Copper drives prion protein phase separation and modulates aggregation

Structural analysis of a micron-sized deposit of Cu0 in an insulin ball from a person with diabetes

BACKGROUND

Protein misfolding is a hallmark of aging, resulting in diabetes and neuroendocrine disorders. Insulin preparations also form aggregates known as insulin balls. Aggregated insulin preparations usually form amyloids and are stable in subcutaneous tissue, some specimens are cytotoxic to cultured cells.

METHODS

A multilayered structural analysis of the detailed morphology of 21 insulin balls was performed by connecting regions of interest along spatial axes. Gross and optical microscopic findings, Raman spectrometric analysis using formalin-fixed paraffin-embedded block specimens, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry, microfocus X-ray computed tomography, scanning electron microscopy-energy dispersive X-ray spectroscopy analysis, and transmission electron microscopy analysis were performed.

RESULTS

Here, we show the presence of 100 µm Cu0 within an insulin ball removed from a woman in her mid-40s with diabetes. The insulin ball is made of insulin lispro in an insoluble state in the lower abdominal subcutaneous adipose tissue. Transmission electron microscopy reveals fibrous structures. Microfocus X-ray computed tomography detects many spots with strong light contrast in the insulin ball. Scanning electron microscopy-energy dispersive X-ray spectroscopic analysis shows that the largest light spot is elemental metallic copper without an oxidation state (Cu0).

CONCLUSIONS

The largest amount of Cu0 found in living things is in a human. Our discovery of 100 µm Cu0 within the insulin ball supports the idea that insulin preparations from outside can disrupt the balance of metals, including Cu. In 2025, the patient continues to inject subcutaneous insulin preparations, but no new insulin balls appear.

Protocols for monitoring condensate formation and dynamics between the phase-separating proteins SET/TAF-Iβ and cytochrome c

The targeting of several nuclear stress-response factors by translocated cytochrome c upon genotoxic stress has been demonstrated in recent years to involve liquid-liquid phase separation. This protocol addresses the need to investigate the mechanisms and features of phase separation of the histone chaperone SET/TAF-Iβ induced by cytochrome c. We provide steps for protein purification and fluorescent labeling, condensate formation, imaging, quantification, and evaluation of their dynamics by fluorescence recovery after photobleaching (FRAP). This protocol can be broadly applied to other protein complexes. For complete details on the use and execution of this protocol, please refer to Casado-Combreras et al.1.

X-Ray Photon Correlation Spectroscopy, Microscopy, and Fluorescence Recovery After Photobleaching to Study Phase Separation and Liquid-to-Solid Transition of Prion Protein Condensates

Biomolecular condensates are macromolecular assemblies constituted of proteins that possess intrinsically disordered regions and RNA-binding ability together with nucleic acids. These compartments formed via liquid-liquid phase separation (LLPS) provide spatiotemporal control of crucial cellular processes such as RNA metabolism. The liquid-like state is dynamic and reversible, containing highly diffusible molecules, whereas gel, glass, and solid phases might not be reversible due to the strong intermolecular crosslinks. Neurodegeneration-associated proteins such as the prion protein (PrP) and Tau form liquid-like condensates that transition to gel- or solid-like structures upon genetic mutations and/or persistent cellular stress. Mounting evidence suggests that progression to a less dynamic state underlies the formation of neurotoxic aggregates. Understanding the dynamics of proteins and biomolecules in condensates by measuring their movement in different timescales is indispensable to characterize their material state and assess the kinetics of LLPS. Herein, we describe protein expression in E. coli and purification of full-length mouse recombinant PrP, our in vitro experimental system. Then, we describe a systematic method to analyze the dynamics of protein condensates by X-ray photon correlation spectroscopy (XPCS). We also present fluorescence recovery after photobleaching (FRAP)-optimized protocols to characterize condensates, including in cells. Next, we detail strategies for using fluorescence microscopy to give insights into the folding state of proteins in condensates. Phase-separated systems display non-equilibrium behavior with length scales ranging from nanometers to microns and timescales from microseconds to minutes. XPCS experiments provide unique insights into biomolecular dynamics and condensate fluidity. Using the combination of the three strategies detailed herein enables robust characterization of the biophysical properties and the nature of protein phase-separated states. Key features • For FRAP in cells, we recommend using a spinning disk confocal microscope coupled with temperature and CO2 incubator. • For fluorescence microscopy, we recommend simultaneously imaging differential interference contrast (DIC) (or phase contrast) and fluorescence channels to obtain morphological details of phase-separated structures. • For XPCS, coherent X-ray beams, fast X-ray detectors in fourth and third synchrotron light sources, and X-ray free-electron lasers are required.

