Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains

Electrokinetic Detection of Single-Molecule Phosphorylation

Current single-molecule fluorescence experiments lack direct sensitivity to molecular phosphorylation states. We show that electrokinetic properties measured with an anti-Brownian trap resolve the number of phosphorylated sites on individual biomolecules and can monitor phosphorylation cycles with single kinase turnovers. As an application, we directly visualize the rate-limiting step in the kinase catalytic cycle.

Emerging connections: Poly(ADP-ribose), FET proteins and RNA in the regulation of DNA damage condensates

Our genome is exposed to thousands of DNA lesions every day, posing a significant threat to cellular viability. To deal with these lesions, cells have evolved sophisticated repair mechanisms collectively known as the DNA damage response. DNA double-strand breaks (DSBs) are very cytotoxic damages, and their repair requires the precise and coordinated recruitment of multiple repair factors to form nuclear foci. Recent research highlighted that these repair structures behave as biomolecular condensates, i.e. membraneless compartments with liquid-like properties. The formation of condensates is driven by weak, multivalent interactions among proteins and nucleic acids, and recent studies highlighted the roles of poly(ADP-ribose) (PAR) and RNA in regulating DSBs-related condensates. Additionally, the FET family of RNA-binding proteins (including FUS, EWS and TAF15), has emerged as a critical player in the DNA damage response, with recent evidence suggesting that FET proteins support the formation and dynamics of repair condensates. Notably, phase separation of FET proteins is implicated also in their pathological functions in cancer biology, highlighting the pervasive role of condensation. This review will provide an overview of biomolecular condensates at DSBs, focusing on the interplay among PAR and RNA in the spatiotemporal regulation of FET proteins at repair complexes. We will also discuss the role of FET condensates in cancer biology and how they are targeted for therapeutic purposes. The study of biomolecular condensates holds great promise for advancing our understanding of key cellular processes and developing novel therapeutic strategies, but requires careful consideration of potential challenges.

Virus-like particles of retroviral origin in protein aggregation and neurodegenerative diseases

A wide range of human diseases are associated with protein misfolding and amyloid aggregates. Recent studies suggest that in certain neurological disorders, including Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD) and various tauopathies, protein aggregation may be promoted by virus-like particles (VLPs) formed by endogenous retroviruses (ERVs). The molecular mechanisms by which these VLPs contribute to protein aggregation, however, remain enigmatic. Here, we discuss possible molecular mechanisms of ERV-derived VLPs in the formation and spread of protein aggregates. An intriguing possibility is that liquid-like condensates may facilitate the formation of both protein aggregates and ERV-derived VLPs. We also describe how RNA chaperoning, and the encapsulation and trafficking of misfolded proteins, may contribute to protein homeostasis through the elimination of protein aggregates from cells. Based on these insights, we discuss future potential therapeutic opportunities.

The evolving role of solid state nuclear magnetic resonance methods in studies of amyloid fibrils

Beginning in the 1990s, solid state nuclear magnetic resonance (ssNMR) methods played a major role in elucidating the molecular structures and properties of amyloid fibrils. General principles that explain these structures and properties were uncovered and experimentally-based structural models were first developed from ssNMR data. Since 2017, cryogenic electron microscopy (cryo-EM) techniques have become capable of solving amyloid structures at near-atomic resolution. Although cryo-EM measurements are now the main approach for structural studies of amyloid fibrils, ssNMR measurements remain essential for studies of certain structures and structural features, as well as studies of dynamical and mechanistic aspects. Recent publications from various research groups illustrate the continuing importance of ssNMR and the unique information available from ssNMR measurements in amyloid research.

Phase separation of the oncogenic fusion protein EWS::FLI1 is modulated by its DNA-binding domain

Ewing sarcoma (EwS) is an aggressive cancer of bone and soft tissue that predominantly affects children and young adults. A chromosomal translocation joins the low-complexity domain (LCD) of the RNA-binding protein EWS (EWSLCD) with the DNA-binding domain of Friend leukemia integration 1 (FLI1DBD), creating EWS::FLI1, a potent fusion oncoprotein essential for EwS development and responsible for over 85% of EwS tumors. EWS::FLI1 forms biomolecular condensates in vivo and promotes tumorigenesis through mediation of aberrant transcriptional changes and by interfering with the normal functions of nucleic acid-binding proteins like EWS through a dominant-negative mechanism. In particular, the expression of EWS::FLI1 in EwS directly interferes with the biological functions of EWS leading to alternate splicing events and defects in DNA-damage repair pathways. Though the EWSLCD is capable of phase separation, here we report a direct interaction between FLI1DBD and EWSLCD that enhances condensate formation and alters the physical properties of the condensate. This effect was conserved for three related E-twenty-six transformation-specific (ETS) DNA-binding domains (DBDs) while DNA binding blocked the interaction with EWSLCD and inhibited EWS::FLI1 condensate formation. NMR spectroscopy and mutagenesis studies confirmed that ETS DBDs transiently interact with EWSLCD via the ETS DBDs "wings." Together these results revealed that ETS DBDs, particularly FLI1DBD, enhance EWSLCD condensate formation and rigidity, supporting a model in which electrostatic and structural interactions drive condensate dynamics with implications for EWS::FLI1-mediated transcriptional regulation in EwS.

Net charge driven recruitment of supercharged GFP mutants into FUS droplets

Liquid droplets recruit their relevant proteins and function together. Previous studies for a series of guest proteins clarified several rules of the recruitment and translational dynamics in the droplets; however, the other guest parameters such as structures, sizes, and amino-acid compositions might mask the single parameter effect. Here, we characterized the properties of GFP mutants with different charged compositions, but the same structure and size, in fused in sarcoma (FUS) droplets using single-molecule fluorescence microscopy. The recruitment of GFP mutants depended on their absolute net charge, whereas the diffusion did not. In the recruitment vs. diffusion plots, GFP mutants with large net charges were distinct from other proteins, demonstrating the importance of long-range electrostatic interaction on the recruitment.

