Publications by authors named "Priya Banerjee"

The material properties of biomolecular condensates govern their dynamics and functions by influencing the molecular diffusion rates and biochemical interactions. A recent report has identified a characteristic timescale of temperature-dependent viscosity in biomolecular condensates arising from an activated dissociation events collectively referred to as flow activation energy. The microscopic origin of this activation energy is a complex function of sequence, stoichiometry, and external conditions.

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Biomolecular condensates are viscoelastic materials. Here, we investigate the determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by the prion-like low-complexity domain of the protein hnRNP A1 and its designed variants. We find that the dominantly viscous forms of the condensates are metastable Maxwell fluids.

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Article Synopsis
  • RNAs and RNA-binding proteins can form liquid-like droplets in cells, acting as important centers for various biological functions; when these processes go wrong, it can lead to diseases.
  • Most research has focused on proteins rather than the role of RNA in the formation and regulation of these ribonucleoprotein condensates, but recent studies are shifting the focus to RNA-driven phase transitions.
  • Future research aims to understand how RNA droplets regulate cellular processes over time and space, possibly leading to new RNA-based therapies.
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  • The internal environment of cells features diverse organelles, including biomolecular condensates, which are unique, membrane-less compartments enriched in specific proteins and nucleic acids.
  • The presence of ion concentration gradients within cells creates non-equilibrium conditions that enhance the transport of biomolecules and promote the formation of these condensates.
  • Using a microfluidic platform, researchers showed that these ion gradients accelerate biomolecule movement, allowing localized formation of condensates and increasing their motility and lifespan.
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  • * The new product is a sprayable hydrogel made from Alginate, Fibrin, and Polylactic acid microcarriers that encapsulate nanoparticles of calcium, copper, and zinc, promoting various healing stages.
  • * In tests against a commercial product, this hydrogel demonstrated better wound healing in a rat model, suggesting its potential as a more effective solution for wound management.
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Biomolecular condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model that leverages information regarding intra- and inter-chain contacts, which we extract from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations of phase separation. The key ingredient of the generalized Rouse model is a graph Laplacian that we compute from equilibrium MMC simulations.

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Extracellular vesicles (EVs), or exosomes, play important roles in physiological and pathological cellular communication and have gained substantial traction as biological drug carriers. EVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. To fully capitalize on the potential of EVs as drug carriers, it is important to study and understand the intricacies of EV function and EV RNA-based communication.

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  • This study examines how intracellular RNA aggregates relate to neurological disorders and the role of biomolecular condensates in RNA clustering.
  • Researchers discovered that certain repeat RNAs can form nanoscale clusters within protein-nucleic acid condensates, leading to distinct structures where solid and fluid phases coexist.
  • The presence of the protein G3BP1 helps prevent unwanted RNA clustering by buffering interactions among similar RNA molecules, underscoring the importance of RNA-binding proteins in regulating RNA phase transitions.
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Article Synopsis
  • The study investigates how biomolecular condensates, which are clusters of proteins and nucleic acids, influence the clustering of repeat expanded RNAs linked to neurological disorders, revealing a phenomenon called age-dependent percolation transition.* -
  • The research shows that these RNAs form nanoscale clusters within the condensates, leading to structures with a solid RNA-rich core and a fluid RNA-depleted shell, driven by specific RNA sequence features and stability.* -
  • Findings emphasize the protective role of RNA-binding proteins like G3BP1, which can prevent excessive RNA clustering within these condensates, suggesting a potential strategy to mitigate aberrant RNA phase transitions in neurological diseases.*
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facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations.

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The form and function of biomolecular condensates are intimately linked to their material properties. Here, we integrate microrheology with molecular simulations to dissect the physical determinants of condensate fluid phase dynamics. By quantifying the timescales and energetics of network relaxation in a series of heterotypic viscoelastic condensates, we uncover distinctive roles of sticker motifs, binding energy, and chain length in dictating condensate dynamical properties.

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Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation.

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Intrinsically disordered regions (IDRs) within human proteins play critical roles in cellular information processing, including signaling, transcription, stress response, DNA repair, genome organization, and RNA processing. Here, we summarize current challenges in the field and propose cutting-edge approaches to address them in physiology and disease processes, with a focus on cancer.

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Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear.

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The internal microenvironment of a living cell is heterogeneous and comprises a multitude of organelles with distinct biochemistry. Amongst them are biomolecular condensates, which are membrane-less, phase-separated compartments enriched in system-specific proteins and nucleic acids. The heterogeneity of the cell engenders the presence of multiple spatiotemporal gradients in chemistry, charge, concentration, temperature, and pressure.

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The internal microenvironment of a living cell is heterogeneous and comprises a multitude of organelles with distinct biochemistry. Amongst them are biomolecular condensates, which are membrane-less, phase-separated compartments enriched in system-specific proteins and nucleic acids. The heterogeneity of the cell engenders the presence of multiple spatiotemporal gradients in chemistry, charge, concentration, temperature, and pressure.

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Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation.

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Biomolecular condensates are viscoelastic materials. Here, we report results from investigations into molecular-scale determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by prion-like low-complexity domains (PLCDs). The terminally viscous forms of PLCD condensates are Maxwell fluids.

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Liquid-liquid phase separation of protein and RNA complexes into biomolecular condensates has emerged as a ubiquitous phenomenon in living systems. These protein-RNA condensates are thought to be involved in many biological functions in all forms of life. One of the most sought-after properties of these condensates is their dynamical properties, as they are a major determinant of condensate physiological function and disease processes.

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Article Synopsis
  • Biomolecular condensates are membraneless organelles that consist of specific proteins and nucleic acids, allowing them to carry out essential biochemical functions through a process known as phase separation.
  • Gene fusions, often resulting from chromosomal translocations, create proteins with altered domains that can disrupt normal protein-protein interactions, leading to abnormal cell behaviors.
  • Recent research suggests that these altered proteins can form ectopic condensates in inappropriate cellular locations, potentially contributing to cancer development by disrupting biological processes through abnormal phase transitions.
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Proteomic studies have shown that cellular condensates are frequently enriched in diverse RNA molecules, which is suggestive of mechanistic links between phase separation and transcriptional activities. Here, we report a systematic experimental and computational study of thermodynamic landscapes and interfacial properties of protein-RNA condensates. We have studied the affinity of protein-RNA condensation as a function of variable RNA sequence length and RNA-protein stoichiometry under different ionic environments and external crowding.

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Liquid-liquid phase separation (LLPS) of multivalent biopolymers is a ubiquitous process in biological systems and is of importance in bio-mimetic soft matter design. The phase behavior of biomolecules, such as proteins and nucleic acids, is typically encoded by the primary chain sequence and regulated by solvent properties. One of the most important physical modulators of LLPS is temperature.

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Liquid-liquid phase separation of multivalent proteins and RNAs drives the formation of biomolecular condensates that facilitate membrane-free compartmentalization of subcellular processes. With recent advances, it is becoming increasingly clear that biomolecular condensates are network fluids with time-dependent material properties. Here, employing microrheology with optical tweezers, we reveal molecular determinants that govern the viscoelastic behavior of condensates formed by multivalent Arg/Gly-rich sticker-spacer polypeptides and RNA.

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Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates.

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