Water access and ligand dissociation at the binding site of proteins

Although water is undoubtedly an essential mediator of protein-ligand interactions, whether or not such water molecules are critical for the progress of ligand dissociation remains unclear. To gain a more complete understanding, molecular dynamics simulations are performed with two molecular systems, rigid model binding sites and trypsin-benzamidine. Free-energy landscapes are calculated with a suitably chosen solvent coordinate, which well describes water access to the ligand binding site. The results of free energy provided clear description of water-ligand exchange process, where two different mechanisms appear depending on whether the binding site is buried or not. As the site is more buried, water access is more difficult. When water does not access the site, ligand dissociation produces a large energy barrier, i.e., slow dissociation kinetics. This indicates that control of ligand dissociation kinetics becomes possible with burying the binding site. However, the results also showed that appropriate burying is important because burying reduces not only water access but also ligand binding. The role of the protein structural change is also discussed; it likely plays a similar role to water access because during ligand dissociation, it can make new coordination with the ligand binding site like water. These results contribute to the future pharmaceutical drug design and will be useful for fundamental exploration of various molecular events.