Liquid-liquid phase separation of membrane-less condensates: from biogenesis to function

Membrane-less condensates (MLCs) are highly concentrated non-membrane-bounded structures in mammalian cells, comprising heterogeneous mixtures of proteins and/or nucleic acids. As dynamic compartments, MLCs can rapidly exchange components with the cellular environment, and their properties are easily altered in response to environmental signals, thus implicating that they can mediate numerous critical biological functions. A basic understanding of these condensates' formation, function, and underlying biomolecular driving forces has been obtained in recent years. For example, MLCs form through a liquid-liquid phase separation (LLPS) phenomenon similar to polymer condensation, which is primarily maintained via multivalent interactions of multi-domain proteins or proteins harboring intrinsically disordered regions (IDRs) as well as RNAs with binding sites. Moreover, an accumulating body of research indicates that MLCs are pathophysiologically relevant and involved in gene expression regulation and cellular stress responses. Here, we review the emerging field and explore what is currently known about the varied progress in LLPS of MLCs and how their features affect various cellular process, focusing on RNAs, including in skeletal myogenesis.

Temperature-Dependent Coarse-Grained Model for Simulations of Intrinsically Disordered Protein LCST and UCST Liquid-Liquid Phase Separations

Many intrinsically disordered proteins (IDPs) can undergo a liquid-liquid phase separation (LLPS) in water, depending on solution conditions (temperature, pH, and ionic strength). There are two types of LLPS that are controlled by temperature: those occurring above a lower critical solution temperature (LCST) and those occurring below an upper critical solution temperature (UCST). IDP coarse-grained (CG) models are particularly appropriate for investigating the physical and chemical factors that govern their LLPS and supramolecular organization. However, the development of CG models allowing simulations of both LCST and UCST behavior of temperature-sensitive IDPs is still in its infancy. In this context, we present here a novel temperature-dependent (TD) CG model for IDP simulations based on the MARTINI 3 force field. The model was developed by modifying the Lennard-Jones potentials between apolar or charged solute beads and water with a TD rescaling factor. It was parametrized to fit the TD potentials of mean force (PMF) between two apolar or two charged molecules computed using all-atom (AA) simulations. We show that the TD CG model is able to reproduce the experimentally known LLPS of both LCST and UCST low-complexity sequences and to estimate phase transition temperatures comparable to experimental measurements.

Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells

Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells.

Molecular Mechanisms of Protein Aggregation in ALS-FTD: Focus on TDP-43 and Cellular Protective Responses

Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share common genes and pathomechanisms and are referred to as the ALS-FTD spectrum. A hallmark of ALS-FTD pathology is the abnormal aggregation of proteins, including Cu/Zn superoxide dismutase (SOD1), transactive response DNA-binding protein 43 (TDP-43), fused in sarcoma/translocated in liposarcoma (FUS/TLS), and dipeptide repeat proteins resulting from C9orf72 hexanucleotide expansions. Genetic mutations linked to ALS-FTD disrupt protein stability, phase separation, and interaction networks, promoting misfolding and insolubility. This review explores the molecular mechanisms underlying protein aggregation in ALS-FTD, with a particular focus on TDP-43, as it represents the main aggregated species inside pathological inclusions and can also aggregate in its wild-type form. Moreover, this review describes the protective mechanisms activated by the cells to prevent protein aggregation, including molecular chaperones and post-translational modifications (PTMs). Understanding these regulatory pathways could offer new insights into targeted interventions aimed at mitigating cell toxicity and restoring cellular function.

Capturing the Conformational Heterogeneity of HSPB1 Chaperone Oligomers at Atomic Resolution

Small heat shock proteins (sHSPs), including HSPB1, are essential regulators of cellular proteostasis that interact with unfolded and partially folded proteins to prevent aberrant misfolding and aggregation. These proteins fulfill a similar role in biological condensates, where they interact with intrinsically disordered proteins to modulate their liquid-liquid and liquid-to-solid phase transitions. Characterizing the sHSP structure, dynamics, and client interactions is challenging due to their partially disordered nature, their tendency to form polydisperse oligomers, and their diverse range of clients. In this work, we leverage various biophysical methods, including fast 1H-based magic angle spinning (MAS) NMR spectroscopy, molecular dynamics (MD) simulations, and modeling, to shed new light on the structure and dynamics of HSPB1 oligomers. Using split-intein-mediated segmental labeling, we provide unambiguous evidence that in the oligomer context, the N-terminal domain (NTD) of HSPB1 is rigid and adopts an ensemble of heterogeneous conformations, the α-Crystallin domain (ACD) forms dimers and experiences multiple distinct local environments, while the C-terminal domain (CTD) remains highly dynamic. Our computational models suggest that the NTDs participate in extensive NTD-NTD and NTD-ACD interactions and are sequestered within the oligomer interior. We further demonstrate that HSPB1 higher order oligomers disassemble into smaller oligomeric species in the presence of a client protein and that an accessible NTD is essential for HSPB1 partitioning into condensates and interactions with client proteins. Our integrated approach provides a high-resolution view of the complex oligomeric landscape of HSPB1 and sheds light on the elusive network of interactions that underlies the function of HSPB1 in biological condensates.

Enzyme-induced liquid-to-solid phase transition of a mitochondria-targeted AIEgen in cancer theranostics

Enzyme-instructed self-assembly (EISA) is a promising approach to anti-cancer therapeutics due to its precise targeting and unique cell death mechanism. In this study, we introduce a small molecule, DN6, which undergoes nitroreductase (NTR)-responsive liquid-liquid phase separation (LLPS) followed by a liquid-to-solid phase transition (LST) through a gel-like intermediate state, resulting in the formation of nanoaggregates with spatiotemporal control. The reduced form of DN6 (DN6R), owing to its aggregation-induced emission (AIE) and mitochondria-targeting capabilities, has been employed for organelle-specific imaging of tumor hypoxia. The red-emissive DN6R nanoaggregates in situ generated by NTR induce mitochondrial damage and oxidative stress, culminating in apoptosis in cancer cells and spheroids. The organelle-specific targeting, visualization, and therapeutic outcomes achieved by leveraging LST of NTR-responsive AIEgenic DN6 render it as a promising agent for cancer theranostics.

