Essential Role of Coiled Coils for Aggregation and Activity of Q/N-Rich Prions and PolyQ Proteins

104

Huntington's disease (HD) is a neurodegenerative disease caused by an abnormal expansion in the polyglutamine (polyQ) track of the Huntingtin (HTT) protein. The severity of the disease depends on the polyQ repeat length, arising only in patients with proteins having 36 repeats or more. Previous studies have shown that the aggregation of N-terminal fragments (encoded by HTT exon 1) underlies the disease pathology in mouse models and that the HTT exon 1 gene product can self-assemble into amyloid structures. Here, we provide detailed structural mechanisms for aggregation of several protein fragments encoded by HTT exon 1 by using the associative memory, water-mediated, structure and energy model (AWSEM) to construct their free energy landscapes. We find that the addition of the N-terminal 17-residue sequence (NT 17 ) facilitates polyQ aggregation by encouraging the formation of prefibrillar oligomers, whereas adding the C-terminal polyproline sequence (P 10 ) inhibits aggregation. The combination of both terminal additions in HTT exon 1 fragment leads to a complex aggregation mechanism with a basic core that resembles that found for the aggregation of pure polyQ repeats using AWSEM. At the extrapolated physiological concentration, although the grand canonical free energy profiles are uphill for HTT exon 1 fragments having 20 or 30 glutamines, the aggregation landscape for fragments with 40 repeats has become downhill. This computational prediction agrees with the critical length found for the onset of HD and suggests potential therapies based on blocking early binding events involving the terminal additions to the polyQ repeats.Huntington's disease | aggregation | solubility | aggregation free energy landscape | critical length H untingtin (HTT) is a huge protein (3,100 amino acid residues) that has been implicated in a variety of physiological functions (1, 2). Having an expanded polyglutamine (polyQ) region of 36 or more glutamine residues in the N terminus of HTT leads to Huntington's disease as witnessed by the deposition of large intracellular protein aggregates or inclusion bodies, which are comprised primarily of N-terminal fragments coded by the exon 1 sequence of the mutant HTT (2-5). These N-terminal fragments, each composed of an N-terminal 17-residue sequence (NT17), a polyQ sequence that has expanded in length, and a proline-rich region afterward, originate from proteolysis of HTT (2, 3). The aggregation of the HTT exon 1 product is, therefore, believed to cause Huntington's disease. Clinical studies have shown an inverse correlation between polyQ length and age of disease onset (5). By implicating polymer physics in the disease process, this regularity has intrigued biophysicists for decades.Expanded polyQ sequences, more generally, are associated with nine known neurodegenerative diseases (4). Biophysical chemists have, therefore, focused on first understanding the aggregation of pure polyQ peptides. The rate of aggregation of polyQ peptides is length-dependent, and primary nucleation is rate-limiti...

Section: Discussionmentioning

confidence: 99%

Section: Aggregation Free Energy Landscapes Of Long Polyq Repeatmentioning

confidence: 99%

Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington’s disease

Chen

Wolynes

2017

104

“…When we tested the capacity of the aggregates formed by these PrD variants to seed the assembly of themselves and each other, only N→Q variants (which we identified as suppressors here) were effective in cross-seeding other sequences. Although these cross-seeded aggregates are often β-sheet-rich amyloids, Q/Nrich proteins can also form coiled coils (27). Cross-seeding by Q-rich PrDs could produce α-helical structures, especially when coaggregating with another protein that has α-helical propensity, such as polyQ-expanded Htt exon-1 (28).…”

