Liquid-liquid Phase Separation Behavior Research Articles

Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA.

The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.

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.

The role of atomistic simulations in predicting liquid-liquid phase separation behavior using RNA structural properties

The role of atomistic simulations in predicting liquid-liquid phase separation behavior using RNA structural properties

Coarse-grained simulation model of protein TDP-43 liquid-liquid phase separation behavior

Coarse-grained simulation model of protein TDP-43 liquid-liquid phase separation behavior

Solute interaction-driven and solvent interaction-driven liquid-liquid phase separation induced by molecular size difference.

We conducted molecular dynamics (MD) simulations in a binary Lennard-Jones system as a model system for molecular solutions and investigated the mechanism of liquid-liquid phase separation (LLPS), which has recently been recognized as a fundamental step in crystallization and organelle formation. Our simulation results showed that LLPS behavior varied drastically with the size ratio of solute to solvent molecules. Interestingly, increasing the size ratio can either facilitate or inhibit LLPS, depending on the combination of interaction strengths. We demonstrated that the unique behavior observed in MD simulation could be reasonably explained by the free energy barrier height calculated using our thermodynamic model based on the classical nucleation theory. Our model proved that the molecular size determines the change in number of interaction pairs through LLPS. Varying the size ratio changes the net number of solute-solvent and solvent-solvent interaction pairs that are either broken or newly generated per solute-solute pair generation, thereby inducing a complicated trend in LLPS depending on the interaction parameters. As smaller molecules have more interaction pairs per unit volume, their contribution is more dominant in the promotion of LLPS. Consequently, as the size ratio of the solute to the solvent increased, the LLPS mode changed from solute-related interaction-driven to solvent-related interaction-driven.

Condensation of the N-terminal domain of human topoisomerase 1 is driven by electrostatic interactions and tuned by its charge distribution

Liquid-liquid phase separation (LLPS) is pivotal in forming biomolecular condensates, which are crucial in several biological processes. Intrinsically disordered regions (IDRs) are typically responsible for driving LLPS due to their multivalency and high content of charged residues that enable the establishment of electrostatic interactions.In our study, we examined the role of charge distribution in the condensation of the disordered N-terminal domain of human topoisomerase I (hNTD). hNTD is densely charged with oppositely charged residues evenly distributed along the sequence. Its LLPS behavior was compared with that of charge permutants exhibiting varying degrees of charge segregation.At low salt concentrations, hNTD undergoes LLPS. However, LLPS is inhibited by high concentrations of salt and RNA, disrupting electrostatic interactions. Our findings show that, in hNTD, moderate charge segregation promotes the formation of liquid condensates that are sensitive to salt and RNA, whereas marked charge segregation results in the formation of aberrant condensates.Although our study is based on a limited set of protein variants, it supports the applicability of the “stickers-and-spacers” model to biomolecular condensates involving highly charged IDRs. These results may help generate reliable models of the overall LLPS behavior of supercharged polypeptides.

Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.

Miscibility and ternary diagram of aqueous polyvinyl alcohols with different degrees of saponification

Liquid–liquid phase separation (LLPS), an important phenomenon in the field of polymer science and material design, plays an essential role in cells and living bodies. Poly(vinyl alcohol) (PVA) is a popular semicrystalline polymer utilized in the synthesis of artificial biomaterials. The aqueous solutions of its derivatives with tuned degrees of saponification (DS) exhibit LLPS. However, the miscibility and LLPS behavior of PVA aqueous solution are still unclear. This study describes the miscibility diagram of the ternary mixture, where water and two types of poly(vinyl alcohol) (PVA) with different DSs [98 (PVA98), 88 (PVA88), 82 (PVA82), and 74 mol% (PVA74)] were blended. UV–Vis measurement was conducted to evaluate the miscibility. Immiscibility was more pronounced at elevated temperatures, exhibiting LLPS. The ternary immiscibility diagram, displaying miscible–immiscible behaviors in the aqueous mixtures of PVA74:PVA98, PVA82:PVA98, and PVA88:PVA98 (blended at a constant volume ratio), indicated that increasing the concentration, temperature, and blend ratio of PVAs at a lower DS increased immiscibility, suggesting that the free energy of mixing increases with increasing these parameters. The miscible–immiscible behaviors of PVAs/water systems provide fundamental knowledge about LLPS and the design of PVA-based materials.

