Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation

Abstract

Recently many cellular functions have been associated with membraneless organelles, or protein droplets, formed by liquid-liquid phase separation (LLPS). Proteins in these droplets often contain RNA-binding domains, but the effects of RNA on LLPS have been controversial. To gain better understanding on the roles of RNA, here we used Gibbs-ensemble simulations to determine phase diagrams of two-component patchy particles, as models for mixtures of proteins with RNA or other regulatory components. Protein-like particles have four patches, with attraction strength ε PP ; regulatory particles experience mutual steric repulsion but have two attractive patches toward proteins, with the strength ε PR tunable. At low ε PR , the regulator, due to steric repulsion, preferentially partitions in the dispersed phase, thereby displacing the protein into the droplet phase and promoting LLPS. At moderate ε PR , the regulator starts to partition and displace the protein in the droplet phase, but only to weaken bonding networks and thereby suppress LLPS. At ε PR > ε PP , the enhanced bonding ability of the regulator initially promotes LLPS, but at higher amounts, the resulting displacement of the protein suppresses LLPS. These results illustrate how RNA can have disparate effects on LLPS, thus able to perform diverse functions in different organelles.

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

“…Standard chemical potential routes are computationally prohibitive for longer chains that we study here. This challenge can be overcome by the use of lattice models (26) or by simplifying the protein chains as patchy particles as done recently by Nguemaha and Zhou (39). We instead prefer an approach that can faithfully capture the polymeric nature of IDPs and their interactions leading to the formation of a dense phase with concentration that is dependent on the protein sequence.…”

Charge-Driven Condensation of RNA and Proteins Suggests Broad Role of Phase Separation in Cytoplasmic Environments

“…Microscopy (23,41,42), nuclear magnetic resonance (NMR) spectroscopy (17,43), fluorescence spectroscopy (10,44,45), X-ray diffraction (46,47) , and scattering methods (44,48,49) have characterized in vitro (10,17,23,42,43,(45)(46)(47)49) and in vivo systems (19,50,51). Theoretical studies have complemented experiments (40,52), including particle-based simulations (53) and analytical approaches based on polymer (54,55) and colloid theories (56)(57)(58). Additional insights into specific interactions have come from molecular dynamics (MD) simulation studies (45,59,60).…”

“…Polymer aspects of IDPs and unstructured RNA were emphasized in applications of Flory-Huggins theory in combination with simulations (10,53,61,62). Related studies in the colloid field have described the phase behavior of macromolecules and nanoparticles as single spherical particles (56)(57)(58). However, most of the latter studies so far have focused on liquid-solid transitions and the formation of finite size clusters in monodisperse systems.…”

A Tug of War Between Condensate Phases in a Minimal Macromolecular System

“…Droplets are a common, liquid phase of bimolecular condensates, and can assemble or disassemble by a simple compositional change, i.e., when the components go above or below their threshold concentrations 15,16 . When a macromolecular mixture can exist in multiple condensate phases, each favored by a different composition, a compositional change can likewise result in the changeover from one condensate phase to another.…”

“…Other components presumably play regulatory roles, and still others are recruited as clients but may nevertheless have regulatory effects. For the thermodynamics of liquid-liquid phase separation, computational studies led us to the notion that macromolecular regulators fall into three archetypical classes 15,51 . Volumeexclusion promotors act by taking up space in the bulk phase and thereby displacing driver proteins into the droplet phase.…”