Liquid-liquid Phase Separation Process Research Articles

Screening of liquid–liquid phase separation conditions for proteins with a mixed solution kit of biomacromolecular crowding agents

Protein liquid–liquid phase separation (LLPS) is a significant process in biology and material sciences. Finding suitable conditions for protein LLPS is essential for its in-depth and systematic study. Here, we provide a mixed solution screening kit based on biomacromolecule crowding agents to find protein LLPS conditions. The screening kit consists of 96 chemical formulations, in which the biomacromolecule crowding agents are used as the key components. The aqueous solution of the target protein is mixed with each chemical agent in the kit and then placed in an incubator for some time. The LLPS conditions for the target protein can be found by examining the LLPS phenomena in the droplets. We used nine proteins as model target proteins—lysozyme, bovine serum albumin, bovine hemoglobin, ovalbumin, catalase, FUS, Aβ, Tau, and α-Synuclein—to evaluate the performance of the screening kit. We found that utilization of the screening kit is efficient and useful to find different conditions for LLPS of proteins. The screening results reveal two types of conditions: those that promote and those that inhibit LLPS. Both conditions are extremely valuable because those that promote LLPS can be used to do extensive studies on the LLPS processes of the proteins of interest, whereas those that inhibit LLPS can be utilized as leads for developing novel medications to treat LLPS-related disorders. Furthermore, novel applications for the kit were investigated by utilizing the screening products.

The evolution of the demixing morphology in quasi 2D water-lutidine mixtures: a fractal dimension analysis

In this work, the evolution of the morphological properties of the liquid-liquid phase separation process of water-lutidine mixtures in a quasi-2D geometry locally heated by laser absorption is studied at different heating rates by videomicroscopy and complemented by a finite element simulation. Morphological changes of the separated domains are characterised using the fractal dimension and the distribution of domain sizes, capturing the main steps of the process: spinodal decomposition derived from the fluctuations in density at the critical point, separation into a bicontinuous structure, breaking of the structures producing a wide distribution of sizes, and the subsequent growth and coalescence of the demixed regions (domains) to produce a complete separation. A comparison with the simplest case of typical nucleation is made by performing the same analysis at a concentration where critical fluctuations are not present. We conclude that the methodology presented here can be used to characterise the main steps of the phase separation process and distinguish between spinodal decomposition and nucleation.

MLOsMetaDB, a meta-database to centralize the information on liquid-liquid phase separation proteins and membraneless organelles.

Over the past few years, there has been a focus on proteins that create separate liquid phases in the intracellular liquid environment, known as membraneless organelles (MLOs). These organelles allow for the spatiotemporal associations of macromolecules that dynamically exchange within the cellular milieu. They provide a form of compartmentalization crucial for organizing key functions in many cells. Metabolic processes and signaling pathways in both the cytoplasm and nucleus are among the functions performed by MLOs, which are facilitated by diverse combinations of proteins and nucleic acids. However, disruptions in these liquid-liquid phase separation processes (LLPS) may lead to several diseases, such as neurodegenerative disorders and cancer, among others. To foster the study of this process and MLO function, we present MLOsMetaDB (http://mlos.leloir.org.ar), a comprehensive resource of information on MLO- and LLPS-related proteins. Our database integrates and centralizes available information for every protein involved in MLOs, which is otherwise disseminated across a plethora of different databases. Our manuscript outlines the development and features of MLOsMetaDB, which provides an interactive and user-friendly environment with modern biological visualizations and easy and quick access to proteins based on LLPS role, MLO location, and organisms. In addition, it offers an advanced search for making complex queries to generate customized information. Furthermore, MLOsMetaDB provides evolutionary information by collecting the orthologs of every protein in the same database. Overall, MLOsMetaDB is a valuable resource as a starting point for researchers studying the many processes driven by LLPS proteins and membraneless organelles.

CRDBP Protein Phase Separation and Its Recruitment to β-Catenin Protein in a Single Living Cell.

