Liquid-Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics.

Alick-O Vweza,Chul-Gyu Song,Kil-To Chong

doi:10.3390/ijms22136675

Alick-O Vweza, Chul-Gyu Song + Show 1 more

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https://doi.org/10.3390/ijms22136675

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Abstract

Biomolecular condensates formed via liquid–liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn–Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.

Highlights

Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in the late-stage coarsening and stabilization of relatively smaller droplets
Note that written in the form (12), the dynamics (1) captures both long- and short-range interactions of the phase separating species
This is important for biomolecular condensates where long-range interactions are inherent in intrinsically disordered proteins (IDPs) that go through LLPS [41,71,72]

Summary

Introduction

Regulated liquid–liquid phase separation (LLPS) is emerging as one of the major processes that facilitates the mixing and demixing of intracellular space into two or more distinct phases to form molecular assemblies termed biomolecular condensates [1,2,3,4,5,6,7,8,9,10,11,12,13].The liquid-like features of the resulting membraneless organelles (MLOs), such as nucleoli and stress granules, enable these condensates to form coherent structures that subcompartmentalize and concentrate a specific set of biomolecules, thereby spatially organizing biochemical reactions [14,15,16]. Regulated liquid–liquid phase separation (LLPS) is emerging as one of the major processes that facilitates the mixing and demixing of intracellular space into two or more distinct phases to form molecular assemblies termed biomolecular condensates [1,2,3,4,5,6,7,8,9,10,11,12,13]. In addition to playing major roles in normal cellular function, the emergent properties from LLPS processes have been implicated in the onset of an array of pathophysiological conditions such as neurodegeneration [11,28,29,30,31,32,33,34,35,36,37] and carcinogenesis [38,39] due to the aberrant phase separation that triggers protein gelation and aggregation in the condensed phases

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Conclusion