Insight into MAPK P38α DFG-Flip mechanism by accelerated molecular dynamics

The DFG motif at the beginning of the activation loop of the MAPK p38a undergoes a local structural reorganizationupon binding of allosteric type-II and type-III inhibitors, which causes the residue F169 to movefrom a buried conformation (defined as DFG-in) to a solvent exposed conformation (defined as DFG-out).Although both experimental and computer simulation studies had been performed with the aim ofunveiling the details of the DFG-in to DFG-out transition, the molecular mechanism is still far from beingunequivocally depicted.Here, the accelerated molecular dynamics (AMD) technique has been applied to model the active loopflexibility of p38a and sample special protein conformations which can be accessible only in some conditionsor time periods. Starting from the assumption of an experimentally known initial and final state ofthe protein, the study allowed the description of the interaction network and the structural intermediateswhich lead the protein to change its loop conformation and active site accessibility. Besides a few importanthydrogen bond interactions, a primary role seems to be played by cation–p interactions, involvingthe DFG-loop residue F169, which participate in the stabilization of an intermediate conformation andin its consequent transition to the DFG-out conformation. From this study, insights which may prove usefulfor inhibitor design and/or site directed mutagenesis studies are derived.