Molecular determinants of arginine versus lysine cation–π interactions in biomolecular condensates

Biomolecular condensates formed by intrinsically disordered regions of proteins are primarily stabilised by amino acid “stickers” that crosslink polypeptide chains. While aromatic and positively charged residues both act as “stickers”, their interaction mechanisms differ. Quantifying these differences is essential since they determine the fate of multicomponent mixtures. Here, we show that the two main positively charged stickers, arginine (Arg) and lysine (Lys), exhibit a consistent hierarchy where Arg promotes phase separation more effectively than Lys. Using molecular dynamics simulations and quantum chemical calculations, we find that, unlike aromatic residues, Arg and Lys consistently maintain this hierarchy across diverse molecular environments. While cation-π interactions are important, the primary factor driving this difference is the higher dehydration penalty of Lys. In contrast, the preferred aromatic partner for these cations depends on the dielectric environment. These results explain at a molecular level the distinct contributions of Arg and Lys to condensate stability. Both aromatic and positively charged residues play a role in stabilizing biomolecular condensates formed by intrinsically disordered regions of proteins, but they differ in their interaction types and relative strengths, which are challenging to quantify. Here, the authors use molecular dynamics simulations and alchemical transformations together with quantum chemical calculations to resolve the differences in arginine and lysine cation-π interaction strengths in different media, showing that these residues maintain a hierarchy of interaction strengths across molecular environments.