Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins

TL;DR

This paper advances the understanding of how sequence-specific electrostatics influence liquid-liquid phase separation in intrinsically disordered proteins using an improved random-phase-approximation theory, with applications to biological systems.

Contribution

It introduces an enhanced RPA heteropolymer theory that accounts for sequence-specific electrostatics and applies it to real IDPs, improving predictions of phase behavior.

Findings

RPA predicts different phase diagrams than mean-field theories.

Charge distribution significantly affects phase separation tendencies.

Concentration-dependent permittivity enhances IDP attraction.

Abstract

Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the living cell. The resulting phase with enhanced IDP concentration can function as a major component of membraneless organelles that, by creating their own IDP-rich microenvironments, stimulate critical biological functions. IDP phase behaviors are governed by their amino acid sequences. To make progress in understanding this sequence-phase relationship, we report further advances in a recently introduced application of random-phase-approximation (RPA) heteropolymer theory to account for sequence-specific electrostatics in IDP phase separation. Here we examine computed variations in phase behavior with respect to block length and charge density of model polyampholytes of alternating equal-length charge blocks to gain insight into trends observed in IDP phase separation. As a real-life example, the theory is applied to rationalize/predict binodal and spinodal phase behaviors of the 236-residue N-terminal disordered region of RNA helicase Ddx4 and its charge-scrambled mutant for which experimental data are available. Fundamental differences are noted between the phase diagrams predicted by RPA and those predicted by mean-field Flory-Huggins and Overbeek-Voorn/Debye-H\"uckel theories. In the RPA context, a physically plausible dependence of relative permittivity on protein concentration can produce a cooperative effect in favor of IDP-IDP attraction and thus a significant increased tendency to phase separate. Ramifications of these findings for future development of IDP phase separation theory are discussed.