Liaisons dangereuses: Intrinsic Disorder in Cellular Proteins Recruited to Viral Infection-Related Biocondensates.

Liquid-liquid phase separation (LLPS) is responsible for the formation of so-called membrane-less organelles (MLOs) that are essential for the spatio-temporal organization of the cell. Intrinsically disordered proteins (IDPs) or regions (IDRs), either alone or in conjunction with nucleic acids, are involved in the formation of these intracellular condensates. Notably, viruses exploit LLPS at their own benefit to form viral replication compartments. Beyond giving rise to biomolecular condensates, viral proteins are also known to partition into cellular MLOs, thus raising the question as to whether these cellular phase-separating proteins are drivers of LLPS or behave as clients/regulators. Here, we focus on a set of eukaryotic proteins that are either sequestered in viral factories or colocalize with viral proteins within cellular MLOs, with the primary goal of gathering organized, predicted, and experimental information on these proteins, which constitute promising targets for innovative antiviral strategies. Using various computational approaches, we thoroughly investigated their disorder content and inherent propensity to undergo LLPS, along with their biological functions and interactivity networks. Results show that these proteins are on average, though to varying degrees, enriched in disorder, with their propensity for phase separation being correlated, as expected, with their disorder content. A trend, which awaits further validation, tends to emerge whereby the most disordered proteins serve as drivers, while more ordered cellular proteins tend instead to be clients of viral factories. In light of their high disorder content and their annotated LLPS behavior, most proteins in our data set are drivers or co-drivers of molecular condensation, foreshadowing a key role of these cellular proteins in the scaffolding of viral infection-related MLOs.

Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins

Intrinsically disordered proteins rich in cationic amino acid groups can undergo Liquid-Liquid Phase Separation (LLPS) in the presence of charge-balancing anionic counterparts. Arginine and Lysine are the two most prevalent cationic amino acids in proteins that undergo LLPS, with arginine-rich proteins observed to undergo LLPS more readily than lysine-rich proteins, a feature commonly attributed to arginine’s ability to form stronger cation-π interactions with aromatic groups. Here, we show that arginine’s ability to promote LLPS is independent of the presence of aromatic partners, and that arginine-rich peptides, but not lysine-rich peptides, display re-entrant phase behavior at high salt concentrations. We further demonstrate that the hydrophobicity of arginine is the determining factor giving rise to the reentrant phase behavior and tunable viscoelastic properties of the dense LLPS phase. Controlling arginine-induced reentrant LLPS behavior using temperature and salt concentration opens avenues for the bioengineering of stress-triggered biological phenomena and drug delivery systems.

A High-Throughput Method to Profile Protein Liquid-Liquid Phase Separation.

Protein liquid-liquid phase separation (LLPS) plays an essential role in the dynamic assembly of various membraneless compartments, which fulfill different biological functions in cells. Numerous proteins were found to undergo LLPS in different conditions. However, a general approach to systemically identify and compare the LLPS ability of different proteins is lacking. Here, we introduce a high-throughput protein phase separation (HiPPS) profiling method to evaluate the LLPS ability of proteins using a combination of crystallization robot/manual mixing mode and high-content analysis system. This method enables us to rapidly and comprehensively explore the LLPS behavior of each individual protein as well as mixture of different proteins.

Morphological evolution during liquid-liquid phase separation governed by composition change pathways

Liquid-liquid phase separation (LLPS) phenomenon are widely recognized to be of vital importance for physics, materials science, and biology. It is highly desired to develop powerful tools to study the LLPS behavior and related physical mechanisms. For this purpose, a phase-field method was developed here which combines the Cahn-Hilliard diffusion equation and the Navier-Stokes equation. The morphological evolution of LLPS behavior with the change in composition was comprehensively investigated under a prototypical ternary theoretical phase diagram. The phase-field simulation results indicated that the microstructural evolution was controlled by the phase diagram and driven by the coupling of diffusion and gravity effect. Moreover, the intermediate morphological microstructures and corresponding interfacial properties during LLPS could be tuned by selecting different composition change pathways. Furthermore, gravity-dependent density overturning and consequent Rayleigh-Taylor instability were observed in a unique LLPS process, demonstrating that the proposed model can capture the critical features of LLPS phenomenon.