The Coding Region Determinant-Binding Protein (CRDBP) is a carcinoembryonic protein, and it is overexpressed in various cancer cells in the form of granules. We speculated the formation of CRDBP granules possibly through liquid-liquid phase separation (LLPS) processes due to the existence of intrinsically disordered regions (IDRs) in CRDBP. So far, we did not know whether or how phase separation processes of CRDBP occur in single living cells due to the lack of in vivo methods for studying intracellular protein phase separation. Therefore, to develop an in situ method for studying protein phase separation in living cells is a very urgent task. In this work, we proposed an efficient method for studying phase separation behavior of CRDBP in a single living cell by combining in situ fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) with a fluorescence protein fusion technique. We first predicted and confirmed that CRDBP has phase separation in solution by conventional fluorescence imaging and FCS methods. And then, we in situ studied the phase separation behaviors of CRDBP in living cells and observed three states of CRDBP phase separation such as monomer state, cluster state, and granule state. We studied the effects of CRDBP truncated forms and its inhibitor on the CRDBP phase separation. Furthermore, we discovered the recruitment of CRDBP to β-catenin protein in living cells and investigated the effects of CRDBP structures and inhibitor on CRDBP recruitment behavior. This finding may help us to further understand the mechanism of CRDBP protein for regulating Wnt signaling pathway. Additionally, our results documented that FCS/FCCS is an efficient and alternative method for studying protein phase separation in situ in living cells.

Lowering spinning temperature for polyketone (PK) hollow fiber membrane fabrication with low-toxic diluent system via thermally induced phase separation

Due to the excellent solvent resistance properties of polyketone (PK), the traditional non-solvent induced phase separation (NIPS) preparation process is both highly toxic and complex. In this work, we successfully and efficiently prepared PK hollow fiber membranes using the thermally induced phase separation (TIPS) method, capitalizing on a low-toxicity diluent system of polyethylene glycol 300 (PEG300) and triethylene glycol (TEG). Moreover, by simply adding TEG to the diluent, we achieved a reduction in the spinning temperature, resulting in membranes that display an interconnected structure formed through the liquid-liquid phase separation process. We systematically investigated the impact of the TEG ratio in the diluent, PK concentration, and propylene carbonate (PC) ratio in the bore liquid on the phase diagram, membrane morphology, and characteristics of PK membranes. Increasing the PC ratio in the bore liquid significantly improves the inner surface porosity due to PC penetration into the dope solution, leading to high water permeability. Additionally, the resulting PK membrane exhibits exceptional resistance to organic solvents. This work introduces a novel approach to lower the spinning temperature for PK membrane preparation in the TIPS process while preserving the membrane structure and properties.

Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates.

Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal that the presence of crowders led to the formation of larger coacervate droplets that remained stable over a 25-day period. While sucrose had a minimal effect on the physical properties of the coacervates, PEG led to the formation of coacervates with distinct characteristics, including higher density, increased protein and polymer content, and a more compact internal structure. These differences in coacervate properties can be attributed to the effects of crowders on individual macromolecules, such as the conformation of model polymers, and nonspecific interactions among model protein molecules. Moreover, our results show that sucrose and PEG have different partition behaviors: sucrose was present in both the coacervate and dilute phases, while PEG was observed to be excluded from the coacervate phase. Collectively, our findings provide insights into the understanding of crowding effects on complex coacervation, shedding light on the formation and properties of coacervates in the context of MLOs.

Protein Condensates and Protein Aggregates: In Vitro, in the Cell, and In Silico.

Similar to other polypeptides and electrolytes, proteins undergo phase transitions, obeying physicochemical laws. They can undergo liquid-to-gel and liquid-to-liquid phase transitions. Intrinsically disordered proteins are particularly susceptible to phase separation. After a general introduction, the principles of in vitro studies of protein folding, aggregation, and condensation are described. Numerous recent and older studies have confirmed that the process of liquid-liquid phase separation (LLPS) leads to various condensed bodies in cells, which is one way cells manage stress. We review what is known about protein aggregation and condensation in the cell, notwithstanding the protective and pathological roles of protein aggregates. This includes membrane-less organelles and cytotoxicity of the prefibrillar oligomers of amyloid-forming proteins. We then describe and evaluate bioinformatic (in silico) methods for predicting protein aggregation-prone regions of proteins that form amyloids, prions, and condensates.

