Tug of War between Condensate Phases in a Minimal Macromolecular System

Fundamental Aspects of Phase-Separated Biomolecular Condensates

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.

Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers

Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.

Determining Thermodynamic and Material Properties of Biomolecular Condensates by Confocal Microscopy and Optical Tweezers

While the roles of biomolecular condensates in health and disease are being intensely studied, it is equally important that their physical properties are characterized in order to achieve mechanistic understanding. Here we share some of the protocols developed in our lab for measuring thermodynamic and materials properties of condensates. These include a simple method for determining the droplet-phase concentrations of condensate components on a confocal microscope, and a method for determining the viscoelasticity of condensates by optical tweezers. These protocols are either generally applicable to biomolecular condensates or are unique for their characterization.

Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In Vivo

Fluorescence microscopy assays enable the investigation of endogenous biomolecular condensates directly in their cellular context. With appropriate experimental designs, these assays yield quantitative information on condensate material properties and inform on biophysical mechanisms of condensate formation. Single-molecule super-resolution and tracking experiments grant access to the smallest condensates and early condensation stages not resolved by conventional imaging approaches. Here, we discuss considerations for using single-molecule assays to extract quantitative information about biomolecular condensates directly in their cellular context.

Unravelling the microscopic characteristics of intrinsically disordered proteins upon liquid–liquid phase separation

Biomolecular condensate formation via liquid–liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the spatiotemporal organization of biomolecules in the cell. These membraneless condensates form and disperse dynamically in response to environmental stimuli. Growing evidence indicates that the liquid-like condensates not only play functional physiological roles but are also implicated in a wide range of human diseases. As a major component of biomolecular condensates, intrinsically disordered proteins (IDPs) are intimately involved in the LLPS process. During the last decade, great efforts have been made on the macroscopic characterization of the physicochemical properties and biological functions of liquid condensates both in vitro and in the cellular context. However, characterization of the conformations and interactions at the molecular level within phase-separated condensates is still at an early stage. In the present review, we summarize recent biophysical studies investigating the intramolecular conformational changes of IDPs upon LLPS and the intermolecular clustering of proteins undergoing LLPS, with a particular focus on single-molecule fluorescence detection. We also discuss how these microscopic features are linked to the macroscopic phase transitions that are relevant to the physiological and pathological roles of the condensates.

Shear relaxation governs fusion dynamics of biomolecular condensates

Phase-separated biomolecular condensates must respond agilely to biochemical and environmental cues in performing their wide-ranging cellular functions, but our understanding of condensate dynamics is lagging. Ample evidence now indicates biomolecular condensates as viscoelastic fluids, where shear stress relaxes at a finite rate, not instantaneously as in viscous liquids. Yet the fusion dynamics of condensate droplets has only been modeled based on viscous liquids, with fusion time given by the viscocapillary ratio (viscosity over interfacial tension). Here we used optically trapped polystyrene beads to measure the viscous and elastic moduli and the interfacial tensions of four types of droplets. Our results challenge the viscocapillary model, and reveal that the relaxation of shear stress governs fusion dynamics. These findings likely have implications for other dynamic processes such as multiphase organization, assembly and disassembly, and aging.

Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates

The interfacial tension of phase-separated biomolecular condensates affects their fusion and multiphase organization, and yet how this important property depends on the composition and interactions of the constituent macromolecules is poorly understood. Here we use molecular dynamics simulations to determine the interfacial tension and phase equilibrium of model condensate-forming systems. The model systems consist of binary mixtures of Lennard-Jones particles or chains of such particles. We refer to the two components as drivers and regulators; the former has stronger self-interactions and hence a higher critical temperature (T_c ) for phase separation. In previous work, we have shown that, depending on the relative strengths of driver-regulator and driver-driver interactions, regulators can either promote or suppress phase separation (i.e., increase or decrease T_c ). Here we find that the effects of regulators on T_c quantitatively match the effects on interfacial tension (γ). This important finding means that, when a condensate-forming system experiences a change in macromolecular composition or a change in intermolecular interactions (e.g., by mutation or posttranslational modification, or by variation in solvent conditions such as temperature, pH, or salt), the resulting change in T_c can be used to predict the change in γ and vice versa. We also report initial results showing that disparity in intermolecular interactions drives multiphase coexistence. These findings provide much needed guidance for understanding how biomolecular condensates mediate cellular functions.

Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies

Multivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases-homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.

Viscoelasticity of biomolecular condensates conforms to the Jeffreys model

Biomolecular condensates, largely by virtue of their material properties, are revolutionizing biology, and yet, the physical understanding of these properties is lagging. Here, I show that the viscoelasticity of condensates can be captured by a simple model, comprising a component where shear relaxation is an exponential function (with time constant τ1) and a component with nearly instantaneous shear relaxation (time constant τ0 → 0). Modulation of intermolecular interactions, e.g., by adding salt, can disparately affect the two components such that the τ1 component may dominate at low salt, whereas the τ0 component may dominate at high salt. Condensates have a tendency to fuse, with the dynamics accelerated by interfacial tension and impeded by viscosity. For fast-fusion condensates, shear relaxation on the τ1 timescale may become rate-limiting such that the fusion speed is no longer in direction proportion to the interfacial tension. These insights help narrow the gap in understanding between the biology and physics of biomolecular condensates.

Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations

Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.

Determinants for Fusion Speed of Biomolecular Droplets

Biomolecular droplets formed through phase separation have a tendency to fuse. The speed with which fusion occurs is a direct indicator of condensate liquidity, which is key to both cellular functions and diseases. Using a dual-trap optical tweezers setup, we found the fusion speeds of four types of droplets to differ by two orders of magnitude. The order of fusion speed correlates with the fluorescence of thioflavin T, which in turn reflects the macromolecular packing density inside droplets. Unstructured protein or polymer chains pack loosely and readily rearrange, leading to fast fusion. In contrast, structured protein domains pack more closely and have to break extensive contacts before rearrangement, corresponding to slower fusion. This molecular interpretation for disparate fusion speeds provides mechanistic insight into the assembly and aging of biomolecular droplets.

Determination of Condensate Material Properties from Droplet Deformation

I derive theoretical results that relate the effective spring constant, χ, of protein droplets to their material properties. χ, defined as the ratio between a uniaxial applied force and the extent of the corresponding deformation, can be measured by optical tweezers. When the deformation is static, where the applied force is balanced by the interfacial tension of the droplet, the spring constant allows for the determination of the surface tension (γ). When a sinusoidal force is applied (at frequency ω), the dynamic spring constant χ(ω) is related to both γ and the complex shear modulus, G*(ω), of the droplet. The results derived here enable accurate extraction of γ and G*(ω) from χ(ω) data.