A Comprehensive Analysis of Anion-Quadrupole Interactions in Protein Structures

The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion–quadrupole interactions, have been well studied. However, the anion–quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein–protein, DNA/RNA–protein, and membrane–protein). Trp/Tyr anion–quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion–quadrupole interaction (−15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA–protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion–quadrupole interactions. At DNA–protein interfaces, the frequency of aromatic ring participation in anion–quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion–quadrupole interactions at DNA–protein (or membrane–protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion–quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion–quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition