The synergic effect of water and biomolecules in intracellular phase separation

Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates

Biomolecular condensates formed via phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids are associated with cell physiology and disease. Water makes up for ∼60-70% of the condensate volume and is thought to influence the complex interplay of chain-chain and chain-solvent interactions, modulating the mesoscale properties of condensates. The behavior of water in condensates and the key roles of protein hydration water in driving the phase separation remain elusive. Here, we employ single-droplet vibrational Raman spectroscopy to illuminate the structural redistribution within protein hydration water during the phase separation of neuronal IDPs. Our Raman measurements reveal the changes in the water hydrogen bonding network during homotypic and heterotypic phase separation governed by various molecular drivers. Such single-droplet water Raman measurements offer a potent generic tool to unmask the intriguing interplay of sequence-encoded chain-chain and chain-solvent interactions governing macromolecular phase separation into membraneless organelles, synthetic condensates, and protocells.

Surface-catalyzed liquid-liquid phase separation and amyloid-like assembly in microscale compartments

Liquid-liquid phase separation is a key phenomenon in the formation of membrane-less structures within the cell, appearing as liquid biomolecular condensates. Protein condensates are the most studied for their biological relevance, and their tendency to evolve, resulting in the formation of aggregates with a high level of order called amyloid. In this study, it is demonstrated that Human Insulin forms micrometric, round amyloid-like structures at room temperature within sub-microliter scale aqueous compartments. These distinctive particles feature a solid core enveloped by a fluid-like corona and form at the interface between the aqueous compartment and the glass coverslip upon which they are cast. Quantitative fluorescence microscopy is used to study in real-time the formation of amyloid-like superstructures. Their formation results driven by liquid-liquid phase separation process that arises from spatially heterogeneous distribution of nuclei at the glass-water interface. The proposed experimental setup allows modifying the surface-to-volume ratio of the aqueous compartments, which affects the aggregation rate and particle size, while also inducing fine alterations in the molecular structures of the final assemblies. These findings enhance the understanding of the factors governing amyloid structure formation, shedding light on the catalytic role of surfaces in this process.

Insights into dynamic properties of water in lipidic cubic phases by 2D nuclear Overhauser effect (NOE) NMR spectroscopy

Two-dimensional NOE (nuclear Overhauser effect) NMR spectroscopy was employed to investigate the dynamic properties of water within lyotropic bicontinuous lipidic cubic phases (LCPs) formed by monoolein (MO). Experiments observed categorically different effective residence times of water molecules: (i) in proximity to the glycerol moiety of MO, and (ii) adjacent to the hydrophobic chain towards the hydrocarbon tail of MO, as evidenced by the opposite signs of intermolecular NOE cross peaks between protons of water and those of MO in 2D 1H-1H NOESY spectra. Spectroscopic data delineating the different effective residence times of water molecules within both the gyroid (QIIG) and diamond (QIID) phase groups corresponding to hydration levels of 35 and 40 wt%, respectively, are presented. Additionally, an increase in effective residence time of water molecules in proximity to the glycerol moiety of MO in LCPs was observed upon storage at ambient temperature and in the presence of an additive lipid, cholesterol. Atom-specific NOE build-up curves for protons of water and those of MO are also given. The results presented herein provide new insight into the physicochemical properties and behaviour of water in LCPs, and demonstrate an additional avenue for experimental study of water-lipid interactions and hydration dynamics in model membranes and nanomaterials using 2D NOE NMR spectroscopy.

Rational Tuning of the Concentration-independent Enrichment of Prion-like Domains in Stress Granules

Stress granules (SGs) are large ribonucleoprotein assemblies that form in response to acute stress in eukaryotes. SG formation is thought to be initiated by liquid-liquid phase separation (LLPS) of key proteins and RNA. These molecules serve as a scaffold for recruitment of client molecules. LLPS of scaffold proteins in vitro is highly concentration-dependent, yet biomolecular condensates in vivo contain hundreds of unique proteins, most of which are thought to be clients rather than scaffolds. Many proteins that localize to SGs contain low-complexity, prion-like domains (PrLDs) that have been implicated in LLPS and SG recruitment. The degree of enrichment of proteins in biomolecular condensates such as SGs can vary widely, but the underlying basis for these differences is not fully understood. Here, we develop a toolkit of model PrLDs to examine the factors that govern efficiency of PrLD recruitment to stress granules. Recruitment was highly sensitive to amino acid composition: enrichment in SGs could be tuned through subtle changes in hydrophobicity. By contrast, SG recruitment was largely insensitive to PrLD concentration at both a population level and single-cell level. These observations point to a model wherein PrLDs are enriched in SGs through either simple solvation effects or interactions that are effectively non-saturable even at high expression levels.