Section: Discussionmentioning

confidence: 99%

Prion-like proteins sequester and suppress the toxicity of huntingtin exon 1

Kayatekin

Matlack

Hesse

et al. 2014

Expansions of preexisting polyglutamine (polyQ) tracts in at least nine different proteins cause devastating neurodegenerative diseases. There are many unique features to these pathologies, but there must also be unifying mechanisms underlying polyQ toxicity. Using a polyQ-expanded fragment of huntingtin exon-1 (Htt103Q), the causal protein in Huntington disease, we and others have created tractable models for investigating polyQ toxicity in yeast cells. These models recapitulate key pathological features of human diseases and provide access to an unrivalled genetic toolbox. To identify toxicity modifiers, we performed an unbiased overexpression screen of virtually every protein encoded by the yeast genome. Surprisingly, there was no overlap between our modifiers and those from a conceptually identical screen reported recently, a discrepancy we attribute to an artifact of their overexpression plasmid. The suppressors of Htt103Q toxicity recovered in our screen were strongly enriched for glutamine-and asparagine-rich prion-like proteins. Separated from the rest of the protein, the prion-like sequences of these proteins were themselves potent suppressors of polyQ-expanded huntingtin exon-1 toxicity, in both yeast and human cells. Replacing the glutamines in these sequences with asparagines abolished suppression and converted them to enhancers of toxicity. Replacing asparagines with glutamines created stronger suppressors. The suppressors (but not the enhancers) coaggregated with Htt103Q, forming large foci at the insoluble protein deposit in which proteins were highly immobile. Cells possessing foci had fewer (if any) small diffusible oligomers of Htt103Q. Until such foci were lost, cells were protected from death. We discuss the therapeutic implications of these findings.protein misfolding | prions P rotein misfolding and aggregation underlie many neurodegenerative diseases. The causes of protein misfolding are numerous and include single amino acid changes and expansions of amino acid repeats. Polyglutamine (polyQ) expansions are an infamous example of the latter and are responsible for at least nine neurodegenerative conditions, including Huntington disease (HD). In most of these diseases the polyQ-expanded protein is expressed throughout the body, but tissue damage is restricted to the nervous system and, often, to a subset of cells depending on the causal protein. Thus, there are important cell type-specific determinants of toxicity, and these are specific to particular proteins. Despite these differences, disease severity is tightly linked to the number of glutamines. Progressively earlier onset occurs as the number of glutamines increases beyond a critical threshold of ∼35-45 residues (1). Moreover, in all cases, pathology is associated with misfolded forms of the polyQ-expanded protein.Thus, common features that arise from the expansions and result from shared aspects of polyQ-driven protein misfolding must contribute to pathology. Given the diverse nature of both the proteins bearing the polyQ tract and t...

“…In the neuron, ApCPEB exists both in a soluble oligomeric form and as an insoluble fiber (13,14). The soluble oligomer form has been confirmed to be an α-helical-rich coiled-coil structure (15). Both solid-state NMR and trypsin proteolysis show that, in the insoluble fibrous form, the glutamine-rich domain constitutes the core of a fiber with β-rich structure (14).…”

mentioning

confidence: 99%

Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory

Chen

Zheng

Wolynes

2016

Aplysia cytoplasmic polyadenylation element binding (CPEB) protein, a translational regulator that recruits mRNAs and facilitates translation, has been shown to be a key component in the formation of long-term memory. Experimental data show that CPEB exists in at least a low-molecular weight coiled-coil oligomeric form and an amyloid fiber form involving the Q-rich domain (CPEB-Q). Using a coarse-grained energy landscape model, we predict the structures of the low-molecular weight oligomeric form and the dynamics of their transitions to the β-form. Up to the decamer, the oligomeric structures are predicted to be coiled coils. Free energy profiles confirm that the coiled coil is the most stable form for dimers and trimers. The structural transition from α to β is shown to be concentration dependent, with the transition barrier decreasing with increased concentration. We observe that a mechanical pulling force can facilitate the α-helix to β-sheet (α-to-β) transition by lowering the free energy barrier between the two forms. Interactome analysis of the CPEB protein suggests that its interactions with the cytoskeleton could provide the necessary mechanical force. We propose that, by exerting mechanical forces on CPEB oligomers, an active cytoskeleton can facilitate fiber formation. This mechanical catalysis makes possible a positive feedback loop that would help localize the formation of CPEB fibers to active synapse areas and mark those synapses for forming a long-term memory after the prion form is established. The functional role of the CPEB helical oligomers in this mechanism carries with it implications for targeting such species in neurodegenerative diseases.long-term memory | mechanical prion | protein aggregation | Q-rich protein I t is widely believed that learning involves the modification in number, strength, and structure of specific localized synaptic connections. Although short-term memory formation occurs without protein synthesis, establishing long-term memory (LTM) involves protein synthesis localized at the synapse area, thus requiring a stable translational regulatory system that activates mRNA and protein synthesis in the synapse (1-3). It has long been recognized that the relatively short half-life of most proteins in eukaryotic cells (4) poses questions about the long timescales over which memories can be retained. It has been suggested that forming a very stable prion could provide a mechanism for achieving memory longevity (5, 6). An excellent candidate species has emerged from the works of Kandel and coworkers (1-3) and Lindquist and coworker (6) on cytoplasmic polyadenylation element binding (CPEB). It has been established, in Aplysia, that Aplysia cytoplasmic polyadenylation element binding (ApCPEB) activates mRNA and mediates synaptic protein synthesis for at least 72 h and that it does so by taking on a functional prion-like form (3, 7). Forming the prion is, thus, a key element in LTM formation and maintenance.Prions were first proposed as protein-only infectious particles causing Creu...