Figure 1.

Simulation system and effects of enzyme conformation on the substrate dynamics. (a) Cartoon representations of the three-dimensional structures at the open conformation (left, PDB code: 4AKE) and closed conformation (right, PDB code: 1AKE). (b) Cartoon representation of the AdK structure with correctly bound substrates. Zoom-in panel shows the native binding pose of the substrate AMP by stick representation. (c) Binding poses of the substrate AMP for the encounter complex structures from 30 independent AMP binding simulations. Binding poses of the substrate AMP were projected onto the reaction coordinates θ_AMP and R_AMP defined in the Methods section. Non-native binding pose for one of the encounter complexes is shown by dark blue in the bottom. For comparison, corresponding native binding pose of AMP is also shown below by light blue. (d and e) Substrate dynamics at the open (d) and closed (e) conformations characterized by the reaction coordinates θ_AMP and R_AMP. (f and g) Free energy landscapes along the reaction coordinates R_AMP and θ_AMP at the open (f) and closed (g) conformations calculated based on one single trajectory. Area around the native binding pose is marked by a red square.