Dynamic metastable long-living droplets formed by sticker-spacer proteins

Multiphasic protein condensation governed by shape and valency

Liquid-liquid phase separation (LLPS) of biological macromolecules leads to the formation of various membraneless organelles. The multilayered and multiphasic form of LLPS can mediate complex cellular functions; however, the determinants of its topological features are not fully understood. Herein, we focus on synaptic proteins consisting of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its interacting partners and present a computational model that reproduces forms of LLPS, including a form of two-phase condensates, phase-in-phase (PIP) organization. The model analyses reveal that the PIP formation requires competitive binding between the proteins. The PIP forms only when CaMKII has high valency and a short linker length. Such CaMKII exhibits low surface tension, a modular structure, and slow diffusion, enabling it to stay in small biochemical domains for a long time, which is necessary for synaptic plasticity. Thus, the computational modeling reveals new structure-function relationships for CaMKII as a synaptic memory unit.

The impact of colloid-solvent dynamic coupling on the coarsening rate of colloidal phase separation

Phase separation, a fundamental phenomenon in both natural and industrial settings, involves the coarsening of domains over time t to reduce interfacial energy. While well-understood for simple viscous liquid mixtures, the physical laws governing coarsening dynamics in complex fluids, such as colloidal suspensions, remain unclear. Here, we investigate colloidal phase separation through particle-based simulations with and without hydrodynamic interactions (HIs). The former incorporates many-body HIs through momentum conservation, while the latter simplifies their effects into a constant friction coefficient on a particle. In cluster-forming phase separation with HIs, the domain size ℓ grows as ℓ∝t1/3, aligning with the Brownian-coagulation mechanism. Without HIs, ℓ∝t1/5, attributed to an improper calculation of cluster thermal diffusion. For network-forming phase separation, ℓ∝t1/2 with HIs, while ℓ∝t1/3 without HIs. In both cases, network coarsening is governed by the mechanical stress relaxation of the colloid-rich phase, yet with distinct mechanisms: slow solvent permeation through densely packed colloids for the former and free draining for the latter. Our results provide a clear and concise physical picture of colloid-solvent dynamic coupling via momentum conservation, offering valuable insights into the self-organization dynamics of particles like colloids, emulsions, and globular proteins suspended in a fluid.

The Origin of the Ionic-strength Dependent Reentrant Behavior in Liquid-Liquid Phase Separation of Neutral IDPs

The effect of salt on coacervation of synthetic or biological polyelectrolytes is well-studied. However, recent experiments showed that largely neutral IDPs like FUS also undergo LLPS at physiological salt concentrations, dissolve at higher salt concentration and again phase separate at higher salt concentrations such as, [C ion ]∼3M. Here we use analytical theory and simulations to reveal the mechanism of these transitions. At low [C ion ], the ionic solution acts as a highly correlated medium conferring long-range effective attractive interactions between spatially distant FUS monomers. In this regime the ion concentration inside the condensate is higher than in the bulk solution. As [C ion ] increases, the correlation length in the ionic plasma decreases, and the condensate dissolves. Second LLPS at high [C ion ] is due to the entropy-driven crowding, and ion concentration inside the condensate is lower than in the bulk. Our study unravels a general physical mechanism of salt-dependent reentrant behavior in LLPS in neutral IDPs.

Emerging biophysical origins and pathogenic implications of amyloid oligomers

The amyloid hypothesis has been a leading narrative concerning the pathophysiological foundation of Alzheimer's and Parkinson's disease. At the two ends of the hypothesis lie the functional protein monomers and the pathology-defining amyloid fibrils, while the early stages of protein aggregation are populated by polymorphic, transient and neurotoxic oligomers. As the structure and activity of oligomers are intertwined, here we show oligomers arising from liquid-liquid phase separation and β-barrel formation, their routes to neurodegeneration, and their role in cerebrovascular perturbation. Together, this Perspective converges on the multifaceted oligomer-axis central to the pathological origin and, hence, the treatment of amyloid diseases.

The mechanobiology of biomolecular condensates

The central goal of mechanobiology is to understand how the mechanical forces and material properties of organelles, cells, and tissues influence biological processes and functions. Since the first description of biomolecular condensates, it was hypothesized that they obtain material properties that are tuned to their functions inside cells. Thus, they represent an intriguing playground for mechanobiology. The idea that biomolecular condensates exhibit diverse and adaptive material properties highlights the need to understand how different material states respond to external forces and whether these responses are linked to their physiological roles within the cell. For example, liquids buffer and dissipate, while solids store and transmit mechanical stress, and the relaxation time of a viscoelastic material can act as a mechanical frequency filter. Hence, a liquid-solid transition of a condensate in the force transmission pathway can determine how mechanical signals are transduced within and in-between cells, affecting differentiation, neuronal network dynamics, and behavior to external stimuli. Here, we first review our current understanding of the molecular drivers and how rigidity phase transitions are set forth in the complex cellular environment. We will then summarize the technical advancements that were necessary to obtain insights into the rich and fascinating mechanobiology of condensates, and finally, we will highlight recent examples of physiological liquid-solid transitions and their connection to specific cellular functions. Our goal is to provide a comprehensive summary of the field on how cells harness and regulate condensate mechanics to achieve specific functions.

