Role of aberrant phase separation in pathological protein aggregation

The prolyl oligopeptidase and α-synuclein connection revisited

The aim of this work was to revisit the connection between prolyl oligopeptidase (PREP) and α-synuclein (aSyn) by presenting novel data from cell free and cellular assays and to discuss the results in a contemporary context. The aSyn aggregation process was studied using fluorescence correlation spectroscopy and thioflavin-T fluorescence. Binding sites for PREP on the aSyn sequence were determined using peptide arrays. Subcellular localisation of PREP and stress markers were studied using double staining immunofluorescence microscopy in SH-SY5Y cells with and without overexpression of aSyn and PREP, before and after differentiation, and with or without proteolytic stress induced by proteasome inhibition. The interaction between PREP and aSyn was found to be weak and transient. It promotes the early phases of aggregation but does not affect the rate of β-fibril formation. Moreover, this interaction is not dependent upon the C-terminal prolines of aSyn, but is affected by PREP inhibitors and interferes with PREP substrate binding. Although present in the same cellular compartments, there is little evidence for a strong physical association of PREP with aggresomes and stress markers. Instead, there is colocalization with aSyn in the cell periphery and neurites. There is evidence for a binding site for peptides much longer than the usual PREP substrates. The modular assembly of molecular machines and the observation that PREP's protein-protein interactions are tuneable by active site inhibitors, lead to the hypothesis that this binding site features in the cross-talk between autophagy and neuron-specific pathways involving vesicle transport and protein secretion.

Assessing amyloid fibrils and amorphous aggregates: A review

Protein misfolding and aggregation play a central role in the progression of neurodegenerative diseases such as Alzheimer's and Parkinson's. These aggregates manifest either as structured amyloid fibrils enriched in β-sheet conformations or as irregular amorphous aggregates with diverse morphologies. Understanding their formation, structure, and behavior is critical for deciphering disease mechanisms and developing targeted diagnostics and therapeutics. This review presents an integrated overview of both conventional and advanced techniques used to detect, distinguish, and structurally characterize these protein aggregates. It covers a range of spectroscopic and spectrometric tools, such as fluorescence, Raman, and mass spectrometry that facilitate aggregate identification. Microscopy methods, including atomic force and electron microscopy, are highlighted for morphological analysis. The review also discusses in situ detection strategies using fluorescent dyes, conformation-specific antibodies, enzymatic reporters, and real-time imaging. Separation methods like centrifugation, electrophoresis, and chromatography are outlined alongside structural analysis tools such as X-ray diffraction. Furthermore, the growing utility of computational approaches and artificial intelligence in predicting aggregation propensities and integrating biological data is emphasized. By critically evaluating each method's capabilities and limitations, this review provides a practical and forward-looking resource for researchers studying the complex landscape of protein aggregation.

Phase separation participates in the genetic regulation mechanism of hematopoietic stem cells: potential therapeutic methods

Hematopoietic stem cells (HSCs) are the primitive cells that give rise to common precursors for all blood cell lineages. Abnormalities in their number and/or function are important factors leading to the decline of immune function and the occurrence of various systemic diseases. Phase separation refers to a physicochemical mechanism in which intracellular liquid-liquid phase separation (LLPS) forms membrane-less organelles. It participates in various physiological activities and is related to the occurrence of diseases. Studies have shown that the functional activity of HSCs is regulated by complex mechanisms, and phase separation is closely related to these complex mechanisms such as genetic regulation, epigenetic regulation, microenvironment regulation, gene expression, autophagy degradation, and cell proliferation. With the deepening of research, the importance of phase separation in the pathogenesis and treatment of diseases such as leukemia and tumors has gradually emerged, but the deep mechanism of its regulation of HSCs genetic regulation still lacks exploration, and the direction of clinical targeted therapy is not yet clear. Here, we will summarize and elaborate the genetic regulation mechanism of HSCs, discuss the relationship between phase separation and the functional regulation of HSCs, and analyze the possibility of phase separation participating in the genetic regulation of HSCs to treat diseases, in order to provide help for the clinical implementation of targeted therapy for HSCs regulation.