Liquid-Liquid Phase Separation Mediated Formation of Chiral 2D Crystalline Nanosheets of a Co-Assembled System

The role of macromolecule-macromolecule and macromolecule-H2O interactions and the resulting perturbation of the H-bonded network of H2O in the liquid-liquid phase separation (LLPS) process of biopolymers are well-known. However, the potential of the hydrated state of supramolecular structures (non-covalent analogs of macromolecules) of synthetic molecules is not widely recognized for playing a similar role in the LLPS process. Herein, LLPS occurred during the co-assembly of hydrated supramolecular vesicles (bolaamphiphile, BA1) with a net positive charge (zeta potential, ζ = +60 ± 2 mV) and a dianionic chiral molecule (disodium l-[+]-tartrate) is reported. As inferred from cryo-transmission electron microscopy (TEM), the LLPS-formed droplets serve as the nucleation precursors, dictating the structure and properties of the co-assembly. The co-assembled structure formed by LLPS effectively integrates the counter anion's asymmetry, resulting in the formation of ultrathin free-standing, chiral 2D crystalline sheets. The significance of the hydrated state of supramolecular structures in influencing LLPS is unraveled through studies extended to a less hydrated supramolecular structure of a comparable system (BA2). The role of LLPS in modulating the hydrophobic interaction in water paves the way for the creation of advanced functional materials in an aqueous environment.

High-throughput and proteome-wide discovery of endogenous biomolecular condensates

Phase separation inside mammalian cells regulates the formation of the biomolecular condensates that are related to gene expression, signalling, development and disease. However, a large population of endogenous condensates and their candidate phase-separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here we demonstrate that endogenously expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation led to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.

Spatiotemporal Regulation of Cell Fate in Living Systems Using Photoactivatable Artificial DNA Membraneless Organelles

Coacervates formed by liquid-liquid phase separation emerge as important biomimetic models for studying the dynamic behaviors of membraneless organelles and synchronously motivating the creation of smart architectures with the regulation of cell fate. Despite continuous progress, it remains challenging to balance the trade-offs among structural stability, versatility, and molecular communication for regulation of cell fate and systemic investigation in a complex physiological system. Herein, we present a self-stabilizing and fastener-bound gain-of-function methodology to create a new type of synthetic DNA membraneless organelle (MO) with high stability and controlled bioactivity on the basis of DNA coacervates. Specifically, long single-strand DNA generated by rolling circle amplification (RCA) is selected as the scaffold that assembles into membraneless coacervates via phase separation. Intriguingly, the as-formed DNA MO can recruit RCA byproducts and other components to achieve self-stabilization, nanoscale condensation, and function encoding. As a proof of concept, photoactivatable DNA MO is constructed and successfully employed for time-dependent accumulation and spatiotemporal management of cancer in a mouse model. This study offers new, important insights into synthetic membraneless organelles for the basic understanding and manipulation of important life processes.

Real-time measure of solvation free energy changes upon liquid-liquid phase separation of α-elastin

Biological condensates are known to retain a large fraction of water to remain in a liquid and reversible state. Local solvation contributions from water hydrating hydrophilic and hydrophobic protein surfaces were proposed to play a prominent role for the formation of condensates through liquid-liquid phase separation (LLPS). However, although the total free energy is accessible by calorimetry, the partial solvent contributions to the free energy changes upon LLPS remained experimentally inaccessible so far. Here, we show that the recently developed THz calorimetry approach allows to quantify local hydration enthalpy and entropy changes upon LLPS of α-elastin in real time, directly from experimental THz spectroscopy data. We find that hydrophobic solvation dominates the entropic solvation term, whereas hydrophilic solvation mainly contributes to the enthalpy. Both terms are in the order of hundreds of kJ/mol, which is more than one order of magnitude larger than the total free energy changes at play during LLPS. However, since we show that entropy/enthalpy mostly compensates, a small entropy/enthalpy imbalance is sufficient to tune LLPS. Theoretically, a balance was proposed before. Here we present experimental evidence based on our spectroscopic approach. We finally show that LLPS can be steered by inducing small changes of solvation entropy/enthalpy compensation via concentration or temperature in α-elastin.

Compressible Hydrogels with Stabilized Chirality from Thermoresponsive Helical Dendronized Poly(phenylacetylene)s

Fabrication of chiral hydrogels from thermoresponsive helical dendronized phenylacetylene copolymers (PPAs) carrying three-fold dendritic oligoethylene glycols (OEGs) is reported. Three different temperatures, i.e. below or above cloud point temperatures (Tcps) of the copolymers, and under freezing condition, were utilized, affording thermoresponsive hydrogels with different morphologies and mechanical properties. At room temperature, transparent hydrogels were obtained through crosslinking among different copolymer chains. Differently, opaque hydrogels with much improved mechanical properties were formed at elevated temperatures through crosslinking from the thermally dehydrated and collapsed copolymer aggregates, leading to heterogeneity for the hydrogels with highly porous morphology. While crosslinking at freezing temperature synergistically through ice templating, these amphiphilic dendronized copolymers formed hydrogels with highly porous lamellar structures, which exhibited remarkable compressible properties as human articular cartilage with excellent fatigue resistance. Amphiphilicity of the dendronized copolymers played a pivotal role in modulating the network formation during the gelation, as well as morphology and mechanical performance of the resulting hydrogels. Through crosslinking, these dendronized copolymers featured with typical dynamic helical conformations were transformed into hydrogels with unprecedently stabilized helicities due to the restrained chain mobilities in the three-dimensional networks.

