Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

Intrinsically disordered regions as facilitators of the transcription factor target search

Transcription factors (TFs) contribute to organismal development and function by regulating gene expression. Despite decades of research, the factors determining the specificity and speed at which eukaryotic TFs detect their target binding sites remain poorly understood. Recent studies have pointed to intrinsically disordered regions (IDRs) within TFs as key regulators of the process by which TFs find their target sites on DNA (the TF target search). However, IDRs are challenging to study because they can confer specificity despite low sequence complexity and can be functionally conserved despite rapid sequence divergence. Nevertheless, emerging computational and experimental approaches are beginning to elucidate the sequence-function relationship within the IDRs of TFs. Additional insights are informing potential mechanisms underlying the IDR-directed search for the DNA targets of TFs, including incorporation into biomolecular condensates, facilitating TF co-localization, and the hypothesis that IDRs recognize and directly interact with specific genomic regions.

Induction and Manipulation of Biomolecular Condensates Through Spatially Heterogeneous Solution Conditions

The study of biomolecular condensates (BMCs) is of great current interest because of the proposed roles of these types of assemblies in biological function and disease. In living cells, BMCs form in a highly heterogeneous environment and are influenced by concentration gradients of various relevant species. Furthermore, the biological functionality of the BMCs requires precise spatial control of their formation in some cases. In recent years, a number of in vitro experimental approaches have emerged that allow the generation, study, and manipulation of BMCs through the creation of well-defined spatially heterogeneous solution conditions relevant for BMC formation. In this concept article, it is presented in what way such methods can contribute to improved understanding and control of BMCs.

Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations

Organisms have evolved various protective mechanisms to survive in complex and dynamic environments. Phase separation is a ubiquitous mechanism in plants, animals, and microorganisms. It facilitates the aggregation of biomolecules through weak interactions, forming membrane-less organelles that help organisms respond effectively to stress signals. These biomolecular condensates include DNA, RNA, and proteins. Proteins are categorized into scaffold and client proteins, whose coordinated actions ensure the compartmentalization of cellular signals, thereby regulating various biological processes. Studies indicate that, in response to stress, phase separation modulates gene expression, signal transduction, cytoskeleton dynamics, and protein homeostasis, ensuring the precise spatiotemporal control of cellular functions. These insights underscore the crucial role of phase separation in maintaining cellular integrity and adaptability.

Tandem-repeat proteins introduce tuneable properties to engineered biomolecular condensates

The cell's ability to rapidly partition biomolecules into biomolecular condensates is linked to a diverse range of cellular functions. Understanding how the structural attributes of biomolecular condensates are linked with their biological roles can be facilitated by the development of synthetic condensate systems that can be manipulated in a controllable and predictable way. Here, we design and characterise a tuneable synthetic biomolecular condensate platform fusing modular consensus-designed tetratricopeptide repeat (CTPR) proteins to intrinsically-disordered domains. Trends between the CTPR structural attributes and condensate propensity were recapitulated across different experimental conditions and by in silico modelling, demonstrating that the CTPR domain can systematically affect the condensates in a predictable manner. Moreover, we show that incorporating short binding motifs into the CTPR domain results in specific target-protein recruitment into the condensates. Our model system can be rationally designed in a versatile manner to both tune condensate propensity and endow the condensates with new functions.

Phosphorylation-dependent charge blocks regulate the relaxation of nuclear speckle networks

Nuclear speckles (NSs) are viscoelastic network fluids formed via phase separation coupled to percolation (PSCP). Intermolecular crosslinks of SRRM2 lead to the emergence of system-spanning networks, although the physicochemical grammar governing SRRM2 PSCP remains poorly decoded. Here, we demonstrate that SRRM2 is extensively phosphorylated within the intrinsically disordered region (IDR), creating alternating charge blocks. We show that this specific charge pattern does not markedly alter the condensation threshold of SRRM2 in cells. Instead, SRRM2 charge blocks intensify intra-network molecular interactions to modulate the material properties of mesoscopic SRRM2 condensates. We further identify casein kinase 2 (CK2) as the upstream enzyme to catalyze SRRM2 phosphorylation. Phosphorylation of SRRM2 IDR by CK2 facilitates NS relaxation, which is associated with enhanced efficiency of mRNA splicing to safeguard genome stability during DNA damage. Our findings reveal important regulatory mechanisms of charge blocks in modulating the material properties and functions of biomolecular condensates in human cells.

Phase separation as a key mechanism in plant development, environmental adaptation, and abiotic stress response

Liquid-liquid phase separation is a fundamental biophysical process in which biopolymers, such as proteins, nucleic acids, and their complexes, spontaneously demix into distinct coexisting phases. This phenomenon drives the formation of membraneless organelles-cellular subcompartments without a lipid bilayer that perform specialized functions. In plants, phase-separated biomolecular condensates play pivotal roles in regulating gene expression, from genome organization to transcriptional and post-transcriptional processes. In addition, phase separation governs plant-specific traits, such as flowering and photosynthesis. As sessile organisms, plants have evolved to leverage phase separation for rapid sensing and response to environmental fluctuations and stress conditions. Recent studies highlight the critical role of phase separation in plant adaptation, particularly in response to abiotic stress. This review compiles the latest research on biomolecular condensates in plant biology, providing examples of their diverse functions in development, environmental adaptation, and stress responses. We propose that phase separation represents a conserved and dynamic mechanism enabling plants to adapt efficiently to ever-changing environmental conditions. Deciphering the molecular mechanisms underlying phase separation in plant stress responses opens new avenues for biotechnological strategies aimed at engineering stress-resistant crops. These advancements have significant implications for agriculture, particularly in addressing crop productivity in the face of climate change.

