The dual nature of amyloids: From pathogenic aggregates to functional biostructures

Protein aggregation is a process in which proteins misfold and accumulate into insoluble clumps. This phenomenon is at the root of over 50 human pathologies including neurodegenerative disorders as well as certain types of diabetes and cancer. When proteins aggregate, they often form amyloids—highly ordered structures characterized by layers of proteins aligned in a distinctive cross-β-sheet pattern. These amyloid fibrils are extremely stable and resistant to mechanical, chemical, and enzymatic degradation, making them difficult for the body to clear and contributing to pathology.

Historically, amyloids were exclusively linked to pathological conditions, given their association with tissue damage and cell death. However, this view has been fundamentally revised with the discovery of functional amyloids, which play beneficial roles in various organisms. These functional amyloids are deliberately formed and have been shown to participate in critical processes, such as controlled hormone storage and release, memory stabilization, and protection against environmental stressors like UV light and microbial infection. Their existence, however, raises questions on the basic biology underlying amyloid pathology. What traits differentiate toxic from functional amyloids? How do biological systems cope and minimize the harmful side effects of amyloid formation?

In this article, we review recent advances in understanding amyloid toxicity and illustrate diverse molecular mechanisms organisms use to control amyloid formation, turning a potentially harmful process into a tool for advantageous functions.

Amyloids were first described in 1854 by Rudolf Virchow, a German scientist who coined the term “amyloid” because he mistakenly thought the deposits observed in pathological tissues resembled starch (amylose). Today, we understand that amyloids are protein aggregates, and their formation is a hallmark of several neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease, and amyotrophic lateral sclerosis. These aggregates exhibit a highly ordered, fibrillar structure that can be specifically detected using amyloid-binding dyes Congo red and Thioflavin-T and appear as regular, helicoidal structures under transmission electron microscopy .

A critical aspect of amyloid research is understanding how uncontrolled aggregation leads to cellular toxicity. When proteins fail to fold into their native 3D shapes, they expose regions rich in hydrophobic residues, which can engage in aberrant interactions with other proteins or cellular structures, leading to aggregation. Misfolded proteins tend to aggregate with copies of themselves, initially forming low-copy complexes that gradually progress into larger, ordered oligomers and eventually deposit as insoluble amyloid fibers. Although mature fibrils are often the most visible hallmark of amyloid diseases, the intermediate oligomeric species are primarily responsible for neurotoxicity.

In AD, one of the defining pathological features is the presence of amyloid plaques formed by aggregated amyloid-beta (Aβ) peptides. Aβ is generated from the cleavage of the amyloid precursor protein (APP), a transmembrane protein normally present in the brain. Cells recycle APP through various pathways, one of which produces Aβ peptides consisting of 42 amino acid residues. These Aβ42 peptides aggregate into toxic species, forming plaques that disrupt neuronal communication, trigger inflammation, and ultimately result in neuronal death. The uncontrolled aggregation of α-synuclein into amyloid deposits causes neuronal degeneration leading to PD. In healthy neurons, α-synuclein remains soluble and regulates vesicle trafficking, fatty acid binding, and neuronal survival. However, in PD, α-synuclein misfolds and aggregates into amyloid-like structures known as Lewy bodies and Lewy neurites. These intranuronal deposits interfere with essential cellular functions, contributing to the progressive loss of neurons and the characteristic motor symptoms of the disease.

Beyond AD and PD, several other amyloid-forming proteins are implicated in neurodegeneration. Recent advances in cryo-electron microscopy (cryo-EM) have revealed the structural diversity of amyloid fibrils, demonstrating not only that different proteins can form a wide array of fibrillar architectures but also that a single protein can generate distinct polymorphs. These polymorphs are linked to diverse disease manifestations and severity, highlighting the complexity of uncontrolled amyloid aggregation in pathologies.

Only a small subset of proteins in living organisms form harmful deposits. Evolution has exerted strong selective pressure against protein aggregation, safeguarding cells from the detrimental effects of misfolded proteins. In most proteins, evolution has favored folding into stable, tightly packed conformations known as native structures, that generally display polar surfaces and thus, a low propensity for aggregation. In contrast, intrinsically disordered proteins lack a stable 3D structure, have evolved distinct features, such as higher net charges and reduced hydrophobicity, making them less likely to aggregate into toxic species.

