Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions.

Yaakov Levy,Milan Kumar Hazra

doi:10.1021/acs.jpcb.0c09975

Yaakov Levy, Milan Kumar Hazra

Open Access

https://doi.org/10.1021/acs.jpcb.0c09975

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Abstract

Intrinsically disordered proteins play a crucial role in cellular phase separation, yet the diverse molecular forces driving phase separation are not fully understood. It is of utmost importance to understand how peptide sequence, and particularly the balance between the peptides’ short- and long-range interactions with other peptides, may affect the stability, structure, and dynamics of liquid–liquid phase separation in protein condensates. Here, using coarse-grained molecular dynamics simulations, we studied the liquid properties of the condensate in a series of polymers in which the ratio of short-range dispersion interactions to long-range electrostatic interactions varied. As the fraction of mutations that participate in short-range interactions increases at the expense of long-range electrostatic interactions, a significant decrease in the critical temperature of phase separation is observed. Nevertheless, sequences with a high fraction of short-range interactions exhibit stabilization, which suggests compensation for the loss of long-range electrostatic interactions. Decreased condensate stability is coupled with decreased translational diffusion of the polymers in the condensate, which may result in the loss of liquid characteristics in the presence of a high fraction of uncharged residues. The effect of exchanging long-range electrostatic interactions for short-range interactions can be explained by the kinetics of breaking intermolecular contacts with neighboring polymers and the kinetics of intramolecular fluctuations. While both time scales are coupled and increase as electrostatic interactions are lost, for sequences that are dominated by short-range interactions, the kinetics of intermolecular contact breakage significantly slows down. Our study supports the contention that different types of interactions can maintain protein condensates, however, long-range electrostatic interactions enhance its liquid-like behavior.

Highlights

Liquid−liquid phase separation (LLPS) mediates several fundamental cellular activities such as signaling,[1] RNA metabolism,[2] and stress adaptation[3] to name a few
Replacing charged residues with hydrophobic or aromatic residues is expected to affect the stability of the condensate formed via LLPS, as these residues are involved in different types of interactions
Whereas charged residues participate in electrostatic interactions that are long-range in nature, hydrophobic and aromatic residues participate in dispersion interactions, such as π−π interactions, that are much shorter range

Summary

Introduction

Liquid−liquid phase separation (LLPS) mediates several fundamental cellular activities such as signaling,[1] RNA metabolism,[2] and stress adaptation[3] to name a few. Recent advances have identified LLPS as the primary mechanism[4−6] for the formation of common membraneless organelles, such as stress granules and nucleoli, as well as heterochromatin assembly,[6,7] centrosomes,[8] presynaptic[9,10] and prosynaptic densities,[11] and membrane receptor clusters.[12] Intrinsically disordered proteins (IDP), which have numerous different chain conformations, play a key role in biological condensates.[13,14] The highly fluctuating and elongated conformations of IDPs are known to govern the protein network in such condensates.[15] This may lead to phase separation at concentrations lower than are needed for folded proteins.[16]. Even stress granule proteins form liquid-like polymer-rich condensate droplets (called coacervates), which in turn mature and solidify.[19]

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