Synapsin Condensation is Governed by Sequence-Encoded Molecular Grammars

Multiple biomolecular condensates coexist at the pre- and post- synapse to enable vesicle dynamics and controlled neurotransmitter release in the brain. In pre-synapses, intrinsically disordered regions (IDRs) of synaptic proteins are drivers of condensation that enable clustering of synaptic vesicles (SVs). Using computational analysis, we show that the IDRs of SV proteins feature evolutionarily conserved non-random compositional biases and sequence patterns. Synapsin-1 is essential for condensation of SVs, and its C-terminal IDR has been shown to be a key driver of condensation. Focusing on this IDR, we dissected the contributions of two conserved features namely the segregation of polar and proline residues along the linear sequence, and the compositional preference for arginine over lysine. Scrambling the blocks of polar and proline residues weakens the driving forces for forming micron-scale condensates. However, the extent of clustering in subsaturated solutions remains equivalent to that of the wild-type synapsin-1. In contrast, substituting arginine with lysine significantly weakens both the driving forces for condensation and the extent of clustering in subsaturated solutions. Co-expression of the scrambled variant of synapsin-1 with synaptophysin results in a gain-of-function phenotype in cells, whereas arginine to lysine substitutions eliminate condensation in cells. We report an emergent consequence of synapsin-1 condensation, which is the generation of interphase pH gradients that is realized via differential partitioning of protons between coexisting phases. This pH gradient is likely to be directly relevant for vesicular ATPase functions and the loading of neurotransmitters. Our studies highlight how conserved IDR grammars serve as drivers of synapsin-1 condensation.

Differential interactions determine anisotropies at interfaces of RNA-based biomolecular condensates

Biomolecular condensates form via macromolecular phase separation. Here, we report results from our characterization of synthetic condensates formed by phase separation of mixtures comprising two types of RNA molecules and the biocompatible polymer polyethylene glycol. Purine-rich RNAs are scaffolds that drive phase separation via heterotypic interactions. Conversely, pyrimidine-rich RNA molecules are adsorbents defined by weaker heterotypic interactions. They adsorb onto and wet the interfaces of coexisting phases formed by scaffolds. Lattice-based simulations reproduce the phenomenology observed in experiments and these simulations predict that scaffolds and adsorbents have different non-random orientational preferences at interfaces. Dynamics at interfaces were probed using single-molecule tracking of fluorogenic probes bound to RNA molecules. These experiments revealed dynamical anisotropy at interfaces whereby motions of probe molecules parallel to the interface are faster than motions perpendicular to the interface. Taken together, our findings have broad implications for designing synthetic condensates with tunable interfacial properties.

Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are semidilute solutions. These can be approximated as solutions of blob-sized segments, which are peptide-sized motifs. We leveraged the blob picture and molecular dynamics simulations to quantify differences between inter-residue interactions in model compound and peptide-based mimics of dense versus dilute phases. The all-atom molecular dynamics simulations use a polarizable forcefield. In model compound solutions, the interactions between aromatic residues are stronger than interactions between cationic and aromatic residues. This holds in dilute and dense phases. Cooperativity within dense phases enhances pairwise interactions leading to finite-sized nanoscale clusters. The results for peptide-based condensates paint a different picture. Backbone amides add valence to the associating molecules. While this enhances pairwise inter-residue interactions in dilute phases, it weakens pair interactions in dense phases, doing so in a concentration-dependent manner. Weakening of pair interactions enables fluidization characterized by short-range order and long-range disorder. The higher valence afforded by the peptide backbone generates system-spanning networks. As a result, dense phases of peptides are best described as percolated network fluids. Overall, our results show how peptide backbones enhance pairwise interactions in dilute phases while weakening these interactions to enable percolation within dense phases.

Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins

The preponderance of intrinsically disordered proteins (IDPs) in the eukaryotic proteome, and their ability to interact with each other, and with folded proteins, RNA, and DNA for functional purposes, have made it important to quantitatively characterize their biophysical properties. Toward this end, we developed the transferable self-organized polymer (SOP-IDP) model to calculate the properties of several IDPs. The values of the radius of gyration (R g $$ {R}_g $$ ) obtained from SOP-IDP simulations are in excellent agreement (correlation coefficient of 0.96) with those estimated from SAXS experiments. For AP180 and Epsin, the predicted values of the hydrodynamic radii (R h s $$ {R}_h\mathrm{s} $$ ) are in nearly quantitative agreement with those from fluorescence correlation spectroscopy (FCS) experiments. Strikingly, the calculated SAXS profiles for 36 IDPs are also nearly superimposable on the experimental profiles. The dependence ofR g $$ {R}_g $$ and the mean end-to-end distance (R ee $$ {R}_{ee} $$ ) on chain length,N $$ N $$ , follows Flory's scaling law,R α ≈ a α N 0.588 $$ {R}_{\alpha}\approx {a}_{\alpha }{N}^{0.588} $$ (α = g , $$ \alpha =g, $$ ande $$ e $$ ), suggesting that globally IDPs behave as synthetic polymers in a good solvent. This finding depends on the solvent quality, which can be altered by changing variables such as pH and salt concentration. The values ofa g $$ {a}_g $$ anda e $$ {a}_e $$ are 0.20 and 0.48 nm, respectively. Surprisingly, finite size corrections to scaling, expected on theoretical grounds, are negligible forR g $$ {R}_g $$ andR ee $$ {R}_{ee} $$ . In contrast, only by accounting for the finite sizes of the IDPs, the dependence of experimentally measurableR h $$ {R}_h $$ onN $$ N $$ can be quantitatively explained usingν = 0.588 $$ \nu =0.588 $$ . Although Flory scaling law captures the estimates forR g $$ {R}_g $$ ,R ee $$ {R}_{ee} $$ , andR h $$ {R}_h $$ accurately, the spread of the simulated data around the theoretical curve is suggestive of of sequence-specific features that emerge through a fine-grained analysis of the conformational ensembles using hierarchical clustering. Typically, the ensemble of conformations partitions into three distinct clusters, having different equilibrium populations and structural properties. Without any further readjustments to the parameters of the SOP-IDP model, we also obtained nearly quantitative agreement with paramagnetic relaxation enhancement (PRE) measurements for α-synuclein. The transferable SOP-IDP model sets the stage for several applications, including the study of phase separation in IDPs and interactions with nucleic acids.