Charge screening and hydrophobicity drive progressive assembly and liquid-liquid phase separation of reflectin protein

The intrinsically disordered reflectin proteins drive tunable reflectivity for dynamic camouflage and communication in the recently evolved Loliginidae family of squid. Previous work revealed that reflectin A1 forms discrete assemblies whose size is precisely predicted by protein net charge density and charge screening by the local anion concentration. Using dynamic light scattering, FRET, and confocal microscopy, we show that these assemblies, of which 95 to 99% of bulk protein in solution is partitioned into, are dynamic intermediates to liquid protein-dense condensates formed by liquid-liquid phase separation (LLPS). Increasing salt concentration drives this progression by anionic screening of the cationic protein's Coulombic repulsion, and by increasing the contribution of the hydrophobic effect which tips the balance between short-range attraction and long-range repulsion to drive protein assembly and ultimately LLPS. Measuring fluorescence recovery after photobleaching and droplet fusion dynamics, we demonstrate that reflectin diffusivity in condensates is tuned by protein net charge density. These results illuminate the physical processes governing reflectin A1 assembly and LLPS and demonstrate the potential for reflectin A1 condensate-based tunable biomaterials. They also compliment previous observations of liquid phase separation in the Bragg lamellae of activated iridocytes and suggest that LLPS behavior may serve a critical role in governing the tunable and reversible dehydration of the membrane-bounded Bragg lamellae and vesicles containing reflectin in biophotonically active cells.

Relating stress fluctuations to rheology in model biopolymer networks

Cross-linked networks of semiflexible biopolymers are one of the essential building blocks of life as they are the scaffolds providing mechanical strength to biological cells to handle external stress and regulate shape. These protein structures experience strain at different rates often under confinement such as a membrane. Here, we compute the steady-state dynamics of stress and stress fluctuations in a wall-confined, continuously sheared, reversibly cross-linked, sticker-spacer model of a semiflexible biopolymer network. We find that the averages and fluctuations of shear stress and pressure increase by orders of magnitude when the strain rate is increased above a certain regime. The shear viscosity decreases with increasing strain rate except near the critical strain rate regime where it exhibits an inflection. Upon increasing the strain rate, we note a shift from a long time autocorrelation to an oscillatory and then to a sharply dropping autocorrelation function, endorsed by corresponding changes in the power spectrum of the stress. These outcomes indicate a transition from stick to stick-slip (stress buildup and relaxation) and then to slip upon increasing the strain rate, and we posit that this has to be a hallmark intermittent response of a dynamically cross-linked network under continuous shear deformations. We suggest that a fluctuation-dissipation type framework, where the stress is a stochastic process and "resistance to stress" is a function of strain rate, can help us understand the stress dynamics in biopolymer networks.

G3BP1 promotes intermolecular RNA-RNA interactions during RNA condensation

Ribonucleoprotein (RNP) granules are biomolecular condensates requiring RNA and proteins to assemble. Stress granules are RNP granules formed upon increases in non-translating messenger ribonucleoprotein particles (mRNPs) during stress. G3BP1 and G3BP2 proteins are proposed to assemble stress granules through multivalent crosslinking of RNPs. We demonstrate that G3BP1 also has "condensate chaperone" functions, which promote the assembly of stress granules but are dispensable following initial condensation. Following granule formation, G3BP1 is dispensable for the RNA component of granules to persist in vitro and in cells when RNA decondensers are inactivated. These results demonstrate that G3BP1 functions as an "RNA condenser," a protein that promotes intermolecular RNA-RNA interactions stabilizing RNA condensates, leading to RNP granule persistence. Moreover, the stability of RNA-only granules highlights the need for active mechanisms limiting RNP condensate stability and lifetime.

Size-controlled assembly of phase separated protein condensates with interfacial protein cages

Phase separation of specific proteins into liquid-like condensates is a key mechanism for forming membrane-less organelles, which organize diverse cellular processes in space and time. These protein condensates hold immense potential as biomaterials capable of containing specific sets of biomolecules with high densities and dynamic liquid properties. Despite their appeal, methods to manipulate protein condensate materials remain largely unexplored. Here, we present a one-pot assembly method to assemble coalescence-resistant protein condensates, ranging from a few μm to 100 nm in sizes, with surface-stabilizing protein cages. We discover that large protein cages (~30 nm), finely tuned to interact with condensates, efficiently localize on condensate surfaces and prevent the merging (coalescence) of condensates during phase separation. We precisely control condensate diameters by modulating condensate/cage ratios. In addition, the 3D structures of intact protein condensates with interfacial cages are visualized with cryo-electron tomography (ET). This work offers a versatile platform for designing size-controlled, surface-engineered protein condensate materials.

Separation of sticker-spacer energetics governs the coalescence of metastable condensates

Biological condensates often emerge as a multidroplet state and never coalesce into one large droplet within the experimental timespan. Previous work revealed that the sticker-spacer architecture of biopolymers may dynamically stabilize the multidroplet state. Here, we simulate the condensate coalescence using metadynamics approach and reveal two distinct physical mechanisms underlying the fusion of droplets. Condensates made of sticker-spacer polymers readily undergo a kinetic arrest when stickers exhibit slow exchange while fast exchanging stickers at similar levels of saturation allow merger to equilibrium states. On the other hand, condensates composed of homopolymers fuse readily until they reach a threshold density. Increase in entropy upon intercondensate mixing of chains drives the fusion of sticker-spacer chains. We map the range of mechanisms of kinetic arrest from slow sticker exchange dynamics to density mediated in terms of energetic separation of stickers and spacers. Our predictions appear to be in qualitative agreement with recent experiments probing dynamic nature of protein-RNA condensates.

