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 X P and 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 X P. 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 a similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependent X P, despite 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 X P. 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.

Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins

“…Membraneless organelles or biomolecular condensates formed through liquid – liquid phase separation (LLPS) have been widely reported in various cellular functions, including gene expression, signal transduction, stress response, and the assembly of macromolecular complexes. − Examples of such condensates include the nucleolus, Cajal bodies, P bodies, and stress granules. Intrinsically disordered proteins (IDPs) play an important role in the formation of biomolecular condensates through LLPS. − Due to the numerous similarities between IDPs and synthetic polymers, classical polymer models offer a powerful approach for investigating the conformations, dynamics, and phase behavior of IDPs. − In particular, such models have been extensively used to reveal the sequence-dependent conformations of IDPs in solution and in condensates. − …”

“…This model is a good approximation for numerous IDPs, such as prion-like low-complexity domains . Recently, we successfully used hydrophobic homopolymers as a reference to establish the biophysics of phase separation of IDPs, revealing that distributed interactions better stabilize the condensed phase than localized interactions . To understand the basic principles governing the chain conformations in the droplet, we focus here on hydrophobic homopolymers.…”

Active learning of the thermodynamics–dynamics tradeoff in protein condensates

“…In all these systems, a negative B 2 value—implying net attractive interactions—is necessary for phase separation to occur. Although this condition turns out to be insufficient to guarantee phase separation in heteropolymer solutions [42, 43], we find that B 2 nonetheless correlates strongly with the difference between the coexisting phase densities for IDP sequences that do phase separate, as we demonstrate using molecular dynamics simulations below. In practice, we compute B 2 by calculating the potential of mean force, u ( r ), between the centers of mass of two polymer chains at 300 K using adaptive biasing force simulations [44] (Fig.…”

Theory and Simulation of Multiphase Coexistence in Biomolecular Mixtures

“…Simulations of recently developed CG IDP models − have demonstrated impressive agreement with experiments on both single-chain and individual condensed-phase properties, suggesting that multicomponent simulations using these models may also be capable of predicting multiphase coexistence with similar accuracy. Further improvement in the chemical accuracy of multicomponent simulations is likely to be achieved through multiscale approaches that incorporate all-atom simulations of ribonucleic condensates. − In future simulation studies, it will also be important to consider the role of competition between sequence-dependent clustering, aggregation, and LLPS behaviors, as observed in simple models of single-component heteropolymer solutions, − in multicomponent mixtures. Accounting for nonequilibrium effects due to kinetic barriers. Within the near-equilibrium framework, kinetic effects can lead to differences between the phase behavior that is observed in simulations and experiments and what is predicted at global thermodynamic equilibrium.…”