Prediction of phase-separation propensities of disordered proteins from sequence

Phase separation is one possible mechanism governing the selective cellular enrichment of biomolecular constituents for processes such as transcriptional activation, mRNA regulation, and immune signaling. Phase separation is mediated by multivalent interactions of macromolecules including intrinsically disordered proteins and regions (IDRs). Despite considerable advances in experiments, theory, and simulations, the prediction of the thermodynamics of IDR phase behavior remains challenging. We combined coarse-grained molecular dynamics simulations and active learning to develop a fast and accurate machine learning model to predict the free energy and saturation concentration for phase separation directly from sequence. We validate the model using computational and previously measured experimental data, as well as new experimental data for six proteins. We apply our model to all 27,663 IDRs of chain length up to 800 residues in the human proteome and find that 1,420 of these (5%) are predicted to undergo homotypic phase separation with transfer free energies < -2 kBT. We use our model to understand the relationship between single-chain compaction and phase separation and find that changes from charge- to hydrophobicity-mediated interactions can break the symmetry between intra- and intermolecular interactions. We also provide proof of principle for how the model can be used in force field refinement. Our work refines and quantifies the established rules governing the connection between sequence features and phase-separation propensities, and our prediction models will be useful for interpreting and designing cellular experiments on the role of phase separation, and for the design of IDRs with specific phase-separation propensities.

Functional specificity in biomolecular condensates revealed by genetic complementation

Biomolecular condensates are thought to create subcellular microenvironments that regulate specific biochemical activities. Extensive in vitro work has helped link condensate formation to a wide range of cellular processes, including gene expression, nuclear transport, signalling and stress responses. However, testing the relationship between condensate formation and function in cells is more challenging. In particular, the extent to which the cellular functions of condensates depend on the nature of the molecular interactions through which the condensates form is a major outstanding question. Here, we review results from recent genetic complementation experiments in cells, and highlight how genetic complementation provides important insights into cellular functions and functional specificity of biomolecular condensates. Combined with observations from human genetic disease, these experiments suggest that diverse condensate-promoting regions within cellular proteins confer different condensate compositions, biophysical properties and functions.

Selective phase separation of transcription factors is driven by orthogonal molecular grammar

Protein production is critically dependent on gene transcription rates, which are regulated by RNA polymerase and a large collection of different transcription factors (TFs). How these transcription factors selectively address different genes is only partially known. Recent discoveries show that the differential condensation of separate TF families through phase separation may contribute to selectivity. Here we address this by conducting phase separation studies on six TFs from three different TF families with residue-scale coarse-grained molecular dynamics simulations. Our exploration of ternary TF phase diagrams reveals four dominant sticker motifs and two orthogonal driving forces that dictate the resultant condensate morphology, pointing to sequence-dependent orthogonal molecular grammar as a generic molecular mechanism that drives selective transcriptional condensation in gene expression.

Genetically-Encoded Phase Separation Sensors Enable High-Fidelity Live-Cell Probing of Biomolecular Condensates

Biomolecular condensates are membraneless compartments with enigmatic roles across intracellular phenomena. Intrinsically disordered proteins (IDPs) often function as condensate scaffolds, fueled by liquid-liquid phase separation (LLPS) dynamics. Intracellular probing of condensates relies on live-cell imaging of IDP-scaffolds tagged with fluorescent proteins. Conformational heterogeneity in IDPs, however, renders them uniquely susceptible to artifacts from tagging. Probing epidermal condensates in skin, we recently introduced genetically-encoded LLPS-sensors that circumvent the need for molecular-level tagging of skin IDPs. Departing from subcellular tracking of IDP-scaffolds, LLPS-sensors report on the assembly and liquid-like dynamics of their condensates. Here, we demonstrate biomolecular approaches for the evolution and tunability of epidermal LLPS-sensors and assess their impact in the early and late stages of intracellular phase separation. Benchmarking against scaffold-bound fluorescent reporters, we discovered that tunable ultraweak scaffold-sensor interactions uniquely enable the sensitive and innocuous probing of nascent and established biomolecular condensates. Our LLPS-sensitive tools pave the way for the high-fidelity intracellular probing of IDP-governed biomolecular condensates across biological systems.

Interaction networks within biomolecular condensates feature topological cliques near the interface

Biomolecular condensates are typically maintained by networks of molecular interactions, with canonical examples including those formed by prion-like low complexity domains (LCDs) of proteins. Single-component LCD condensates have been predicted to exhibit small-world network topologies and spatial inhomogeneities in protein compaction. Here, we systematically characterize molecular networks underlying condensates and investigate the relationship between single molecule properties and network topologies. We employ a chemically specific coarse-grained model to probe LCD condensates and generalize our findings by varying sequence hydrophobicity via a generic model that describes "hydrophobic-polar" (HP) polymers. For both model systems, we find that condensates are sustained by small-world network topologies featuring molecular "hubs" and "cliques". Molecular hubs with high network betweenness centrality localize near the centers of condensates and adopt more elongated conformations. In contrast, network cliques-densely interacting molecules that form locally fully connected subgraphs-are bridged by hubs and tend to localize near the condensate interface. Interestingly, we find power-law relationships between the structure and dynamics of individual molecules and network betweenness centrality, which describes molecular connectivity. Thus, our work demonstrates that inhomogeneities in condensate network connectivity can be predicted from single-molecule properties. Furthermore, we find that network cliques have longer lifetimes and that their constituent molecules remain spatially constrained, suggesting a role in shaping interface material properties.

Uncovering the mechanism for polar sequestration of the major bacterial sugar regulator by high-throughput screens and 3D interaction modeling

The poles of rod-shaped bacteria emerge as regulatory hubs. We have shown that enzyme I (EI), the major bacterial sugar metabolism regulator, is sequestered when not needed in TmaR phase-separated condensates in Escherichia coli cell poles. Here, we combined genetic and automated microscopy screens to identify residues in EI and TmaR that are important for their interaction and colocalization. Mutating these residues affects EI-TmaR interaction in bacteria and impairs co-phase separation in yeast. The results were used to generate an EI-TmaR interaction model, which agrees with coevolution data and is supported by conservation of the interacting residues and EI-TmaR colocalization in other species. Mutating residues predicted to interact electrostatically further supports our model. The model explains how TmaR controls EI activity and its interaction with the phosphoprotein HPr and, hence, sugar uptake. Our study highlights the importance of sugar metabolism spatial regulation during evolution and presents a way to unravel protein-protein interactions.

