Role of Strong Localized vs. Weak Distributed Interactions in Disordered Protein Phase Separation

Abstract

Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomers XPand employ two distinct particle-based models that include either strong localized attractions between only H-H pairs (HP model) or weak distributed attractions between both H-H and H-P pairs (HP+ model). To compare different sequences and models, we first carefully tune the attraction strength for all sequences to match the single-chain radius of gyration. Interestingly, we find that this procedure produces similar conformational ensembles, nonbonded potential energies, and chain-level dynamics for single chains of almost all sequences in both models, with some deviations for the HP model at large XP. However, we observe a surprisingly rich phase behavior for the sequences in both models that deviates from the expectation that similarity at the single-chain level will translate to similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependent XPdespite the presence of favorable interchain interactions, which we quantify using the second virial coefficient. Instead, the limited number of attractive sites (H monomers) leads to the self-assembly of finite-sized clusters of different sizes depending on XP. Our findings strongly suggest that models with distributed interactions favor the formation of liquid-like condensates over a much larger range of sequence compositions compared to models with localized interactions.

The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins

“…In some proteins, specific residues or subregions were identified as contact hotspots. This includes the aliphatic residues in ACTR, and hydrophobic residues in the p53 transactivation domains, in line with recent work identifying aliphatic residues as driving intramolecular interactions 61,82 . Most visually noticeable, aromatic residues in the A1-LCD appear as spikes that uniformly punctuate the sequence, highlighting their previously-identified role as evenly-spaced stickers 25 .…”

The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins

“…This includes the aliphatic residues in ACTR and the hydrophobic residues in the p53 transactivation domains, in line with recent work identifying aliphatic residues as driving intramolecular interactions. 68,84 Most visually noticeable, aromatic residues in the A1-LCD appear as spikes that uniformly punctuate the sequence, highlighting their previously identified role as evenly-spaced stickers. 25 Intriguingly, in alpha-synuclein, several regions in the aggregation-prone non-amyloid core region (residues 61− 95) appear as contact score spikes, potentially highlighting the ability of intramolecular interactions to guide regions or residues that may mediate inter-molecular interaction.…”

Expanding the molecular language of protein liquid-liquid phase separation

“…Based on experiments and simulations of repetitive model polypeptides, we find that polar and nonpolar residues that have not been considered as significant for phase separation propensity in the current literature in fact form a multitude of interactions with all other residues in the sequence, aiding in phase separation. The collective presence of a sufficient number of such interacting residues in an IDP tips the balance towards phase separation 52 . This work therefore points to the diverse range of IDP sequences that can phase separate under biologically relevant conditions.…”