Kinetic control of shape deformations and membrane phase separation inside giant vesicles

A variety of cellular processes use liquid-liquid phase separation (LLPS) to create functional levels of organization, but the kinetic pathways by which it proceeds remain incompletely understood. Here in real time, we monitor the dynamics of LLPS of mixtures of segregatively phase-separating polymers inside all-synthetic, giant unilamellar vesicles. After dynamically triggering phase separation, we find that the ensuing relaxation-en route to the new equilibrium-is non-trivially modulated by a dynamic interplay between the coarsening of the evolving droplet phase and the interactive membrane boundary. The membrane boundary is preferentially wetted by one of the incipient phases, dynamically arresting the progression of coarsening and deforming the membrane. When the vesicles are composed of phase-separating mixtures of common lipids, LLPS within the vesicular interior becomes coupled to the membrane's compositional degrees of freedom, producing microphase-separated membrane textures. This coupling of bulk and surface phase-separation processes suggests a physical principle by which LLPS inside living cells might be dynamically regulated and communicated to the cellular boundaries.

Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates

Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.

Chirality-Selected Coacervate by Chiral Gemini Surfactant

Chiral surfactants present opportunities to self-assemble into supramolecules with a chiral trait; however, the effects of stereochemistry on the formation of simple coacervates remain unclear. Here, we investigate the chirality-selected phase behavior in mixtures of chiral gemini surfactant 1,4-bis(dodecyl-N,N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)2-12) with an oppositely charged chiral mandelic acid (MA). It demonstrates that altering the chirality of surfactants yields a heightened ability to regulate the phase behavior, leading to the formation of three different network-like structures, i.e., wormlike micelle, coacervate, and hydrogel, in the racemate, enantiomer, and mesomer, respectively. The different aggregate structures arise from the intermolecular and intramolecular hydrogen-bond interactions of the two hydroxyl groups located at stereogenic centers. Intriguingly, although they contain similar microstructures, the solid-like hydrogel and liquid-like wormlike micelle show similar low hydration ability and have no encapsulation capability, whereas only coacervate formed by the enantiomers of 12-4(OH)2-12 displays liquid-like characteristics, strong capacity to sequester diverse solutes, and high affinity for tightly bound water simultaneously. These findings further highlight the unique and advantageous properties of coacervates as a promising model for exploring the biological process and understanding how chirality plays a crucial role in early life scenarios and cell evolution at the molecular level.

3D Printable Gelatin Methacryloyl (GelMA)-Dextran Aqueous Two-Phase System with Tunable Pores Structure and Size Enables Physiological Behavior of Embedded Cells In Vitro

The restricted porosity of most hydrogels established for in vitro 3D tissue engineering applications limits embedded cells with regard to their physiological spreading, proliferation, and migration behavior. To overcome these confines, porous hydrogels derived from aqueous two-phase systems (ATPS) are an interesting alternative. However, while developing hydrogels with trapped pores is widespread, the design of bicontinuous hydrogels is still challenging. Herein, an ATPS consisting of photo-crosslinkable gelatin methacryloyl (GelMA) and dextran is presented. The phase behavior, monophasic or biphasic, is tuned via the pH and dextran concentration. This, in turn, allows the formation of hydrogels with three distinct microstructures: homogenous nonporous, regular disconnected-pores, and bicontinuous with interconnected-pores. The pore size of the latter two hydrogels can be tuned from ≈4 to 100 µm. Cytocompatibility of the generated ATPS hydrogels is confirmed by testing the viability of stromal and tumor cells. Their distribution and growth pattern are cell-type specific but are also strongly defined by the microstructure of the hydrogel. Finally, it is demonstrated that the unique porous structure is sustained when processing the bicontinuous system by inkjet and microextrusion techniques. The proposed ATPS hydrogels hold great potential for 3D tissue engineering applications due to their unique tunable interconnected porosity.

Macromolecular condensation buffers intracellular water potential

Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of 'structured' water molecules within their hydration layers, reducing the available 'free' bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2,3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function.

Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain

Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These results provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.

