Stochastic resonance represents one of the mechanisms that trigger protein ligand unbinding

The unbinding of the Vorapaxar (VPX) from the β-sheet of the Endothelial cell Protein C Receptor (EPCR) can be observed during a 100 ns unbiased Molecular Dynamics simulation while VPX in the hydrophobic cleft remained in a bound state during a microsecond-long simulation. Three sites of VPX participate in binding to the EPCR: the carbamic acid tail, the central naphthol-furan group, and the fluoro-phenyl tail. Empirical Mode Decomposition of the EPCR-VPX interface distances in the trajectories revealed a resonant increase in the vibration amplitudes for the frequency range of 1-10 GHz associated with the unbinding of the VPX sites from β-sheet of EPCR. The VPX molecule in the hydrophobic cleft experienced occasional reorientations without unbinding. The main difference between the two VPX-binding sites of EPCR was the direction of the ligand vibrations relative to the ligand escape route: collinear for the β-sheet and perpendicular to the escape direction for cleft-bound VPX. The observed residence times of VPX bound to the β-sheet were 1-10 ns at 10 °C and more than 100 ns at 37 °C for soluble EPCR. The residence time was 1-10 ns for both temperatures for full-length EPCR (mEPCR). The resonant conditions for soluble EPCR were achieved by reducing the thermal noise, suggesting the involvement of stochastic resonance. The mEPCR, which has lower frequencies of normal modes than sEPCR, could afford the resonant conditions for both temperatures. Thus, ligand unbinding in the EPCR-VPX model was triggered by enhanced vibrations induced by the stochastic resonance.