Fig. 4: Synthetic thioredoxin fold.
From: Sampling of structure and sequence space of small protein folds
a Connectivity of the basic thioredoxin fold showing N and C motifs; the N motif (βαβ element) represents the structural feature that allows domain extensions. The commonly found α0, also called α2, was replaced with the L3 loop for a minimized thioredoxin fold. b Thioredoxin folds found in nature (left and middle) and the designed synthetic thioredoxin (right). c SEC of ThioM_802 shows a single defined peak using a Superdex S75 column. d NMR structure (grey) ensemble (PDB 7LDF) compared to the model (rainbow coloring from N-terminus (blue) to C-terminus (red) of Thio_802. The His-tag was omitted. e Distances in Å, measured between secondary structure elements. f Correlation of distances in stable (blue) and unstable (red) designs. g Several occurrences of L3 loop variations (represented by their ABEGO sequences) in unstable (red) and stable (blue) designs. L3 replaces the α2 helix of natural thioredoxins; several conformations allow a stable protein. h Definition of geometric descriptions measured to evaluate shape diversity, including how the sheet dihedrals were calculated. i Interdependence of structural factors, such as the helix midpoint distances (Hm-d), helix dihedrals (H-dih), helix 1 and 2 opening angles (H1a and H2a), reveal several correlations within a fold. Red indicates correlated, whereas blue shades indicate a negative correlation. Source data is provided as Source Data File.