Cells also tightly regulate gene expression levels to maintain proteins at safe concentrations. Proteins at higher risk of aggregation are generally maintained at lower numbers to minimize the chances of misfolding and deposition. Beyond these intrinsic defenses, cells are equipped with robust quality control systems that actively manage polypeptides that fail to fold correctly.

Chaperones act as specialized assistants in the cell, aiding in the proper folding of newly synthesized proteins and refolding misfolded ones. Chaperones like Hsp70 and Hsp90 bind to exposed hydrophobic regions allowing proteins another opportunity to achieve their correct native conformation. The proteasome is a large multiprotein complex that serves as a cellular recycling center, where damaged, misfolded, or unnecessary proteins are broken down into their constituent amino acids, which can be recycled for new protein synthesis.

For larger protein aggregates and dysfunctional components, cells rely on autophagy, a degradation pathway that clears out bulky cellular debris, including entire organelles like mitochondria. In autophagy, cellular components are sequestered into a membrane-bound vesicle where acidic pH, proteases, and other lysosomal enzymes degrade biomolecules into their monomers.

Together, these three mechanisms form a comprehensive protein quality control network that safeguards cellular health by preventing the buildup of toxic protein aggregates.

Remarkably, the potential toxicity of amyloid fibrils has not deterred evolution from co-opting their unique material properties for beneficial purposes.

While toxic amyloids result from undesired and uncontrolled protein misfolding, functional amyloids are intentionally formed by organisms to carry out specialized tasks that extend beyond the capabilities of individual proteins. A well-studied example of functional amyloids is found in the silk-producing glands of spiders, where silk proteins are stored in an amyloid-like state. These proteins undergo a controlled process of fibril formation to produce silk fibers, which are exceptionally strong, flexible, and resistant to environmental stress. Functional amyloids like these have evolved to perform specialized tasks, leveraging the stability, self-assembly nature, and mechanical resilience conferred by the amyloid fold.

Despite their advantages, their production requires precise cellular regulation of protein synthesis, concentration, and localization to minimize casing harm. Unlike the structural variability seen in pathogenic amyloids, functional amyloids generally adopt a single, well-defined fibrillar conformation. This structure is often reversible and features fewer exposed hydrophobic surfaces, which reduces the risk of unwanted interactions with other biomolecules, membrane destabilization, and the sequestration of molecular chaperones into futile cycles.

Below, we highlight various examples of functional amyloids focusing on the cellular and molecular strategies organisms use to precisely regulate them and mitigate the potential risks associated with their formation.

Yeasts synthesize the amyloid-forming protein Sup35p, which plays a key role in gene regulation at the post-transcriptional level. When in its soluble form, Sup35p ensures proper termination of protein synthesis. In its aggregated amyloid state, however, Sup35p allows ribosomes to read-through stop codons on messenger RNAs, producing elongated proteins that can provide selective advantages under certain conditions, such as growth in environments with limited adenine, enhancing the adaptability of the yeast population.

Several bacteria including Escherichia coli, Salmonella, and Pseudomonas, produce extracellular amyloid fibers known as curli. These fibers, which were identified in the 1980s by researchers studying bacterial communities, aid in surface attachment and biofilm formation. Biofilms serve as a protective shield, enhancing bacterial survival, and posing significant challenges in clinical settings. Biofilms can form on implanted medical devices—such as artificial heart valves, catheters, stents, and joint prostheses—complicating treatment and potentially seeding persistent infections. The production of curli is highly regulated in these organisms (Figure 1). The major amyloid-forming component, CsgA, is synthesized alongside specialized chaperones and a channel protein, which keeps CsgA in a soluble state until it reaches the extracellular milieu. Once secreted, a dedicated nucleator protein initiates the amyloid formation of CsgA, ensuring that amyloid formation only occurs outside the cell.

In plants, the seed storage protein vicilin in garden peas undergoes amyloid aggregation. Vicilin self-assembles into amyloid fibrils that enhance the seed’s resistance to desiccation and provide anti-fungal protection. To minimize potential toxicity, vicilin amyloids are sequestered within specialized membrane-bound compartments in the seeds. Upon germination, these amyloid structures quickly disassemble, releasing amino acids that supply vital building blocks for the growing seedling.

