Mesoscale properties of protein clusters determine the size and nature of liquid-liquid phase separation (LLPS)

TL;DR

This paper presents a mesoscale core-shell model to analyze protein clusters involved in liquid-liquid phase separation, revealing how cluster properties influence the size and stability of phase-separated domains in cells.

Contribution

It introduces a theoretical core-shell model to interpret experimental cluster size distributions and compares conformational states of proteins affecting LLPS stability.

Findings

CPEB4 clusters are more stable than FUS clusters.

FUS forms micron-scale LLPS domains, while CPEB4 forms large aggregates.

Protein conformations influence cluster stabilization and phase separation.

Abstract

The observation of Liquid-Liquid Phase Separation (LLPS) in biological cells has dramatically shifted the paradigm that soluble proteins are uniformly dispersed in the cytoplasm or nucleoplasm. The LLPS region is preceded by a one-phase solution, where recent experiments have identified clusters in an aqueous solution with 102-103 proteins. Here, we theoretically consider a core-shell model with mesoscale core, surface, and bending properties of the cluster shell and contrast two experimental paradigms for the measured cluster size distributions of the Cytoplasmic Polyadenylation Element Binding-4 (CPEB4) and Fused in Sarcoma (FUS) proteins. The fits to the theoretical model and earlier electron paramagnetic resonance (EPR) experiments suggest that the same protein may exhibit hydrophilic, hydrophobic, and amphiphilic conformations, which act to stabilize the clusters. We find that CPEB4 clusters are much more stable compared to FUS clusters, which are less energetically favorable. This suggests that in CPEB4, LLPS consists of large-scale aggregates of clusters, while for FUS, clusters coalesce to form micron-scale LLPS domains.