A simple method for mapping the location of cross-β-forming regions within protein domains of low sequence complexity

Protein domains of low sequence complexity are unable to fold into stable, three-dimensional structures. In test tube studies, these unusual polypeptide regions can self-associate in a manner causing phase separation from aqueous solution. This form of protein:protein interaction has been implicated in numerous examples of dynamic morphological organization within eukaryotic cells. In several cases, the basis for low complexity domain (LCD) self-association and phase separation has been traced to the formation of labile cross-β structures. The primary energetic force favoring formation of these transient and reversible structures is enabled by polypeptide backbone interactions. Short, contiguous networks of peptide backbone amino groups and carbonyl oxygens are zippered together intermolecularly by hydrogen bonding as described by Linus Pauling seven decades ago. Here, we describe a simple, molecular biological method useful for the identification of localized, self-associating regions within larger protein domains of low sequence complexity.

A non-tethering role for the Drosophila Pol θ linker domain in promoting damage resolution

DNA polymerase theta (Pol θ) is an error-prone translesion polymerase that becomes crucial for DNA double-strand break repair when cells are deficient in homologous recombination or non-homologous end joining. In some organisms, Pol θ also promotes tolerance of DNA interstrand crosslinks. Due to its importance in DNA damage tolerance, Pol θ is an emerging target for treatment of cancer and disease. Prior work has characterized the functions of the Pol θ helicase-like and polymerase domains, but the roles of the linker domain are largely unknown. Here, we show that the Drosophila melanogaster Pol θ linker domain promotes proper egg development and is required for repair of DNA double-strand breaks and interstrand crosslink tolerance. While a linker domain with scrambled amino acid residues is sufficient for DNA repair, replacement of the linker with part of the Homo sapiens Pol θ linker or a disordered region from the FUS RNA-binding protein does not restore function. These results demonstrate that the linker domain is not simply a random tether between the catalytic domains and suggest that intrinsic amino acid residue properties, rather than protein interaction motifs, are more critical for Pol θ linker functions in DNA repair.

Nanoscale domains govern local diffusion and aging within FUS condensates

Biomolecular condensates regulate cellular physiology by sequestering and processing RNAs and proteins, yet how these processes are locally tuned within condensates remains unclear. Moreover, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), condensates undergo liquid-to-solid phase transitions, but capturing early intermediates in this process has been challenging. Here, we present a surface multi-tethering approach to achieve intra-condensate single-molecule tracking of fluorescently labeled RNA and protein molecules within liquid-like condensates. Using RNA-binding protein Fused in Sarcoma (FUS) as a model for condensates implicated in ALS, we discover that RNA and protein diffusion is confined within distinct nanometer-scale domains, or nanodomains, which exhibit unique connectivity and chemical environments. During condensate aging, these nanodomains reposition, facilitating FUS fibrilization at the condensate surface, a transition enhanced by FDA-approved ALS drugs. Our findings demonstrate that nanodomain formation governs condensate function by modulating biomolecule sequestration and percolation, offering insights into condensate aging and disease-related transitions.

Probing the Formation and Liquid-to-Solid Transition of FUS Condensates via the Lifetimes of Fluorescent Proteins

Liquid-liquid phase separation (LLPS) of biomolecules is a fundamental cellular process that is essential for maintaining homeostasis and facilitating biochemical activities. On the other hand, aberrant phase separation alters condensate fluidity and causes a transition from liquid-like condensates to solid-like condensates, which may lead to the formation of the pathological aggregations often observed in neurodegenerative diseases. Condensate fluidity is usually assessed by the fluorescence recovery after photobleaching. Here, we reveal that the fluorescence lifetimes of several fluorescent proteins are sensitive to LLPS and the liquid-to-solid transition. Furthermore, we identify several key residues that regulate the sensitivity of fluorescence lifetimes toward phase separation. Thus, we apply fluorescence lifetime imaging microscopy (FLIM) to visualize LLPS and the liquid-to-solid transition in living cells, demonstrating that FLIM is a nondestructive method for tracking changes in condensate fluidity in real time.

Nanoscale domains govern local diffusion and aging within FUS condensates

Biomolecular condensates regulate cellular physiology by sequestering and processing RNAs and proteins, yet how these processes are locally tuned within condensates remains unclear. Moreover, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), condensates undergo liquid-to-solid phase transitions, but capturing early intermediates in this process has been challenging. Here, we present a surface multi-tethering approach to achieve intra-condensate single-molecule tracking of fluorescently labeled RNA and protein molecules within liquid-like condensates. Using RNA-binding protein Fused in Sarcoma (FUS) as a model for condensates implicated in ALS, we discover that RNA and protein diffusion is confined within distinct nanometer-scale domains, or nanodomains, which exhibit unique connectivity and chemical environments. During condensate aging, these nanodomains reposition, facilitating FUS fibrilization at the condensate surface, a transition enhanced by FDA-approved ALS drugs. Our findings demonstrate that nanodomain formation governs condensate function by modulating biomolecule sequestration and percolation, offering insights into condensate aging and disease-related transitions.