Tunable metastability of condensates reconciles their dual roles in amyloid fibril formation

Stress granules form via co-condensation of RNA-binding proteins containing prion-like low complexity domains (PLCDs) with RNA molecules. Homotypic interactions among PLCDs can drive amyloid fibril formation that is enhanced by ALS-associated mutations. We report that condensation- versus fibril-driving homotypic interactions are separable for A1-LCD, the PLCD of hnRNPA1. Separable interactions lead to thermodynamically metastable condensates and globally stable fibrils. Interiors of condensates suppress fibril formation whereas interfaces have the opposite effect. ALS-associated mutations enhance the stability of fibrils and weaken condensate metastability, thus enhancing the rate of fibril formation. We designed mutations to enhance A1-LCD condensate metastability and discovered that stress granule disassembly in cells can be restored even when the designed variants carry ALS-causing mutations. Therefore, fibril formation can be suppressed by condensate interiors that function as sinks. Condensate sink potentials are influenced by their metastability, which is tunable through separable interactions even among minority components of stress granules.

Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces

The localization of biomolecular condensates to intracellular membrane surfaces has emerged as an important feature of sub-cellular organization. In this work, we study the wetting behavior of biomolecular condensates on various substrates. We use confocal microscopy to measure the contact angles of model condensates formed by intrinsically disordered protein Ddx4N. We show the importance of taking optical aberrations into account, as these impact apparent contact angle measurements. Ddx4N condensates are seen to partially dry (contact angles above 90°) a model membrane, with little dependence on the magnitude of charge on, or tyrosine content of, Ddx4N. Further contact angle measurements on surfaces of varying hydrophilicity reveal a preference of Ddx4N condensates for hydrophobic surfaces, suggesting an intrinsic repulsion between protein condensates and hydrophilic membrane surfaces. This observation is in line with previous studies relating protein adsorption to surface hydrophilicity. Our work advances the understanding of the molecular details governing the localization of biomolecular condensates.

Extreme pH Tolerance in Peptide Coacervates Mediated by Multivalent Hydrogen Bonds for Enzyme-Triggered Oral Drug Delivery

Biopolymer-based complex coacervates hold promising prospects in the field of biomedicine. However, their low stability in environments with extreme pH and high salt concentrations, largely due to weakly charged biomacromolecules and insufficient understanding of their assembly processes, has hindered their practical applications in oral drug delivery. Here, we have developed Dopa-containing peptide-based complex coacervates that are stable across a wide range of pH (1-11) and salt concentrations. Large-scale all-atom molecular dynamics simulations reveal that multivalent hydrogen bonds control the assembly pathway of the coacervates and boost their stability. Systematic point mutations reveal that various multivalent molecular interactions can synergistically tune the properties of complex coacervates. Such peptide coacervates show high drug encapsulation efficacy and trypsin-triggered release, presenting great potential for oral drug delivery applications. Our multivalent hydrogen bond-mediated peptide coacervates provide new design principles of engineering functional coacervates for diverse applications.

Multiphasic condensates formed with mono-component of tetrapeptides via phase separation

Biomolecular condensates, formed by liquid-liquid phase separation of biomacromolecules, play crucial roles in regulating physiological events in biological systems. While multiphasic condensates have been extensively studied, those derived from a single component of short peptides have not yet been reported. Here, we report the symmetrical core-shell structural biomolecular condensates formed with a programmable tetrapeptide library via phase separation. Our findings reveal that tryptophan is essential for core-shell structure formation due to its strongest homotypical π-π interaction, enabling us to modulate the structure of condensates from core-shell to homogeneous by altering the amino acid composition. Molecular dynamics simulation combined with cryogenic focused ion beam scanning electron microscopy and cryogenic electron microscopy show that the inner core of multiphasic tetrapeptide condensates is solid-like, consisting of ordered structures. The core is enveloped by a liquid-like shell, stabilizing the core structure. Furthermore, we demonstrate control over multiphasic condensate formation through intrinsic redox reactions or post-translational modifications, facilitating the rational design of synthetic multiphasic condensates for various applications on demand.

Crosstalk Between Phase-Separated Membraneless Condensates and Membrane-Bound Organelles in Cellular Function and Disease

Compartmentalization in eukaryotic cells allows the spatiotemporal regulation of biochemical processes, in addition to allowing specific sets of proteins to interact in a regulated as well as stochastic manner. Although membrane-bound organelles are thought to be the key players of cellular compartmentalization, membraneless biomolecular condensates such as stress granules, P bodies, and many others have recently emerged as key players that are also thought to bring order to a highly chaotic environment. Here, we have evaluated the latest studies on biomolecular condensates, specifically focusing on how they interact with membrane-bound organelles and modulate each other's functions. We also highlight the importance of this interaction in neurodegenerative and cardiovascular diseases as well as in cancer.

Single-fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates

Biomolecular condensates are viscoelastic materials. Simulations predict that condensates formed by intrinsically disordered proteins are network fluids defined by spatially inhomogeneous organization of the underlying molecules. Here, we test these predictions and find that molecules within condensates are organized into slow-moving nanoscale clusters and fast-moving dispersed molecules. These results, obtained using single-fluorogen tracking and super-resolution imaging of different disordered protein-based condensates, affirm the predicted spatially inhomogeneous organization of molecules within condensates. We map the internal environments and interfaces of condensates using fluorogens that localize differently to the interiors versus interface between dilute phase and condensate. We show that nanoscale clusters within condensates are more hydrophobic than regions outside the clusters, and regions within condensates that lie outside clusters are more hydrophobic than coexisting dilute phases. Our findings provide a structural and dynamical basis for the viscoelasticity of condensates.