The stability of NPM1 oligomers regulated by acidic disordered regions controls the quality of liquid droplets.

The nucleolus is a membrane-less nuclear body that typically forms through the process of liquid-liquid phase separation (LLPS) involving its components. NPM1 drives LLPS within the nucleolus and its oligomer formation and inter-oligomer interactions play a cooperative role in inducing LLPS. However, the molecular mechanism underlaying the regulation of liquid droplet quality formed by NPM1 remains poorly understood. In this study, we demonstrate that the N-terminal and central acidic residues within the intrinsically disordered regions (IDR) of NPM1 contribute to attenuating oligomer stability, although differences in the oligomer stability were observed only under stringent conditions. Furthermore, the impact of the IDRs is augmented by an increase in net negative charges resulting from phosphorylation within the IDRs. Significantly, we observed an increase in fluidity of liquid droplets formed by NPM1 with decreased oligomer stability. These results indicate that the difference in oligomer stability only observed biochemically under stringent conditions has a significant impact on liquid droplet quality formed by NPM1. Our findings provide new mechanistic insights into the regulation of nucleolar dynamics during the cell cycle.

Single-Molecular Dissection of Liquid-Liquid Phase Transitions.

Interaction between peptides and nucleic acids is a ubiquitous process that drives many cellular functions, such as replications, transcriptions, and translations. Recently, this interaction has been found in liquid-liquid phase separation (LLPS), a process responsible for the formation of newly discovered membraneless organelles with a variety of biological functions inside cells. In this work, we studied the molecular interaction between the poly-l-lysine (PLL) peptide and nucleic acids during the early stage of an LLPS process at the single-molecule level using optical tweezers. By monitoring the mechanical tension of individual nucleic acid templates upon PLL addition, we revealed a multistage LLPS process mediated by the long-range interactions between nucleic acids and polyelectrolytes. By varying different types (ssDNA, ssRNA, and dsDNA) and sequences (A-, T-, G-, or U-rich) of nucleic acids, we pieced together transition diagrams of the PLL-nucleic acid condensates from which we concluded that the propensity to form rigid nucleic acid-PLL complexes reduces the condensate formation during the LLPS process. We anticipate that these results are instrumental in understanding the transition mechanism of LLPS condensates, which allows new strategies to interfere with the biological functions of LLPS condensates inside cells.

Dynamic Control of Functional Coacervates in Synthetic Cells.

Membrane-less compartments formed via liquid-liquid phase separation (LLPS) are regulated dynamically via enzyme reactions in cells. Giant unilamellar vesicles (GUVs) provide a promising chassis to control, mimic, and understand the LLPS process; however, they are challenging to construct. Here, we engineer the dynamic assembly and disassembly of LLPS compartments using complex coacervates as models inside synthetic cells. Semipermeable GUVs constructed with defined lipid composition encapsulate the biomolecules, including enzymes required to regulate coacervates. Assembly and disassembly of coacervates are triggered in independent systems by the diffusion of substrates through the membrane into the vesicle lumen. The coupling of enzyme networks in a single synthetic cell system allows for reversible and out-of-equilibrium regulation of coacervates. The functional properties of the coacervates are revealed by sequestering biomolecules, including drugs and enzymes. GUVs, with functional LLPS compartment assembly, open avenues in constructing programmable autonomous synthetic cells with membrane-less organelles. The coacervate-in-vesicle platform has significant implications for understanding LLPS regulation mechanisms in cells.

Crosslink-Induced Conformation Change of Intrinsically Disordered Proteins Have a Nontrivial Effect on Phase Separation Dynamics and Thermodynamics.

