General structural motifs of amyloid protofilaments

Abstract

Human CA150, a transcriptional activator, binds to and is co-deposited with huntingtin during Huntington's disease. The second WW domain of CA150 is a three-stranded β-sheet that folds in vitro in microseconds and forms amyloid fibers under physiological conditions. We found from exhaustive alanine scanning studies that fibrillation of this WW domain begins from its denatured conformations, and we identified a subset of residues critical for fibril formation. We used high-resolution magic-angle-spinning NMR studies on site-specific isotopically labeled fibrils to identify abundant long-range interactions between side chains. The distribution of critical residues identified by the alanine scanning and NMR spectroscopy, along with the electron microscopy data, revealed the protofilament repeat unit: a 26-residue nonnative β-hairpin. The structure we report has similarities to the hairpin formed by the A β (1–40) protofilament, yet also contains closely packed side-chains in a “steric zipper” arrangement found in the cross-β spine formed from small peptides from the Sup35 prion protein. Fibrillation of unrelated amyloidogenic sequences shows the common feature of zippered repeat units that act as templates for fiber elongation.

Truncated β-amyloid peptide channels provide an alternative mechanism for Alzheimer’s Disease and Down syndrome

“…Using the two available Aβ oligomer coordinate sets (27,28), we constructed annular channels based on the U-shaped β-strand-turn-β-strand motif. Previously, U-shaped motifs were also observed in the ssNMR structure of a β 2 -microglobulin fragment (29) and in the CA150 WW domain (30), and they could also form ion channels similar to prion and to β 2 -microglobulin (31,32). We constructed perfectly annular channels as the starting points for the atomistic simulations with 12 to 36 monomers per channel and lipid-favorable topology (5, 25) (SI Materials and Methods).…”

“…Early MD simulations of amyloidogenic peptides (5,25) consisting of U-shaped β-strandturn-β-strand peptides in the bilayer predicted ion-permeable channels formed by loosely attached mobile subunits with morphologies and dimensions similar to the AFM-images of amyloid channels (7,8). U-shaped motifs, first predicted by modeling of Aβ [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] (26), appear as a general feature of amyloid organization, suggesting that other U-shaped amyloid organizations may also form dynamic ion channels in the fluidic membrane (8). Because N9 and p3 have membrane-spanning segments, we modeled their 3D structures in the bilayer using the previous successful protocol (5,25).…”

Quantitative approaches to defining normal and aberrant protein homeostasis

“…69 In addition to information about the structure of the amyloid fibrils formed by an 11-residue fragment of human transthyretin, these approaches have provided great insight into the structures of amyloid fibrils formed by several other peptides and proteins, including Het-S and Ab. [70][71][72] Together with the strategy mentioned above, nanoscience techniques are also emerging as powerful tools that can provide insight into the factors that stabilise amyloid fibrils. 30,42,44 In an initial study, by using atomic force microscopy (AFM) imaging we described the changes in the distribution of inter-versus intra-molecular bonding interactions associated with the transition of proteins from their native globular structures into ordered supramolecular assemblies.…”

Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid-State NMR

“…From the standpoint of molecular structure, the defining feature of an amyloid fibril is the presence of cross-β supramolecular structure, meaning that the β-sheets within the fibril are formed by β-strand segments that run approximately perpendicular to the long axis of the fibril and are linked by hydrogen bonds that run approximately parallel to this axis (11)(12)(13). Although determination of the molecular structures of amyloid fibrils is made difficult by their inherent noncrystallinity and insolubility, techniques such as solid state nuclear magnetic resonance (NMR) (12,(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33), electron paramagnetic resonance (EPR) (34)(35)(36), electron microscopy (37)(38)(39)(40)(41)(42)(43), hydrogen/deuterium exchange (29,(44)(45)(46)(47), scanning mutagenesis (48), chemical crosslinking (27,49,50), and x-ray diffraction of amyloid-like crystals …”