In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and
computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently
change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence
of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled,
the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states
when provided with the structures of the unbound proteins and their complex; however, the modeling becomes much more complicated if
the bound state has to be predicted in a docking protocol or if the structures of either bound or unbound receptor-ligand are not available.
The major challenges that arise in these situations are the coupling between binding and protonation states, and the conformational
changes induced by the binding and ionization states of titratable groups. In addition, any assessment of the protonation state, either before
or after binding, must refer to the pH of binding, which is frequently unknown. Thus, even if the pKa’s of ionizable groups can be
correctly assigned for both unbound and bound state, without knowing the experimental pH one cannot assign the corresponding protonation
states, and consequently one cannot calculate the resulting proton uptake/release. It is pointed out, that while experimental pH may
not be the physiological pH and binding may involve proton uptake/release, there is a tendency that the native receptor-ligand complexes
have evolved toward specific either subcellular or tissue characteristic pH at which the proton uptake/release is either minimal or absent.