Emerging regulatory mechanisms and functions of biomolecular condensates: implications for therapeutic targets

Cells orchestrate their processes through complex interactions, precisely organizing biomolecules in space and time. Recent discoveries have highlighted the crucial role of biomolecular condensates-membrane-less assemblies formed through the condensation of proteins, nucleic acids, and other molecules-in driving efficient and dynamic cellular processes. These condensates are integral to various physiological functions, such as gene expression and intracellular signal transduction, enabling rapid and finely tuned cellular responses. Their ability to regulate cellular signaling pathways is particularly significant, as it requires a careful balance between flexibility and precision. Disruption of this balance can lead to pathological conditions, including neurodegenerative diseases, cancer, and viral infections. Consequently, biomolecular condensates have emerged as promising therapeutic targets, with the potential to offer novel approaches to disease treatment. In this review, we present the recent insights into the regulatory mechanisms by which biomolecular condensates influence intracellular signaling pathways, their roles in health and disease, and potential strategies for modulating condensate dynamics as a therapeutic approach. Understanding these emerging principles may provide valuable directions for developing effective treatments targeting the aberrant behavior of biomolecular condensates in various diseases.

Sequence complexity and monomer rigidity control the morphologies and aging dynamics of protein aggregates

Understanding the biophysical basis of protein aggregation is important in biology because of the potential link to several misfolding diseases. Although experiments have shown that protein aggregates adopt a variety of morphologies, the dynamics of their formation are less well characterized. Here, we introduce a minimal model to explore the dependence of the aggregation dynamics on the structural and sequence features of the monomers. Using simulations, we demonstrate that sequence complexity (codified in terms of word entropy) and monomer rigidity profoundly influence the dynamics and morphology of the aggregates. Flexible monomers with low sequence complexity (corresponding to repeat sequences) form liquid-like droplets that exhibit ergodic behavior. Strikingly, these aggregates abruptly transition to more ordered structures, reminiscent of amyloid fibrils, when the monomer rigidity is increased. In contrast, aggregates resulting from monomers with high sequence complexity are amorphous and display nonergodic glassy dynamics. The heterogeneous dynamics of the low and high-complexity sequences follow stretched exponential kinetics, which is one of the characteristics of glassy dynamics. Importantly, at nonzero values of the bending rigidities, the aggregates age with the relaxation times that increase with the waiting time. Informed by these findings, we provide insights into aging dynamics in protein condensates and contrast the behavior with the dynamics expected in RNA repeat sequences. Our findings underscore the influence of the monomer characteristics in shaping the morphology and dynamics of protein aggregates, thus providing a foundation for deciphering the general rules governing the behavior of protein condensates.

Continuity of Short-Time Dynamics Crossing the Liquid-Liquid Phase Separation in Charge-Tuned Protein Solutions

Liquid-liquid phase separation (LLPS) constitutes a crucial phenomenon in biological self-organization, not only intervening in the formation of membraneless organelles but also triggering pathological protein aggregation, which is a hallmark in neurodegenerative diseases. Employing incoherent quasi-elastic neutron spectroscopy (QENS), we examine the short-time self-diffusion of a model protein undergoing LLPS as a function of phase splitting and temperature to access information on the nanosecond hydrodynamic response to the cluster formation both within and outside the LLPS regime. We investigate the samples as they dissociate into microdroplets of a dense protein phase dispersed in a dilute phase as well as the separated dense and dilute phases obtained from centrifugation. By interpreting the QENS results in terms of the local concentrations in the two phases determined by UV-vis spectroscopy, we hypothesize that the short-time transient protein cluster size distribution is conserved at the transition point while the local volume fractions separate.

Nonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding

Biomolecular condensates are essential in various cellular processes, and their misregulation has been demonstrated to underlie disease. Small molecules that modulate condensate stability and material properties offer promising therapeutic approaches, but mechanistic insights into their interactions with condensates remain largely lacking. We employ a multiscale approach to enable long-time, equilibrated all-atom simulations of various condensate-ligand systems. Systematic characterization of the ligand binding poses reveals that condensates can form diverse and heterogeneous chemical environments with one or multiple chains to bind small molecules. Unlike traditional protein-ligand interactions, these chemical environments are dominated by nonspecific hydrophobic interactions. Nevertheless, the chemical environments feature unique amino acid compositions and physicochemical properties that favor certain small molecules over others, resulting in varied ligand partitioning coefficients within condensates. Notably, different condensates share similar sets of chemical environments but at different populations. This population shift drives ligand selectivity toward specific condensates. Our approach can enhance the interpretation of experimental screening data and may assist in the rational design of small molecules targeting specific condensates.

