Extended Data Fig. 5: Time evolution of the active site center of mass (COM) and ligand distance during total 5 × 1 μs of MD simulations.
From: Complete computational design of high-efficiency Kemp elimination enzymes
a. Des27 and b. Des27.7. The dotted gray line at 4 Å marks the threshold for defining the ligand as being within the active site. In two out of ten replicas across the two systems, we observe ligand dissociation without rebinding towards the end of the trajectory on the timescale of our simulations; in a third, in the case of Des27.7, we observe substantial dissociation mid-trajectory with ligand rebinding within the simulation timeframes.