Purification of Low-Complexity Domain Proteins FUS, EWSR1, and Their Fusions

FET proteins are large multifunctional proteins that have several key roles in biology. The FET family of proteins, including FUS, EWSR1, and TAF15, play critical roles in transcription regulation, RNA processing, and DNA damage repair. These multifunctional RNA- and DNA-binding proteins are ubiquitously expressed and conserved across vertebrate species. They contain low-complexity (LC) domains that allow them to assemble and phase separate but also makes the proteins prone to aggregation. Aberrations in FET proteins, such as point mutations, aggregation, or translocations leading to fusion proteins, have been implicated in several pathologies, including frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), and Ewing sarcoma. In vitro study of FET proteins is hampered by their propensity to aggregate, their disordered structure, and their susceptibility to proteolysis, making high-yield production difficult. Here, we present optimized methods for the purification of full-length FUS, EWSR1, and their fusion proteins. These protocols enable researchers to overcome issues related to aggregation and solubility, facilitating biochemical and biophysical studies of these critical yet complex proteins. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Purification of EWSR1 and FUS proteins Alternate Protocol: Purification for fusion proteins.

Selective translational control by PABPC1 phase separation regulates blast crisis and therapy resistance in chronic myeloid leukaemia

Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukaemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten patients with CML. Accumulating evidence suggests that translational control is crucial for cancer progression. Our high-throughput CRISPR-Cas9 screening identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML progression in the BC stage. PABPC1 preferentially improved the translation efficiency of multiple leukaemogenic mRNAs with long and highly structured 5' untranslated regions by forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, with minimal effects on normal haematopoiesis. Moreover, we identified two PABPC1 inhibitors that inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identifies PABPC1 as a selective translation enhancing factor in CML-BC, with its genetic or pharmacological inhibition overcoming TKI resistance and suppressed BC progression.

Liquid-liquid phase separation in cell physiology and cancer biology: recent advances and therapeutic implications

Liquid-liquid phase separation (LLPS) is a pivotal biophysical phenomenon that plays a critical role in cellular organization and has garnered significant attention in the fields of molecular mechanism and pathophysiology of cancer. This dynamic process involves the spontaneous segregation of biomolecules, primarily proteins and nucleic acids, into condensed, liquid-like droplets under specific conditions. LLPS drives the formation of biomolecular condensates, which are crucial for various cellular functions. Increasing evidences link alterations in LLPS to the onset and progression of various diseases, particularly cancer. This review explores the diverse roles of LLPS in cancer, highlighting its underlying molecular mechanisms and far-reaching implications. We examine how dysregulated LLPS contributes to cancer development by influencing key processes such as genomic instability, metabolism, and immune evasion. Furthermore, we discuss emerging therapeutic strategies aimed at modulating LLPS, underscoring their potential to revolutionize cancer treatment.

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.

Exploring liquid-liquid phase separation in vitro and in vivo using multimodal nonlinear optical imaging

Liquid-liquid phase separation leads to the formation of liquid droplets (LqDs) such as P granules in Caenorhabditis elegans (C. elegans). In this study, we demonstrate the label-free visualization of LqDs using multimodal nonlinear optical imaging both in vitro and in vivo. In vitro measurements with polymerized adenine [poly(A)], we found significantly higher poly(A) concentrations in LqDs compared to surrounding solutions, with the limit of detection (LoD) of 32 mg/mL. In vivo measurements, we performed label-free imaging of C. elegans. Despite efforts to detect P granules within P lineage cells in both wild-type C. elegans and green fluorescent protein (GFP)-tagged strains, no clear RNA-specific signals were observed. This indicates that the RNA concentration in P granules is lower than anticipated and falls below our in vitro LoD. These results underscore the challenges of label-free RNA detection in P granules.

The mechanobiology of biomolecular condensates

The central goal of mechanobiology is to understand how the mechanical forces and material properties of organelles, cells, and tissues influence biological processes and functions. Since the first description of biomolecular condensates, it was hypothesized that they obtain material properties that are tuned to their functions inside cells. Thus, they represent an intriguing playground for mechanobiology. The idea that biomolecular condensates exhibit diverse and adaptive material properties highlights the need to understand how different material states respond to external forces and whether these responses are linked to their physiological roles within the cell. For example, liquids buffer and dissipate, while solids store and transmit mechanical stress, and the relaxation time of a viscoelastic material can act as a mechanical frequency filter. Hence, a liquid-solid transition of a condensate in the force transmission pathway can determine how mechanical signals are transduced within and in-between cells, affecting differentiation, neuronal network dynamics, and behavior to external stimuli. Here, we first review our current understanding of the molecular drivers and how rigidity phase transitions are set forth in the complex cellular environment. We will then summarize the technical advancements that were necessary to obtain insights into the rich and fascinating mechanobiology of condensates, and finally, we will highlight recent examples of physiological liquid-solid transitions and their connection to specific cellular functions. Our goal is to provide a comprehensive summary of the field on how cells harness and regulate condensate mechanics to achieve specific functions.

The roles of functional bacterial amyloids in neurological physiology and pathophysiology: Pros and cons for neurodegeneration

Bacterial biofilms, which are complex communities of microorganisms encapsulated in a self-produced extracellular matrix, play critical roles in various diseases. Recent research has underscored the dualistic nature of amyloids, structural proteins within these biofilms, in human health, particularly highlighting the significant role in neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's disease (PD). These amyloids modulate the immune response by inducing the production of interleukin-10 (IL-10), which plays a role in anti-inflammatory processes. Additionally, they inhibit the aggregation of human amyloids and enhance the integrity of the intestinal barrier. Detrimentally, they exacerbate neuroinflammation by elevating inflammatory cytokines and promoting the aggregation of human amyloid proteins-amyloid-β (Aβ) in AD and α-synuclein (αS) in PD-through a process known as cross-seeding. Moreover, bacterial amyloids have also been shown to stimulate the production of anti-curli/DNA antibodies, which are implicated in the pathogenesis of autoimmune diseases. Given their dualistic nature, bacterial amyloids may, under specific conditions, function as beneficial proteins for human health. This understanding holds promise for the development of targeted therapeutic strategies aimed at modulating bacterial amyloids in the context of neurodegenerative diseases, such as AD and PD.