Separation of sticker-spacer energetics governs the coalescence of metastable condensates

Biological condensates often emerge as a multi-droplet state and never coalesce into one large droplet within the experimental timespan. Previous work revealed that the sticker-spacer architecture of biopolymers may dynamically stabilize the multi-droplet state. Here, we simulate the condensate coalescence using metadynamics approach and reveal two distinct physical mechanisms underlying the fusion of droplets. Condensates made of sticker-spacer polymers readily undergo a kinetic arrest when stickers exhibit slow exchange while fast exchanging stickers at similar levels of saturation allow merger to equilibrium states. On the other hand, condensates composed of homopolymers fuse readily until they reach a threshold density. Increase in entropy upon inter-condensate mixing of chains drives the fusion of sticker-spacer chains. We map the range of mechanisms of kinetic arrest from slow sticker exchange dynamics to density mediated in terms of energetic separation of stickers and spacers. Our predictions appear to be in qualitative agreement with recent experiments probing dynamic nature of protein-RNA condensates.

Disordered regions of human eIF4B orchestrate a dynamic self-association landscape

Eukaryotic translation initiation factor eIF4B is required for efficient cap-dependent translation, it is overexpressed in cancer cells, and may influence stress granule formation. Due to the high degree of intrinsic disorder, eIF4B is rarely observed in cryo-EM structures of translation complexes and only ever by its single structured RNA recognition motif domain, leaving the molecular details of its large intrinsically disordered region (IDR) unknown. By integrating experiments and simulations we demonstrate that eIF4B IDR orchestrates and fine-tunes an intricate transition from monomers to a condensed phase, in which large-size dynamic oligomers form before mesoscopic phase separation. Single-molecule spectroscopy combined with molecular simulations enabled us to characterize the conformational ensembles and underlying intra- and intermolecular dynamics across the oligomerization transition. The observed sensitivity to ionic strength and molecular crowding in the self-association landscape suggests potential regulation of eIF4B nanoscopic and mesoscopic behaviors such as driven by protein modifications, binding partners or changes to the cellular environment.

Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop

The nanoscale organization of enzymes associated with the dynamics of second messengers is critical for ensuring compartmentation and localization of signaling molecules in cells. Specifically, the spatiotemporal orchestration of cAMP and Ca2+ oscillations is critical for many cellular functions. Previous experimental studies have shown that the formation of nanodomains of A-kinase anchoring protein 79/150 (AKAP150) and adenylyl cyclase 8 (AC8) on the surface of pancreatic MIN6 β cells modulates the phase of Ca2+-cAMP oscillations from out-of-phase to in-phase. In this work, we develop computational models of the Ca2+/cAMP pathway and AKAP/AC nanodomain formation that give rise to the two important predictions: instead of an arbitrary phase difference, the out-of-phase Ca2+/cAMP oscillation reaches Ca2+ trough and cAMP peak simultaneously, which is defined as inversely out-of-phase; the in-phase and inversely out-of-phase oscillations associated with Ca2+-cAMP dynamics on and away from the nanodomains can be explained by an incoherent feedforward loop. Factors such as cellular surface-to-volume ratio, compartment size, and distance between nanodomains do not affect the existence of in-phase or inversely out-of-phase Ca2+/cAMP oscillation, but cellular surface-to-volume ratio and compartment size can affect the time delay for the inversely out-of-phase Ca2+/cAMP oscillation while the distance between two nanodomains does not. Finally, we predict that both the Turing pattern-generated nanodomains and experimentally measured nanodomains demonstrate the existence of in-phase and inversely out-of-phase Ca2+/cAMP oscillation when the AC8 is at a low level, consistent with the behavior of an incoherent feedforward loop. These findings unveil the key circuit motif that governs cAMP and Ca2+ oscillations and advance our understanding of how nanodomains can lead to spatial compartmentation of second messengers.

The exchange dynamics of biomolecular condensates

A hallmark of biomolecular condensates formed via liquid-liquid phase separation is that they dynamically exchange material with their surroundings, and this process can be crucial to condensate function. Intuitively, the rate of exchange can be limited by the flux from the dilute phase or by the mixing speed in the dense phase. Surprisingly, a recent experiment suggests that exchange can also be limited by the dynamics at the droplet interface, implying the existence of an 'interface resistance'. Here, we first derive an analytical expression for the timescale of condensate material exchange, which clearly conveys the physical factors controlling exchange dynamics. We then utilize sticker-spacer polymer models to show that interface resistance can arise when incident molecules transiently touch the interface without entering the dense phase, i.e., the molecules 'bounce' from the interface. Our work provides insight into condensate exchange dynamics, with implications for both natural and synthetic systems.

Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation

Biomolecular condensation involving proteins and nucleic acids has been recognized to play crucial roles in genome organization and transcriptional regulation. However, the biophysical mechanisms underlying the droplet fusion dynamics and microstructure evolution during the early stage of liquid-liquid phase separation (LLPS) remain elusive. In this work, we study the phase separation of linker histone H1, which is among the most abundant chromatin proteins, in the presence of single-stranded DNA (ssDNA) capable of forming a G-quadruplex by using molecular simulations and experimental characterization. We found that droplet fusion is a rather stochastic and kinetically controlled process. Productive fusion events are triggered by the formation of ssDNA-mediated electrostatic bridges within the droplet contacting zone. The droplet microstructure is size-dependent and evolves driven by maximizing the number of electrostatic contacts. We also showed that the folding of ssDNA to the G-quadruplex promotes LLPS by increasing the multivalency and strength of protein-DNA interactions. These findings provide deep mechanistic insights into the growth dynamics of biomolecular droplets and highlight the key role of kinetic control during the early stage of ssDNA-protein condensation.

Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are prevalent participants in liquid-liquid phase separation due to their inherent potential for promoting multivalent binding. Understanding the underlying mechanisms of phase separation is challenging, as phase separation is a complex process, involving numerous molecules and various types of interactions. Here, we used a simplified coarse-grained model of IDPs to investigate the thermodynamic stability of the dense phase, conformational properties of IDPs, chain dynamics, and kinetic rates of forming condensates. We focused on the IDP system, in which the oppositely charged IDPs are maximally segregated, inherently possessing a high propensity for phase separation. By varying interaction strengths, salt concentrations, and temperatures, we observed that IDPs in the dense phase exhibited highly conserved conformational characteristics, which are more extended than those in the dilute phase. Although the chain motions and global conformational dynamics of IDPs in the condensates are slow due to the high viscosity, local chain flexibility at the short timescales is largely preserved with respect to that at the free state. Strikingly, we observed a non-monotonic relationship between interaction strengths and kinetic rates for forming condensates. As strong interactions of IDPs result in high stable condensates, our results suggest that the thermodynamics and kinetics of phase separation are decoupled and optimized by the speed-stability balance through underlying molecular interactions. Our findings contribute to the molecular-level understanding of phase separation and offer valuable insights into the developments of engineering strategies for precise regulation of biomolecular condensates.

Sequence-specific interactions determine viscoelasticity and aging dynamics of protein condensates

Biomolecular condensates are viscoelastic materials. Here, we investigate the determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by the prion-like low-complexity domain of the protein hnRNP A1 and its designed variants. We find that the dominantly viscous forms of the condensates are metastable Maxwell fluids. A Rouse-Zimm model that accounts for the network-like organization of proteins within condensates reproduces the measured viscoelastic moduli. We show that the strengths of aromatic inter-sticker interactions determine sequence-specific amplitudes of elastic and viscous moduli, and the timescales over which elastic properties dominate. These condensates undergo physical ageing on sequence-specific timescales. This is driven by mutations to spacer residues that weaken the metastability of dominantly viscous phases. The ageing of condensates is accompanied by disorder-to-order transitions, leading to the formation of non-fibrillar, beta-sheet-containing, semi-crystalline, elastic, Kelvin-Voigt solids. Our results suggest that sequence grammars, which refer to amino acid identities of stickers versus spacers in prion-like low-complexity domains, have evolved to afford control over metastabilities of dominantly viscous fluid phases of condensates. This selection is likely to render barriers for conversion from metastable fluids to globally stable solids insurmountable on functionally relevant timescales.

Measurement of solubility product reveals the interplay of oligomerization and self-association for defining condensate formation

Cellular condensates often consist of 10s to 100s of distinct interacting molecular species. Because of the complexity of these interactions, predicting the point at which they will undergo phase separation is daunting. Using experiments and computation, we therefore studied a simple model system consisting of polySH3 and polyPRM designed for pentavalent heterotypic binding. We tested whether the peak solubility product, or the product of the dilute phase concentration of each component, is a predictive parameter for the onset of phase separation. Titrating up equal total concentrations of each component showed that the maximum solubility product does approximately coincide with the threshold for phase separation in both experiments and models. However, we found that measurements of dilute phase concentration include small oligomers and monomers; therefore, a quantitative comparison of the experiments and models required inclusion of small oligomers in the model analysis. Even with the inclusion of small polyPRM and polySH3 oligomers, models did not predict experimental results. This led us to perform dynamic light scattering experiments, which revealed homotypic binding of polyPRM. Addition of this interaction to our model recapitulated the experimentally observed asymmetry. Thus, comparing experiments with simulation reveals that the solubility product can be predictive of the interactions underlying phase separation, even if small oligomers and low affinity homotypic interactions complicate the analysis.

Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions

The coacervation of alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is central to amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work shows that factors promoting or inhibiting aggregation have similar effects on LLPS. This study provides a detailed scanning of a wide range of parameters, including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and LLPS. The influence of salt on aggregation under crowding conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, this study finds a monotonic salt dependence of LLPS due to intermolecular interactions. Furthermore, it observes time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving aggregates through heterotypic interactions, thus preventing αSyn from its dynamically arrested state.

Non-specific yet selective interactions contribute to small molecule condensate partitioning behavior

Biomolecular condensates are essential in various cellular processes, and their misregulation has been demonstrated to be underly disease. Small molecules that modulate condensate stability and material properties offer promising therapeutic approaches, but mechanistic insights into their interactions with condensates remain largely lacking. We employ a multiscale approach to enable long-time, equilibrated all-atom simulations of various condensate-ligand systems. Systematic characterization of the ligand binding poses reveals that condensates can form diverse and heterogeneous chemical environments with one or multiple chains to bind small molecules. Unlike traditional protein-ligand interactions, these chemical environments are dominated by non-specific hydrophobic interactions. Nevertheless, the chemical environments feature unique amino acid compositions and physicochemical properties that favor certain small molecules over others, resulting in varied ligand partitioning coefficients within condensates. Notably, different condensates share similar sets of chemical environments but at different populations. This population shift drives ligand selectivity towards specific condensates. Our approach can enhance the interpretation of experimental screening data and may assist in the rational design of small molecules targeting specific condensates.

Multi-condensate state as a functional strategy to optimize the cell signaling output

The existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combine Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.