Thermodynamically controlled multiphase separation of heterogeneous liquid crystal colloids

Phase separation is a universal physical transition process whereby a homogeneous mixture splits into two distinct compartments that are driven by the component activity, elasticity, or compositions. In the current work, we develop a series of heterogeneous colloidal suspensions that exhibit both liquid-liquid phase separation of semiflexible binary polymers and liquid crystal phase separation of rigid, rod-like nanocellulose particles. The phase behavior of the multicomponent mixture is controlled by the trade-off between thermodynamics and kinetics during the two transition processes, displaying cholesteric self-assembly of nanocellulose within or across the compartmented aqueous phases. Upon thermodynamic control, two-, three-, and four-phase coexistence behaviors with rich liquid crystal stackings are realized. Among which, each relevant multiphase separation kinetics shows fundamentally different paths governed by nucleation and growth of polymer droplets and nanocellulose tactoids. Furthermore, a coupled multiphase transition can be realized by tuning the composition and the equilibrium temperature, which results in thermotropic behavior of polymers within a lyotropic liquid crystal matrix. Finally, upon drying, the multicomponent mixture undergoes a hierarchical self-assembly of nanocellulose and polymers into stratified cholesteric films, exhibiting compartmentalized polymer distribution and anisotropic microporous structure.

RNA-mediated demixing transition of low-density condensates

Biomolecular condensates play a key role in organizing cellular reactions by concentrating a specific set of biomolecules. However, whether condensate formation is accompanied by an increase in the total mass concentration within condensates or by the demixing of already highly crowded intracellular components remains elusive. Here, using refractive index imaging, we quantify the mass density of several condensates, including nucleoli, heterochromatin, nuclear speckles, and stress granules. Surprisingly, the latter two condensates exhibit low densities with a total mass concentration similar to the surrounding cyto- or nucleoplasm. Low-density condensates display higher permeability to cellular protein probes. We find that RNA tunes the biomolecular density of condensates. Moreover, intracellular structures such as mitochondria heavily influence the way phase separation proceeds, impacting the localization, morphology, and growth of condensates. These findings favor a model where segregative phase separation driven by non-associative or repulsive molecular interactions together with RNA-mediated selective association of specific components can give rise to low-density condensates in the crowded cellular environment.

Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia

The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.

Micro-Raman spectroscopic analysis of liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) plays a significant role in various biological processes, including the formation of membraneless organelles and pathological protein aggregation. Although many studies have found various factors that modulate the LLPS process or the liquid-to-solid phase transition (LSPT) using microscopy or fluorescence-based methods, the molecular mechanistic details underlying LLPS and protein aggregation within liquid droplets remain uncharacterized. Therefore, structural information on proteins inside liquid droplets is required to understand the mechanistic link to amyloid formation. In the present study, we monitored droplet formation related to protein fibrillation using micro-Raman spectroscopy in combination with differential interference contrast (DIC) microscopy to study the conformational change in proteins and the hydrogen-bonding (H-bonding) structure of water during LLPS. Interestingly, we found that the O-D stretching band for water (HOD in H₂O) inside the droplets exhibited a distinct Raman spectrum from that of the bulk water, suggesting that the time-dependent change in the hydration environment in the protein droplets during the process of LLPS can be studied. These results demonstrate that the superior spatial resolution of micro-Raman spectroscopy offers significant advantages in investigating the molecular mechanisms of LLPS and following LSPT processes.

Sequence Context and Complex Hofmeister Salt Interactions Dictate Phase Separation Propensity of Resilin-like Polypeptides

Resilin is an elastic material found in insects with exceptional durability, resilience, and extensibility, making it a promising biomaterial for tissue engineering. The monomeric precursor, pro-resilin, undergoes thermo-responsive self-assembly through liquid-liquid phase separation (LLPS). Understanding the molecular details of this assembly process is critical to developing complex biomaterials. The present study investigates the interplay between the solvent, sequence syntax, structure, and dynamics in promoting LLPS of resilin-like-polypeptides (RLPs) derived from domains 1 and 3 of Drosophila melanogaster pro-resilin. NMR, UV-vis, and microscopy data demonstrate that while kosmotropic salts and low pH promote LLPS, the effects of chaotropic salts with increasing pH are more complex. Subtle variations between the repeating amino acid motifs of resilin domain 1 and domain 3 lead to significantly different salt and pH dependence of LLPS, with domain 3 sequence motifs more strongly favoring phase separation under most conditions. These findings provide new insight into the molecular drivers of RLP phase separation and the complex roles of both RLP sequence and solution composition in fine-tuning assembly conditions.

Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions

Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.

A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates

Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.

A Cohesive Shear-Thinning Biomaterial for Catheter-Based Minimally Invasive Therapeutics

