Liquid-liquid Phase Separation Research Articles

Liquid-liquid phase separation of microtubule-binding proteins in the regulation of spindle assembly.

Cell division is a highly regulated process essential for the accurate segregation of chromosomes. Central to this process is the assembly of a bipolar mitotic spindle, a highly dynamic microtubule (MT)-based structure responsible for chromosome movement. The nucleation and dynamics of MTs are intricately regulated by MT-binding proteins. Over the recent years, various MT-binding proteins have been reported to undergo liquid-liquid phase separation, forming either single- or multi-component condensates on MTs. Herein, we provide a comprehensive summary of the phase separation characteristics of these proteins. We underscore their critical roles in MT nucleation, spindle assembly and kinetochore-MT attachment during the cell division process. Furthermore, we discuss the current challenges and various remaining unsolved problems, highlights the ongoing research efforts aimed at a deeper understanding of the role of the phase separation process during spindle assembly and orientation. Our review aims to contribute to the collective knowledge in this area and stimulate further investigations that will enhance our comprehension of the intricate mechanisms governing cell division.

Kinetic Study of the Esterase-like Activity of Albumin following Condensation by Macromolecular Crowding.

The ability of bovine serum albumin (BSA) to form condensates in crowded environments has been discovered only recently. Effects of this condensed state on the secondary structure of the protein have already been unraveled as some aging aspects, but the pseudo-enzymatic behavior of condensed BSA has never been reported yet. This article investigates the kinetic profile of para-nitrophenol acetate hydrolysis by BSA in its condensed state with poly(ethylene) glycol (PEG) as the crowding agent. Furthermore, the initial BSA concentration was varied between 0.25 and 1 mM which allowed us to modify the size distribution, the volume fraction, and the partition coefficient (varying from 136 to 180). Hence, the amount of BSA originally added was a simple way to modulate the size and density of the condensates. Compared with dilute BSA, the initial velocity (vi) with condensates was dramatically reduced. From the Michaelis-Menten fits, the extracted Michaelis constant Km and the maximum velocity Vmax decreased in control samples without condensates when the BSA concentration increased, which was attributed to BSA self-oligomerization. In samples containing condensates, the observed vi was interpreted as an effect of diluted BSA remaining in the supernatants and from the condensates. In supernatants, the crowding effect of PEG increased the kcat and catalytic efficiency. Last, Vmax was proportional to the volume fraction of the condensates, which could be controlled by varying its initial concentration. Hence, the major significance of this article is the control of the size and volume fraction of albumin condensates, along with their kinetic profile using liquid-liquid phase separation.

The Role of Lysozyme in the Formation of Bioinspired Silicon Dioxide.

Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon (IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase-separation and recent experimental evidence appears to confirm this model. At the same time, polycationic proteins like lysozyme can also promote polycondensation of silicon (IV) dioxide, and they do so under conditions that are not compatible with liquid-liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations. Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon (IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase-separation and recent experimental evidence appears to confirm this model. At thesame time, polycationic proteins like lysozyme can also promote polycondensation of silicon (IV) dioxide, and they doso under conditions that are not compatible with liquid-liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations.

Ionic Effect on the Microenvironment of Biomolecular Condensates

Ionic Effect on the Microenvironment of Biomolecular Condensates

MeCP2 binds to methylated DNA independently of phase separation and heterochromatin organisation

Correlative evidence has suggested that the methyl-CpG-binding protein MeCP2 contributes to the formation of heterochromatin condensates via liquid-liquid phase separation. This interpretation has been reinforced by the observation that heterochromatin, DNA methylation and MeCP2 co-localise within prominent foci in mouse cells. The findings presented here revise this view. MeCP2 localisation is independent of heterochromatin as MeCP2 foci persist even when heterochromatin organisation is disrupted. Additionally, MeCP2 foci fail to show hallmarks of phase separation in live cells. Importantly, we find that mouse cellular models are highly atypical as MeCP2 distribution is diffuse in most mammalian species, including humans. Notably, MeCP2 foci are absent in Mus spretus which is a mouse subspecies lacking methylated satellite DNA repeats. We conclude that MeCP2 has no intrinsic tendency to form condensates and its localisation is independent of heterochromatin. Instead, the distribution of MeCP2 in the nucleus is primarily determined by global DNA methylation patterns.

Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor.

Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.

