Fig. 1: Overview of the procedure for designing modular peptide binders.

a, Like all repeating structures, repeat proteins and peptides form superhelices with constant axial displacement (ΔZ) and angular twist (ω) between adjacent repeat units (shown in green and yellow). For in-register binding, the protein and peptide parameters must match (for some integral multiple of repeat units). b, Construction of hash tables for privileged residue–residue interactions. Top row: classes of side-chain–backbone interactions for which hash tables were built. The side-chain amide group of asparagine or glutamine forms bidentate interactions with the N–H and C=O groups on the backbone of a single residue (left) or consecutive residues (middle), or with the backbone N–H group and side-chain oxygen atom of a serine or threonine residue (right). Second row: as illustrated for the case of the glutamine–backbone bidentate interaction, to build the hash table we perform Monte Carlo sampling over the rigid-body orientation between the terminal amide group and the backbone, and the backbone torsions φ and ψ, saving configurations with low-energy bidentate hydrogen bonds. For each configuration, the possible placements for the backbone of the glutamine are enumerated by growing side-chain rotamers back from the terminal amide. Third row: from the six rigid-body degrees of freedom relating the backbones of the two residues, together with the two φ and ψ torsion angle degrees of freedom, a hash key is calculated using an eight-dimensional hashing scheme. The hash key is then added to the hash table with the side-chain name and torsions as the value. CA, α-carbon; OG, γ-oxygen. c, To dock repeat proteins and repeat peptides with compatible superhelical parameters, their superhelical axes are first aligned, and the repeat peptide is then rotated around and slid along this axis. For each of these docks, for each pair of repeat protein–repeat peptide residues within a threshold distance, the hash key is calculated from the rigid-body transform between backbones and the backbone torsions of the peptide residue, and the hash table is interrogated. If the key is found in the hash table, side chains with the stored identities and torsion angles are installed in the docking interface. d, The sequence of the remainder of the interface is optimized using Rosetta for high-affinity binding. Two representative designed binding complexes are shown to highlight the peptide-binding groove and the shape complementarity. The magnified views illustrate hydrophobic interactions (right), salt bridges (middle) and π–π stacks (left) incorporated during design.