Tam reseptör tirozin kinaz ailesinin farklı ligandlara karşı seçiciliği

TAM (Tyro3, Axl, Mer) proteins belong to the receptor tyrosine kinase family. One of the prominent TAM activation pathways involves the interaction of TAM's extracellular Ig domains with a ligand. The most commonly studied TAM ligands are two paralogous Vitamin K-dependent proteins, i.e. Gas6 and Pros1. Although Gas6 and Pros1 sequences are significantly similar, Gas6 can bind to all TAM receptors (with the highest affinity towards Axl) while Pros1 can interact only with Tyro3 and Mer (with little or no affinity towards Axl). Expanding on this knowledge, in this thesis, we aim at characterizing the molecular grounds of Axl's ligand selectivity through a structure-based approach. For this, we modeled the complex structures of all possible TAM-ligand interactions, by using the available Axl-Gas6 complex structure as a template. This process was followed by refinement of each complex with HADDOCK. Strikingly, HADDOCK score of each complex, obtained at the end of each refinement session, correlated very well with the observed experimental binding affinities. In order to have a deeper understanding of Axl-ligand selectivity, we later focused on two extremities: the best binder, i.e. Axl-Gas6 and the worst one, i.e. Axl-Pros1. To that end, we run four parallel 200 ns molecular dynamics simulations yielding 800 ns ensembles of Axl-Gas6 and Axl-Pros1. Detailed interaction analyses of these pairs highlighted that electrostatic interactions are dominating Axl's partner selection, which disappear in the case of Axl-Pros1. By combining these results with the conservation and comparative analysis, we identified three specificity determining positions directing Axl's ligand selectivity, i.e. ARG 48Axl, GLU 70Axl and GLU 83Axl.