Amyloid structure: conformational diversity and consequences

Abstract

Many, perhaps most, proteins, are capable of forming self-propagating, β-sheet (amyloid) aggregates. Amyloid-like aggregates are found in a wide range of diseases and underlie prion-based inheritance. Despite intense interest in amyloids, structural details have only recently begun to be revealed as advances in biophysical approaches, such as hydrogen-deuterium exchange, X-ray crystallography, solid-state nuclear magnetic resonance (SSNMR), and cryoelectron microscopy (cryoEM), have enabled high-resolution insights into their molecular organization. Initial studies found that despite the highly divergent primary structure of different amyloid-forming proteins, amyloids from different sources share many structural similarities. With higher-resolution information, however, it has become clear that, on the molecular level, amyloids comprise a wide diversity of structures. Particularly surprising has been the finding that identical polypeptides can fold into multiple, distinct amyloid conformations and that this structural diversity can lead to distinct heritable prion states or strains.

Figure 1

Classification of different amyloid folds and techniques to distinguish between them. (a) Amyloid β-sheet structures have largely fallen into three broad categories, all of which can be distinguished from each other by the introduction of a single probe (red rectangle) in identical positions for every monomer and by measuring the distance between probes. In one antiparallel arrangement (left), the probe alternates positions in the fiber structure, resulting in a distance between probes greater than 4.7 Å. In the parallel in-register sheet, the probes are directly adjacent to each other, with a probe distance of ~4.7 Å. In a β-solenoid in which a single monomer forms two layers of the fiber structure, the distance between probes is ~9.4 Å. (b) In systems in which two probes have been introduced (yellow and red rectangles), intramolecular distances can be distinguished from intermolecular distances by diluting labeled protein with unlabeled protein. Dilution increases intermolecular distances while preserving intramolecular distances (right). (c) Types of β-solenoids are depicted schematically. A β-solenoid is a structure in which a monomer loops around in a coil-like manner and forms multiple layers of the fiber structure. Two types of β-solenoid include the β-helix (top), where three β-sheets form a triangular interface, and the β-roll, where two sheets form an interface akin to the β-sandwich.

Figure 2

(a–c) Model structure of the Het-s prion fiber [Protein Data Bank (PDB): 2RNM]. (a) A single Het-s monomer is shown in the fiber conformation down the fiber axis. Here, the eight β-strands and the β-helix structure are clearly seen. β1a/β 3a, β1b/β3b, and β2a/β4a for the three β-sheets, respectively, with β2b/β4b lying outside the helix structure. (b) Similar view of the Het-s fiber structure with specific acidic side chains (red) and basic side chains (blue) shown to illustrate the salt bridges that form in the fiber structure. (c) The full fiber structure from a view perpendicular to the fiber axis. A single monomer is highlighted in dark gray. (d–f) Model structure of Aβ1-42 (PDB: 2BEG). (d) A single Aβ1–42 monomer in the fiber conformation is shown down the fiber axis. The N-terminal β-strand and the C-terminal β-strand are labeled β1 and β2, respectively. (e) A view of Aβ1-42 fiber structure from the side, perpendicular to the fiber axis. A single Aβ1-42 monomer is shown in red, with the neighboring monomer in gray. This illustrates how the side chains from one unit in this structure (Aβ 3, strand β2) form an interface with the neighboring molecule (Aβ 4, strand β1). (f) Full structure of Aβ1-42 viewed perpendicular to the fiber axis. A single monomer is displayed in red, with the others in gray.

Figure 3

(a–c) X-ray structure of the peptide GNNQQNY. (a) A view of the peptide structure down the fiber axis. Visible is the interdigitation of side chains from opposing sheets forming a dry interface devoid of water. (b) The peptide structure viewed from the side, perpendicular to the fiber axis. Visible is the interdigitation of one set of side chains between side chains of opposed peptides above and below. Hydrogen bonds (yellow) that form between asparagine side chains are shown, forming the asparagine ladder structure. (c) Peptide structure viewed face on, perpendicular to the fiber axis. (d–e) Different orientations of the peptide structures. (d) A schematic of some of the possible peptide structures. Peptide structures can differ in three main criteria: parallel versus antiparallel β-sheets, sheets that are face-to-face versus face-to-back, and sheets that are ipsidirectional versus contradirectional. Only parallel arrangements are displayed, where the individual β-strands within a sheet are all oriented in the same direction. Face-to-face versus face-to-back depends on the face of the sheets that forms the interface between the sheets. If this interface is formed by identical faces, it is classified as face-to-face, whereas if the interface is formed by opposite faces, it is classified as face-to-back. The different faces in the schematic are represented by a letter and color (face 1 is labeled a and gray, and face 2 is b and red). Ipsi- versus contradirectional is distinguished by the direction of a particular reference hydrogen bond within a sheet. If the direction of this hydrogen bond is the same for both opposing sheets, it is classified as ipsidirectional, whereas if the hydrogen bond is in opposing directions, it is classified as contradirectional. The direction of each sheet is illustrated by the orientation of the letter of each strand (correct side up versus upside down). (e) The NNQQ peptide in two different conformations, with the corresponding schematic to illustrate the orientations. On the left is NNQQ in a parallel, face-to-face ipsidirectional orientation. On the right is NNQQ peptide in a parallel, face-to-back contradirectional orientation.

Figure 4

(a–b) Demonstration of the conformational differences between the yeast prion, strong and weak, derived from the fibers Sc4 and Sc37, respectively. (a) HXNMR data after 1 min of exchange for SupNM residues 4–150 in the Sc4 (blue) and Sc37 (red) conformations. (b) Mutation analysis of Sc4 and Sc37 conformations. Indicated mutants on the horizontal axis were made, and their ability to form the Sc4 (blue) and Sc37 (red) conformations evaluated. The larger the defect in forming these conformations, the higher the value on the y-axis. (c) Conformational diversity of Aβ fibers. Shown are the cross-sectional views of several models of Aβ fiber structures based on SSNMR (left: 108, 109) and cryoEM (middle: 51, right: 49) Light gray areas approximate the electron density observed in the cryoEM structures.