Electrokinetic detection of single-molecule phosphorylation

Current single-molecule fluorescence experiments lack direct sensitivity to molecular phosphorylation state. We show that electrokinetic properties measured with an anti-Brownian trap resolve the number of phosphorylated sites on individual biomolecules and can monitor phosphorylation cycles with single kinase turn overs. As an application, we directly visualize the rate limiting step in the kinase catalytic cycle.

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.

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.

Structural Characteristics and Properties of the RNA-Binding Protein hnRNPK at Multiple Physical States

Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA-binding protein containing low-complexity domains (LCDs), which are known to regulate protein behavior under stress conditions. This study demonstrates the ability to control hnRNPK's transitions into four distinct material states-monomer, soluble aggregate, liquid droplet, and fibrillar hydrogel-by modulating environmental factors such as temperature and protein concentration. Importantly, the phase-separated and hydrogel states are newly identified for eGFP-hnRNPK, marking a significant advancement in understanding its material properties. A combination of biophysical techniques, including DLS and SEC-LS, were used to further characterize hnRNPK in monomeric and soluble aggregate states. Structural methods, such as SANS, SAXS, and TEM, revealed the elongated morphology of the hnRNPK monomer. Environmental perturbations, such as decreased temperature or crowding agents, drove hnRNPK into phase-separated or gel-like states, each with distinct biophysical characteristics. These novel states were further analyzed using SEM, X-ray diffraction, and fluorescence microscopy. Collectively, these results demonstrate the complex behaviors of hnRNPK under different conditions and illustrate the properties of the protein in each material state. Transitions of hnRNPK upon condition changes could potentially affect functions of hnRNPK, playing a significant role in regulation of hnRNPK-involved processes in the cell.

Amyotrophic lateral sclerosis caused by FUS mutations: advances with broad implications

Autosomal dominant mutations in the gene encoding the DNA and RNA binding protein FUS are a cause of amyotrophic lateral sclerosis (ALS), and about 0·3-0·9% of patients with ALS are FUS mutation carriers. FUS-mutation-associated ALS (FUS-ALS) is characterised by early onset and rapid progression, compared with other forms of ALS. However, different pathogenic mutations in FUS can result in markedly different age at symptom onset and rate of disease progression. Most FUS mutations disrupt its nuclear localisation, leading to its cytoplasmic accumulation in the CNS. FUS also forms inclusions in around 5% of patients with the related neurodegenerative condition frontotemporal dementia. However, there are key differences between the two diseases at the genetic and neuropathological level, which suggest distinct pathogenic processes. Experimental models have uncovered potential pathogenic mechanisms in FUS-ALS and informed therapeutic strategies that are currently in development, including the silencing of FUS expression using an intrathecally administered antisense oligonucleotide.

Accelerated amyloid fibril formation at the interface of liquid-liquid phase-separated droplets by depletion interactions

Amyloid fibril formation of α-synuclein (αSN) is a hallmark of synucleinopathies. Although the previous studies have provided numerous insights into the molecular basis of αSN amyloid formation, it remains unclear how αSN self-assembles into amyloid fibrils in vivo. Here, we show that αSN amyloid formation is accelerated in the presence of two macromolecular crowders, polyethylene glycol (PEG) (MW: ~10,000) and dextran (DEX) (MW: ~500,000), with a maximum at approximately 7% (w/v) PEG and 7% (w/v) DEX. Under these conditions, the two crowders induce a two-phase separation of upper PEG and lower DEX phases with a small number of liquid droplets of DEX and PEG in PEG and DEX phases, respectively. Fluorescence microscope images revealed that the interfaces of DEX droplets in the upper PEG phase are the major sites of amyloid formation. We consider that the depletion interactions working in micro phase-segregated state with DEX and PEG systems causes αSN condensation at the interface between solute PEG and DEX droplets, resulting in accelerated amyloid formation. Ultrasonication further accelerated the amyloid formation in both DEX and PEG phases, confirming the droplet-dependent amyloid formation. Similar PEG/DEX-dependent accelerated amyloid formation was observed for amyloid β peptide. In contrast, amyloid formation of β2-microglobulin or hen egg white lysozyme with a native fold was suppressed in the PEG/DEX mixtures, suggesting that the depletion interactions work adversely depending on whether the protein is unfolded or folded.

Recent advances in the synthesis and application of biomolecular condensates

Biomolecular condensates (BMCs) represent a group of organized and programmed systems that participate in gene transcription, chromosome organization, cell division, tumorigenesis, and aging. However, the understanding of BMCs in terms of internal organizations and external regulations remains at an early stage. Recently, novel approaches such as synthetic biology have been used for de novo synthesis of BMCs. These synthesized BMCs (SBMCs) driven by phase separation adeptly resemble the self-assembly and dynamics of natural BMCs, offering vast potentials in basic and applied research. This review introduces recent progresses in phase separation-induced SBMCs, attempting to elaborate on the intrinsic principles and regulatory methodologies used to construct SBMCs. Furthermore, the scientific applications of SBMCs are illustrated, as indicated by the studies of chromosome structure, pathogenesis, biomanufacturing, artificial cell design, and drug delivery. The controllable SBMCs offer a powerful tool for understanding metabolic regulations, cellular organizations, and disease-associated protein aggregations, raising both opportunities and challenges in the future of biomaterial, biotechnology, and biomedicine.