In silk moths, amyloid fibrils constitute the primary structural component of eggshells, providing the developing oocyte and embryo with both mechanical and environmental resistance. The silk moth’s eggshell proteins initially exist in a liquid crystalline phase, separated from other cellular components, and gradually transition into stable amyloid fibers occur as the eggshell matures, providing a robust barrier while still allowing essential gas exchange for respiration.

These examples illustrate how amyloid structures have been adapted for durability while preserving the organism’s physiological functions.

Functional amyloids are integral to the process of melanin production, the pigment responsible for the coloration of our skin, hair, and eyes. A key player in this process is the protein Pmel17, which undergoes several post-translational modifications (PTMs) in the endoplasmic reticulum. The mature protein assembles into amyloid fibrils within specialized acidic organelles called melanosomes, serving as scaffolds for the efficient deposition of melanin.

The acidic environment within melanosomes permits a fast Pmel17 fibrillization. In contrast, the protein does not assemble at physiological pH, preventing the accidental formation of toxic amyloids before reaching this compartment. The entire process is tightly regulated, involving precise control over Pmel17 trafficking, sorting, and proteolytic processing. Additionally, the aggregation kinetics of Pmel17 are significantly faster than pathological amyloids, allowing for rapid scaffold formation while minimizing the risk of accumulating intermediate, toxic oligomers. The precise spatial and temporal control prevents Pmel17 aggregation and exemplifies how functional amyloids can be harnessed safely for essential physiological roles.

In mammals, functional amyloids play a critical role in the storage and regulated release of peptide hormones, including growth hormone, oxytocin, prolactin, and vasopressin. These peptide hormones are stored in high concentrations within membrane-enclosed secretory granules, where they form reversible amyloid-like structures, providing a stable reservoir for efficient release when needed.

A prototypical example is the storage of insulin in the pancreatic β cells. Once synthesized and processed, mature insulin is packed into amyloid-like aggregates within secretory granules. These ordered structures allow for safe insulin storage at high concentrations while preventing its premature release and degradation. Similar to the process observed in melanin formation, insulin amyloid aggregation is facilitated by the acidic environment within the secretory granules. Recent cryo-EM studies have elucidated the structure of these insulin amyloids, revealing two tightly packed protofilaments with a characteristic β-sheet conformation.

When blood glucose levels rise, pancreatic β cells receive a signal to release insulin into the bloodstream. The shift to a neutral pH environment causes the amyloid fibrils to rapidly disassemble, releasing insulin molecules in their functional, monomeric form and regulating glucose uptake throughout the body. This reversible amyloid-based storage provides a highly efficient mechanism to maintain a large reservoir of hormones for extended periods, ensuring their rapid availability in quantities that far exceed the rate of new synthesis.

Long-term memory formation and consolidation in animals rely on the controlled aggregation of CPEB proteins (known as Orb2 in fruit flies) into amyloid-like deposits. This process is highly regulated at the cellular level and requires repeated activation by neurotransmitters released from neighboring neurons. The formation of CPEB/Orb2 amyloids is orchestrated through multiple layers of control, including the expression levels of different protein isoforms. An increase in the expression of the most aggregation-prone variant induces the controlled aggregation of the entire CPEB/Orb2 pool, stabilizing synaptic changes necessary for memory storage.

PTMs, such as phosphorylation, dephosphorylation, and sumoylation, provide an extra layer of regulation that fine-tunes the aggregation process to prevent the buildup of potentially toxic intermediates. In fruit flies, the transition of Orb2 from its monomeric to amyloid-like state can occur within minutes, minimizing the risk of forming harmful oligomers and ensuring that the aggregation process contributes effectively to memory consolidation.

Recently, the atomic structure of polymeric Orb2 was unveiled using cryo-EM, revealing an elegant triangular cross-section in the core of the amyloid. This core is built from three identical protofilaments, each containing a high proportion of polar glutamine residues, contributing to the amyloid structure’s overall stability and functionality. The reliance on polar residues and hydrogen bonding for structural stabilization is a common strategy observed in other functional amyloid assemblies. In contrast, pathological amyloids are often glued by hydrophobic amino acids, resulting in sticky surfaces that establish promiscuous interactions with cellular components that contribute to their toxicity.

Although amyloids are frequently associated with neuronal damage in neurodegenerative diseases, neurons themselves utilize controlled amyloid formation of CPEB/Orb2 to support memory processes. This dual nature of amyloids—as both potential agents of toxicity and essential components of normal physiology—highlights the complex interplay between the beneficial and pathological aspects of amyloid aggregation.

