De novo amyloid proteins from designed combinatorial libraries

Amyloid deposits are associated with several neurodegenerative diseases, in cluding Alzheimer's disease and the prion diseases. The amyloid fibrils iso lated from these different diseases share similar structural features. Howe ver, the protein sequences that assemble into these fibrils differ substant ially from one disease to another. To probe the relationship between amino acid sequence and the propensity to form amyloid, we studied a combinatoria l library of sequences designed de novo. All sequences in the library were designed to share an identical pattern of alternating polar and nonpolar re sidues, but the precise identities of these side chains were not constraine d and were varied combinatorially. The resulting proteins self-assemble int o large oligomers visible by electron microscopy as amyloid-like fibrils. L ike natural amyloid, the de novo fibrils are composed of beta-sheet seconda ry structure and bind the diagnostic dye, Congo red. Thus, binary patternin g of polar and nonpolar residues arranged in alternating periodicity can di rect protein sequences to form fibrils resembling amyloid. The model amyloi d fibrils assemble and disassemble reversibly, providing a tractable system for both basic studies into the mechanisms of fibril assembly and the deve lopment of molecular therapies that interfere with this assembly.