Fig. 1: Pipeline for rationally seeded computational design of de novo protein folds.
From: Rationally seeded computational protein design of ɑ-helical barrels
a, Robust sequence-to-structure relationships for coiled-coil oligomers were used as rules to seed the design of new protein scaffolds. b,c, Antiparallel (b) and parallel (c) α-helical barrel protein design targets. For both targets, MASTER51,52 was used to search known experimental protein structures for segments with the potential to connect adjacent helices and generate single-chain models. For the antiparallel designs (b), the sequences and structures of identified short connectors were used directly. However, the parallel targets required longer structured loops (c), for which we targeted helix–turn–helix–turn–helix motifs. ProteinMPNN8 and AlphaFold2 (refs. 55,56) were then used iteratively to optimize the sequences and models of these three-helix bundle motifs. d, For each design, a small number of synthetic genes were made and expressed in E. coli for biophysical and structural characterization. Peptide and protein chains are shown in chainbows from the N termini to the C termini (blue to red), except for the initially placed central helices of the helix–turn–helix–turn–helix motifs in the parallel designs, which are shown in white. α-HB, α-helical barrel.