Shear-thinning hydrogels are suitable biomaterials for catheter-based minimally invasive therapies; however, the tradeoff between injectability and mechanical integrity has limited their applications, particularly at high external shear stress such as that during endovascular procedures. Extensive molecular crosslinking often results in stiff, hard-to-inject hydrogels that may block catheters, whereas weak crosslinking renders hydrogels mechanically weak and susceptible to shear-induced fragmentation. Thus, controlling molecular interactions is necessary to improve the cohesion of catheter-deployable hydrogels. To address this material design challenge, we have developed an easily injectable, nonhemolytic, and noncytotoxic shear-thinning hydrogel with significantly enhanced cohesion via controlling noncovalent interactions. We show that enhancing the electrostatic interactions between weakly bound biopolymers (gelatin) and nanoparticles (silicate nanoplatelets) using a highly charged polycation at an optimum concentration increases cohesion without compromising injectability, whereas introducing excessive charge to the system leads to phase separation and loss of function. The cohesive biomaterial is successfully injected with a neuroendovascular catheter and retained without fragmentation in patient-derived three-dimensionally printed cerebral aneurysm models under a physiologically relevant pulsatile fluid flow, which would otherwise be impossible using the noncohesive hydrogel counterpart. This work sheds light on how charge-driven molecular and colloidal interactions in shear-thinning physical hydrogels improve cohesion, enabling complex minimally invasive procedures under flow, which may open new opportunities for developing the next generation of injectable biomaterials.

An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions

Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of protein phase-separation-prediction algorithms are available, with many being specific for particular classes of proteins and others providing results that are not amenable to the interpretation of the contributing biophysical interactions. Here, we describe LLPhyScore, a new predictor of IDR-driven phase separation, based on a broad set of physical interactions or features. LLPhyScore uses sequence-based statistics from the RCSB PDB database of folded structures for these interactions, and is trained on a manually curated set of phase-separation-driving proteins with different negative training sets including the PDB and human proteome. Competitive training for a variety of physical chemical interactions shows the greatest contribution of solvent contacts, disorder, hydrogen bonds, pi–pi contacts, and kinked beta-structures to the score, with electrostatics, cation–pi contacts, and the absence of a helical secondary structure also contributing. LLPhyScore has strong phase-separation-prediction recall statistics and enables a breakdown of the contribution from each physical feature to a sequence’s phase-separation propensity, while recognizing the interdependence of many of these features. The tool should be a valuable resource for guiding experiments and providing hypotheses for protein function in normal and pathological states, as well as for understanding how specificity emerges in defining individual biomolecular condensates.

The role of ATP in solubilizing RNA-binding protein fused in sarcoma

Intrinsically disordered protein (IDP) plays an important role in liquid-liquid phase separation (LLPS). RNA-binding protein fused in sarcoma (FUS) is a well-studied IDP that induces LLPS since its low-complexity core region (FUS-LC-core) is essential for droplet formation through contacts between FUS-LC-cores. Several experimental studies have reported that adenosine triphosphate (ATP) concentrations modulate LLPS-driven droplet formation through the dissolution of FUS. To elucidate the role of ATP in this dissolution, microsecond-order all-atom molecular dynamics (MD) simulations were performed for a crowded system of FUS-LC-cores in the presence of multiple ATP molecules. Our analysis revealed that the adenine group of ATP frequently contacted the FUS-LC-core, and the phosphoric acid group of ATP was exposed to the external solvent, which promoted both hydration and solubilization of FUS.

Impact of Chain Conformation on Structural Heterogeneity in Polymer Network

Polymer networks generally consist of an ensemble of single chains. However, understanding how chain conformation affects the structure and properties of polymer networks remains a challenge for optimizing their functionality. Here, we present the fabrication and comparative study of a polymer network composed of collapsed self-entangled chains (intrachain entangled network) and a standard polymer network in which random-coil chains are entangled with each other (interchain entangled network). For poly(methyl methacrylate) thin films composed of these networks, we coupled solvent vapor swelling and single-molecule tracking techniques to examine the anomalies in the dynamics of a small-molecular probe included in the system. We demonstrate that when compared to the interchain entangled network the intrachain one exhibits a more substantial structural heterogeneity, particularly under highly crowded conditions. This network also exhibits physical compactness, which keeps the heterogeneous network structure frozen over time and impedes network plasticization through solvent uptake by the film.

The Role of Ubiquitin in Regulating Stress Granule Dynamics

Stress granules (SGs) are dynamic, reversible biomolecular condensates, which assemble in the cytoplasm of eukaryotic cells under various stress conditions. Formation of SGs typically occurs upon stress-induced translational arrest and polysome disassembly. The increase in cytoplasmic mRNAs triggers the formation of a protein-RNA network that undergoes liquid-liquid phase separation when a critical interaction threshold has been reached. This adaptive stress response allows a transient shutdown of several cellular processes until the stress is removed. During the recovery from stress, SGs disassemble to re-establish cellular activities. Persistent stress and disease-related mutations in SG components favor the formation of aberrant SGs that are impaired in disassembly and prone to aggregation. Recently, posttranslational modifications of SG components have been identified as major regulators of SG dynamics. Here, we summarize new insights into the role of ubiquitination in affecting SG dynamics and clearance and discuss implications for neurodegenerative diseases linked to aberrant SG formation.