Multimodal Profiling of Iron Heterogeneity at the Nanoscale

Life is inherently heterogeneous, and visualizing this heterogeneity in the spatial distribution of biometals offers valuable insights into various biological processes. While biometal mapping provides superior spatial resolution compared to other bioanalytical techniques, it alone cannot fully explain the functional roles of biometals in health and disease. In this study, we introduced a novel method using specially designed sample grids to facilitate beam-, X-ray-, and ion-beam-based imaging of biometals on the same tissue section. This innovative approach aligns and integrates nanoscale-resolved iron profiles across spatial, chemical, and isotopic dimensions. By combining these analyses, we achieved unprecedented spatial resolution and detail, revealing the complex regulatory framework of iron homeostasis in liver tissues following iron overload. These findings demonstrate that enhancing both the information content and spatial resolution of biometal analysis can overcome current limitations, providing new insights into the molecular mechanisms underlying biometal functions.

Zinc ions trigger the prion protein liquid-liquid phase separation

Prion diseases are characterized by the misfolding and conversion of the monomeric prion protein (PrP) to a multimeric aggregated pathogenic form, known as PrPSc. We and others have recently shown that biomolecular condensates formed via liquid-liquid phase separation of PrP can undergo maturation to solid-like species that resemble pathological aggregates, and this process is modulated by DNA, RNA, and oxidative conditions. Conversely, the most well-studied ligand of PrP, copper ions, induce liquid-like condensates of PrP that accumulate Cu2+in vitro, and live PrPC-expressing cells show condensation at the cell surface as triggered by physiologically relevant conditions of Cu2+ and protein concentrations. Since PrP can also bind to Zn2+ through its intrinsically disordered N-terminal domain, though with different affinities and binding modes than Cu2+, we hypothesized that Zn2+ could modulate PrP phase separation differently from copper ions. Using an appropriate buffer with negligible metal ion binding, as well as relevant pH, ionic strength, molecular crowding, and Zn2+ concentrations, we show that recombinant PrP undergoes phase separation with Zn2+. Furthermore, we show that metal ion-induced condensation of PrP is dependent on the N-terminal domain (residues 23-90). In vitro Fluorescence Recovery After Photobleaching (FRAP) experiments and thioflavin T aggregation kinetics support key differences in the molecular properties of PrP:Zn2+versus PrP:Cu2+ phase separated states. FRAP analysis indicated that both Cu2+ and Zn2+ promote liquid-like PrP condensates; however, PrP:Zn2+condensates exhibit a faster recovery. Cu2+ pronouncedly inhibits seed-induced PrP misfolding, whereas Zn2+ provides a milder delay in PrP aggregation. Our findings provide insights on Zn2+-induced phase separation of PrP, supporting a variety of previously proposed functions of PrP in metal sequestering and uptake, processes that could be effectively regulated through biomolecular condensation.

BR-Bodies Facilitate Adaptive Responses and Survival During Copper Stress in Caulobacter crescentus

Microbes must rapidly adapt to environmental stresses, including toxic heavy metals like copper, by sensing and mitigating their harmful effects. Here, we demonstrate that the phase separation properties of bacterial ribonucleoprotein bodies (BR-bodies) enhance Caulobacter crescentus fitness under copper stress. To uncover the underlying mechanism, we identified two key interactions between copper and the central scaffold of BR-bodies, RNase E. First, biochemical assays and fluorescence microscopy experiments show that reductive chelation of Cu2+ leads to cysteine oxidation, driving the transition of BR-bodies into more solid-like condensates. Second, tryptophan fluorescence and EPR assays reveal that RNase E binds Cu2+ at histidine sites, creating a protective microenvironment that prevents mismetallation and preserves PNPase activity. More broadly, this example highlights how metal-condensate interactions can regulate condensate material properties and establish specialized chemical environments that safeguard enzyme function.

Mammalian copper homeostasis: physiological roles and molecular mechanisms

In the past decade, evidence for the numerous roles of copper (Cu) in mammalian physiology has grown exponentially. The discoveries of Cu involvement in cell signaling, autophagy, cell motility, differentiation, and regulated cell death (cuproptosis) have markedly extended the list of already known functions of Cu, such as a cofactor of essential metabolic enzymes, a protein structural component, and a regulator of protein trafficking. Novel and unexpected functions of Cu transporting proteins and enzymes have been identified, and new disorders of Cu homeostasis have been described. Significant progress has been made in the mechanistic studies of two classic disorders of Cu metabolism, Menkes disease and Wilson's disease, which paved the way for novel approaches to their treatment. The discovery of cuproptosis and the role of Cu in cell metastatic growth have markedly increased interest in targeting Cu homeostatic pathways to treat cancer. In this review, we summarize the established concepts in the field of mammalian Cu physiology and discuss how new discoveries of the past decade expand and modify these concepts. The roles of Cu in brain metabolism and in cell functional speciation and a recently discovered regulated cell death have attracted significant attention and are highlighted in this review.

Phase separation of microtubule-binding proteins - implications for neuronal function and disease

Protein liquid-liquid phase separation (LLPS) is driven by intrinsically disordered regions and multivalent binding domains, both of which are common features of diverse microtubule (MT) regulators. Many in vitro studies have dissected the mechanisms by which MT-binding proteins (MBPs) regulate MT nucleation, stabilization and dynamics, and investigated whether LLPS plays a role in these processes. However, more recent in vivo studies have focused on how MBP LLPS affects biological functions throughout neuronal development. Dysregulation of MBP LLPS can lead to formation of aggregates - an underlying feature in many neurodegenerative diseases - such as the tau neurofibrillary tangles present in Alzheimer's disease. In this Review, we highlight progress towards understanding the regulation of MT dynamics through the lens of phase separation of MBPs and associated cytoskeletal regulators, from both in vitro and in vivo studies. We also discuss how LLPS of MBPs regulates neuronal development and maintains homeostasis in mature neurons.