Genome-Wide Characterization of Wholly Disordered Proteins in Arabidopsis

Intrinsically disordered proteins (IDPs) include two types of proteins: partial disordered regions (IDRs) and wholly disordered proteins (WDPs). Extensive studies focused on the proteins with IDRs, but less is known about WDPs because of their difficult-to-form folded tertiary structure. In this study, we developed a bioinformatics method for screening more than 50 amino acids in the genome level and found a total of 27 categories, including 56 WDPs, in Arabidopsis. After comparing with 56 randomly selected structural proteins, we found that WDPs possessed a more wide range of theoretical isoelectric point (PI), a more negative of Grand Average of Hydropathicity (GRAVY), a higher value of Instability Index (II), and lower values of Aliphatic Index (AI). In addition, by calculating the FCR (fraction of charged residue) and NCPR (net charge per residue) values of each WDP, we found 20 WDPs in R1 (FCR < 0.25 and NCPR < 0.25) group, 15 in R2 (0.25 ≤ FCR ≤ 0.35 and NCPR ≤ 0.35), 19 in R3 (FCR > 0.35 and NCPR ≤ 0.35), and two in R4 (FCR > 0.35 and NCPR > 0.35). Moreover, the gene expression and protein-protein interaction (PPI) network analysis showed that WDPs perform different biological functions. We also showed that two WDPs, SIS (Salt Induced Serine rich) and RAB18 (a dehydrin family protein), undergo the in vitro liquid-liquid phase separation (LLPS). Therefore, our results provide insight into understanding the biochemical characters and biological functions of WDPs in plants.

The Balbiani body is formed by microtubule-controlled molecular condensation of Buc in early oogenesis

Vertebrate oocyte polarity has been observed for two centuries and is essential for embryonic axis formation and germline specification, yet its underlying mechanisms remain unknown. In oocyte polarization, critical RNA-protein (RNP) granules delivered to the oocyte's vegetal pole are stored by the Balbiani body (Bb), a membraneless organelle conserved across species from insects to humans. However, the mechanisms of Bb formation are still unclear. Here, we elucidate mechanisms of Bb formation in zebrafish through developmental biomolecular condensation. Using super-resolution microscopy, live imaging, biochemical, and genetic analyses in vivo, we demonstrate that Bb formation is driven by molecular condensation through phase separation of the essential intrinsically disordered protein Bucky ball (Buc). Live imaging, molecular analyses, and fluorescence recovery after photobleaching (FRAP) experiments in vivo reveal Buc-dependent changes in the Bb condensate's dynamics and apparent material properties, transitioning from liquid-like condensates to a solid-like stable compartment. Furthermore, we identify a multistep regulation by microtubules that controls Bb condensation: first through dynein-mediated trafficking of early condensing Buc granules, then by scaffolding condensed granules, likely through molecular crowding, and finally by caging the mature Bb to prevent overgrowth and maintain shape. These regulatory steps ensure the formation of a single intact Bb, which is considered essential for oocyte polarization and embryonic development. Our work offers insight into the long-standing question of the origins of embryonic polarity in non-mammalian vertebrates, supports a paradigm of cellular control over molecular condensation by microtubules, and highlights biomolecular condensation as a key process in female reproduction.

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.

Sequence complexity and monomer rigidity control the morphologies and aging dynamics of protein aggregates

Understanding the biophysical basis of protein aggregation is important in biology because of the potential link to several misfolding diseases. Although experiments have shown that protein aggregates adopt a variety of morphologies, the dynamics of their formation are less well characterized. Here, we introduce a minimal model to explore the dependence of the aggregation dynamics on the structural and sequence features of the monomers. Using simulations, we demonstrate that sequence complexity (codified in terms of word entropy) and monomer rigidity profoundly influence the dynamics and morphology of the aggregates. Flexible monomers with low sequence complexity (corresponding to repeat sequences) form liquid-like droplets that exhibit ergodic behavior. Strikingly, these aggregates abruptly transition to more ordered structures, reminiscent of amyloid fibrils, when the monomer rigidity is increased. In contrast, aggregates resulting from monomers with high sequence complexity are amorphous and display nonergodic glassy dynamics. The heterogeneous dynamics of the low and high-complexity sequences follow stretched exponential kinetics, which is one of the characteristics of glassy dynamics. Importantly, at nonzero values of the bending rigidities, the aggregates age with the relaxation times that increase with the waiting time. Informed by these findings, we provide insights into aging dynamics in protein condensates and contrast the behavior with the dynamics expected in RNA repeat sequences. Our findings underscore the influence of the monomer characteristics in shaping the morphology and dynamics of protein aggregates, thus providing a foundation for deciphering the general rules governing the behavior of protein 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%.

From molecular descriptions to cellular functions of intrinsically disordered protein regions

Molecular descriptions of intrinsically disordered protein regions (IDRs) are fundamental to understanding their cellular functions and regulation. NMR spectroscopy has been a leading tool in characterizing IDRs at the atomic level. In this review, we highlight recent conceptual breakthroughs in the study of IDRs facilitated by NMR and discuss emerging NMR techniques that bridge molecular descriptions to cellular functions. First, we review the assemblies formed by IDRs at various scales, from one-to-one complexes to non-stoichiometric clusters and condensates, discussing how NMR characterizes their structural dynamics and molecular interactions. Next, we explore several unique interaction modes of IDRs that enable regulatory mechanisms such as selective transport and switch-like inhibition. Finally, we highlight recent progress in solid-state NMR and in-cell NMR on IDRs, discussing how these methods allow for atomic characterization of full-length IDR complexes in various phases and cellular environments. This review emphasizes recent conceptual and methodological advancements in IDR studies by NMR and offers future perspectives on bridging the gap between in vitro molecular descriptions and the cellular functions of IDRs.

ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules

Stress granules (SG) are part of a cellular protection mechanism where untranslated messenger RNAs and RNA-binding proteins are stored upon conditions of cellular stress. Compositional variations due to qualitative or quantitative protein changes can disrupt their functionality and alter their structure. This is the case of different forms of amyotrophic lateral sclerosis (ALS) where a causative link has been proposed between the cytoplasmic de-localization of mutant proteins, such as FUS (Fused in Sarcoma), and the formation of cytotoxic inclusions. Here, we describe the SG transcriptome in neuroblastoma cells and define several features for RNA recruitment in these condensates. We demonstrate that SG dynamics and RNA content are strongly modified by the incorporation of mutant FUS, switching to a more unstructured, AU-rich SG transcriptome. Moreover, we show that mutant FUS, together with its protein interactors and their target RNAs, are responsible for the reshaping of the mutant SG transcriptome with alterations that can be linked to neurodegeneration. Our data describe the molecular differences between physiological and pathological SG in ALS-FUS conditions, showing how FUS mutations impact the RNA and protein composition of these condensates.

