The Energetic Origins of Pi–Pi Contacts in Proteins

[Image: see text] Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein’s stability and structure. Pi–pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi–pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi–pi contact motifs. We find that neutral pi–pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter–Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi–pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi–pi contacts in polar media and like typical ion–pi interactions in nonpolar environments. Like-charged pairs such as arginine–arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi–pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.