X-ray fiber diffraction experiments on Alzheimer Aβ(1–40) fibrils formed in an assembly process thought to simulate a portion of the pathophysiological process in Alzheimer's disease, indicated protofilaments with tilted β-strands rather than strands oriented perpendicular to the fibril axis as is usually interpreted from cross-β patterns. The protofilament width and tilt angle determined by these experiments were used to predict a β-strip helix model–a β-helix-like structure in which multiple identical polypeptide molecules assemble in-register to form a helical sheet structure such that the outer strands 1 and m join with a register shift t–with m = 11 and t = 22. Starting from untwisted β-sheets comprising 10, 11, and 12 strands, multiple explicit solvent molecular dynamics (MD) simulations were performed to determine whether the sheets form β-strip helices matching the dimensions of the experimentally measured protofilament. In the simulations, the predicted 11-strand sheets curled up to form a closed β-strip helix-like structure with dimensions matching experimental values, whereas the 10- and 12-strand sheets did not form a closed helical structure. The 12-strand structure did, however, show similarity to a cross-β structure determined by a solid-state NMR experiment. The 11-strand β-strip helix resembles a trans-membrane β-barrel which could explain the ability of small oligomers of Aβ(1–40) to form toxic ion channels. A further consequence of opposite sides of the 11-strand strip coming together at a register shift of 22 is end-to-end joins between neighboring β-strip helices, resulting in a protofilament that keeps growing in both directions. Communicated by Ramaswamy H. Sarma.
- molecular dynamics simulation
- shear number