Systematic Evaluation and Application of IDR Domain-Mediated Transcriptional Activation of NUP98 in Saccharomyces cerevisiae

Implementing dynamic control over gene transcription to decouple cell growth is essential for regulating protein expression in microbial cells. However, the availability of efficient regulatory elements in Saccharomyces cerevisiae remains limited. In this study, we present a novel β-estradiol-inducible gene expression system, termed DEN. This system combines a DNA-binding domain with an estradiol-binding domain and an intrinsically disordered region (IDR) from NUP98. Comparative analysis shows that the DEN system outperforms IDRs from other proteins, achieving an approximately 60-fold increase in EGFP expression upon β-estradiol induction. Moreover, our system is tightly controlled; nontoxic gene expression makes it a powerful tool for rapid and precise modulation of target gene expression. This system holds great potential for unlocking new functionalities from existing proteins in future research.

Prion-like Spreading of Disease in TDP-43 Proteinopathies

TDP-43 is a ubiquitous nuclear protein that plays a central role in neurodegenerative disorders collectively known as TDP-43 proteinopathies. Under physiological conditions, TDP-43 is primarily localized to the nucleus, but in its pathological form it aggregates in the cytoplasm, contributing to neuronal death. Given its association with numerous diseases, particularly ALS and FTLD, the mechanisms underlying TDP-43 aggregation and its impact on neuronal function have been extensively investigated. However, little is still known about the spreading of this pathology from cell to cell. Recent research has unveiled the possibility that TDP-43 may possess prion-like properties. Specifically, misfolded TDP-43 aggregates can act as templates inducing conformational changes in native TDP-43 molecules and propagating the misfolded state across neural networks. This review summarizes the mounting and most recent evidence from in vitro and in vivo studies supporting the prion-like hypothesis and its underlying mechanisms. The prion-like behavior of TDP-43 has significant implications for diagnostics and therapeutics. Importantly, emerging strategies such as small molecule inhibitors, immunotherapies, and gene therapies targeting TDP-43 propagation offer promising avenues for developing effective treatments. By elucidating the mechanisms of TDP-43 spreading, we therefore aim to pave the way for novel therapies for TDP-43-related neurodegenerative diseases.

Operando Decoding Ion-Conductive Switch in Stimuli-Responsive Hydrogel by Nanodiamond-Based Quantum Sensing

Thermal-responsive hydrogels are developed as ion-conductive switchs for energy storage devices, however, the molecule mechanism of switch on/off remains unclear. Here, poly(N-isopropylacrylamide-co-acrylamide) hydrogel is synthesized as a model material and nanodiamond (ND) based quantum sensing for phase change study is developed. First, micro-scale phase separation with cross-linked mesh structure after sol-gel transition is visualized in situ and water molecules are trapped by polymer chains and on a chemically "frozen" state. Then, the nano-scale inhomogeneous distributions of viscosity, thermal conductivity and ionic mobility in hydrogel at high temperature are observed by measuring the rotation, translation and zero-field splitting of NDs. Besides, the ionic mobility of hydrogel is found to be dependent not only on temperature but also on polymer concentration. These observations suggested that the physical "wall" induced by inhomogeneous phase separation at microscopic scale blocked the ion conduction pathways, providing a potential intrinsic explanation for ion migration shut-down of ionic hydrogels at high temperature.

Metals at the Helm: Revolutionizing Protein Assembly and Applications

Protein assembly is an essential process in biological systems, where proteins self-assemble into complex structures with diverse functions. Inspired by the exquisite control over protein assembly in nature, scientists have been exploring ways to design and assemble protein structures with precise control over their topologies and functions. One promising approach for achieving this goal is through metal coordination, which utilizes metal-binding motifs to mediate protein-protein interactions and assemble protein complexes with controlled stoichiometry and geometry. Metal coordination provides a modular and tunable approach for protein assembly and de novo structure design, where the metal ion acts as a molecular glue that holds the protein subunits together in a specific orientation. Metal-coordinated protein assemblies have shown great potential for developing functional metalloproteinase, novel biomaterials and integrated drug delivery systems. In this review, an overview of the recent advances in protein assemblies benefited from metal coordination is provided, focusing on various protein arrangements in different dimensions including protein oligomers, protein nanocage and higher-order protein architectures. Moreover, the key metal-binding motifs and strategies used to assemble protein structures with precise control over their properties are highlighted. The potential applications of metal-mediated protein assemblies in biotechnology and biomedicine are also discussed.

The role of liquid-liquid phase separation in the disease pathogenesis and drug development

Misfolding and aggregation of specific proteins are associated with liquid-liquid phase separation (LLPS), and these protein aggregates can interfere with normal cellular functions and even lead to cell death, possibly affecting gene expression regulation and cell proliferation. Therefore, understanding the role of LLPS in disease may help to identify new mechanisms or therapeutic targets and provide new strategies for disease treatment. There are several ways to disrupt LLPS, including screening small molecules or small molecule drugs to target the upstream signaling pathways that regulate the LLPS process, selectively dissolve and destroy RNA droplets or protein aggregates, regulate the conformation of mutant protein, activate the protein degradation pathway to remove harmful protein aggregates. Furthermore, harnessing the mechanism of LLPS can improve drug development, including preparing different kinds of drug delivery carriers (microneedles, nanodrugs, imprints), regulating drug internalization and penetration behaviors, screening more drugs to overcome drug resistance and enhance receptor signaling. This review initially explores the correlation between aberrant LLPS and disease, highlighting the pivotal role of LLPS in preparing drug development. Ultimately, a comprehensive investigation into drug-mediated regulation of LLPS processes holds significant scientific promise for disease management.

