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Key Points Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins that may also contain structured domains mediate crucial signalling processes in eukaryotic cells. Disorder is advantageous in cell signalling because disordered sequences have the potential to bind to multiple partners, often using different structures. Disordered regions are relatively accessible, often contain multiple binding motifs and are frequently the sites for post-translational modification, an important mediator of the control of signalling pathways. Disordered proteins have central roles in the formation of higher-order signalling assemblies and in the operation of circadian clocks. Intrinsically disordered proteins (IDPs) are key components of the cellular signalling machinery. Their flexible conformation enables them to interact with different partners and to participate in the assembly of signalling complexes and membrane-less organelles; this leads to different cellular outcomes. Post-translational modification of IDPs and alternative splicing add complexity to regulatory networks. Intrinsically disordered proteins (IDPs) are important components of the cellular signalling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signalling. These proteins participate in the assembly of signalling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles. Experimental, computational and bioinformatic analyses combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread roles in biological processes.

Key Points The phenomenon of amyloid formation is associated with protein misfolding disorders, including Alzheimer's disease, Parkinson's disease and type II diabetes. The amyloid state is a 'generic state' of proteins and its study can provide great insight into the nature of functional structures and into that of disease-related assemblies. A multitude of quality control, or 'housekeeping', mechanisms exist in living organisms to prevent the conversion of normally soluble proteins into the aberrant amyloid state and to maintain protein homeostasis. The failure of these quality control mechanisms can give rise to 'protein metastasis', the uncontrolled conversion of these molecules into aberrant self-propagating assemblies that ultimately lead to a cascade of cytotoxic processes. Our increasing ability to monitor and characterize the molecular structures and formation mechanisms of the protein species that are involved in amyloid formation is suggesting novel strategies to treat or prevent protein misfolding disorders. Ultimately, the results of this field of research will result in great changes in the way we are able to manage modern lifestyles and maintain healthy ageing. Protein aggregation and amyloid deposition are associated with a wide range of medical disorders, including Alzheimer's disease and type II diabetes. Studies into the amyloid state are revealing fundamental principles that underlie the maintenance of protein homeostasis, and the origins of aberrant protein behaviour and disease. The phenomenon of protein aggregation and amyloid formation has become the subject of rapidly increasing research activities across a wide range of scientific disciplines. Such activities have been stimulated by the association of amyloid deposition with a range of debilitating medical disorders, from Alzheimer's disease to type II diabetes, many of which are major threats to human health and welfare in the modern world. It has become clear, however, that the ability to form the amyloid state is more general than previously imagined, and that its study can provide unique insights into the nature of the functional forms of peptides and proteins, as well as understanding the means by which protein homeostasis can be maintained and protein metastasis avoided.

The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.

Key Points Many neurodegenerative diseases share a common pathological hallmark: the accumulation of characteristic proteins into insoluble aggregates in vulnerable neurons and glial cells. Converging lines of evidence from cell culture studies and animal models indicate that progression of these diseases is driven by the template-directed misfolding, seeded aggregation and cell-to-cell transmission of characteristic disease-related proteins. Although such mechanisms of propagation are similar to prions, important differences to prions exists, namely the lack of inter-individual infectivity and the lack of zoonoses. Neuropathological studies in humans identified stereotypical patterns of pathology in various neurodegenerative diseases, and progression of these patterns can be correlated with increasing severity of the clinical phenotype, enabling the development of staging systems for these diseases. Human tissue pathology-staging studies are limited by the relative lack of early (prodromal) cases and by the fact that the resulting neuropathological data are, by definition, cross-sectional. Imaging biomarkers specific to the different disease proteins are necessary to validate the sequential involvement of different CNS regions proposed by human autopsy studies. Currently, the most promising markers are positron emission tomography ligands that should enable the in vivo detection and monitoring of the spread of protein pathology in longitudinal studies. Various neurodegenerative diseases are characterized by aggregates of pathological proteins, and increasing evidence suggests these disease-associated proteins may 'spread' via neuronal connections. Trojanowski and colleagues describe the molecular mechanisms of such spreading, and present the findings from neuropathological and imaging studies in humans that support this process. The progression of many neurodegenerative diseases is thought to be driven by the template-directed misfolding, seeded aggregation and cell–cell transmission of characteristic disease-related proteins, leading to the sequential dissemination of pathological protein aggregates. Recent evidence strongly suggests that the anatomical connections made by neurons — in addition to the intrinsic characteristics of neurons, such as morphology and gene expression profile — determine whether they are vulnerable to degeneration in these disorders. Notably, this common pathogenic principle opens up opportunities for pursuing novel targets for therapeutic interventions for these neurodegenerative disorders. We review recent evidence that supports the notion of neuron–neuron protein propagation, with a focus on neuropathological and positron emission tomography imaging studies in humans.