Spatially Resolved Hydration Thermodynamics in Biomolecular Systems

Water is essential for the structure, dynamics, energetics, and thus the function of biomolecules. It is a formidable challenge to elicit, in microscopic detail, the role of the solvation-related driving forces of biomolecular processes, such as the enthalpy and entropy contributions to the underlying free-energy landscape. In this Perspective, we discuss recent developments and applications of computational methods that provide a spatially resolved map of hydration thermodynamics in biomolecular systems and thus yield atomic-level insights to guide the interpretation of experimental observations. An emphasis is on the challenge of quantifying the hydration entropy, which requires characterization of both the motions of the biomolecules and of the water molecules in their surrounding.

Ubiquitination of Alzheimer's-related tau protein affects liquid-liquid phase separation in a site- and cofactor-dependent manner

The formation of biomolecular condensates has emerged as a crucial player both in neuronal physiology and neurodegeneration. Phase separation of the Alzheimer's related protein tau into liquid condensates is facilitated by polyanions and is regulated by post-translational modifications. Given the central role of ubiquitination in proteostasis regulation and signaling, we investigated the behavior of monoubiquitinated tau during formation of condensates. We ubiquitinated the lysine-rich, four-repeat domain of tau either unspecifically via enzymatic conjugation or in a position-specific manner by semisynthesis. Ubiquitin conjugation at specific sites weakened multivalent tau/RNA interactions and disfavored tau/heparin condensation. Yet, heterogeneous ubiquitination was tolerated during phase separation and stabilized droplets against aggregation-linked dissolution. Thus, we demonstrated that cofactor chemistry and site of modification affect the mesoscopic and molecular signatures of ubiquitinated tau condensates. Our findings suggest that ubiquitination could influence the physiological states and pathological transformations of tau in cellular condensates.

Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability

Stress granules (SGs) are among the most studied membraneless organelles that form upon heat stress (HS) to sequester unfolded, misfolded, or aggregated protein, supporting protein quality control (PQC) clearance. The folding states that are primarily associated with SGs, as well as the function of the phase separated environment in adjusting the energy landscapes, remain unknown. Here, we investigate the association of superoxide dismutase 1 (SOD1) proteins with different folding stabilities and aggregation propensities with condensates in cells, in vitro and by simulation. We find that irrespective of aggregation the folding stability determines the association of SOD1 with SGs in cells. In vitro and in silico experiments however suggest that the increased flexibility of the unfolded state constitutes only a minor driving force to associate with the dynamic biomolecular network of the condensate. Specific protein-protein interactions in the cytoplasm in comparison to SGs determine the partitioning of folding states between the respective phases during HS.

The protein hydration layer in high glucose concentration: Dynamical responses in folded and intrinsically disordered dimeric states

This exposition reveals the effect of glucose as a molecular crowder on the solvent environment in proximity of the protein surface in putative folded (Ubiquitin) and intrinsically disordered (dimeric Amyloid beta) states. Atomistic simulations reveal markedly higher structural perturbation in the disordered systems due to crowding effects, while the folded state retains overall structural fidelity. Key hydrophobic contacts in the disordered dimer are lost. However, glucose induced crowding results in elevated hydration on surfaces of both protein systems. Despite evident differences in their structural responses, the hydration layer of both the folded and disordered states display a distinct enhancement in lifetimes of mean residence and rotational relaxation under the hyperglycemic conditions. The results are crucial in the light of emergent co-solvent induced biological phenomena in crowded media.

Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions

Multivalent proteins and nucleic acids can self-assemble into biomolecular condensates that contribute to compartmentalize the cell interior. Computer simulations offer a unique view to elucidate the mechanisms and key intermolecular interactions behind the dynamic formation and dissolution of these condensates. In this work, we present a novel approach to include explicit water and salt in sequence-dependent coarse-grained (CG) models for proteins and RNA, enabling the study of biomolecular condensate formation in a salt-dependent manner. Our framework combines a reparameterized version of the HPS protein force field with the monoatomic mW water model and the mW-ion potential for NaCl. We show how our CG model qualitatively captures the experimental radius of the gyration trend of a subset of intrinsically disordered proteins and reproduces the experimental protein concentration and water percentage of the human fused in sarcoma (FUS) low-complexity-domain droplets at physiological salt concentration. Moreover, we perform seeding simulations as a function of salt concentration for two antagonist systems: the engineered peptide PR₂₅ and poly-uridine/poly-arginine mixtures, finding good agreement with their reported in vitro phase behavior with salt concentration in both cases. Taken together, our work represents a step forward towards extending sequence-dependent CG models to include water and salt, and to consider their key role in biomolecular condensate self-assembly.