Acetylation of Short Glycopeptides Enables Phase Separation

Liquid-liquid phase separation (LLPS) of biomacromolecules is crucial for regulating cellular functions. To explore their molecular mechanisms, peptide-based coacervates mimicking natural proteins have been developed, but the role of side chain modifications such as glycosylation remains underexplored. Here, we demonstrate that acetylation of short glycopeptides can induce pH- and concentration-dependent phase separation, while removing acetyl groups abolishes this behavior. Circular dichroism spectroscopy revealed a strong link between peptide structural ordering and the phase separation propensity. Peptides capable of forming liquid droplets displayed a significant ellipticity change at 205 nm upon changing solution pH. Moreover, these peptide coacervates can interact with cells and enhance the antiproliferative property of doxorubicin. Therefore, this work highlights the critical role of O-acetylation in LLPS and provides a valuable tool for studying the parameters regulating LLPS and its implications in cellular processes.

Accurate prediction of thermoresponsive phase behavior of disordered proteins

Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermoresponsive properties. While UCST-type (upper critical solution temperature) phase behavior has been studied extensively and can now be predicted reliably using computational models, LCST-type (lower critical solution temperature) phase transitions remain less explored, with a lack of computational models capable of accurate prediction. This gap limits our ability to probe fully how proteins undergo phase transitions in response to temperature changes. Here, we introduce Mpipi-T, a residue-level coarse-grained model designed to predict LCST-type phase behavior of proteins. Parametrized using both atomistic simulations and experimental data, Mpipi-T accounts for entropically driven protein phase separation that occurs upon heating. Accordingly, Mpipi-T predicts temperature-driven protein behavior quantitatively in both single- and multi-chain systems. Beyond its predictive capabilities, we demonstrate that Mpipi-T provides a framework for uncovering the molecular mechanisms underlying heat stress responses, offering new insights into how proteins sense and adapt to thermal changes in biological systems.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

Electrostatics of salt-dependent reentrant phase behaviors highlights diverse roles of ATP in biomolecular condensates

Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, for example, reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP's involvement in π-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.

Scale-free Spatio-temporal Correlations in Conformational Fluctuations of Intrinsically Disordered Proteins

The self-assembly of intrinsically disordered proteins (IDPs) into condensed phases and the formation of membrane-less organelles (MLOs) can be considered as the phenomenon of collective behavior. The conformational dynamics of IDPs are essential for their interactions and the formation of a condensed phase. From a physical perspective, collective behavior and the emergence of phase are associated with long-range correlations. Here the conformational dynamics of IDPs and the correlations therein are analyzed, using µs-scale atomistic molecular dynamics (MD) simulations and single-molecule Förster resonance energy transfer (smFRET) experiments. The existence of typical scale-free spatio-temporal correlations in IDP conformational fluctuations is demonstrated. Their conformational evolutions exhibit "1/f noise" power spectra and are accompanied by the appearance of residue domains following a power-law size distribution. Additionally, the motions of residues present scale-free behavioral correlation. These scale-free correlations resemble those in physical systems near critical points, suggesting that IDPs are poised at a critical state. Therefore, IDPs can effectively respond to finite differences in sequence compositions and engender considerable structural heterogeneity which is beneficial for IDP interactions and phase formation.

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.

Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates

Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely regulated by electrostatic interactions. Residue-resolution coarse-grained models that describe solvent and ions implicitly are widely used to gain mechanistic insights into the biophysical properties of condensates, offering transferability, computational efficiency, and accurate predictions for multiple systems. However, their predictive accuracy diminishes for charge-rich condensates due to the implicit treatment of solvent and ions. Here, we present Mpipi-Recharged, a residue-resolution coarse-grained model that improves the description of charge effects in biomolecular condensates containing disordered proteins, multidomain proteins, and/or disordered single-stranded RNAs. Mpipi-Recharged introduces a pair-specific asymmetric Yukawa electrostatic potential, informed by atomistic simulations. We show that this asymmetric coarse-graining of electrostatic forces captures intricate effects, such as charge blockiness, stoichiometry variations in complex coacervates, and modulation of salt concentration, without requiring explicit solvation. Mpipi-Recharged provides excellent agreement with experiments in predicting the phase behavior of highly charged condensates. Overall, Mpipi-Recharged improves the computational tools available to investigate the physicochemical mechanisms regulating biomolecular condensates, enhancing the scope of computer simulations in this field.

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Decoding phase separation of prion-like domains through data-driven scaling laws

Proteins containing prion-like low complexity domains (PLDs) are common drivers of the formation of biomolecular condensates and are prone to misregulation due to amino acid mutations. Here, we exploit the accuracy of our residue-resolution coarse-grained model, Mpipi, to quantify the impact of amino acid mutations on the stability of 140 PLD mutants from six proteins (hnRNPA1, TDP43, FUS, EWSR1, RBM14, and TIA1). Our simulations reveal the existence of scaling laws that quantify the range of change in the critical solution temperature of PLDs as a function of the number and type of amino acid sequence mutations. These rules are consistent with the physicochemical properties of the mutations and extend across the entire family tested, suggesting that scaling laws can be used as tools to predict changes in the stability of PLD condensates. Our work offers a quantitative lens into how the emergent behavior of PLD solutions vary in response to physicochemical changes of single PLD molecules.

A Single Amino Acid Model for Hydrophobically Driven Liquid-Liquid Phase Separation

This study proposes fluorenylmethoxycarbonyl (Fmoc)-protected single amino acids (Fmoc-AAs) as a minimalistic model system to investigate liquid-liquid phase separation (LLPS) and the elusive liquid-to-solid transition of condensates. We demonstrated that Fmoc-AAs exhibit LLPS depending on the pH and ionic strength, primarily driven by hydrophobic interactions. Systematic examination of the conditions under which each Fmoc-AA undergoes LLPS revealed distinct residue-dependent trends in the critical concentrations and phase behavior. Importantly, we elucidated the liquid-to-solid transition process, suggesting that it may be driven by a molecular mechanism different from that of LLPS. Fmoc-AA condensates showed promise for biomolecular enrichment and catalytic applications. This work provides significant insights into the molecular mechanisms of LLPS and the subsequent liquid-to-solid transition, offering a robust platform for future studies related to protocells and protein aggregation diseases.