Preserving condensate structure and composition by lowering sequence complexity

Biomolecular condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating heterogeneous, nonspecific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that although spacer interactions contribute to phase separation and co-condensation, their nonspecific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined networked structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low-complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.

Direct computations of viscoelastic moduli of biomolecular condensates

In vitro facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations. The key ingredient of the generalized Rouse model is the Zimm matrix that we compute from equilibrium MMC simulations. We compute two flavors of Zimm matrices, one referred to as the single-chain model that accounts only for intra-chain contacts, and the other referred to as a collective model, that accounts for inter-chain interactions. The single-chain model systematically overestimates the storage and loss moduli, whereas the collective model reproduces the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two models proves to be most accurate. In line with the theory of Rouse, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic versus dominantly viscous behaviors is influenced by the totality of the relaxation modes. Hence, our analysis suggests that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain distributions of relaxation times that underlie the dynamics within condensates.

Multi-condensate state as a functional strategy to optimize the cell signaling output

The existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combined Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.

Multiscale Computational Framework for the Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins

The reversible assembly of intrinsically disordered proteins (IDPs) to form membraneless organelles (MLOs) is a fundamental process involved in the spatiotemporal regulation in living cells. MLOs formed via liquid-liquid phase separation (LLPS) serve as molecule-enhancing hubs to regulate cell functions. Owing to the complexity and dynamic nature of the protein assembly via a network of weak inter- and intra-molecular interactions, it is challenging to describe and predict the LLPS behavior. We have developed a multiscale computational model for IDPs, using the fused in sarcoma (FUS) protein and its variants as illustrative examples. To simplify the description of protein, FUS is represented as a linear chain of stickers interspaced by spacers, as inspired by the associative polymer theory. Low-complexity aromatic-rich kinked segments (LARKS) available in FUS were identified using LARKSdb and represented as "stickers". The pairwise potential energies of each pair of stickers and their β-sheet-forming propensity were estimated via molecular docking and all atomistic molecular dynamics (AA-MD) simulations. Subsequently, FUS chains were randomly positioned in a cubic lattice as coarse-grained (CG) beads, with the bead assignment based on the Kuhn length estimation of stickers and spacers. Stochastic FUS movements were modeled by Monte Carlo (MC) simulations. In addition to the Metropolis algorithm, discretized pair potential distributions between stickers were considered in the move acceptance criteria. The chosen pair potential represents one of the possible binding energy states, with its probability determined by the frequency of the binding energy distribution histogram. The fluctuations of averaged radial distribution functions (RDFs) in successive MC trial move intervals of equilibrated lattice MC simulations were used to indicate the dynamic nature of assembly/disassembly of the protein chains. This multiscale computational framework provides an economical and efficient way of predicting and describing the LLPS behavior of IDPs.

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions

The coacervation and structural rearrangement of the protein alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is recognized as the key element of amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work showed that factors promoting or inhibiting amyloid formation have similar effects on phase separation. Here, we provide a detailed scanning of a wide range of parameters including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and phase separation. The influence of salt on aggregation under crowded conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, we find a monotonic salt dependence of phase separation due to the intermolecular interaction. Furthermore, we observe the time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving the aggregates through a variety of heterotypic interactions, thus preventing αSyn from its dynamically arrested state.

Measurement of solubility product in a model condensate reveals the interplay of small oligomerization and self-association

Cellular condensates often consist of 10s to 100s of distinct interacting molecular species. Because of the complexity of these interactions, predicting the point at which they will undergo phase separation into discrete compartments is daunting. Using experiments and computation, we therefore studied a simple model system consisting of 2 proteins, polySH3 and polyPRM, designed for pentavalent heterotypic binding. We tested whether the peak solubility product, the product of dilute phase monomer concentrations, is a predictive parameter for the onset of phase separation. Titrating up equal total concentrations of each component showed that the maximum solubility product does approximately coincide with the threshold for phase separation in both the experiments and models. However, we found that measurements of dilute phase concentration include contributions from small oligomers, not just monomers; therefore, a quantitative comparison of the experiments and models required inclusion of small oligomers in the model analysis. We also examined full phase diagrams where the model results were almost symmetric along the diagonal, but the experimental results were highly asymmetric. This led us to perform dynamic light scattering experiments, where we discovered a weak homotypic interaction for polyPRM; when this was added to the computational model, it was able to recapitulate the experimentally observed asymmetry. Thus, comparing experiments to simulation reveals that the solubility product can be predictive of phase separation, even if small oligomers and low affinity homotypic interactions preclude experimental measurement of monomer concentration.

RNAs undergo phase transitions with lower critical solution temperatures

Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.

Preserving condensate structure and composition by lowering sequence complexity

Biological condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross-talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent, non-specific interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating non-specific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that while spacer interactions contribute to phase separation and co-condensation, their non-specific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.