Prion diseases are fatal neurodegenerative disorders affecting several mammalian species, characterized by the accumulation of the misfolded form of the prion protein, which is followed by the induction of endoplasmic reticulum (ER) stress and the activation of the unfolded protein response (UPR). GRP78, also called BiP, is a master regulator of the UPR, reducing ER stress levels and apoptosis due to an enhancement of the cellular folding capacity. Here, we studied the role of GRP78 in prion diseases using several in vivo and in vitro approaches. Our results show that a reduction in the expression of this molecular chaperone accelerates prion pathogenesis in vivo . In addition, we observed that prion replication in cell culture was inversely related to the levels of expression of GRP78 and that both proteins interact in the cellular context. Finally, incubation of PrP Sc with recombinant GRP78 led to the dose-dependent reduction of protease-resistant PrP Sc in vitro . Our results uncover a novel role of GRP78 in reducing prion pathogenesis, suggesting that modulating its levels/activity may offer a novel opportunity for designing therapeutic approaches for these diseases. These findings may also have implications for other diseases involving the accumulation of misfolded proteins.

It is shown that the formation of amyloid-β oligomers, one of the histopathological signatures of Alzheimer’s disease, can be triggered by small quantities of a specifically truncated and post-translationally modified version of amyloid-β. Hypertoxic amyloid variants Here it is demonstrated that the formation of hypertoxic amyloid-β (Aβ) oligomers can be triggered by small quantities of a specifically truncated and post-translationally modified (pyroglutamylated) version of Aβ, called pEAβ. Previous studies have shown that pE modification of Aβ enhances its aggregation kinetics, toxicity and resistance to degradation, but a mechanistic explanation for these observations was lacking. This study shows that pEAβ causes template-induced misfolding of Aβ 1–42 into small hypertoxic structurally distinct oligomers that propagate through a prion-like mechanism. Tau expression is required for the cytotoxicity of these oligomers, and similar molecules can be isolated from the brains of people with Alzheimer's disease. Extracellular plaques of amyloid-β and intraneuronal neurofibrillary tangles made from tau are the histopathological signatures of Alzheimer’s disease. Plaques comprise amyloid-β fibrils that assemble from monomeric and oligomeric intermediates, and are prognostic indicators of Alzheimer’s disease. Despite the importance of plaques to Alzheimer’s disease, oligomers are considered to be the principal toxic forms of amyloid-β 1 , 2 . Interestingly, many adverse responses to amyloid-β, such as cytotoxicity 3 , microtubule loss 4 , impaired memory and learning 5 , and neuritic degeneration 6 , are greatly amplified by tau expression. Amino-terminally truncated, pyroglutamylated (pE) forms of amyloid-β 7 , 8 are strongly associated with Alzheimer’s disease, are more toxic than amyloid-β, residues 1–42 (Aβ 1–42 ) and Aβ 1–40 , and have been proposed as initiators of Alzheimer’s disease pathogenesis 9 , 10 . Here we report a mechanism by which pE-Aβ may trigger Alzheimer’s disease. Aβ 3(pE)–42 co-oligomerizes with excess Aβ 1–42 to form metastable low- n oligomers (LNOs) that are structurally distinct and far more cytotoxic to cultured neurons than comparable LNOs made from Aβ 1–42 alone. Tau is required for cytotoxicity, and LNOs comprising 5% Aβ 3(pE)–42 plus 95% Aβ 1–42 (5% pE-Aβ) seed new cytotoxic LNOs through multiple serial dilutions into Aβ 1–42 monomers in the absence of additional Aβ 3(pE)–42 . LNOs isolated from human Alzheimer’s disease brain contained Aβ 3(pE)–42 , and enhanced Aβ 3(pE)–42 formation in mice triggered neuron loss and gliosis at 3 months, but not in a tau-null background. We conclude that Aβ 3(pE)–42 confers tau-dependent neuronal death and causes template-induced misfolding of Aβ 1–42 into structurally distinct LNOs that propagate by a prion-like mechanism. Our results raise the possibility that Aβ 3(pE)–42 acts similarly at a primary step in Alzheimer’s disease pathogenesis.

