Fig. 2: Design rules for cross-β motifs in β-sandwiches.
a Cartoon representation of a 7-stranded immunoglobulin-like domain model formed by two β-sheets packing face-to-face, and the corresponding cross-β motif, which generates translations and rotations between the two opposing β-sheets. b Topology diagram of a cross-β motif with circles and arrows representing β-strand residue positions and connections, respectively. Dark- and light-colored circles correspond to residues with sidechains pointing inwards or outwards from the β-sandwich, respectively. c Efficiency of pairs of common β-arch loop geometries (described with ABEGO backbone torsions) in forming cross-β motifs obtained from Rosetta folding simulations (gray shaded squares). Loop geometries were classified in four groups according to the sidechain directions of the adjacent residues. Colored squares group pairs of loops that, due to their sidechain orientations, have different requirements in β-strand length: in red or blue, if all β-strands need an odd or even number of residues, respectively; in green, if the β-strands of the first and second sheet need an odd and even number of residues, respectively; and in yellow for the opposite case (even and odd number of residues for the first and second sheet, respectively). Black-outlined boxes highlight loop combinations observed in natural Ig domains. On the right, examples of changes in cross-β motif geometry linked to β-arch loop geometry. d β-arch helices are formed by a short ɑ-helix connected to the adjacent β-strands with short loops, and are complementary to β-arch loops for connecting cross-β motifs. e Topology diagram of a 7-stranded Ig domain. β-strands and β-arch loops are indicated as Si and Li, respectively, where i is the corresponding number. f Examples of de novo designed Ig backbones generated with different geometries and β-arch connections following the described rules, colored from N-terminus (blue) to C-terminus (red).
