Étude numérique de la formation du complexe protéique formé du canal potassique humain Kv4.2 et de sa sous-unité bêta DPP6.2

The homeostasis of all living organism results from the concerted action of a unfanthomable number of biochemical actors. Among them, proteins play a fundamental role by range of functions as diverse as crucial that they fulfill, whether it is on a structural or enzymatic level, or on a transportation and signaling one. For instance, voltage-dependent potassium channels (Kv) form a family of transmembrane proteins responsible for the transportation of potassium ions across the membrane of excitable cells. The electric currants resulting from their activity constitute an essential component of a wide variety of vital physiological processes. The action potential is such an example, omnipresent in all vertebrates to relay information between the nervous and other systems, such as the muscles, glands, organs, or the nervous system itself. The present study looks at the molecular origin of two other potassium currents, referred by I_{to,f} et I_SA, that play a similar regulatory role for cardiac and neuronal cells, respectively. While it has been clearly established that the isoforme Kv4 is the molecular basis for the conducting pore of these currents, the kinetics of this Kv channel are too slow to reproduce the currents on its own. Indeed, these currents are the manifestation of a larger protein-protein complex that imply two auxiliary subunits that modulate Kv4's biophysical propreties, namely KChIP (Kv Channel Interacting Proteins) and DPP (dipepdyl-aminopeptidase like proteins). Many of Kv4's properties are affected by these interactions, like the acceleration Kv4's gating and inactivation kinetics by DPP -- a crucial effect for the regulation I_SA et I_{to,f} exert on other neuronal or cardiac currents. A handful of molecular details about this interaction are known, especially for the cytosolic part, but very little is known about the main interaction, at the level of the transmembrane domains. This study aims at filling this void by precising the mode of action of DPP6.2 on Kv4.2 with the help of molecular dynamics.   Initially, since only partial crystal structure data is available for both proteins, predictive models for the structure of the models will have to be constructed. Then, a combination of docking algorithms, complemented with molecular dynamics, will help refine the mode of interaction. The most probable model will be identified by comparing the structural stability and the strenght of the affinity of the different complexes proposed by docking algorithms. The preferential pose thereby predicted will allow to compare with the litterature and to formulate further hypotheses to test the models. Then, we will look at the effect of the binding of auxiliary subunits of Kv4's substructures to gain insight into how DPP6.2 disturb the normal gating process. We could corroborate an hypothesis, formulated by Jerng et Pfaffinger (2014), according to which the pore would be constrained by the interaction. We also predicted that the voltage sensing domain was less stable, and we suggest that this could be the basis of the faster activation of Kv4.2 in presence of DPP6.2. Moreover, the region of interaction identified by docking algorithms are consistant with preliminary data (Ren et al., 2003). As for the N-terminal part of the interaction, the only (realist) region of interaction predicted was highly consistant with functionnal studies available, and we predicted a few other interactions. We also showed that the first N-terminal residues form a flexible chain, readily available to interact with the pore and its mecanism, as suggested by the prevalent model of the ball and chain that applies for Kv4.2.

Keyphrases: Voltage-gated potassium channels, Auxiliary subunits, Protein-protein interaction, Molecular dynamics, Structure-function relationship