Effect of Zr addition on metastable Liquid-Liquid Phase Separation of Cu-Fe alloys

The liquid-liquid phase separation (LLPS) behavior was investigated in Cu-Fe alloys that consisted of 60 wt % or 80 wt % Cu and balance iron, without or with addition of 1 wt% Zr. Both Zr-free alloys clearly showed LLPS at metastable spinodal temperatures prior to γ-Fe nucleation, whereas Zr-added showed γ-Fe phase evolution without LLPS. Addition of Zr was highly effective to activate γ-Fe nucleation by decreasing the mixing enthalpy and also accelerating heterogeneous nucleation. A combination of thermal instrumental analysis and classical nucleation theory yielded an effective assessment made of LLPS behavior below the liquidus temperature of Cu-Fe alloys. Furthermore, it was possible to control the solidification mechanism of Cu-Fe alloy by zirconium addition.

Emerging Roles of Liquid-Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling.

Liquid–liquid Phase Separation (LLPS) of proteins and nucleic acids has emerged as a new paradigm in the study of cellular activities. It drives the formation of liquid-like condensates containing biomolecules in the absence of membrane structures in living cells. In addition, typical membrane-less condensates such as nuclear speckles, stress granules and cell signaling clusters play important roles in various cellular activities, including regulation of transcription, cellular stress response and signal transduction. Previous studies highlighted the biophysical and biochemical principles underlying the formation of these liquid condensates. The studies also showed how these principles determine the molecular properties, LLPS behavior, and composition of liquid condensates. While the basic rules driving LLPS are continuously being uncovered, their function in cellular activities is still unclear, especially within a pathological context. Therefore, the present review summarizes the recent progress made on the existing roles of LLPS in cancer, including cancer-related signaling pathways, transcription regulation and maintenance of genome stability. Additionally, the review briefly introduces the basic rules of LLPS, and cellular signaling that potentially plays a role in cancer, including pathways relevant to immune responses and autophagy.

In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention.

Proteins able to undergo liquid-liquid phase separation (LLPS) in vivo and in vitro are drawing a lot of interest, due to their functional relevance for cell life. Nevertheless, the proteome-scale experimental screening of these proteins seems unfeasible, because besides being expensive and time-consuming, LLPS is heavily influenced by multiple environmental conditions such as concentration, pH and temperature, thus requiring a combinatorial number of experiments for each protein. To overcome this problem, we propose a neural network model able to predict the LLPS behavior of proteins given specified experimental conditions, effectively predicting the outcome of in vitro experiments. Our model can be used to rapidly screen proteins and experimental conditions searching for LLPS, thus reducing the search space that needs to be covered experimentally. We experimentally validate Droppler's prediction on the TAR DNA-binding protein in different experimental conditions, showing the consistency of its predictions. A python implementation of Droppler is available at https://bitbucket.org/grogdrinker/droppler. Supplementary data are available at Bioinformatics online.

N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins

Liquid-liquid phase separation (LLPS) of proteins is involved in a growing number of cellular processes. Most proteins with LLPS harbor intrinsically disordered regions (IDR), which serve as a guideline to search for cellular proteins that potentially phase separate. Herein, we reveal that oligomerization lowers the barriers for LLPS and could act as a general mechanism to enhance LLPS of proteins domains independent of IDR. Using TDP43 as a model system, we found that deleting its IDR resulted in LLPS that was dependent on the oligomerization of the N-terminal domain (NTD). Replacing TDP43′s NTD with other oligomerization domains enhanced the LLPS proportionately to the state of oligomerization. In addition to TDP43, fusing NTD to other globular proteins without known LLPS behavior also drove their phase separation in a manner dependent on oligomerization. Finally, we demonstrate that heterooligomers composed of NTD-fused proteins can be driven into droplets through NTD interactions. Our results potentiate a new paradigm for using oligomerization domains as a signature to systematically identify cellular proteins with LLPS behavior, thus broadening the scope of this exciting research field.

Small heat shock protein 22 kDa can modulate the aggregation and liquid-liquid phase separation behavior of tau.