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Serum Amyloid A Binding to Glycosaminoglycans is Synergistic with Amyloid Formation: Therapeutic Targeting in the Inflammation-linked Amyloidosis

Serum amyloid A (SAA), a small lipophilic plasma protein elevated in inflammation, is a precursor of amyloid A (AA) amyloidosis, the major life-threatening complication of chronic inflammation in animals and humans. Although heparan sulfate (HS) is a potent amyloid agonist, particularly in AA amyloidosis, therapeutic targeting of SAA-HS interactions using a small-molecule HS/heparin decoy was unsuccessful. To understand molecular underpinnings, we used recombinant lipid-free human and murine SAA1 and human SAA2 to explore their interactions with various glycosaminoglycans at pH 5.5-7.4 during amyloid formation, from native protein to amyloid oligomers and fibrils. Effects of pH and glycosaminoglycan sulfation/charge supported by prior computational studies indicate electrostatic origin of SAA-glycosaminoglycan interactions. HS/heparin can promote amyloidogenesis by inducing non-native β-sheet and apparently causing liquid droplet formation in SAA in solution. Structural and binding studies by spectroscopy and ELISA reveal previously unknown synergy between amyloid formation and heparin/HS binding by SAA. We propose that this synergy potentially extends to other protein amyloids and stems from longitudinal binding of HS polyanions to basic residue arrays on amyloid oligomers or fibrils. This binding mode explains our finding that a minimal heparin chain length exceeding 20 monosaccharides is necessary to compete with HS for binding to amyloid oligomers. The results help explain prior failure of a small-molecule drug in targeting of SAA-HS interactions and consider alternative HS-targeting approaches for AA and, potentially, other amyloid diseases.

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.

The Regulation of TDP-43 Structure and Phase Transitions: A Review

The transactive response DNA binding protein 43 (TDP-43) is an RNA/DNA-binding protein that is involved in a number of cellular functions, including RNA processing and alternative splicing, RNA transport and translation, and stress granule assembly. It has attracted significant attention for being the primary component of cytoplasmic inclusions in patients with amyotrophic lateral sclerosis or frontotemporal dementia. Mounting evidence suggests that both cytoplasmic aggregation of TDP-43 and loss of nuclear TDP-43 function contribute to TDP-43 pathology. Furthermore, recent studies have demonstrated that TDP-43 is an important component of many constitutive or stress-induced biomolecular condensates. Dysregulation or liquid-to-gel transition of TDP-43 condensates can lead to alterations in TDP-43 function and the formation of TDP-43 amyloid fibrils. In this review, we summarize recent research progress on the structural characterization of TDP-43 and the TDP-43 phase transition. In particular, the roles that disease-associated genetic mutations, post-translational modifications, and extrinsic stressors play in the transitions among TDP-43 monomers, liquid condensates, solid condensates, and fibrils are discussed. Finally, we discuss the effectiveness of available regulators of TDP-43 phase separation and aggregation. Understanding the underlying mechanisms that drive the pathological transformation of TDP-43 could help develop therapeutic strategies for TDP-43 pathology.

Phase Separation and Prion-Like Aggregation of p53 Family Tumor Suppressors: From Protein Evolution to Cancer Treatment

