A bottom-up approach for the de novo design of functional proteins
Yang, C.; Sesterhenn, F.; Bonet, J.; Aalen, E. v.; Scheller, L.; Abriata, L.; Cramer, J.; Wen, X.; Rosset, S.; Georgeon, S.; Jardetzky, T. S.; Krey, T.; Fussenegger, M.; Merkx, M.; Correia, B.
Show abstract
De novo protein design has enabled the creation of novel protein structures. To design novel functional proteins, state-of-the-art approaches use natural proteins or first design protein scaffolds that subsequently serve as templates for the transplantation of functional motifs. In these approaches, the templates are function-agnostic and motifs have been limited to those with regular secondary structure. Here, we present a bottom-up approach to build de novo proteins tailored to structurally complex functional motifs. We applied a bottom-up strategy to design scaffolds for four different binding motifs, including one bi-functionalized protein with two motifs. The de novo proteins were functional as biosensors to quantify epitope-specific antibody responses and as orthogonal ligands to activate a signaling pathway in engineered mammalian cells. Altogether, we present a versatile strategy for the bottom-up design of functional proteins, applicable to a wide range of functional protein design challenges.
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