Intermolecular energy migration via homoFRET captures the modulation in the material property of phase-separated biomolecular condensates

Physical properties of biomolecular condensates formed via phase separation of proteins and nucleic acids are associated with cell physiology and disease. Condensate properties can be regulated by several cellular factors including post-translational modifications. Here, we introduce an application of intermolecular energy migration via homo-FRET (Förster resonance energy transfer), a nanometric proximity ruler, to study the modulation in short- and long-range protein-protein interactions leading to the changes in the physical properties of condensates of fluorescently-tagged FUS (Fused in Sarcoma) that is associated with the formation of cytoplasmic and nuclear membraneless organelles. We show that homoFRET captures modulations in condensate properties of FUS by RNA, ATP, and post-translational arginine methylation. We also extend the homoFRET methodology to study the in-situ formation of cytoplasmic stress granules in mammalian cells. Our studies highlight the broad applicability of homoFRET as a potent generic tool for studying intracellular phase transitions involved in function and disease.

Distinguishing Protein Corona from Nanoparticle Aggregate Formation in Complex Biological Media Using X-ray Photon Correlation Spectroscopy

In biological systems, nanoparticles interact with biomolecules, which may undergo protein corona formation that can result in noncontrolled aggregation. Therefore, comprehending the behavior and evolution of nanoparticles in the presence of biological fluids is paramount in nanomedicine. However, traditional lab-based colloid methods characterize diluted suspensions in low-complexity media, which hinders in-depth studies in complex biological environments. Here, we apply X-ray photon correlation spectroscopy (XPCS) to investigate silica nanoparticles (SiO2) in various environments, ranging from low to high complex biological media. Interestingly, SiO2 revealed Brownian motion behavior, irrespective of the complexity of the chosen media. Moreover, the SiO2 surface and media composition were tailored to underline the differences between a corona-free system from protein corona and aggregates formation. Our results highlighted XPCS potential for real-time nanoparticle analysis in biological media, surpassing the limitations of conventional techniques and offering deeper insights into colloidal behavior in complex environments.

Cuproptosis and Cu: a new paradigm in cellular death and their role in non-cancerous diseases

Cuproptosis, a newly characterized form of regulated cell death driven by copper accumulation, has emerged as a significant mechanism underlying various non-cancerous diseases. This review delves into the complex interplay between copper metabolism and the pathogenesis of conditions such as Wilson's disease (WD), neurodegenerative disorders, and cardiovascular pathologies. We examine the molecular mechanisms by which copper dysregulation induces cuproptosis, highlighting the pivotal roles of key copper transporters and enzymes. Additionally, we evaluate the therapeutic potential of copper chelation strategies, which have shown promise in experimental models by mitigating copper-induced cellular damage and restoring physiological homeostasis. Through a comprehensive synthesis of recent advancements and current knowledge, this review underscores the necessity of further research to translate these findings into clinical applications. The ultimate goal is to harness the therapeutic potential of targeting cuproptosis, thereby improving disease management and patient outcomes in non-cancerous conditions associated with copper dysregulation.

Liquid-liquid phase separation of the prion protein is regulated by the octarepeat domain independently of histidines and copper

Liquid-liquid phase separation (LLPS) of the mammalian prion protein is mainly driven by its intrinsically disordered N-terminal domain (N-PrP). However, the specific intermolecular interactions that promote LLPS remain largely unknown. Here, we used extensive mutagenesis and comparative analyses of evolutionarily distant PrP species to gain insight into the relationship between protein sequence and phase behavior. LLPS of mouse PrP is dependent on two polybasic motifs in N-PrP that are conserved in all tetrapods. A unique feature of mammalian N-PrP is the octarepeat domain with four histidines that mediate binding to copper ions. We now show that the octarepeat is critical for promoting LLPS and preventing the formation of PrP aggregates. Amphibian N-PrP, which contains the polybasic motifs but lacks a repeat domain and histidines, does not undergo LLPS and forms nondynamic protein assemblies indicative of aggregates. Insertion of the mouse octarepeat domain restored LLPS of amphibian N-PrP, supporting its essential role in regulating the phase transition of PrP. This activity of the octarepeat domain was neither dependent on the four highly conserved histidines nor on copper binding. Instead, the regularly spaced tryptophan residues were critical for regulating LLPS, presumably via cation-π interactions with the polybasic motifs. Our study reveals a novel role for the tryptophan residues in the octarepeat in controlling phase transition of PrP and indicates that the ability of mammalian PrP to undergo LLPS has evolved with the octarepeat in the intrinsically disordered domain but independently of the histidines.

Protein misfolding and amyloid nucleation through liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.