Extended Data Fig. 7: Designing proteins of the (αβ)n-barrel and the (β4)n-propeller architectures.
(a) Left: an example initial structure ‘sketched’ according to the (αβ)15-barrel architecture. Right: example backbones (blue) generated for the (αβ)n-barrel architectures superimposed with structures predicted by AlphaFold2 (gray) for amino acid sequences designed for these backbones with ProteinMPNN. The scRMSDs of the superimpositions are indicated. For each value of the repeat number n from 9 to 15, one example is shown. (b) The same as A, but for the (β4)n-propeller architectures with n ranging from 7 to 11. (c) Left: the crystal structure (gold and salmon) and the designed backbone (blue) of the designed (αβ)9-barrel protein T01. The crystal structure presents a domain-swapped dimer, with the monomers colored differently. The designed backbone is superimposed with one of the monomers. Right: the results of SEC (black curve) and static light scattering (red curve) experiments on T01, which indicate that the protein exists in the monomeric state in solution. (d) Left: the crystal structure (gold, yellow, and salmon) and the designed backbone (blue) of the designed (αβ)9-barrel protein T11. The crystal structure presents a domain-swapped trimer, with the monomers colored differently. The designed backbone is superimposed with one of the monomers. Right: the results of SEC (black curve) and static light scattering (red curve) experiments on T11, which indicate that the protein exists in the monomeric state in solution.