Alzheimer's disease is a progressive fatal neurodegenerative disease with no cure or effective treatments. The hallmarks of disease include extracellular plaques and intracellular tangles of aggregated protein. The intracellular tangles consist of the microtubule associated protein tau. Preventing the pathological aggregation of tau may be an important therapeutic approach to treat disease. In this study we show that small heat shock protein 22 kDa (Hsp22) can prevent the aggregation of tau in vitro. Additionally, tau can undergo liquid-liquid phase separation (LLPS) in the presence of crowding reagents which causes it to have an increased aggregation rate. We show that Hsp22 can modulate both the aggregation and LLPS behavior of tau in vitro.

Liquid-Liquid Phase Separation of Tau Protein Is Encoded at the Monomeric Level.

Liquid-liquid phase separation (LLPS) is involved in both physiological and pathological processes. The intrinsically disordered protein Tau and its K18 construct can undergo LLPS in a distinct temperature-dependent manner, and the LLPS of Tau protein can initiate Tau aggregation. However, the underlying mechanism driving Tau LLPS remains largely elusive. To understand the temperature-dependent LLPS behavior of Tau at the monomeric level, we explored the conformational ensemble of Tau at different temperatures by performing all-atom replica-exchange molecular dynamic simulation on K18 monomer with an accumulated simulation time of 26.4 μs. Our simulation demonstrates that the compactness, β-structure propensity, and intramolecular interaction of K18 monomer exhibit nonlinear temperature-dependent behavior. 295DNIKHV300/326GNIHHK331/337VEVKSE342 make significant contributions to the temperature dependence of the β propensity of K18 monomer, while the two fibril-nucleating cores display relatively high β propensity at all temperatures. At a specific temperature, K18 monomer adopts the most collapsed state with exposed sites for both persistent and transient interactions. Given that more collapsed polypeptide chains were reported to be more prone to phase separate, our results suggest that K18 monomer inherently possesses conformational characteristics favoring LLPS. Our simulation predicts the importance of 295DNIKHV300/326GNIHHK331/337VEVKSE342 to the temperature-dependent conformational properties of K18, which is corroborated by CD spectra, turbidity assays, and DIC microscopy. Taken together, we offer a computational and experimental approach to comprehend the structural basis for LLPS by amyloidal building blocks.

Influence of high magnetic field on the liquid-liquid phase separation behavior of an undercooled Cu–Co immiscible alloy

Abstract In this work, the influence of 10 T high magnetic field on the liquid-liquid phase separation behavior of Cu-33.33 at.%Co immiscible alloy was systematically investigated. The results show that the separation behavior was significantly altered via the application of a high magnetic field. Both the Co-rich phase and the non-ferromagnetic Cu-rich phase are found to be elongated along the magnetic field direction due to the action of static magnetic energy and the coordinating of deformation. The relatively homogeneous microstructure of uniform dispersion of Co-rich phase on the matrix is obtained in the direction perpendicular to the magnetic field. The drag force induced by the thermoelectric magnetic convection under a high magnetic field hinders the solute transport of Co-rich phase, leading to a decline in the number of Cu-rich phase produced by the secondary decomposition. Moreover, the applied high magnetic field results in the variations of the undercooling during rapid solidification. The finally solidified Cu–Co alloy in a magnetic field of 10 T with higher undercooling exhibited a slightly lower saturation magnetization and higher coercivity and residual magnetizations. The present research provides new insights into the influence of high magnetic field on the liquid-liquid phase separation behavior of immiscible alloys.

Phase-equilibrium measurement of a carbon dioxide/toluene/polystyrene ternary system using laser turbidimetry

The phase behavior of a carbon dioxide (CO2)/toluene (Tol)/polystyrene (PS) ternary system was measured. The measurements were performed using a synthetic method combined with a reflected light intensity measurement. The bubble points were determined by visual observation, and the cloud points were determined from the change in the reflected light intensity. The phase boundaries were measured at temperatures ranging from 313.2 K to 373.2 K and CO2 weight fractions ranging from 0.10 to 0.41. The homogeneous phase area decreased when the molecular weight of PS and/or the ratio of PS to Tol increased. It was found that the phase behavior of ternary systems, especially the liquid-liquid phase separation behavior, was altered by a change in the mutual solubility between the three components.