Functional Amyloids

Abstract

When protein/peptides aggregate, they usually form the amyloid state consisting of cross β-sheet structure built by repetitively stacked β-strands forming long fibrils. Amyloids are usually associated with disease including Alzheimer's. However, amyloid has many useful features. It efficiently transforms protein from the soluble to the insoluble state in an essentially two-state process, while its repetitive structure provides high stability and a robust prion-like replication mechanism. Accordingly, amyloid is used by nature in multifaceted and ingenious ways of life, ranging from bacteria and fungi to mammals. These include (1) Structure: Templating for small chemical molecules (Pmel17), biofilm formation in bacteria (curli), assisting aerial hyphae formation in streptomycetes (chaplins) or monolayer formation at a surface (hydrophobins). (2) Reservoirs: A storage state for peptide/proteins to protect them from their surroundings or vice versa (storage of peptide hormones in mammalian secretory granules or major basic protein in eosinophils). (3) Information carriers: The fungal immune system (HET-s prion in Podospora anserina, yeast prions) or long-term memory (e.g., mnemons in yeast, cytoplasmic polyadenylation element-binding protein in aplysia). Aggregation is also used to (4) "suppress" the function of the soluble protein (e.g., Cdc19 in yeast stress granules), or (5) "signaling" through formation of oligomers (e.g., HET-s prion, necroptosis-related proteins RIP1/RIP3). This review summarizes current knowledge on functional amyloids with a focus on the amyloid systems curli in bacteria, HET-s prion in P. anserina, and peptide hormone storage in mammals together with an attempt to highlight differences between functional and disease-associated amyloids.

Figure 1.

The 3D structures of amyloids. An electron micrograph of a peptide amyloid (top left). The zoom box (top right) depicts a cartoon version of the cross-β-sheet motif, with arrows indicating β-strands of individual peptides stabilized by both intermolecular hydrogen bonds and intermolecular side-chain interactions. Three 3D structures of peptide amyloids are shown below, illustrating three of the eight possible symmetry classes of steric zippers, with views both down the protofilament axis (middle row) and perpendicular to the axis (bottom row). One sheet is black and the other gray. Note that the water molecules (aqua spheres) are excluded from the tight interface between the sheets that form a dry zipper. Nitrogen atoms are colored blue, oxygen atoms red, and sulfur atoms yellow. β-Strands are shown as arrows. The structure on the left is composed of the peptide sequence QNNQQNY (protein data bank [PDB code]: 1YJP), the middle one of AIIGLM (2Y3J), and the right one of MVGGVVIA (2Y3K). (Figure created from data in Greenwald et al. 2018 and Riek and Eisenberg 2016.)

Figure 2.

Structural models of the monomeric units of CsgA and FapC in Fap and curli fibrils and a model for Fap biogenesis. The models are computed by combining inter-residue constraints (based on sequence covariation) with molecular simulations. Plot showing predicted contacts between (A) CsgA, and (B) FapC residues based on sequence data. The individual amyloid repeats of the two proteins are indicated by arrows. The darker the blue dots, the greater the coevolutionary strength. Distances calculated from the resulting coordinate file are depicted with gray spheres. The model of CsgA is based on data in Tian et al. (2015), with the model of the FapC core highlighting the three repeats and the unstructured linker regions (figure reprinted from Rouse et al. 2018 under the terms of the Creative Commons Attribution License CC BY). (C) Proposed model for how Fap fibrils are produced in Pseudomonas. All Fap components enter the periplasm via the Sec pathway. FapB (blue), FapC (red), and FapE (magenta) remain unfolded in the periplasm. The membrane protein FapF (gray) forms a stable trimer within the outer membrane (OM), although its amino-terminal coiled–coil domain extends into the periplasm. The channel is gated by plugs (violet) whose conformational changes permit substrate secretion through the OM. For clarity, only one plug is shown. FapD (green) proteolytic activity is essential for secretion. FapE may associate in different ways with the FapC/B fibrils extending from the surface. IM, Inner membrane (figure reprinted from Rouse et al. 2018 under the terms of the Creative Commons Attribution License CC BY).

Figure 3.