Spatiotemporal control of kinases and the biomolecular tools to trace activity

The delicate balance of cell physiology is implicitly tied to the expression and activation of proteins. Post-translational modifications offer a tool to dynamically switch protein activity on and off to orchestrate a wide range of protein-protein interactions to tune signal transduction during cellular homeostasis and pathological responses. There is a growing acknowledgment that subcellular locations of kinases define the spatial network of potential scaffolds, adaptors, and substrates. These highly ordered and localized biomolecular microdomains confer a spatially distinct bias in the outcomes of kinase activity. Furthermore, they may hold essential clues to the underlying mechanisms that promote disease. Developing tools to dissect the spatiotemporal activation of kinases is critical to reveal these mechanisms and promote the development of spatially targeted kinase inhibitors. Here, we discuss the spatial regulation of kinases, the tools used to detect their activity, and their potential impact on human health.

NMR studies of amyloid interactions

Amyloid fibrils are insoluble, fibrous nanostructures that accumulate extracellularly in biological tissue during the progression of several human disorders, including Alzheimer's disease (AD) and type 2 diabetes. Fibrils are assembled from protein monomers via the transient formation of soluble, cytotoxic oligomers, and have a common molecular architecture consisting of a spinal core of hydrogen-bonded protein β-strands. For the past 25 years, NMR spectroscopy has been at the forefront of research into the structure and assembly mechanisms of amyloid aggregates. Until the recent boom in fibril structure analysis by cryo-electron microscopy, solid-state NMR was unrivalled in its ability to provide atomic-level models of amyloid fibril architecture. Solution-state NMR has also provided complementary information on the early stages in the amyloid assembly mechanism. Now, both NMR modalities are proving to be valuable in unravelling the complex interactions between amyloid species and a diverse range of physiological metal ions, molecules and surfaces that influence the assembly pathway, kinetics, morphology and clearance in vivo. Here, an overview is presented of the main applications of solid-state and solution-state NMR for studying the interactions between amyloid proteins and biomembranes, glycosaminoglycan polysaccharides, metal ions, polyphenols, synthetic therapeutics and diagnostics. Key NMR methodology is reviewed along with examples of how to overcome the challenges of detecting interactions with aggregating proteins. The review heralds this new role for NMR in providing a comprehensive and pathologically-relevant view of the interactions between protein and non-protein components of amyloid. Coverage of both solid- and solution-state NMR methods and applications herein will be informative and valuable to the broad communities that are interested in amyloid proteins.

RNA granules in flux: dynamics to balance physiology and pathology

The life cycle of an mRNA is a complex process that is tightly regulated by interactions between the mRNA and RNA-binding proteins, forming molecular machines known as RNA granules. Various types of these membrane-less organelles form inside cells, including neurons, and contribute critically to various physiological processes. RNA granules are constantly in flux, change dynamically and adapt to their local environment, depending on their intracellular localization. The discovery that RNA condensates can form by liquid-liquid phase separation expanded our understanding of how compartments may be generated in the cell. Since then, a plethora of new functions have been proposed for distinct condensates in cells that await their validation in vivo. The finding that dysregulation of RNA granules (for example, stress granules) is likely to affect neurodevelopmental and neurodegenerative diseases further boosted interest in this topic. RNA granules have various physiological functions in neurons and in the brain that we would like to focus on. We outline examples of state-of-the-art experiments including timelapse microscopy in neurons to unravel the precise functions of various types of RNA granule. Finally, we distinguish physiologically occurring RNA condensation from aberrant aggregation, induced by artificial RNA overexpression, and present visual examples to discriminate both forms in neurons.

Homologous Peptide Foldamer Promotes FUS Aggregation and Triggers Cancer Cell Death

Fused in sarcoma (FUS), a multifunctional deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein, has been implicated in various cancer types, including sarcoma and leukemia. Despite its association with these diseases, there has been limited exploration of FUS as a cancer therapy target, primarily because its dynamic nature makes it difficult to target specifically. In this study, we explored a kind of β-sheet peptide foldamer, named β4-TAT, to influence FUS aggregation by targeting its RNA recognition motifs (RRM). This approach leverages the noncovalent interaction characteristics of peptide self-assembly processes. The β4 sequence, derived from the FUS RRM β-sheet, in combination with TAT, a peptide known for its nuclear targeting capability, enables β4-TAT to bind specifically to the analogous β4 sequence within FUS. Notably, β4-TAT effectively induces FUS aggregation within cells, leading to the death of cancer cells. Our work developed a novel peptide foldamer-based strategy for inducing protein aggregation, paving the way for innovative therapeutic approaches in targeting FUS-associated cancers.

Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils

The tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.

Osmotic stress induces formation of both liquid condensates and amyloids by a yeast prion domain

Liquid protein condensates produced by phase separation are involved in the spatiotemporal control of cellular functions, while solid fibrous aggregates (amyloids) are associated with diseases and/or manifest as infectious or heritable elements (prions). Relationships between these assemblies are poorly understood. The Saccharomyces cerevisiae release factor Sup35 can produce both fluid liquid-like condensates (e.g., at acidic pH) and amyloids (typically cross-seeded by other prions). We observed acidification-independent formation of Sup35-based liquid condensates in response to hyperosmotic shock in the absence of other prions, both at increased and physiological expression levels. The Sup35 prion domain, Sup35N, is both necessary and sufficient for condensate formation, while the middle domain, Sup35M antagonizes this process. Formation of liquid condensates in response to osmotic stress is conserved within yeast evolution. Notably, condensates of Sup35N/NM protein originated from the distantly related yeast Ogataea methanolica can directly convert to amyloids in osmotically stressed S. cerevisiae cells, providing a unique opportunity for real-time monitoring of condensate-to-fibril transition in vivo by fluorescence microscopy. Thus, cellular fate of stress-induced condensates depends on protein properties and/or intracellular environment.

Biomolecular condensates in plant cells: Mediating and integrating environmental signals and development

In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.