Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank

We
conduct a statistical analysis of the molecular environment
of common ionizable functional groups in both protein–ligand
complexes and inside proteins from the Protein Data Bank (PDB). In
particular, we characterize the frequency, type, and density of the
interacting atoms as well as the presence of a potential counterion.
We found that for ligands, most guanidinium groups, half of primary
and secondary amines, and one-fourth of imidazole neighbor a carboxylate
group. Tertiary amines bind more rarely near carboxylate groups, which
may be explained by a crowded neighborhood and hydrophobic character.
In comparison to the environment seen by the ligands, inside proteins,
an environment enriched in main-chain atoms is found, and the prevalence
of direct charge neutralization by carboxylate groups is different.
When the ionizable character of water molecules and phenolic or hydroxyl
groups is accounted, considering a high-resolution dataset (less than
1.5 Å), charge neutralization could occur for well above 80%
of the ligand functional groups considered, but for tertiary amines.