Technical note: Characterization of a single-beam gradient force aerosol optical tweezer for droplet trapping, phase transition monitoring, and morphology studies

Abstract. Single particle analysis is essential for a better understanding of the particle transformation process and to predict its environmental impact. In this study, we developed an aerosol optical tweezer (AOT) Raman spectroscopy system to investigate the phase state and morphology of suspended aerosol droplets in real time. The system comprises four modules: optical trapping, reaction, illumination and imaging, and detection. The optical trapping module utilizes a 532 nm laser and a 100 × oil immersion objective to stably trap aerosol droplets within 30 s. The reaction module allows us to adjust relative humidity (RH) and introduce reaction gases into the droplet levitation chamber, facilitating experiments to study liquid–liquid phase transitions. The illumination and imaging module employs a high-speed camera to monitor the trapped droplets, while the detector module records Raman scattering light. We trapped sodium chloride (NaCl) and 3-methyl glutaric acid (3-MGA) mixed droplets to examine RH-dependent morphology changes. Liquid–liquid phase separation (LLPS) occurred when RH was decreased. Additionally, we introduced ozone and limonene/pinene to generate secondary organic aerosol (SOA) particles in situ, which collided with the trapped droplet and dissolved in it. To determine the trapped droplet's characteristics, we utilized an open-source program based on Mie theory to retrieve diameter and refractive index from the observed whispering gallery modes (WGMs) in Raman spectra. It is found that mixed droplets formed core–shell morphology when RH was decreased, and the RH dependence of the droplets' phase transitions generated by different SOA precursors varied. Our AOT system serves as an essential experimental platform for in situ assessment of morphology and phase state during dynamic atmospheric processes.

CAR and PPARα do not perform liquid-liquid phase separation in cells

<b>CAR and PPARα do not perform liquid-liquid phase separation in cells</b>

Isolation of nucleic acids using liquid–liquid phase separation of pH-sensitive elastin-like polypeptides

Extraction of nucleic acids (NAs) is critical for many methods in molecular biology and bioanalytical chemistry. NA extraction has been extensively studied and optimized for a wide range of applications and its importance to society has significantly increased. The COVID-19 pandemic highlighted the importance of early and efficient NA testing, for which NA extraction is a critical analytical step prior to the detection by methods like polymerase chain reaction. This study explores simple, new approaches to extraction using engineered smart nanomaterials, namely NA-binding, intrinsically disordered proteins (IDPs), that undergo triggered liquid–liquid phase separation (LLPS). Two types of NA-binding IDPs are studied, both based on genetically engineered elastin-like polypeptides (ELPs), model IDPs that exhibit a lower critical solution temperature in water and can be designed to exhibit LLPS at desired temperatures in a variety of biological solutions. We show that ELP fusion proteins with natural NA-binding domains can be used to extract DNA and RNA from physiologically relevant solutions. We further show that LLPS of pH responsive ELPs that incorporate histidine in their sequences can be used for both binding, extraction and release of NAs from biological solutions, and can be used to detect SARS-CoV-2 RNA in samples from COVID-positive patients.

The Enigma of Tau Protein Aggregation: Mechanistic Insights and Future Challenges.

Tau protein misfolding and aggregation are pathological hallmarks of Alzheimer's disease and over twenty neurodegenerative disorders. However, the molecular mechanisms of tau aggregation in vivo remain incompletely understood. There are two types of tau aggregates in the brain: soluble aggregates (oligomers and protofibrils) and insoluble filaments (fibrils). Compared to filamentous aggregates, soluble aggregates are more toxic and exhibit prion-like transmission, providing seeds for templated misfolding. Curiously, in its native state, tau is a highly soluble, heat-stable protein that does not form fibrils by itself, not even when hyperphosphorylated. In vitro studies have found that negatively charged molecules such as heparin, RNA, or arachidonic acid are generally required to induce tau aggregation. Two recent breakthroughs have provided new insights into tau aggregation mechanisms. First, as an intrinsically disordered protein, tau is found to undergo liquid-liquid phase separation (LLPS) both in vitro and inside cells. Second, cryo-electron microscopy has revealed diverse fibrillar tau conformations associated with different neurodegenerative disorders. Nonetheless, only the fibrillar core is structurally resolved, and the remainder of the protein appears as a "fuzzy coat". From this review, it appears that further studies are required (1) to clarify the role of LLPS in tau aggregation; (2) to unveil the structural features of soluble tau aggregates; (3) to understand the involvement of fuzzy coat regions in oligomer and fibril formation.

Nucleic acid liquids.

The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by basepairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.

The liquid-liquid phase separation in programmed cell death

In recent years, the physical phenomenon of liquid-liquid phase separation has been widely introduced into biological research. Membrane-free organelles have been found to exist in cells that were driven by liquid-liquid phase separation. Intermolecular multivalent interactions can drive liquid-liquid phase separation to form condensates that are independent of other substances in the environment and thus can play an effective role in regulating multiple biological processes in the cell. The way of cell death has also long been a focus in multiple research. In the face of various stresses, cell death-related mechanisms are crucial for maintaining cellular homeostasis and regulating cell fate. With the in-depth study of cell death pathways, it has been found that the process of cell death was also accompanied by the regulation of liquid-liquid phase separation and played a key role. Therefore, this review summarized the roles of liquid-liquid phase separation in various cell death pathways, and explored the regulation of cell fate by liquid-liquid phase separation, with the expectation that the exploration of the mechanism of liquid-liquid phase separation would provide new insights into the treatment of diseases caused by regulated cell death.