Biomolecule condensates formed via liquid-liquid phase separation (LLPS) play crucial roles within various cellular processes. Despite numerous theoretical and experimental discoveries, the general principle by which the protein conformation affects the propensity for LLPS remains poorly understood. Here, we systematically address this issue using a general coarse-grained model of intrinsically disordered proteins (IDPs) with different degrees of intrachain crosslinks. We find that an increased conformation collapse due to higher intrachain crosslink ratio f enhances the thermodynamic stability of protein phase separation and found the critical temperature Tc has a good scaling law with the proteins' average radius of gyration Rg. Such correlation is robust regardless of interaction types and sequence patterns. Strikingly, the growth dynamics of the LLPS process, contrary to the thermodynamic observation, is generally more favored at proteins with extended conformation. Faster condensate growing speed is again observed for higher-f collapsed IDPs, resulting altogether in a nonmonotonic dynamics as a function of f. A phenomenological understanding of the phase behavior is provided by a mean-field model with an effective Flory interaction parameter χ, which is found to have a good scaling law with conformation expansion. Our study shed lights on the general mechanism for understanding and modulation of phase separation with different conformation profiles and may provide new evidence in reconciling the contradictions in thermodynamic- and dynamic-controlled experimental LLPS observations.

FUS fibrillation occurs through a nucleation-based process below the critical concentration required for liquid–liquid phase separation

FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid–liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.

Study liquid-liquid phase separation with optical microscopy: A methodology review.

Intracellular liquid-liquid phase separation (LLPS) is a critical process involving the dynamic association of biomolecules and the formation of non-membrane compartments, playing a vital role in regulating biomolecular interactions and organelle functions. A comprehensive understanding of cellular LLPS mechanisms at the molecular level is crucial, as many diseases are linked to LLPS, and insights gained can inform drug/gene delivery processes and aid in the diagnosis and treatment of associated diseases. Over the past few decades, numerous techniques have been employed to investigate the LLPS process. In this review, we concentrate on optical imaging methods applied to LLPS studies. We begin by introducing LLPS and its molecular mechanism, followed by a review of the optical imaging methods and fluorescent probes employed in LLPS research. Furthermore, we discuss potential future imaging tools applicable to the LLPS studies. This review aims to provide a reference for selecting appropriate optical imaging methods for LLPS investigations.

Stochastic Monte Carlo Model for Simulating the Dynamic Liquid-Liquid Phase Separation in Bacterial Cells.

There is growing evidence showing that many critical biological processes are driven by biomolecule condensates through liquid-liquid phase separation (LLPS). Although the qualitative observation and description of LLPS have been well documented, quantitative simulations of the time-dependent progression of LLPS in live cells are generally lacking. In this work, we build a stochastic Monte Carlo model to simulate the dynamic LLPS process during the formation of bacterial aggresomes. We demonstrate that the size distribution of the protein condensates evolves from an exponential-like to a bimodal-like pattern, and the number of condensates increases at the beginning and then decreases after reaching a maximum. Incorporating diffusion and collision, our simplified model recapitulates the two-step LLPS process in which many smaller condensates are formed in the first step and then merged into a few larger ones. We further reveal that the condensation speed, which can be defined by the condensates formed in unit time during the first step, is mainly determined by both the collision energy barrier and the initial protein density, while the number of condensates at the equilibrium is mainly associated with the dissociation energy barrier. Moreover, the LLPS process is not sensitive to temperature changes ranging around physiological conditions. Additionally, we consider the effect of the nucleation energy barrier on LLPS. We find that a higher nucleation energy barrier brings a slower condensation speed. Overall, we simulate the spatiotemporal dynamics of the LLPS process and provide qualitative guidance for understanding the dynamics of LLPS in bacterial cells, which can faithfully recapitulate experimental observations and facilitate the design of future experimental tests.

Flexibility of the Rotavirus NSP2 C-Terminal Region Supports Factory Formation via Liquid-Liquid Phase Separation.

