Thermodynamics of Huntingtin Aggregation

Phan, Tam Thi Minh; Schmit, Jeremy D.

doi:10.1016/j.bpj.2020.05.013

Cited by 17 publications

(13 citation statements)

References 36 publications

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“…In our model, and consistent with early proposals by Wetzel and colleagues (Kar et al, 2011), the termini of the hairpin fold back toward the beta turn. Unlike other models for the polyQ nucleus (Chen and Wolynes, 2017; Chen et al, 2016; Miettinen et al, 2014; T. T. M. Phan and Schmit, 2020), the AHA monomer contains an embryo of exquisitely ordered Q zipper structure necessary for the entropic bottleneck. We note that the AHA conformer is one of a small number of configurations for a minimal tertiary motif known as a beta-arcade, which was previously proposed to serve as an amyloid nucleus based on its favorable energetics and characteristic occurrence in amyloid fibrils (Kajava et al, 2010).…”

Section: Discussionmentioning

confidence: 97%

The polyglutamine amyloid nucleus in living cells is a monomer with competing dimensions of order

Kandola

Zhang

Venkatesan

et al. 2021

Preprint

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A long-standing goal of the study of amyloids has been to characterize the physical nature of the rate-determining nucleating event. However, the transience and rarity of that event within the heterogeneous ensemble of states populated by amyloid-forming proteins make it inaccessible to classical biochemistry, structural biology, and computational approaches. Here, we address these limitations by measuring the dependence of amyloid formation on concentration and conformational templates in living cells, whose volumes are sufficiently small to resolve independent nucleation events. We characterized over one hundred rationally designed sequence variants of polyglutamine (polyQ), a polypeptide that precipitates Huntingtons and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. We deduce that amyloid formation by polyQ begins with a steric zipper embryo of approximately twelve interdigitated glutamine side chains within an individual polypeptide molecule. Formation of the embryo was limited to polypeptides longer than the pathogenic threshold, and involved neither phase separation nor oligomerization. We found that different amyloid propensities of polyQ sequence variants can be rationalized by steric zipper ordering orthogonally to the axis of polymerization, and validated this intuition using all-atom molecular dynamics simulations. The unique ability of the polyQ sequence to fold in this fashion not only allowed for polyQ amyloid to nucleate from low concentrations; it also stalled amyloid growth with a concomitant accumulation of partially-ordered oligomers. By illuminating the structural mechanism of polyQ amyloid formation in cells, our findings reveal a potential molecular etiology for polyQ diseases, and may provide a roadmap for the design of new therapies.

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Section: Discussionmentioning

confidence: 97%

The polyglutamine amyloid nucleus in living cells is a monomer with competing dimensions of order

Kandola

Zhang

Venkatesan

et al. 2021

Preprint

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“…Prolines from the C-terminal domain cannot adopt the extended β-sheet conformation. The large positively charged side chain of lysine from the N-terminal domain (ATLEKLMKAFESLKSF) also limits out-of-register shifts due to the large free-energy penalty of charge desolvation 26,45 .…”

Section: Discussionmentioning

confidence: 99%

The structural basis of huntingtin (Htt) fibril polymorphism, revealed by cryo-EM of exon 1 Htt fibrils

Nazarov

Chiki

Boudeffa

et al. 2021

Preprint

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The lack of detailed insight into the structure of aggregates formed by the huntingtin protein has hampered efforts to develop therapeutics and diagnostics targeting pathology formation in the brain of patients with Huntington's disease. To address this knowledge gap, we investigated the structural properties of in vitro generated fibrils from exon1 of the huntingtin protein by electron cryo-microscopy and single- particle analysis. We show that wildtype and mutant exon1 of the huntingtin protein form non-helical fibrils with a polygultamine amyloid core composed of β-hairpins with unique characteristics that have not been previously observed with other amyloid filaments. The stacks of β-hairpins form long planar β- sheets (protofilaments) with variable stacking angle and occasional out-of-register state of individual β-hairpins. These features and the propensity of protofilament to undergo lateral association results in a high degree of fibril polymorphism, including fibrils composed of varying numbers of protofilaments. Our results also represent the first direct observation of how the flanking domains are organized around the polyglutamine core of the fibril and provide insight into how they might affect huntingtin fibril structure, polymorphism, and stacking of β-hairpins within its core structure. Removal of the first 17 amino acids at the N-terminus resulted in surprising intra-fibril structural heterogeneity and reduced fibril's propensity to lateral associations. Overall, this work provides valuable insights that could guide future mechanistic studies to elucidate the sequence and structural determinants of huntingtin aggregation, as well as cryo- EM and structural studies of fibrils derived from huntingtin proteins and other disease-associated polyglutamine-containing proteins.

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“…1). The registry variable can take positive or negative values − L +1 ≤ R ≤ L −1, where L is the number of base pairs in a strand and R = 0 indicates the in-register (native) alignment 45,46 . Each registry has a binding lifetime t reg ( R ) in which the molecules search for in-register base pairs.…”

Section: Methodsmentioning

confidence: 99%

“…The registry variable can take positive or negative values −L+1 ≤ R ≤ L−1, where L is the number of base pairs in a strand and R = 0 indicates the in-register (native) alignment 45,46 .…”

Section: Registry Stagementioning

confidence: 99%

Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization

Phan

Schmit

2022

Preprint

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DNA strands have to sample numerous states to find the alignment that maximizes Watson-Crick-Franklin base pairing. This process depends strongly on sequence, which affects the stability of the native duplex as well as the prevalence of non-native inter- and intra-molecular helices. We present a theory which describes DNA hybridization as a three stage process: diffusion, registry search, and zipping. We find that non-specific binding affects each of these stages in different ways. Mis-registered intermolecular binding in the registry search stage helps DNA strands sample different alignments and accelerates the hybridization rate. Non-native intramolecular structure affects all three stages by rendering portions of the molecule inert to intermolecular association, limiting mis-registered alignments to be sampled, and impeding the zipping process. Once in register base-pairs are formed, the stability of the native structure is important to hold the molecules together long enough for non-native contacts to break.

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Thermodynamics of Huntingtin Aggregation

Cited by 17 publications

References 36 publications

The polyglutamine amyloid nucleus in living cells is a monomer with competing dimensions of order

The polyglutamine amyloid nucleus in living cells is a monomer with competing dimensions of order

The structural basis of huntingtin (Htt) fibril polymorphism, revealed by cryo-EM of exon 1 Htt fibrils

Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization

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