HSD17B13 liquid-liquid phase separation promotes leukocyte adhesion in chronic liver inflammation.

The rs72613567:TA polymorphism in 17-beta hydroxysteroid dehydrogenase 13 (HSD17B13) has been found to reduce the progression from steatosis to nonalcoholic steatohepatitis. In this study, we sought to define the pathogenic role of HSD17B13 in triggering liver inflammation. Here we find that HSD17B13 forms liquid-liquid phase separation (LLPS) around lipid droplets in the livers of nonalcoholic steatohepatitis patients. The dimerization of HSD17B13 supports the LLPS formation and promotes its enzymatic function. HSD17B13 LLPS increases the biosynthesis of platelet activating factor (PAF), which in turn promotes fibrinogen synthesis and leukocyte adhesion. Blockade of PAFR or STAT3 pathway inhibited the fibrinogen synthesis and leukocyte adhesion. Importantly, adeno-associated viral-mediated xeno-expression of human HSD17B13 exacerbated western diet/carbon tetrachloride-induced liver inflammation in Hsd17b13-/- mice. In conclusion, our results suggest that HSD17B13 LLPS triggers liver inflammation by promoting PAF-mediated leukocyte adhesion, and targeting HSD17B13 phase transition could be a promising therapeutic approach for treating hepatic inflammation in chronic liver disease.

Mung bean protein colloid mixtures and their fractions - a novel and excellent foam stabiliser

Protein aggregates are known to enhance foam stability by either increasing the thin film viscosity or by blocking the lamellae of a foam. In this study, we produced a mung bean protein colloids mixture (MPCM) by heating protein coacervates that were formed by liquid-liquid phase separation. The functionality of MPCM was compared to a mildly purified mung bean protein extract (MIL). The MPCM showed extraordinary foaming properties, much better than MIL, with foamability of 324 % and a half-life time of 400 min. This work focused on elucidating the exact interface and foam stabilising mechanism of the MPCM by separating the colloids (COL) from the supernatant/continuous phase of the MPCM (SUP). Their interfacial properties were studied by performing surface dilatational rheology and microstructure analysis. Finally, foaming properties, such as foamability, foam stability, and air bubble size, were studied.It was found that the highest foam capacity was observed for the SUP fraction by generating stiffer interfaces. This fraction also contributed to the high foam stability of the MPCM. The COL fraction was found to form a viscoelastic thin film between air bubbles, thereby decreasing the drainage rate of the foam. In brief, SUP and COL fractions co-operate in the formation of highly stable MPCM foam, leading to a promising plant-derived candidate for producing stable foams in food products.

Biomolecular condensates of Chlorocatechol 1,2-Dioxygenase as prototypes of enzymatic microreactors for the degradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are molecules with two or more fused aromatic rings that occur naturally in the environment due to incomplete combustion of organic substances. However, the increased demand for fossil fuels in recent years has increased anthropogenic activity, contributing to the environmental concentration of PAHs. The enzyme chlorocatechol 1,2-dioxygenase from Pseudomonas putida (Pp 1,2-CCD) is responsible for the breakdown of the aromatic ring of catechol, making it a potential player in bioremediation strategies. Pp 1,2-CCD can tolerate a broader range of substrates, including halogenated compounds, than other dioxygenases. Here, we report the construction of a chimera protein able to form biomolecular condensates with potential application in bioremediation. The chimera protein was built by conjugating Pp 1,2-CCD to low complex domains (LCDs) derived from the DEAD-box protein Dhh1. We showed that the chimera could undergo liquid-liquid phase separation (LLPS), forming a protein-rich liquid droplet under different conditions (variable protein and PEG8000 concentrations and pH values), in which the protein maintained its structure and main biophysical properties. The condensates were active against 4-chlorocatechol, showing that the chimera droplets preserved the enzymatic activity of the native protein. Therefore, it constitutes a prototype of a microreactor with potential use in bioremediation.

Single-Step Control of Liquid-Liquid Crystalline Phase Separation by Depletion Gradients.

