin decreases melanoma progression through FAK/PI 3 K/Akt pathway inhibition

Tetrastatin, a 230 amino acid sequence from collagen IV, was previously demonstrated to inhibit melanoma progression. In the present paper, we identified the minimal active sequence (QKISRCQVCVKYS: QS-13) that reproduced the anti-tumor effects of whole Tetrastatin in vivo and in vitro on melanoma cell proliferation, migration and invasion. We demonstrated that QS-13 binds to SK-MEL-28 melanoma cells through the αvβ3 integrin using blocking antibody and β3 integrin subunit siRNAs strategies. Relevant QS-13 conformations were extracted from molecular dynamics simulations and their interactions with αVβ3 integrin were analyzed by docking experiments to determine the binding areas and the QS-13 amino acids crucial for the binding. The in silico results were confirmed by in vitro experiments. Indeed, QS-13 binding to SK-MEL-28 was dependent on the presence of a disulfide-bound as shown by mass spectroscopy and the binding site on αVβ3 was located in close vicinity to the RGD binding site. QS-13 binding inhibits the FAK/PI3K/Akt pathway, a transduction pathway that is largely involved in tumor cell proliferation and migration. Taken together, our results demonstrate that the QS-13 peptide binds αvβ3 integrin in a conformation-dependent manner and is a potent antitumor agent that could target cancer cells through αVβ3.