Fig. 8

Interaction contact maps between glutamate dehydrogenase residues and XEG for the main a and replica b simulations, depicting the presence of hydrophobic (yellow), hydrogen bonds (green), and rare π-cation (purple) interactions. c–k Dynamic binding of epicatechin-3-gallate (XEG) to glutamate dehydrogenase (GDH). Analysis of the water-mediated binding for the first cluster (snapshots 0-598) simulation, showing the c entire medoid (409) snapshot, d zoomed-in binding site, and e the Bridge2 output of water-mediated H-bonding interactions. f–h panels corresponding to the second cluster (snapshots 599-745) and i–k panels corresponding to the third cluster (snapshots 746-1000). Blue cartoons in panels represent the backbone of GDH and sticks with grey carbons the amino-acid residues forming H-bonding interactions (cyan lines) with XEG. Sticks with green carbons represent the XEG ligand.The numbers on the edges represent the average number of water molecules bridging the H-bonding interaction