Atomic structure and hierarchical assembly of a cross-β amyloid fibril

Abstract

The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale-including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy-we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. It is well established that a wide variety of peptides or proteins without any evident sequence similarity can self-assemble into amyloid fibrils (1, 2). These structures have many common characteristics, typically being 100-200 Å in diameter and containing a universal "cross-β" core structure composed of arrays of β-sheets running parallel to the long axis of the fibrils (3). These fibrillar states are highly ordered, with persistence lengths of the order of microns (4) and mechanical properties comparable to those of steel and dragline silk, and much greater than those typical of biological filaments such as actin and microtubules (5). Amyloid fibrils can also possess very high kinetic and thermodynamic stabilities, often exceeding those of the functional folded states of proteins (6), as well as a greater resistance to degradation by chemical or biological means (7). Several functional forms of proteins that exploit these properties have been observed in biological systems (8). More generally, however, the conversion of normally soluble functional proteins into the amyloid state is associated with many debilitating human disorders, ranging from Alzheimer's disease to type II diabetes (1, 9). Our understanding of the nature of this type of filamentous aggregate has greatly improved in recent years (3,(10)(11)(12)(13)(14)(15)(16)(17)(18)(19), particularly through the structural determination of their elementary β-strand building blocks (20) and the characterization of their assembly into cross-β steric zippers (21,22). However, a thorough understanding of the hierarchical assembly of these individual structural elements into fully-formed fibrils, which display polymorphism but possess a range of generic features (23), has so far been limited by the absence of a complete atomicresolution cross-β amyloid structures (2).We report here the simultaneous determination of the a...

On the lack of polymorphism in Aβ‐peptide aggregates derived from patient brains

“…10 The average number of water molecules around each side-chain is shown in Figure 7 for both the in vivo model and the in vitro systems with three-fold symmetry. The presence of water in the central pore 22,26 observed in our molecular dynamics simulations suggests cell membrane leakage as a possible mechanism for oligomer-mediated toxicity. 17 The possibility that oligomers of Ab could be formed outside the membrane, bind to the cell surface and then span the membrane for the formation of active channels has been proposed by Shafrir et al 31 Further computational studies of Ab aggregation with three-fold symmetry in the presence of lipid membranes may help to identify which of the amyloid peptide models are stable and remain sufficiently open for ion diffusion.…”

“…25 The hydrophobic contacts (Table IV) measured between F 19 and L 34 in each strand-loop-strand units for the two-fold in vitro models are around 10 Å , close to experimental values. 26 The side-chain contacts in the hydrophobic core of the double layer Table IV indicate that Ca-Ca distances are within the range of 9.5-10.0 Å , which is characteristic for lateral association of two b-sheet. Visual inspection of the two-fold structures indicates that the larger steric zipper interface stabilizes such contacts much better than in the three-fold fibril models characterized by small steric zipper (with Ca-Ca at interface being 19.0 Å ) and less efficient packing between U-shaped units.…”

Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses

“…Unfortunately none of these data fully explain the mechanism of TTR amyloid fibril formation. There are increasing efforts in exploiting other techniques such as NMR and neutron crystallography as alternative methods to study the assembly processes 3, 4, 5. A number of these techniques require deuteration of the protein, or some other form of isotope labeling.…”

Quantitative detection of amyloid-β peptides by mass spectrometry: state of the art and clinical applications

“…Aβ peptide aggregation is mainly triggered by conformational changes [23]. These peptides which are initially part of the APP transmembrane domain acquire after proteolytic cleavage a β-sheet structure.…”

“…Then, they aggregate in an antiparallel arrangement to form filaments. Several filaments constitute fibrils which eventually form amyloid plaques [23]. While Aβ peptides auto-aggregate, they also Graphic representation of the generation of Aβ peptide isoforms from the amyloid precursor protein (APP).…”