Dynamical control enables the formation of demixed biomolecular condensates

Cellular matter can be organized into compositionally distinct biomolecular condensates. For example, in Ashbya gossypii, the RNA-binding protein Whi3 forms distinct condensates with different RNA molecules. Using criteria derived from a physical framework for explaining how compositionally distinct condensates can form spontaneously via thermodynamic considerations, we find that condensates in vitro form mainly via heterotypic interactions in binary mixtures of Whi3 and RNA. However, within these condensates, RNA molecules become dynamically arrested. As a result, in ternary systems, simultaneous additions of Whi3 and pairs of distinct RNA molecules lead to well-mixed condensates, whereas delayed addition of an RNA component results in compositional distinctness. Therefore, compositional identities of condensates can be achieved via dynamical control, being driven, at least partially, by the dynamical arrest of RNA molecules. Finally, we show that synchronizing the production of different RNAs leads to more well-mixed, as opposed to compositionally distinct condensates in vivo.

Formation, function, and pathology of RNP granules

Ribonucleoprotein (RNP) granules are diverse membrane-less organelles that form through multivalent RNA-RNA, RNA-protein, and protein-protein interactions between RNPs. RNP granules are implicated in many aspects of RNA physiology, but in most cases their functions are poorly understood. RNP granules can be described through four key principles. First, RNP granules often arise because of the large size, high localized concentrations, and multivalent interactions of RNPs. Second, cells regulate RNP granule formation by multiple mechanisms including posttranslational modifications, protein chaperones, and RNA chaperones. Third, RNP granules impact cell physiology in multiple manners. Finally, dysregulation of RNP granules contributes to human diseases. Outstanding issues in the field remain, including determining the scale and molecular mechanisms of RNP granule function and how granule dysfunction contributes to human disease.

Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation

Our current understanding of biomolecular condensate formation is largely based on observing the final near-equilibrium condensate state. Despite expectations from classical nucleation theory, pre-critical protein clusters were recently shown to form under subsaturation conditions in vitro; if similar long-lived clusters comprising more than a few molecules are also present in cells, our understanding of the physical basis of biological phase separation may fundamentally change. Here, we combine fluorescence microscopy with photobleaching analysis to quantify the formation of clusters of NELF proteins in living, stressed cells. We categorise small and large clusters based on their dynamics and their response to p38 kinase inhibition. We find a broad distribution of pre-condensate cluster sizes and show that NELF protein cluster formation can be explained as non-classical nucleation with a surprisingly flat free-energy landscape for a wide range of sizes and an inhibition of condensation in unstressed cells.

Condensation Goes Viral: A Polymer Physics Perspective

The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.

Theoretical and Data-Driven Approaches for Biomolecular Condensates

Biomolecular condensation processes are increasingly recognized as a fundamental mechanism that living cells use to organize biomolecules in time and space. These processes can lead to the formation of membraneless organelles that enable cells to perform distinct biochemical processes in controlled local environments, thereby supplying them with an additional degree of spatial control relative to that achieved by membrane-bound organelles. This fundamental importance of biomolecular condensation has motivated a quest to discover and understand the molecular mechanisms and determinants that drive and control this process. Within this molecular viewpoint, computational methods can provide a unique angle to studying biomolecular condensation processes by contributing the resolution and scale that are challenging to reach with experimental techniques alone. In this Review, we focus on three types of dry-lab approaches: theoretical methods, physics-driven simulations and data-driven machine learning methods. We review recent progress in using these tools for probing biomolecular condensation across all three fields and outline the key advantages and limitations of each of the approaches. We further discuss some of the key outstanding challenges that we foresee the community addressing next in order to develop a more complete picture of the molecular driving forces behind biomolecular condensation processes and their biological roles in health and disease.

Phase Transitions of Associative Biomacromolecules

Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.

Sequence variations of phase-separating proteins and resources for studying biomolecular condensates

Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein's phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.

Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories

Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather and coordinate viral transcription, replication, and assembly. Key to viral factory function is the recruitment of EBOV polymerase, a multifunctional machine that mediates transcription and replication of the viral RNA genome. We show that intracellularly reconstituted EBOV viral factories are biomolecular condensates, with composition-dependent internal exchange dynamics that likely facilitates viral replication. Within the viral factory, we found the EBOV polymerase clusters into foci. The distance between these foci increases when viral replication is enabled. In addition to the typical droplet-like viral factories, we report the formation of network-like viral factories during EBOV infection. Unlike droplet-like viral factories, network-like factories are inactive for EBOV nucleocapsid assembly. This unique view of EBOV propagation suggests a form-to-function relationship that describes how physical properties and internal structures of biomolecular condensates influence viral biogenesis.

Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity

Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate. In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains. Here we show that phase separation propensity underpins Ccc1 function. Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate effects on formation of Ccc1 condensates in vivo, which are enriched for PRC2. Notably, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains. Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro whereas HP1 droplets do so only weakly. These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.

Ribozyme activity modulates the physical properties of RNA-peptide coacervates

Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into long chains. Our results show that the formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype-phenotype linkage.

Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid

Biomolecular condensates are membraneless organelles formed via phase separation of macromolecules, typically consisting of bond-forming "stickers" connected by flexible "linkers". Linkers have diverse roles, such as occupying space and facilitating interactions. To understand how linker length relative to other lengths affects condensation, we focus on the pyrenoid, which enhances photosynthesis in green algae. Specifically, we apply coarse-grained simulations and analytical theory to the pyrenoid proteins of Chlamydomonas reinhardtii: the rigid holoenzyme Rubisco and its flexible partner EPYC1. Remarkably, halving EPYC1 linker lengths decreases critical concentrations by ten-fold. We attribute this difference to the molecular "fit" between EPYC1 and Rubisco. Varying Rubisco sticker locations reveals that the native sites yield the poorest fit, thus optimizing phase separation. Surprisingly, shorter linkers mediate a transition to a gas of rods as Rubisco stickers approach the poles. These findings illustrate how intrinsically disordered proteins affect phase separation through the interplay of molecular length scales.

Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates

Assemblies of multivalent RNA-binding protein fused in sarcoma (FUS) can exist in the functional liquid-like state as well as less dynamic and potentially toxic amyloid- and hydrogel-like states. How could then cells form liquid-like condensates while avoiding their transformation to amyloids? Here, we show how posttranslational phosphorylation can provide a "handle" that prevents liquid-solid transition of intracellular condensates containing FUS. Using residue-specific coarse-grained simulations, for 85 different mammalian FUS sequences, we show how the number of phosphorylation sites and their spatial arrangement affect intracluster dynamics preventing conversion to amyloids. All atom simulations further confirm that phosphorylation can effectively reduce the β-sheet propensity in amyloid-prone fragments of FUS. A detailed evolutionary analysis shows that mammalian FUS PLDs are enriched in amyloid-prone stretches compared to control neutrally evolved sequences, suggesting that mammalian FUS proteins evolved to self-assemble. However, in stark contrast to proteins that do not phase-separate for their function, mammalian sequences have phosphosites in close proximity to these amyloid-prone regions. These results suggest that evolution uses amyloid-prone sequences in prion-like domains to enhance phase separation of condensate proteins while enriching phosphorylation sites in close proximity to safeguard against liquid-solid transitions.

The maximum solubility product marks the threshold for condensation of multivalent biomolecules

Clustering of weakly interacting multivalent biomolecules underlies the formation of membraneless compartments known as condensates. As opposed to single-component (homotypic) systems, the concentration dependence of multicomponent (heterotypic) condensate formation is not well understood. We previously proposed the solubility product (SP), the product of monomer concentrations in the dilute phase, as a tool for understanding the concentration dependence of multicomponent systems. In this study, we further explore the limits of the SP concept using spatial Langevin dynamics and rule-based stochastic simulations. We show, for a variety of idealized molecular structures, how the maximum SP coincides with the onset of the phase transition, i.e., the formation of large clusters. We reveal the importance of intracluster binding in steering the free and cluster phase molecular distributions. We also show how structural features of biomolecules shape the SP profiles. The interplay of flexibility, length, and steric hindrance of linker regions controls the phase transition threshold. Remarkably, when SPs are normalized to nondimensional variables and plotted against the concentration scaled to the threshold for phase transition, the curves all coincide independent of the structural features of the binding partners. Similar coincidence is observed for the normalized clustering versus concentration plots. Overall, the principles derived from these systematic models will help guide and interpret in vitro and in vivo experiments on the biophysics of biomolecular condensates.

RNA granules: functional compartments or incidental condensates?

RNA granules are mesoscale assemblies that form in the absence of limiting membranes. RNA granules contain factors for RNA biogenesis and turnover and are often assumed to represent specialized compartments for RNA biochemistry. Recent evidence suggests that RNA granules assemble by phase separation of subsoluble ribonucleoprotein (RNP) complexes that partially demix from the cytoplasm or nucleoplasm. We explore the possibility that some RNA granules are nonessential condensation by-products that arise when RNP complexes exceed their solubility limit as a consequence of cellular activity, stress, or aging. We describe the use of evolutionary and mutational analyses and single-molecule techniques to distinguish functional RNA granules from "incidental condensates."

Condensation of LINE-1 is critical for retrotransposition

LINE-1 (L1) is the only autonomously active retrotransposon in the human genome, and accounts for 17% of the human genome. The L1 mRNA encodes two proteins, ORF1p and ORF2p, both essential for retrotransposition. ORF2p has reverse transcriptase and endonuclease activities, while ORF1p is a homotrimeric RNA-binding protein with poorly understood function. Here, we show that condensation of ORF1p is critical for L1 retrotransposition. Using a combination of biochemical reconstitution and live-cell imaging, we demonstrate that electrostatic interactions and trimer conformational dynamics together tune the properties of ORF1p assemblies to allow for efficient L1 ribonucleoprotein (RNP) complex formation in cells. Furthermore, we relate the dynamics of ORF1p assembly and RNP condensate material properties to the ability to complete the entire retrotransposon life-cycle. Mutations that prevented ORF1p condensation led to loss of retrotransposition activity, while orthogonal restoration of coiled-coil conformational flexibility rescued both condensation and retrotransposition. Based on these observations, we propose that dynamic ORF1p oligomerization on L1 RNA drives the formation of an L1 RNP condensate that is essential for retrotransposition.

A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins

The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding of the viral RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support the assembly of ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, and analysis of the mutational landscape, we describe a heretofore unknown oligomerization site that contributes to LLPS, is required for the assembly of higher-order protein-nucleic acid complexes, and is coupled to large-scale conformational changes of N-protein upon nucleic acid binding. The self-association interface is located in a leucine-rich sequence of the intrinsically disordered linker between N-protein folded domains and formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic and electrostatic interactions between adjacent helices are highly protected against mutations in viable SARS-CoV-2 genomes, and the oligomerization motif is conserved across related coronaviruses, thus presenting a target for antiviral therapeutics.