Many viruses sequester the materials needed for their replication into discrete subcellular factories. For rotaviruses (RVs), these factories are called viroplasms, and they are formed in the host cell cytosol via the process of liquid-liquid phase separation (LLPS). The nonstructural protein 2 (NSP2) and its binding partner, nonstructural protein 5 (NSP5), are critical for viroplasm biogenesis. Yet it is not fully understood how NSP2 and NSP5 cooperate to form factories. The C-terminal region (CTR) of NSP2 (residues 291 to 317) is flexible, allowing it to participate in domain-swapping interactions that promote interoctamer interactions and, presumably, viroplasm formation. Molecular dynamics simulations showed that a lysine-to-glutamic acid change at position 294 (K294E) reduces NSP2 CTR flexibility in silico. To test the impact of reduced NSP2 CTR flexibility during infection, we engineered a mutant RV bearing this change (rRV-NSP2K294E). Single-cycle growth assays revealed a >1.2-log reduction in endpoint titers for rRV-NSP2K294E versus the wild-type control (rRV-WT). Using immunofluorescence assays, we found that rRV-NSP2K294E formed smaller, more numerous viroplasms than rRV-WT. Live-cell imaging experiments confirmed these results and revealed that rRV-NSP2K294E factories had delayed fusion kinetics. Moreover, NSP2K294E and several other CTR mutants formed fewer viroplasm-like structures in NSP5 coexpressing cells than did control NSP2WT. Finally, NSP2K294E exhibited defects in its capacity to induce LLPS droplet formation in vitro when incubated alongside NSP5. These results underscore the importance of NSP2 CTR flexibility in supporting the biogenesis of RV factories. IMPORTANCE Viruses often condense the materials needed for their replication into discrete intracellular factories. For rotaviruses, agents of severe gastroenteritis in children, factory formation is mediated in part by an octameric protein called NSP2. A flexible C-terminal region of NSP2 has been proposed to link several NSP2 octamers together, a feature that might be important for factory formation. Here, we created a change in NSP2 that reduced C-terminal flexibility and analyzed the impact on rotavirus factories. We found that the change caused the formation of smaller and more numerous factories that could not readily fuse together like those of the wild-type virus. The altered NSP2 protein also had a reduced capacity to form factory-like condensates in a test tube. Together, these results add to our growing understanding of how NSP2 supports rotavirus factory formation-a key step of viral replication.

Cofactor-dependent structural transition of SOD1 modulates its ability to undergo liquid-liquid phase separation.

Impetus leading to the toxic gain of function of Cu/Zn superoxide dismutase (SOD1) whose aggregation forms the hallmark of amyotrophic lateral sclerosis (ALS) is still a controversial area. The formation of membraneless organelles such as stress granules (SGs) is believed to occur through the process of liquid-liquid phase separation (LLPS) and involves numerous proteins containing intrinsically disordered regions. Whether SOD1, which is also associated with SGs and whose aggregation is associated with Amyotrophic lateral sclerosis (ALS), can independently undergo LLPS, is not known. Using a combination of experiments and computational methods, we report here that local structural disorder in two loop regions of SOD1 induced by the absence of metal cofactor - Zn, triggers its LLPS. The liquid condensates give rise to aggregates which eventually form toxic amyloids in a longer timescale. The addition of exogenous Zn to immature, metal-free SOD1 and the disease-relate ALS mutant - I113T, stabilized the loops and restored the folded structure, thereby inhibiting LLPS and subsequent aggregation. On the contrary, the Zn-induced inhibition of phase separation and aggregation was found to be partial in the case of another severe ALS-associated mutant - G85R, which exhibits reduced Zn-binding. Moreover, a less-severe ALS mutant - G37R with perturbed Cu binding does not undergo LLPS. In this work, we want to highlight the modulation of SOD1 LLPS propensity in a Zn-dependent manner due to underlying conformational transitions between folded and partially disordered states. Our work establishes a link between SOD1 LLPS and aggregation, which is relevant to ALS pathogenesis.

Phase separation underlies interactions of the SARS-CoV-2 nucleocapsid protein with nucleoli.