Expanding the molecular grammar of polar residues and arginine in FUS phase separation

A molecular grammar governing low-complexity prion-like domain phase separation (PS) has identified tyrosine and arginine as primary drivers via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues and contacts contribute to PS, highlighting the need to include these contributions in PS theories and models. Tyrosine and arginine make important contacts beyond tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine contributes to PS with sequence and position specificity, contacting tyrosine, arginine and other residues, both before PS and in condensed phases. The flexibility of glycine enhances PS by allowing favorable contacts between adjacent residues and inhibits the liquid-to-solid transition. Polar residues also make sequence-specific contributions to liquid-to-solid transition, with serine positions linked to the formation of an amyloid-core structure by the FUS low-complexity domain. Hence, an extended molecular grammar expands the role of arginine and polar residues in prion-like domain protein PS and reveals the position dependence of residue contribution to solidification.

Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.

Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains

Disordered regions are an important functional feature of many multidomain proteins. A prime example is proteins in membraneless organelles, which contain folded domains that engage in specific interactions and disordered low-complexity (LC) domains that mediate liquid-liquid phase separation. Studying these complex architectures remains challenging due to their conformational variability. Native mass spectrometry (nMS) is routinely employed to analyze conformations and interactions of folded or disordered proteins; however, its ability to analyze proteins with disordered LC domains has not been investigated. Here, we analyze the ionization and conformational states of designed model proteins that recapitulate key features of proteins found in membraneless organelles. Our results show that charge state distributions (CSDs) in nMS reflect partial disorder regardless of the protein sequence, providing insights into their conformational plasticity and interactions. By applying the same CSD analysis to a spider silk protein fragment, we find that interactions between folded domains that trigger silk assembly simultaneously induce conformational changes in the LC domains. Lastly, using intact nucleosomes, we demonstrate that CSDs are a good predictor for the disorder content of complex native assemblies. We conclude that nMS reliably informs about the conformational landscape of proteins with LC domains, which is crucial for understanding protein condensates in cellular environments.

Charge Arrangement Determines the Sensitivity of Aggregation Patterns between Peptide-Chains to the Surrounding Ionic Environment

The molecular basis for the liquid-liquid phase separation (LLPS) behavior of various biomolecular components in the cell is the formation of multivalent and low-affinity interactions. When the content of these components exceeds a certain critical concentration, the molecules will spontaneously coalesce to form a new liquid phase; i.e., LLPS occurs. Intrinsically disordered proteins (IDPs) are usually rich in amino acids with charged side-chains, and thus, LLPS-involving interactions between their side-chains are of great interest. However, the molecular details of the coalescence of such charged IDPs in a salt solution are still lacking. Here, we focus on two types of peptide-chains with oppositely charged amino acids in extreme arrangements and investigate their aggregation patterns in various ionic environments. The results show that the interaction patterns between peptide-chains with nonuniform charge arrangement sequences are more sensitive to the surrounding cationic environment, and Na+ ions are more likely to cause aggregation of ASP residues compared to Mg2+ ions. As the ionic concentration increases, the electrostatic interactions between oppositely charged residues are gradually converted into a negative-negative amino acid interaction network bridged by Na+ ions, while the positive charge-rich regions are more strongly inclined to be exposed to the solvent environment and gain greater freedom of movement. Simultaneously, this effect will reach saturation with a further increase of salt concentration. The present study enriches insights into the electrostatic dominant factors in phase separation phenomena at the atomic level, which will hopefully inspire the design and application of targeted LLPS in the future.

Mechano-dependent sorbitol accumulation supports biomolecular condensate

Condensed droplets of protein regulate many cellular functions, yet the physiological conditions regulating their formation remain largely unexplored. Increasing our understanding of these mechanisms is paramount, as failure to control condensate formation and dynamics can lead to many diseases. Here, we provide evidence that matrix stiffening promotes biomolecular condensation in vivo. We demonstrate that the extracellular matrix links mechanical cues with the control of glucose metabolism to sorbitol. In turn, sorbitol acts as a natural crowding agent to promote biomolecular condensation. Using in silico simulations and in vitro assays, we establish that variations in the physiological range of sorbitol concentrations, but not glucose concentrations, are sufficient to regulate biomolecular condensates. Accordingly, pharmacological and genetic manipulation of intracellular sorbitol concentration modulates biomolecular condensates in breast cancer-a mechano-dependent disease. We propose that sorbitol is a mechanosensitive metabolite enabling protein condensation to control mechano-regulated cellular functions.

Molecular determinants of condensate composition

Cells use membraneless compartments to organize their interiors, and recent research has begun to uncover the molecular principles underlying their assembly. Here, we explore how site-specific and chemically specific interactions shape the properties and functions of condensates. Site-specific recruitment involves precise interactions at specific sites driven by partially or fully structured interfaces. In contrast, chemically specific recruitment is driven by complementary chemical interactions without the requirement for a persistent bound-state structure. We propose that site-specific and chemically specific interactions work together to determine the composition of condensates, facilitate biochemical reactions, and regulate enzymatic activities linked to metabolism, signaling, and gene expression. Characterizing the composition of condensates requires novel experimental and computational tools to identify and manipulate the molecular determinants guiding condensate recruitment. Advancing this research will deepen our understanding of how condensates regulate cellular functions, providing valuable insights into cellular physiology and organization.

Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning

Elucidating how protein sequence determines the properties of disordered proteins and their phase-separated condensates is a great challenge in computational chemistry, biology, and biophysics. Quantitative molecular dynamics simulations and derived free energy values can in principle capture how a sequence encodes the chemical and biological properties of a protein. These calculations are, however, computationally demanding, even after reducing the representation by coarse-graining; exploring the large spaces of potentially relevant sequences remains a formidable task. We employ an "active learning" scheme introduced by Yang et al. (bioRxiv, 2022, https://doi.org/10.1101/2022.08.05.502972) to reduce the number of labelled examples needed from simulations, where a neural network-based model suggests the most useful examples for the next training cycle. Applying this Bayesian optimisation framework, we determine properties of protein sequences with coarse-grained molecular dynamics, which enables the network to establish sequence-property relationships for disordered proteins and their self-interactions and their interactions in phase-separated condensates. We show how iterative training with second virial coefficients derived from the simulations of disordered protein sequences leads to a rapid improvement in predicting peptide self-interactions. We employ this Bayesian approach to efficiently search for new sequences that bind to condensates of the disordered C-terminal domain (CTD) of RNA Polymerase II, by simulating molecular recognition of peptides to phase-separated condensates in coarse-grained molecular dynamics. By searching for protein sequences which prefer to self-interact rather than interact with another protein sequence we are able to shape the morphology of protein condensates and design multiphasic protein condensates.