O-Linked-N-Acetylglucosaminylation of the RNA-Binding Protein EWS N-Terminal Low Complexity Region Reduces Phase Separation and Enhances Condensate Dynamics

Many membraneless organelles are thought to be biomolecular condensates formed by phase separation of proteins and other biopolymers. Post-translational modifications (PTMs) can impact protein phase separation behavior, although for many PTMs this aspect of their function is unknown. O-linked β-D-N-acetylglucosaminylation (O-GlcNAcylation) is an abundant form of intracellular glycosylation whose roles in regulating biomolecular condensate assembly and dynamics have not been delineated. Using an in vitro approach, we found that O-GlcNAcylation reduces the phase separation propensity of the EWS N-terminal low complexity region (LCR_N) under different conditions, including in the presence of the arginine- and glycine-rich RNA-binding domains (RBD). O-GlcNAcylation enhances fluorescence recovery after photobleaching (FRAP) within EWS LCR_N condensates and causes the droplets to exhibit more liquid-like relaxation following fusion. Following extended incubation times, EWS LCR_N+RBD condensates exhibit diminished FRAP, indicating a loss of fluidity, while condensates containing the O-GlcNAcylated LCR_N do not. In HeLa cells, EWS is less O-GlcNAcylated following OGT knockdown, which correlates with its increased accumulation in a filter retardation assay. Relative to the human proteome, O-GlcNAcylated proteins are enriched with regions that are predicted to phase separate, suggesting a general role of O-GlcNAcylation in regulation of biomolecular condensates.

Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses

This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.

Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels

Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.

Taurine suppresses liquid-liquid phase separation of lysozyme protein

Taurine is a compatible osmolyte that confers stability to proteins. Recent studies have revealed that liquid-liquid phase separation (LLPS) of proteins underlie the formation of membraneless organelles in cells. In the present study, we evaluated the role of taurine on LLPS of hen egg lysozyme. We demonstrated that taurine decreases the turbidity of the polyethylene glycol-induced crowding solution of lysozyme. We also demonstrated that taurine attenuates LLPS-dependent cloudiness of lysozyme solution with 0.5 or 1 M NaCl at a critical temperature. Moreover, we observed that taurine inhibits LLPS formation of a heteroprotein mix solution of lysozyme and ovalbumin. These data indicate that taurine can modulate the formation of LLPS of proteins.

The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS

Formation of biomolecular condensates through liquid-liquid phase separation (LLPS) has emerged as a pervasive principle in cell biology, allowing compartmentalization and spatiotemporal regulation of dynamic cellular processes. Proteins that form condensates under physiological conditions often contain intrinsically disordered regions with low-complexity domains. Among them, the RNA-binding proteins FUS and TDP-43 have been a focus of intense investigation because aberrant condensation and aggregation of these proteins is linked to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. LLPS occurs when protein-rich condensates form surrounded by a dilute aqueous solution. LLPS is per se entropically unfavorable. Energetically favorable multivalent protein-protein interactions are one important aspect to offset entropic costs. Another proposed aspect is the release of entropically unfavorable preordered hydration water into the bulk. We used attenuated total reflection spectroscopy in the terahertz frequency range to characterize the changes in the hydrogen bonding network accompanying the FUS enrichment in liquid-liquid phase-separated droplets to provide experimental evidence for the key role of the solvent as a thermodynamic driving force. The FUS concentration inside LLPS droplets was determined to be increased to 2.0 mM independent of the initial protein concentration (5 or 10 μM solutions) by fluorescence measurements. With terahertz spectroscopy, we revealed a dewetting of hydrophobic side chains in phase-separated FUS. Thus, the release of entropically unfavorable water populations into the bulk goes hand in hand with enthalpically favorable protein-protein interaction. Both changes are energetically favorable, and our study shows that both contribute to the thermodynamic driving force in phase separation.

Convergence behaviour of solvation shells in simulated liquids

A convenient way to analyse solvent structure around a solute is to use solvation shells, whereby solvent position around the solute is discretised by the size of a solvent molecule, leading to multiple shells around the solute. The two main ways to define multiple shells around a solute are either directly with respect to the solute, called solute-centric, or locally for both solute and solvent molecules alike. It might be assumed that both methods lead to solvation shells with similar properties. However, our analysis suggests otherwise. Solvation shells are analysed in a series of simulations of five pure liquids of differing polarity. Shells are defined locally working outwards from each molecule treated as a reference molecule using two methods: the cutoff at the first minimum in the radial distribution function and the parameter-free Relative Angular Distance method (RAD). The molecular properties studied are potential energy, coordination number and coordination radius. Rather than converging to bulk values, as might be expected for pure solvents, properties are found to deviate as a function of shell index. This behaviour occurs because molecules with larger coordination numbers and radius have more neighbours, which make them more likely to be connected to the reference molecule via fewer shells. The effect is amplified for RAD because of its more variable coordination radii and for water with its more open structure and stronger interactions. These findings indicate that locally defined shells should not be thought of as directly comparable to solute-centric shells or to distance. As well as showing how box size and cutoff affect the non-convergence, to restore convergence we propose a hybrid method by defining a new set of shells with boundaries at the uppermost distance of each locally derived shell.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