Proteins are incredibly versatile molecules, capable of carrying out diverse tasks and responding to ever-changing conditions. Properly functioning proteins are the foundation of life, but devastating illnesses can occur when their structure or function is compromised. The ongoing research into amyloid formation has uncovered not only the mechanisms underlying these diseases but also the widespread occurrence and functional roles of amyloids across different species. This has propelled the intriguing proposal that early life could have started by functional amyloids capable of self-replicating, performing enzymatic reactions, transmitting information, and withstand extreme environmental conditions.

The use of amyloids, however, comes with an inherent risk of cytotoxicity, requiring sophisticated mechanisms to minimize potential damage. Amyloid-induced toxicity has shaped the evolution of protein sequences, folding and aggregation pathways, but also important control strategies such as the enclosure of aggregates within membrane-separated compartments and the need for specific signals (such as protein modification, changes in environmental conditions, or the presence of aggregation accelerators).

In this scenario, understanding the controlled fibrillation of functional amyloids allows the creation of innovative, biodegradable, and sustainable amyloid-based materials, set to offer new tools that could make significant advances in medicine, nanotechnology, biotechnology, cell biology, and other industries. By leveraging the unique properties of functional amyloids, we are on the cusp of unlocking novel applications that could redefine our approach to materials science and therapeutic design.

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Valentín Iglesias is an associate professor and researcher at the Clinical Research Center from the Medical University of Białystok in Poland. He developed his PhD at the Department of Biochemistry and Molecular Biology and the Institute of Biotechnology and Biomedicine at the Autonomous University of Barcelona (UAB, Spain) under the supervision of Prof. Salvador Ventura. Valentín was awarded a Margarita Salas postdoctoral fellowship in a joint project between Xavier Fernàndez-Busquets’ laboratory in the Institute for Bioengineering of Catalonia (IBEC, Spain) and the Barcelona Institute for Global Health (ISGlobal, Spain) and Salvador Ventura’s lab at IBB-UAB. In 2024 Valentín moved to Michał Burdukiewicz’s laboratory at the Medical University of Białystok after he was awarded the Ulam grant from the Polish National Agency for Academic Exchange (NAWA) to focus on the molecular mechanisms promoting heterotypic amyloid formation. Email: [email protected].

Javier Garcia-Pardo is an associate professor and researcher at the Department of Biochemistry and Molecular Biology and the Institute of Biotechnology and Biomedicine (IBB-UAB, Spain). He earned his PhD from the Autonomous University of Barcelona under the supervision of Prof. FX Avilés at IBB-UAB. Following his PhD, he visited Sir Tom Blundell's lab at the University of Cambridge (UK), where he developed extensive expertise in structural biology techniques. A major achievement during this period was his discovery of a key mechanism regulating the substrate specificity of carboxypeptidase O, a novel digestive enzyme with a unique affinity for acidic residues. This groundbreaking discovery was made possible through collaborations with Prof. Robert Huber at the Max Planck Institute in Germany and Prof. David Reverter at IBB-UAB. In 2018, Javier moved to Frankfurt am Main to join Prof. Ivan Dikic's group at the Buchmann Institute for Molecular Life Sciences (BMLS, Germany) as a senior scientist. During his time in Frankfurt, his research focused on identifying novel compounds targeting the NF-kB pathway and providing structural insights into reticulons, a group of conserved ER-resident proteins involved in membrane curvature. More recently, Javier has returned to IBB-UAB, where he has centered his research on understanding the structure and mechanism of pathological and functional amyloid fibrils using cryo-EM, as well as exploring their applications in nanotechnology. Email: [email protected].

Salvador Ventura is Professor of Biochemistry and Molecular Biology at the Autonomous University of Barcelona (UAB) and the Director of the Institute for Research and Innovation Parc Taulí (I3PT-CERCA). He has received numerous prestigious awards, including the Bruker 'Manuel Rico' Prize, three ICREA Academia awards, and the Narcís Monturiol Medal. Salvador is also a member of the Academia Europaea. As a senior researcher at the Institute of Biotechnology and Biomedicine (IBB) of UAB, where he previously served as Director, he has authored over 300 scientific publications and holds 18 patents. His research focuses on the relationship between protein misfolding and degenerative diseases, with the aim develop novel therapeutic molecules. Email: [email protected].