Fragment­ based modeling of protein­-GAG complexes

International audienceGlycosaminoglycans (GAGs) are linear anionic periodic poly-saccharides that bind to their protein targets in the extracellular matrix, and so participate in many cell-signaling processes. They are very promising targets for the design of novel functional biomaterials with medical applications such as bone and skin regeneration [Scharnweber et al, JMSM 2015].Useful biological and therapeutical insights can be obtained from the structure of complexes between GAGs and their target proteins. However the experimental resolution as well as the modeling of their structure is highly challenging. The reasons are both GAG intrinsic properties, such as the high flexibility and conformational diversity of glycans, and the lack for computational tools particularly designed for protein-GAG systems. This currently limits the success of GAG docking to very short fragments [Samsonov and Pisabarro, Glycobiology 2016].We present here a new fragment-based method to dock GAGs on a coarsly known protein binding site. We combine flexible docking of trimeric GAG fragments with Autodock and combinatorial assembly of the compatible poses into GAGs chains, followed by fully flexible refinement. Tested on a benchmark of 13 complexes with various GAG types (heparin, chondroitin sulfate and hyaluronic acids), the method could model 5-mers to 7-mers with the accuracy of 5 Å RMSD to the experimental structure for all of them, and 3 Å RMSD for half of them. This is the first reported automatized fragment-based docking method to successfully dock such diverse GAGs. In principle, the independence of this approach on the ligand's length allows to dock very long GAG chains, which has been a bottleneck for previously applied docking approaches for these systems. The results of this work contribute to enrich the sparse pool of computational tools specifically developed for protein-GAG complexes

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites

Encore quelques mots sur l’emploi du temps

Chauvot A. Encore quelques mots sur l’emploi du temps . In: Manuel général de l'instruction primaire : journal hebdomadaire des instituteurs. 50e année, tome 19, 1883. pp. 59-61