The role of water in the primary nucleation of protein amyloid aggregation

The understanding of the complex conformational landscape of amyloid aggregation and its modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating some of the molecular basis of pathology in amyloid related diseases, and for developing and evaluating effective disease-specific therapeutics to reduce or eliminate the underlying sources of toxicity in these diseases. Interactions of proteins with solvating water have been long considered to be fundamental in mediating their function and folding; however, the relevance of water in the process of protein amyloid aggregation has been largely overlooked. Here, we provide a perspective on the role water plays in triggering primary amyloid nucleation of intrinsically disordered proteins (IDPs) based on recent experimental evidences. The initiation of amyloid aggregation likely results from the synergistic effect between both protein intermolecular interactions and the properties of the water hydration layer of the protein surface. While the self-assembly of both hydrophobic and hydrophilic IDPs would be thermodynamically favoured due to large water entropy contributions, large desolvation energy barriers are expected, particularly for the nucleation of hydrophilic IDPs. Under highly hydrating conditions, primary nucleation is slow, being facilitated by the presence of nucleation-active surfaces (heterogeneous nucleation). Under conditions of poor water activity, such as those found in the interior of protein droplets generated by liquid-liquid phase separation, however, the desolvation energy barrier is significantly reduced, and nucleation can occur very rapidly in the bulk of the solution (homogeneous nucleation), giving rise to structurally distinct amyloid polymorphs. Water, therefore, plays a key role in modulating the transition free energy of amyloid nucleation, thus governing the initiation of the process, and dictating the type of preferred primary nucleation and the type of amyloid polymorph generated, which could vary depending on the particular microenvironment that the protein molecules encounter in the cell.

Size and charge correlations in spherical electric double layers: a case study with fully asymmetric mixed electrolytes within the solvent primitive model

Size and charge correlations in spherical electric double layers are investigated through Monte Carlo simulations and density functional theory, through a solvent primitive model representation. A fully asymmetric mixed electrolyte is used for the small ions, whereas the solvent, apart from being a continuum dielectric, is also treated as an individual component. A partially perturbative density functional theory is adopted here, and for comparison, a standard canonical ensemble Monte Carlo simulation is used. The hard-sphere free energy is treated within a weighted density approach and the residual ionic contribution is estimated through perturbation around the uniform density. The results from both methods corroborate each other quantitatively over a wide range of physical parameters. The importance of structural correlations is envisaged through the size and charge asymmetry of the supporting electrolytes that includes the solvent as a component.

Size and charge correlations in spherical electric double layers are investigated through Monte Carlo simulations and density functional theory, through a solvent primitive model representation.

Interface Engineering in Multiphase Systems toward Synthetic Cells and Organelles: From Soft Matter Fundamentals to Biomedical Applications

Synthetic cells have a major role in gaining insight into the complex biological processes of living cells; they also give rise to a range of emerging applications from gene delivery to enzymatic nanoreactors. Living cells rely on compartmentalization to orchestrate reaction networks for specialized and coordinated functions. Principally, the compartmentalization has been an essential engineering theme in constructing cell-mimicking systems. Here, efforts to engineer liquid-liquid interfaces of multiphase systems into membrane-bounded and membraneless compartments, which include lipid vesicles, polymer vesicles, colloidosomes, hybrids, and coacervate droplets, are summarized. Examples are provided of how these compartments are designed to imitate biological behaviors or machinery, including molecule trafficking, growth, fusion, energy conversion, intercellular communication, and adaptivity. Subsequently, the state-of-art applications of these cell-inspired synthetic compartments are discussed. Apart from being simplified and cell models for bridging the gap between nonliving matter and cellular life, synthetic compartments also are utilized as intracellular delivery vehicles for nuclei acids and nanoreactors for biochemical synthesis. Finally, key challenges and future directions for achieving the full potential of synthetic cells are highlighted.

Charge pattern affects the structure and dynamics of polyampholyte condensates

Proteins with intrinsically disordered regions have a tendency to condensate via liquid-liquid phase separation both in vitro and in vivo. Such biomolecular coacervates play various significant roles in biologically important regulatory processes. The present work explores the structural and dynamic features of coacervates formed by model polyampholytes, being intrinsically disordered proteins, that differ in terms of their charged amino acid patterns. Differences in the distribution of charged amino acids along the polyampholyte sequence lead to distinctly different structural features in the dense phase and hence to different liquid properties. Increased charge clustering raises the critical temperature for phase separation and results in each polyampholyte experiencing a larger number of inter-chain contacts with neighboring proteins in the condensate. Consequently, polyampholytes with greater charge clustering adopt a much more extended conformation, having a radius of gyration up to twice that observed in the dilute bulk phase. Translational diffusion within the droplet is pronounced, being just 4-20 times slower than in the bulk, consistently with the high conformational entropy in the dense phase and high exchange rate of the network of intermolecular interactions in the condensate. Coupled to the faster diffusion, the condensate also adopts a more elongated shape and exhibits imperfect packing, which results in cavities. This study quantifies the fundamental microscopic properties of condensates including the effect of long-range electrostatic forces and particularly how they can be modulated by the charge pattern.

Amino acid homorepeats in proteins

Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.

Artificial Intracellular Filaments

Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the in situ formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.