RNA viruses hijack host cell functions to promote viral replication. During infection, viral components enter membrane-bound and membrane-less cellular organelles, including the phase-separated nucleolus, where they perturb nucleolar proteins to aid virus replication. Recently, viruses have been shown to utilize the process of liquid-liquid phase separation (LLPS) to package their genome and promote viral RNA synthesis. The viral nucleocapsid (N) protein is critically involved in several aspects of virus replication. Importantly, the nucleolar phosphoprotein, Nucleophosmin (NPM1), with roles in ribosome biogenesis, was reported to interact with the N protein of several different RNA viruses and facilitate viral replication. However, the impact of this interaction and SARS CoV-2 N protein (NCoV-2) nucleolar localization on ribosome biogenesis and viral life cycle remains poorly understood. Our in vitro studies show that NPM1 undergoes heterotypic phase separation with NCoV-2, causing the formation of liquid-like droplets or condensates with restricted NPM1 mobility. Sequence analysis of NCoV-2 revealed enrichment of positively charged (Arg and Lys) amino acids, an important “sequence feature” that governs nuclear and nucleolar localization. Importantly, our cellular studies reveal the colocalization of NCoV-2 with NPM1 in the nucleoli of Vero E6 cells. These results suggest that there is a direct interaction between NPM1 and NCoV-2. Strikingly, NCoV-2 displaces NPM1 from reconstituted, granular component-like condensates and from nucleoli. Based on our collective findings, we propose that displacement of regulatory proteins (e.g., NPM1) from nucleoli by NCoV-2 through interactions of its Arg residues with ribosomal RNA (rRNA), may promote protein synthesis and the viral life cycle. These mechanistic insights will provide new avenues for the development of novel antiviral therapies for inhibition of nucleolar localization of NCoV-2.

LLPS vs. LLCPS: analogies and differences.

We compare the process of Liquid-Liquid Phase Separation (LLPS) of flexible macromolecular solutions, with the Liquid-Liquid Crystalline Phase Separation (LLCPS) of semiflexible polymers and rigid filamentous colloids, which involves the formation of a liquid phase that possesses a directional alignment. Although the observed phase separation follows a similar dynamic path, namely nucleation and growth or spinodal decomposition separating two phases of dilute and concentrated compositions, the underlying physics that defines the theoretical framework of LLCPS is completely different from the one of LLPS. We review the main theories that describe the phase separation processes and relying on thermodynamics and dynamical arguments, we highlight the differences and analogies between these two phase separation phenomena, attempting to clarify the inner mechanisms that regulate those two processes. A particular focus is given to metastable phases, as these intermediate states represent a key element in understanding how phase separation works.

Fused in sarcoma undergoes cold denaturation: Implications for phase separation.

The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.

Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects.

Liquid-liquid phase separation (LLPS) in macromolecular solutions (e.g., coacervation) is relevant both to technology and to the process of mesoscale structure formation in cells. The LLPS process is characterized by a phase diagram, i.e., binodal lines in the temperature/concentration plane, which must be quantified to predict the system's behavior. Experimentally, this can be difficult due to complications in handling the dense macromolecular phase. Here, we develop a method for accurately quantifying the phase diagram without direct handling: We confine the sample within micron-scale, water-in-oil emulsion droplets and then use precision fluorescent imaging to measure the volume fraction of the condensate within the droplet. We find that this volume fraction grows linearly with macromolecule concentration; thus, by applying the lever rule, we can directly extract the dense and dilute binodal concentrations. We use this approach to study a model LLPS system of self-assembled, fixed-valence DNA particles termed nanostars (NSs). We find that temperature/concentration phase diagrams of NSs display, with certain exceptions, a larger co-existence regime upon increasing salt or valence, in line with expectations. Aspects of the measured phase behavior validate recent predictions that account for the role of valence in modulating the connectivity of the condensed phase. Generally, our results on NS phase diagrams give fundamental insight into limited-valence phase separation, while the method we have developed will likely be useful in the study of other LLPS systems.