Biomolecular condensates, formed through phase separation (PS), are essential in various physiological processes, but they can also transition into amyloid-like structures, contributing to diseases like cancer and neurodegenerative disorders. This review centers on the tumor suppressor protein p53 and its paralogs, p63 and p73, which play significant roles in cancer biology. Mutations in the TP53 gene, present in over half of all malignant tumors, disrupt the function of p53 and contribute to cancer progression. Mutant p53 not only misfolds but also forms biomolecular condensates and amyloid-like aggregates, like the toxic amyloids seen in neurodegenerative diseases. These amyloid-like structures, characteristic of mutant p53, might be associated with its gain of function (GoF) in cancer. Recent in vitro and in cell studies demonstrate that mutant p53 can exert a prion-like effect on its paralogs, p63 and p73, which typically do not form amyloids under physiological conditions. Heparin inhibits the prion-like effect of mutant p53 on p63 and p73. These findings underscore the critical role of mutant p53 in promoting the aggregation of p63 and p73, and likely of other transcription factors, suggesting new therapeutic targets. The amyloid-like aggregation of mutant p53 is an excellent candidate target for cancer, as evidenced by recent studies. By understanding the phase transitions and amyloid formation of mutant p53, innovative diagnostic and treatment strategies have been explored to reveal and disrupt these processes, offering hope for improved cancer therapies.

The roles of intrinsically disordered proteins in neurodegeneration

Neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, and Huntington's disease share a common pathological hallmark: the accumulation of misfolded proteins, particularly involving intrinsically disordered proteins (IDPs) like TDP-43, FUS, Tau, α-synuclein, and Huntingtin. These proteins undergo pathological aggregation, forming toxic inclusions that disrupt cellular function. The dysregulation of proteostasis mechanisms, including the ubiquitin-proteasome system (UPS), ubiquitin-independent proteasome system (UIPS), autophagy, and molecular chaperones, exacerbates these proteinopathies by failing to clear misfolded proteins effectively. Emerging therapeutic strategies aim to restore proteostasis through proteasome activators, autophagy enhancers, and chaperone-based interventions to prevent the toxic accumulation of IDPs. Additionally, understanding liquid-liquid phase separation (LLPS) and its role in stress granule dynamics offers novel insights into how aberrant phase transitions contribute to neurodegeneration. By targeting the molecular pathways involved in IDP aggregation and proteostasis regulation, and better understanding the specificity of each component, research in this area will pave the way for innovative therapeutic approaches to combat these neurodegenerative diseases. This review discusses the molecular mechanisms underpinning IDP pathology, highlights recent advancements in drug discovery, and explores the potential of targeting proteostasis machinery to develop effective therapies.

Caffeine Inhibits Tau Aggregation and Destabilizes the Fibril Associated with Chronic Traumatic Encephalopathy: A REST2 and Conventional MD Simulations Study

Chronic traumatic encephalopathy (CTE) is a unique tauopathy mostly diagnosed in contact sports athletes, such as those active in American football, boxing, soccer, etc. The hyperphosphorylated fibrillar aggregates composed of self-assembled tau protein are the pathological hallmark of CTE, and inhibiting the aggregation or disassociating the fibrillar aggregates has been considered a promising avenue to prevent or treat CTE. Caffeine (CA) is a well-known psychostimulant and can be found in coffee, tea, and soft drinks. In vitro experiments revealed that CA could effectively inhibit wild-type tau aggregation and disassemble preformed fibrils. However, the atomic effect and the underlying molecular mechanisms remain largely elusive. In this study, we performed a multitude of replica exchange with solute tempering 2 (REST2) and conventional molecular dynamics (CMD) simulations of 43.8 μs in total on tau models with and without CA, including the third and fourth microtubule-binding repeats (R3-R4) tau monomer and CTE-related R3-R4 tau protofibril and fibril. The results revealed that CA could prominently inhibit the β-sheet formation of the monomer and disrupt the β-sheet structure of the protofibril, inducing the monomer and protofibril to adopt loosely packed or extended conformations. H-bonding and π-π stacking interactions drove the binding of CA on the monomer, while hydrophobic interactions made an extra contribution to the binding of CA on the protofibril. Strikingly, CA could stably bind to the hydrophobic cavity of the protofibril, which might occupy the space and prevent the entering of the aggregation cofactor. What is more, CA destabilized the fibril and played a role in reversing the liquid-to-solid phase transition (LSPT) of tau. Our study systematically uncovered the atomic-level effect of CA on tau aggregation, which offers a theoretical foundation for the design of drugs to prevent or treat CTE.