Discrimination between Purine and Pyrimidine-Rich RNA in Liquid-Liquid Phase-Separated Condensates with Cationic Peptides and the Effect of Artificial Crowding Agents

Membraneless organelles, often referred to as condensates or coacervates, are liquid-liquid phase-separated systems formed between noncoding RNAs and intrinsically disordered proteins. While the importance of different amino acid residues in short peptide-based condensates has been investigated, the role of the individual nucleobases or the type of heterocyclic structures, the purine vs pyrimidine nucleobases, is less researched. The cell's crowded environment has been mimicked in vitro to demonstrate its ability to induce the formation of condensates, but more research in this area is required, especially with respect to RNA-facilitated phase separation and the properties of the crowding agent, poly(ethylene glycol) (PEG). Herein, we have shown that the nucleotide base sequence of RNA can greatly influence its propensity to undergo phase separation with cationic peptides, with the purine-only RNA decamer (AG)5 readily doing so while the pyrimidine-only (CU)5 does not. Furthermore, we show that the presence and size of a PEG macromolecular crowder affects both the ability to phase separate and the stability of coacervates formed, possibly due to co-condensation of PEG with the RNA and peptides. This work sheds light on the presence of low-complexity long purine- or pyrimidine-rich noncomplementary repeat (AG or CU) sequences in various noncoding RNAs found in biology.

The molecular mechanism of temperature-dependent phase separation of heat shock factor 1

Heat shock factor 1 (HSF1) is the critical orchestrator of cell responses to heat shock, and its dysfunction is linked to various diseases. HSF1 undergoes phase separation upon heat shock, and its activity is regulated by post-translational modifications (PTMs). The molecular details underlying HSF1 phase separation, temperature sensing and PTM regulation remain poorly understood. Here, we discovered that HSF1 exhibits temperature-dependent phase separation with a lower critical solution temperature behavior, providing a new conceptual mechanism accounting for HSF1 activation. We revealed the residue-level molecular details of the interactions driving the phase separation of wild-type HSF1 and its distinct PTM patterns at various temperatures. The mapped interfaces were validated experimentally and accounted for the reported HSF1 functions. Importantly, the molecular grammar of temperature-dependent HSF1 phase separation is species specific and physiologically relevant. These findings delineate a chemical code that integrates accurate phase separation with physiological body temperature control in animals.

Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

Intracellular liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a fundamental mechanism by which cells compartmentalize their components and perform essential biological functions. Molecular simulations play a crucial role in providing microscopic insights into the physicochemical processes driving this phenomenon. In this study, we systematically compare six state-of-the-art sequence-dependent residue-resolution models to evaluate their performance in reproducing the phase behaviour and material properties of condensates formed by seven variants of the low-complexity domain (LCD) of the hnRNPA1 protein (A1-LCD)-a protein implicated in the pathological liquid-to-solid transition of stress granules. Specifically, we assess the HPS, HPS-cation-π, HPS-Urry, CALVADOS2, Mpipi, and Mpipi-Recharged models in their predictions of the condensate saturation concentration, critical solution temperature, and condensate viscosity of the A1-LCD variants. Our analyses demonstrate that, among the tested models, Mpipi, Mpipi-Recharged, and CALVADOS2 provide accurate descriptions of the critical solution temperatures and saturation concentrations for the multiple A1-LCD variants tested. Regarding the prediction of material properties for condensates of A1-LCD and its variants, Mpipi-Recharged stands out as the most reliable model. Overall, this study benchmarks a range of residue-resolution coarse-grained models for the study of the thermodynamic stability and material properties of condensates and establishes a direct link between their performance and the ranking of intermolecular interactions these models consider.

Mis-splicing of a neuronal microexon promotes CPEB4 aggregation in ASD

The inclusion of microexons by alternative splicing occurs frequently in neuronal proteins. The roles of these sequences are largely unknown, and changes in their degree of inclusion are associated with neurodevelopmental disorders1. We have previously shown that decreased inclusion of a 24-nucleotide neuron-specific microexon in CPEB4, a RNA-binding protein that regulates translation through cytoplasmic changes in poly(A) tail length, is linked to idiopathic autism spectrum disorder (ASD)2. Why this microexon is required and how small changes in its degree of inclusion have a dominant-negative effect on the expression of ASD-linked genes is unclear. Here we show that neuronal CPEB4 forms condensates that dissolve after depolarization, a transition associated with a switch from translational repression to activation. Heterotypic interactions between the microexon and a cluster of histidine residues prevent the irreversible aggregation of CPEB4 by competing with homotypic interactions between histidine clusters. We conclude that the microexon is required in neuronal CPEB4 to preserve the reversible regulation of CPEB4-mediated gene expression in response to neuronal stimulation.

Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations

It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facilitate a systematic investigation of these sequence-ensemble relationships, we selected a set of 16 naturally occurring intrinsically disordered regions of identical length but with large differences in amino acid composition, hydrophobicity, and charge patterning. We probed their conformational ensembles with single-molecule Förster resonance energy transfer (FRET), complemented by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as small-angle X-ray scattering (SAXS). The set of disordered proteins shows a strong dependence of the chain dimensions on sequence composition, with chain volumes differing by up to a factor of 6. The residue-specific intrachain interaction networks that underlie these pronounced differences were identified using atomistic simulations combined with ensemble reweighting, revealing the important role of charged, aromatic, and polar residues. To advance a transferable description of disordered protein regions, we further employed the experimental data to parametrize a coarse-grained model for disordered proteins that includes an explicit representation of the FRET fluorophores and successfully describes experiments with different dye pairs. Our findings demonstrate the value of integrating experiments and simulations for advancing our quantitative understanding of the sequence features that determine the conformational ensembles of intrinsically disordered proteins.