This 96-well-plate ‘real-time quaking-induced conversion’ assay allows the detection of abnormal prion protein in human brain and CSF samples. It can be applied to study many protein misfolding diseases, as well as for drug screening and prion strain discrimination. The development and adaption of in vitro misfolded protein amplification systems has been a major innovation in the detection of abnormally folded prion protein scrapie (PrP Sc ) in human brain and cerebrospinal fluid (CSF) samples. Herein, we describe a fast and efficient protein amplification technique, real-time quaking-induced conversion (RT-QuIC), for the detection of a PrP Sc seed in human brain and CSF. In contrast to other in vitro misfolded protein amplification assays—such as protein misfolding cyclic amplification (PMCA)—which are based on sonication, the RT-QuIC technique is based on prion seed–induced misfolding and aggregation of recombinant prion protein substrate, accelerated by alternating cycles of shaking and rest in fluorescence plate readers. A single RT-QuIC assay typically analyzes up to 32 samples in triplicate, using a 96-well-plate format. From sample preparation to analysis of results, the protocol takes ∼87 h to complete. In addition to diagnostics, this technique has substantial generic analytical applications, including drug screening, prion strain discrimination, biohazard screening (e.g., to reduce transmission risk related to prion diseases) and the study of protein misfolding; in addition, it can potentially be used for the investigation of other protein misfolding diseases such as Alzheimer's and Parkinson's disease.

Amino-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. Although loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [ PSI + ], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype. While N-terminal acetylation has been shown to regulate the function or stability of a limited number of specific proteins, Holmes et al. report that global loss of this modification results in widespread protein misfolding, and show that the resulting stress response contributes to the suppression of a yeast prion phenotype.

Although Bovine Spongiform Encephalopathy (BSE) is the cause of variant Creutzfeldt Jakob disease (vCJD) in humans, the zoonotic potential of scrapie prions remains unknown. Mice genetically engineered to overexpress the human prion protein (tgHu) have emerged as highly relevant models for gauging the capacity of prions to transmit to humans. These models can propagate human prions without any apparent transmission barrier and have been used used to confirm the zoonotic ability of BSE. Here we show that a panel of sheep scrapie prions transmit to several tgHu mice models with an efficiency comparable to that of cattle BSE. The serial transmission of different scrapie isolates in these mice led to the propagation of prions that are phenotypically identical to those causing sporadic CJD (sCJD) in humans. These results demonstrate that scrapie prions have a zoonotic potential and raise new questions about the possible link between animal and human prions. Scrapie, a form of prion disease that affects sheep and goats, is believed not to be transmissible to humans. Using transgenic mice expressing human prion protein as a model of cross-species prion transmission, the authors show that ovine scrapie may possess potential to be passed on to humans.

There is an urgent need to develop disease-modifying therapies to treat neurodegenerative diseases which pose increasing challenges to global healthcare systems. Prion diseases, although rare, provide a paradigm to study neurodegenerative dementias as similar disease mechanisms involving propagation and spread of multichain assemblies of misfolded protein (“prion-like” mechanisms) are increasingly recognised in the commoner conditions such as Alzheimer’s disease. However, studies of prion disease pathogenesis in mouse models showed that prion propagation and neurotoxicity can be mechanistically uncoupled and in vitro assays confirmed that highly purified prions are indeed not directly neurotoxic. To aid development of prion disease therapeutics we have therefore developed a cell-based assay for the specific neurotoxicity seen in prion diseases rather than to simply assess inhibition of prion propagation. We applied this assay to examine an anti-prion protein mouse monoclonal antibody (ICSM18) known to potently cure prion-infected cells and to delay onset of prion disease in prion-infected mice. We demonstrate that whilst ICSM18 itself lacks inherent neurotoxicity in this assay, it potently blocks prion disease-associated neurotoxicity.