Insight into the thermo-responsive phase behavior of the P1 domain of α-synuclein using atomistic simulations

Biomolecular condensate formation driven by intrinsically disordered proteins (IDPs) is regulated by interactions between various domains of the proteins. Such condensates are implicated in various neurodegenerative diseases. The presynaptic intrinsically disordered protein, α-Syn is involved in the pathogenesis of Parkinson's disease. The central non-amyloid β-component (NAC) domain in the protein is considered to be a major driver of pathogenic aggregation, although recent studies have suggested that the P1 domain from the flanking N-terminal region can act as a 'master controller' for α-Syn function and aggregation. To gain molecular insight into the phase behavior of the P1 domain itself, we investigate how assemblies of P1 (residues 36-42) chains phase separate with varying temperatures using all-atom molecular dynamics simulations. The simulations reveal that P1 is able to phase separate above a lower critical solution temperature. Formation of a condensed phase is driven by exclusion of water molecules by the hydrophobic chains. P1 chain density in the condensate is determined by weak multi-chain interactions between the residues. Moreover, tyrosine (Y39) is involved in the formation of strongest contacts between residue pairs in the dense phase. These results provide a detailed picture of condensate formation by a key segment of the α-Syn molecule.

Synaptic sabotage: How Tau and α-Synuclein undermine synaptic health

Synaptic dysfunction is one of the earliest cellular defects observed in Alzheimer's disease (AD) and Parkinson's disease (PD), occurring before widespread protein aggregation, neuronal loss, and cognitive decline. While the field has focused on the aggregation of Tau and α-Synuclein (α-Syn), emerging evidence suggests that these proteins may drive presynaptic pathology even before their aggregation. Therefore, understanding the mechanisms by which Tau and α-Syn affect presynaptic terminals offers an opportunity for developing innovative therapeutics aimed at preserving synapses and potentially halting neurodegeneration. This review focuses on the molecular defects that converge on presynaptic dysfunction caused by Tau and α-Syn. Both proteins have physiological roles in synapses. However, during disease, they acquire abnormal functions due to aberrant interactions and mislocalization. We provide an overview of current research on different essential presynaptic pathways influenced by Tau and α-Syn. Finally, we highlight promising therapeutic targets aimed at maintaining synaptic function in both tauopathies and synucleinopathies.

Deciphering the Monomeric and Dimeric Conformational Landscapes of the Full-Length TDP-43 and the Impact of the C-Terminal Domain

The aberrant aggregation of TAR DNA-binding protein 43 kDa (TDP-43) in cells leads to the pathogenesis of multiple fatal neurodegenerative diseases. Decoding the proposed initial transition between its functional dimeric and aggregation-prone monomeric states can potentially design a viable therapeutic strategy, which is presently limited by the lack of structural detail of the full-length TDP-43. To achieve a complete understanding of such a delicate phase space, we employed a multiscale simulation approach that unearths numerous crucial features, broadly summarized in two categories: (1) state-independent features that involve inherent chain collapsibility, rugged polymorphic landscape dictated by the terminal domains, high β-sheet propensity, structural integrity preserved by backbone-based intrachain hydrogen bonds and electrostatic forces, the prominence of the C-terminal domain in the intrachain cross-domain interfaces, and equal participation of hydrophobic and hydrophilic (charged and polar) residues in cross-domain interfaces; and (2) dimerization-modulated characteristics that encompass slower collapsing dynamics, restricted polymorphic landscape, the dominance of side chains in interchain hydrogen bonds, the appearance of the N-terminal domain in the dimer interface, and the prominence of hydrophilic (specifically polar) residues in interchain homo- and cross-domain interfaces. In our work, the ill-known C-terminal domain appears as the most crucial structure-dictating domain, which preferably populates a compact conformation with a high β-sheet propensity in its isolated state stabilized by intrabackbone hydrogen bonds, and these signatures are comparatively faded in its integrated form. Validation of our simulated observables by a complementary spectroscopic approach on multiple counts ensures the robustness of the computationally predicted features of the TDP-43 aggregation landscape.

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%.

Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation

Emerging evidence suggests that physiological C-terminal truncation of α-synuclein (αS) plays a critical role in regulating liquid-liquid phase separation and promoting amyloid aggregation, processes implicated in neurodegenerative diseases such as Parkinson's disease (PD). However, the molecular mechanisms through which C-terminal truncation influences αS conformation and modulates its aggregation remain poorly understood. In this study, we investigated the impact of C-terminal truncation on αS conformational dynamics by comparing full-length αS1-140 with truncated αS1-103 monomers using atomistic discrete molecular dynamics simulations. Our findings revealed that both αS1-140 and αS1-103 primarily adopted helical conformations around residues 7-32, while residues 36-95, located in the second half of the N-terminal and NAC domains, predominantly formed a dynamic β-sheet core. The C-terminus of αS1-140 was largely unstructured and dynamically wrapped around the β-sheet core. While residues 1-95 exhibited similar secondary structure propensities in both αS1-140 and αS1-103, the dynamic capping by the C-terminus in αS1-140 slightly enhanced β-sheet formation around residues 36-95. In contrast, key aggregation-driving regions (residues 2-9, 36-42, 45-57, and 68-78) were dynamically shielded by the C-terminus in αS1-140, reducing their exposure and potentially preventing interpeptide interactions that drive aggregation. C-terminal truncation, on the other hand, increased the exposed surface area of these aggregation-prone regions, thereby enhancing interpeptide interactions, phase separation, and amyloid aggregation. Overall, our simulations provide valuable insights into the conformational effects of C-terminal truncation on αS and its role in promoting pathological aggregation.

Membraneless organelles in health and disease: exploring the molecular basis, physiological roles and pathological implications

Once considered unconventional cellular structures, membraneless organelles (MLOs), cellular substructures involved in biological processes or pathways under physiological conditions, have emerged as central players in cellular dynamics and function. MLOs can be formed through liquid-liquid phase separation (LLPS), resulting in the creation of condensates. From neurodegenerative disorders, cardiovascular diseases, aging, and metabolism to cancer, the influence of MLOs on human health and disease extends widely. This review discusses the underlying mechanisms of LLPS, the biophysical properties that drive MLO formation, and their implications for cellular function. We highlight recent advances in understanding how the physicochemical environment, molecular interactions, and post-translational modifications regulate LLPS and MLO dynamics. This review offers an overview of the discovery and current understanding of MLOs and biomolecular condensate in physiological conditions and diseases. This article aims to deliver the latest insights on MLOs and LLPS by analyzing current research, highlighting their critical role in cellular organization. The discussion also covers the role of membrane-associated condensates in cell signaling, including those involving T-cell receptors, stress granules linked to lysosomes, and biomolecular condensates within the Golgi apparatus. Additionally, the potential of targeting LLPS in clinical settings is explored, highlighting promising avenues for future research and therapeutic interventions.

β-synuclein regulates the phase transitions and amyloid conversion of α-synuclein

Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB) are neurodegenerative disorders characterized by the accumulation of α-synuclein aggregates. α-synuclein forms droplets via liquid-liquid phase separation (LLPS), followed by liquid-solid phase separation (LSPS) to form amyloids, how this process is physiologically-regulated remains unclear. β-synuclein colocalizes with α-synuclein in presynaptic terminals. Here, we report that β-synuclein partitions into α-synuclein condensates promotes the LLPS, and slows down LSPS of α-synuclein, while disease-associated β-synuclein mutations lose these capacities. Exogenous β-synuclein improves the movement defects and prolongs the lifespan of an α-synuclein-expressing NL5901 Caenorhabditis elegans strain, while disease-associated β-synuclein mutants aggravate the symptoms. Decapeptides targeted at the α-/β-synuclein interaction sites are rationally designed, which suppress the LSPS of α-synuclein, rescue the movement defects, and prolong the lifespan of C. elegans NL5901. Together, we unveil a Yin-Yang balance between α- and β-synuclein underlying the normal and disease states of PD and DLB with therapeutical potentials.

Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis

The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.

Detection of TurboID fusion proteins by fluorescent streptavidin outcompetes antibody signals and visualises targets not accessible to antibodies

Immunofluorescence localises proteins via fluorophore-labelled antibodies. However, some proteins evade detection due to antibody-accessibility issues or because they are naturally low abundant or antigen density is reduced by the imaging method. Here, we show that the fusion of the target protein to the biotin ligase TurboID and subsequent detection of biotinylation by fluorescent streptavidin offers an 'all in one' solution to these restrictions. For all proteins tested, the streptavidin signal was significantly stronger than an antibody signal, markedly improving the sensitivity of expansion microscopy and correlative light and electron microscopy. Importantly, proteins within phase-separated regions, such as the central channel of the nuclear pores, the nucleolus, or RNA granules, were readily detected with streptavidin, while most antibodies failed. When TurboID is used in tandem with an HA epitope tag, co-probing with streptavidin and anti-HA can map antibody-accessibility and we created such a map for the trypanosome nuclear pore. Lastly, we show that streptavidin imaging resolves dynamic, temporally, and spatially distinct sub-complexes and, in specific cases, reveals a history of dynamic protein interaction. In conclusion, streptavidin imaging has major advantages for the detection of lowly abundant or inaccessible proteins and in addition, provides information on protein interactions and biophysical environment.

Tannic acid as a biphasic modulator of tau protein liquid-liquid phase separation

Tannic acid (TA) is a natural polyphenol that shows great potential in the field of biomedicine due to its anti-inflammatory, anti-oxidant, anti-bacterial, anti-tumor, anti-virus, and neuroprotective activities. Recent studies have revealed that liquid-liquid phase separation (LLPS) is closely associated with protein aggregation. Therefore, modulating LLPS offers new insights into the treatment of neurodegenerative diseases. In this study, we investigated the influence of TA on the LLPS of the Alzheimer's-related protein tau and the underlying mechanism. Our findings indicate that TA affects the LLPS of tau in a biphasic manner, with initial promotion and subsequent suppression as the TA to tau molar ratio increases. TA modulates tau phase separation through a combination of hydrophobic interactions and hydrogen bonds. The balance between TA-tau and tau-tau interactions is found to be relevant to the material properties of TA-induced tau condensates. We further illustrate that the modulatory activity of TA in phase separation is highly dependent on the target proteins. These findings enhance our understanding of the forces driving tau LLPS under different conditions, and may facilitate the identification and optimization of compounds that can rationally modulate protein phase transition in the future.

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 temperatures TLLPS in the 20-40° C range. To investigate whether local conformational distributions are detectably different in the homogeneous and phase-separated states of FUS-LC, we performed solid state nuclear magnetic resonance (ssNMR) measurements on solutions that were frozen on sub-millisecond time scales 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 (2D) 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 2D crosspeak patterns to an enhanced population of β-strand-like conformations suggests that changes in conformational distributions are no larger than 5-10%.

Statement of Significance

Liquid-liquid phase separation (LLPS) in solutions of proteins with intrinsically disordered domains has attracted recent attention because of its relevance to multiple biological processes and its inherent interest from the standpoint of protein biophysics. The high protein concentrations and abundant intermolecular interactions within protein-rich, phase-separated "droplets" suggests that conformational distributions of intrinsically disordered proteins may differ in homogeneous and phase-separated solutions. To investigate whether detectable differences exist, we performed experiments on the low-complexity domain of the FUS protein (FUS-LC) in which FUS-LC solutions were first equilibrated at temperatures well above or well below their LLPS transition temperatures, then rapidly frozen and examined at very low temperatures by solid state nuclear magnetic resonance (ssNMR) spectroscopy. The ssNMR data for homogeneous and phase-separated frozen solutions of FUS-LC were found to be nearly identical, showing that LLPS is not accompanied by substantial changes in the local conformational distributions of this intrinsically disordered protein.

Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.

Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation

When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.

The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome

Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.