Extended Data Fig. 8: EVB equilibration dynamics and representative structures of the Des27 system.

a-b Root mean square deviations (rmsd, Å) of all solute atoms of the Des27 and Des27.7 calculated for the equilibration phase prior to our EVB simulations. Data were collected every 10 ps from the initial equilibration runs and shown as averages and standard deviations over ten individual 25 ns MD simulations per system (i.e., 750 ns cumulative simulation time per system). The average rmsd per system is denoted by the colored solid line, and the standard deviations per point over all trajectories are illustrated by the shaded area on each plot. a. rmsd for EVB equilibration from “out” substrate conformation. b. rmsd for EVB equilibration from “in” substrate conformation. c-d EVB Representative structures of the Des27 system. c. For the “in” ligand conformation. d. For the “out” ligand conformation. Michaelis complex (MC, left panel), transition state (TS, middle panel), and product complex (PC, right panel) for the KE reaction catalyzed by this enzyme, extracted from EVB trajectories of this reaction. Structures were selected based on clustering analysis. The clustering was performed at the MC, TS and PC independently, in order to obtain representative structures for each state. Donor-acceptor distances (Å) are shown for each stationary point. These values are averages of the snapshots taken every 5 ps of the trajectory, determined based on the combined evaluation of 30 replicas.