The amyloid activities in the secretory granule biogenesis. The amyloid state of peptide hormones in secretory granules (shown by an alignment of several clothes pins) may explain the processes of granule formation, selection, storage, and release of hormones in the granules. It is suggested that in the Golgi (shown as a blue bathing cap), the amyloid aggregation of the prohormone (shown by individually colored clothespins with a tail) is initiated spontaneously above a critical prohormone concentration or/and in presence of helper molecules such as glycosaminoglycans (GAGs). This may occur in parallel with prohormone processing (indicated by scissors) that could also initiate the aggregation. Because formation of amyloid fibrils is highly sequence-specific, amyloid aggregation of the (pro)hormone is selective. This excludes nonaggregation-prone constitutively secreted proteins and yields granule cores composed of single hormones or multiple distinct hormone coaggregates only. Because the amyloid entity is usually able to interact with membranes (shown in blue), the hormone amyloid is spontaneously coated with membranes during the aggregation process, followed by the formation of granules. Thanks to the high stability of amyloids, mature secretory granules can exist for extended periods. On stimulation, secretory granules are secreted and release monomeric, functional hormone (indicated by an extended red stick) in a controlled manner. The scissors indicate the convertases. The cytoplasm is shown as sand, the extracellular space as a bath towel. The red colored stick represents the released soluble hormone. (From Seuring et al. 2013; reprinted with permission from the authors.)

Figure 4.

Proposed mechanism for the generation of toxicity by the HET-s prion/HET-S system. (1) In the fusion cell, HET-S (in blue with a red transmembrane segment) encounters the β-solenoid structure of the HET-s prion (in brown). (2) HET-S binds to the β-solenoid structure through its own prion-forming domain (PFD) segment, itself adopting the β-solenoid structure. The structural overlap of the HeLo domain and the PFD causes a partial unfolding of the HeLo domain of HET-S, represented here by the transition to a random coil conformation of its three carboxy-terminal helices. (3) The destabilized HeLo domain of HET-S then expels its amino-terminal transmembrane segment (residues 1–34, in red). (4) The exposed transmembrane segment targets the activated HET-s/HET-S complex to the membrane where it is able to penetrate the membrane through the formation of a transmembrane helix and oligomerization. Membrane integrity is thus disrupted by hole-like structures triggering cell death. The model for the HET-s fibril was created from the PFD fibril structure (Wasmer et al. 2009) and the HeLo domain structure (Greenwald et al. 2010) with an unwinding of the last three helices of the HeLo domain (residues 177–222) to make space for the HeLo domains around the fibril. The HET-s HeLo domains are depicted as dimers between adjacent monomers in the fibril, but these are speculative and it should be emphasized that the structures of the HeLo domains of HET-s and HET-S, in the context of a fibril, are not known except that they lose tertiary structure (i.e., become more molten globule-like), and also locally lose secondary structure around residues 190–220 (Wasmer et al. 2009).

Figure 5.

3D structures of disease versus functional amyloid systems. (A) 3D structure of a fragment of provasopressin comprising vasopressin (represented in red) and neurophysin II (represented by a white ribbon including secondary structural elements; the 1jk4 Protein Data Bank (PDB) (Wu et al. 2001) shows the tight packing of the amyloid-prone vasopressin by neurophysin. Neurophysin II is a segment of provasopressin just carboxy terminal to vasopressin linked by a few amino acid residues indicated by a dashed ribbon. (B) 3D structure of HET-s(218–289) fibrils (Wasmer et al. 2009). (C) 3D structure of β-endorphin fibrils. (D) 3D structure of Aβ(1–42) fibrils (Wälti et al. 2016), (E) 3D structure of α-synuclein fibrils (Guerrero-Ferreira et al. 2018), (F) 3D structure of tau filaments (Fitzpatrick et al. 2017). Three protein layers for each fibril are shown. The top layer is shown as a bond representation, while for the two lower levels only the surface is shown. The color code for the surfaces and side chains shown are white for hydrophobic, green for polar, red for negatively charged, and blue for positively charged side chains. For HET-s(218–289) fibrils, three molecules per fibril are shown, but each molecule spans two layers. The protonated Glu8 of β-endorphin fibrils is shown in red, although it is not charged.