Fine-tuning nucleation and growth of colloidal liquid crystalline (LC) droplets, also known as tactoids, is highly desirable in both fundamental science and technological applications. However, the tactoid structure results from the trade-off between thermodynamics and non-equilibrium kinetics effects, and controlling liquid-liquid crystalline phase separation (LLCPS) in these systems is still work in progress. Here we introduce a single-step strategy to obtain a rich palette of morphologies for tactoids formed via nucleation and growth within an initially isotropic phase exposed to a gradient of depletants. We show the simultaneous appearance of rich LC structures along the depleting potential gradient, where the position of each LC structure is correlated with the magnitude of the depleting potential. Changing the size (nanoparticles) or the nature (polymers) of the depleting agent provides additional, precise control over the resulting LC structures through a size-selective mechanism, where the depletant may be found both within and outside the LC droplets. The use of depletion gradients from depletants of varying size and nature offers a powerful toolbox to manipulation, templating, imaging and understanding heterogeneous colloidal LC structures. This article is protected by copyright. All rights reserved.

Phosphorylation in the Ser/Arg-Rich Region of the Nucleocapsid of SARS-CoV-2 Regulates Phase Separation by Inhibiting Self-Association of a Distant Helix

The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and virus maturation. N is a multidomain protein composed of an independently folded monomeric N-terminal domain that is the primary site for RNA binding, and a dimeric C-terminal domain that is essential for efficient phase separation and condensate formation with RNA. The domains are separated by a disordered Ser/Arg-rich region preceding a self-associating Leu-rich helix. Phosphorylation in the Ser/Arg region in infected cells decreases the viscosity of N:RNA condensates promoting viral replication and host immune evasion. The molecular level effect of phosphorylation, however, is missing from our current understanding. Using NMR spectroscopy and analytical ultracentrifugation we show that phosphorylation destabilizes the self-associating Leu-rich helix 30 amino acids distant from the phosphorylation site. NMR and gel shift assays demonstrate that RNA binding by the linker is dampened by phosphorylation, whereas RNA binding to the full-length protein is not significantly affected presumably due to retained strong interactions with the primary RNA binding domain. Introducing a switchable self-associating domain to replace the Leu-rich helix confirms the importance of linker self-association to droplet formation and suggests that phosphorylation not only increases solubility of the positively charged elongated Ser/Arg region as observed in other RNA binding proteins but can also inhibit self-association of the Leu-rich helix. These data highlight the effect of phosphorylation both at local sites and at a distant self-associating hydrophobic helix in regulating liquid-liquid phase separation of the entire protein.

Diffusion mediated thermally induced phase separation for preparing poly(vinylidene fluoride) membranes with enhanced separation performances

Thermally induced phase separation (TIPS) process is an appealing method for preparing poly(vinylidene fluoride) (PVDF) membranes for separation. In this work, we developed a diffusion mediated thermally induced phase separation (d-TIPS) to prepare PVDF membranes with great molecules separation performances. We investigated the thermodynamics of ternary polymer solutions including PVDF, caprolactam (CPL), and Polyethylene glycol (PEG). We controlled liquid–liquid phase separation and the CPL diffusion by adjusting the addition of PEG and molecular weight to modulate the evolution of morphology from spherulitic to bicontinuous structure. The resulting membrane was characterized by morphology, surface chemistry, tensile strength, water contact angle, and perm-selectivity. The membrane was further stretched for enhanced strength, permeance, and rejection. This work provides a fundamental understanding of the diffusion mediated thermally induced phase separation and shows the great potential of PVDF membranes in macromolecules separation.

The utilization of open-source microcontroller boards and single-board computers in liquid chromatography.

Electronic system control of analytical instrumentation remains a critical aspect of modern measurement science. Within the field of liquid chromatography (LC), this is especially relevant for automation, module operation, detection, data acquisition, and data analysis. Increasingly, home-built analytical tools used for liquid-phase separations rely upon open-source microcontrollers and single-board computers to aid in simplifying these operations. In this review, we detail literature reported within the past 5 years in which these types of devices were used to advance various aspects of the LC research field, including sample preparation, instrument control, and data collection.

Biophysical Mechanisms of Liquid–Liquid Phase Separation in Biological Systems

A key biophysical process in biological systems, liquid–liquid phase separation (LLPS) is responsible for constructing membrane-less organelles and modulating cellular activities. The biophysical mechanisms underlying LLPS are explored in this paper, with an emphasis on multivalent interactions, entropy-driven processes, and how they affect cellular organization. We investigate the impact of external stimuli on phase behavior and clarify the physiological roles of biomolecular condensates, from stress response modulation to gene expression regulation. In addition, we study dysregulated LLPS in human disorders, providing information about possible therapeutic targets and approaches to innovative therapeutics. Through this interdisciplinary approach, we aim to improve our knowledge of LLPS and its effects on health and illness, opening the door to new therapeutic approaches that focus on the behavior of proteins and the structure of cells.