Biophysical Analysis of Therapeutic Antibodies in the Early Development Pipeline

The successful progression of therapeutic antibodies and other biologics from the laboratory to the clinic depends on their possession of "drug-like" biophysical properties. The techniques and the resultant biophysical and biochemical parameters used to characterize their ease of manufacture can be broadly defined as developability. Focusing on antibodies, this review firstly discusses established and emerging biophysical techniques used to probe the early-stage developability of biologics, aimed towards those new to the field. Secondly, we describe the inter-relationships and redundancies amongst developability assays and how in silico methods aid the efficient deployment of developability to bring a new generation of cost-effective therapeutic proteins from bench to bedside more quickly and sustainably.

C. elegans nucleolar RG repeats are sufficient for nucleolar accumulation but insufficient for sub-nucleolar compartmentalization

Intrinsically disordered arginine-glycine (RG) repeat domains are enriched in multilayered biomolecular condensates such as the nucleolus. C. elegans nucleolar RG repeats are dispensable for nucleolar accumulation and instead contribute to the organization of sub-nucleolar compartments. The sufficiency of RG repeats to facilitate sub-nucleolar compartmentalization is unclear. In this study, we drive expression of full-length RG repeats in the C. elegans germline to test their ability to localize to nucleoli and organize into nucleolar sub-compartments in vivo . We find that repeats accumulate within germ cell nucleoli but do not enrich in the correct sub-compartment. Our results suggest RG repeats may indirectly influence nucleolar organization by creating an environment favorable for sub-nucleolar compartmentalization of proteins primarily based on their function within the nucleolus.

Nucleo-cytoplasmic environment modulates spatiotemporal p53 phase separation

Liquid-liquid phase separation of various transcription factors into biomolecular condensates plays an essential role in gene regulation. Here, using cellular models and in vitro studies, we show the spatiotemporal formation and material properties of p53 condensates that might dictate its function. In particular, p53 forms liquid-like condensates in the nucleus of cells, which can bind to DNA and perform transcriptional activity. However, cancer-associated mutations promote misfolding and partially rigidify the p53 condensates with impaired DNA binding ability. Irrespective of wild-type and mutant forms, the partitioning of p53 into cytoplasm leads to the condensate formation, which subsequently undergoes rapid solidification. In vitro studies show that abundant nuclear components such as RNA and nonspecific DNA promote multicomponent phase separation of the p53 core domain and maintain their liquid-like property, whereas specific DNA promotes its dissolution into tetrameric functional p53. This work provides mechanistic insights into how the life cycle and DNA binding properties of p53 might be regulated by phase separation.

Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation

The self-assembly of intrinsically disordered proteins into biomolecular condensates shows a dependence on the primary sequence of the protein, leading to sequence-dependent phase separation. Methods to investigate this sequence-dependent phase separation rely on effective residue-level interaction potentials that quantify the propensity for the residues to remain in the dilute phase versus the dense phase. The most direct measure of these effective potentials are the distribution coefficients of the different amino acids between the two phases, but due to the lack of availability of these coefficients, proxies, most notably hydropathy, have been used. However, recent work has demonstrated the limitations of the assumption of hydropathy-driven phase separation. In this work, we address this fundamental gap by calculating the transfer free energies associated with transferring each amino acid side chain analog from the dilute phase to the dense phase of a model biomolecular condensate. We uncover an interplay between favorable protein-mediated and unfavorable water-mediated contributions to the overall free energies of transfer. We further uncover an asymmetry between the contributions of positive and negative charges in the driving forces for condensate formation. The results presented in this work provide an explanation for several non-trivial trends observed in the literature and will aid in the interpretation of experiments aimed at elucidating the sequence-dependent driving forces underlying the formation of biomolecular condensates.

Conformations of a low-complexity protein in homogeneous and phase-separated frozen solutions

Solutions of the intrinsically disordered, low-complexity domain of the FUS protein (FUS-LC) undergo liquid-liquid phase separation (LLPS) below a temperature TLLPS. To investigate whether local conformational distributions are detectably different in the homogeneous (i.e., single-phase) and phase-separated states of FUS-LC, we performed solid-state NMR (ssNMR) measurements on solutions that were frozen on submillisecond timescales after equilibration at temperatures well above (50°C) or well below (4°C) TLLPS. Measurements were performed at 25 K with signal enhancements from dynamic nuclear polarization. Crosspeak patterns in two-dimensional ssNMR spectra of rapidly frozen solutions in which FUS-LC was uniformly 15N,13C labeled were found to be nearly identical for the two states. Similar results were obtained for solutions in which FUS-LC was labeled only at Thr, Tyr, and Gly residues, as well as solutions of a FUS construct in which five specific residues were labeled by ligation of synthetic and recombinant fragments. These experiments show that local conformational distributions are nearly the same in the homogeneous and phase-separated solutions, despite the much greater protein concentrations and more abundant intermolecular interactions within phase-separated, protein-rich "droplets." Comparison of the experimental results with simulations of the sensitivity of two-dimensional ssNMR crosspeaks to changes in populations of β strand-like conformations suggests that changes in conformational distributions are no larger than 5-10%.

Recent advances in engineering synthetic biomolecular condensates

Biomolecular condensates are intriguing entities found within living cells. These structures possess the ability to selectively concentrate specific components through phase separation, thereby playing a crucial role in the spatiotemporal regulation of a wide range of cellular processes and metabolic activities. To date, extensive studies have been dedicated to unraveling the intricate connections between molecular features, physical properties, and cellular functions of condensates. This collective effort has paved the way for deliberate engineering of tailor-made condensates with specific applications. In this review, we comprehensively examine the underpinnings governing condensate formation. Next, we summarize the material states of condensates and delve into the design of synthetic intrinsically disordered proteins with tunable phase behaviors and physical properties. Subsequently, we review the diverse biological functions demonstrated by synthetic biomolecular condensates, encompassing gene regulation, cellular behaviors, modulation of biochemical reactions, and manipulation of endogenous protein activities. Lastly, we discuss future challenges and opportunities in constructing synthetic condensates with tunable physical properties and customized cellular functions, which may shed light on the development of new types of sophisticated condensate systems with distinct functions applicable to various scenarios.