Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates

Abstract

ABSTRACTIntrinsically disordered regions (IDRs) of proteins with specific sequence grammars can be drivers of phase separation and percolation that enable the formation of biomolecular condensates. Measurements have shown that dense phases of protein-based condensates are semidilute solutions. In these solutions, the probability of realizing intermolecular interactions is higher than the probability of intramolecular interactions. Accordingly, to zeroth order, dense phases may be viewed as concentrated solutions of peptide-sized motifs. Here, we report results from all-atom molecular dynamics simulations that were used to quantify differences between inter-residue interactions in mimics of dense versus dilute phases. The simulations use the polarizable AMOEBA forcefield for peptides, ions, and water molecules. In simulations that treat coexisting phases as solutions of model compounds, we find that the interactions between aromatic residues are stronger than interactions between cationic and aromatic residues. Cooperativity within dense phases formed by freely diffusing model compounds is manifest as enhanced pairwise interactions and the formation of nanoscale clusters of aromatic sidechains. Simulations that account for the effects of peptide backbones reveal contrasting results. While peptide backbones maintain or enhance pairwise inter-residue interactions in dilute phases, these interactions are weakened within dense phases. Backbone-mediated weakening of pairwise inter-residue interactions within dense phases is accompanied by the gain of higher-order interactions that enables percolation, whereby molecules within a dense phase become part of a system-spanning network. Our findings provide a physico-chemical rationale for phase separation and percolation as joint drivers of condensate formation.