De Novo Design of Peptides That Bind Specific Conformers of Α-Synuclein

Insoluble amyloids rich in cross-beta fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloids in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of alpha-synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of alpha-synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by alpha-synuclein, tau, or A beta 40. This designed peptide also markedly slowed the formation of alpha-synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.