Fig. 1: Backbone blueprints and design models for target folds.
From: Role of backbone strain in de novo design of complex α/β protein structures
(top) Backbone blueprints for a P-loop2×3-fold: Pl2×3_BP, b Rossmann2×3-fold: R2x3_BP1, c Rossmann3×3-fold: R3×3_BP1 and R3x3_BP2. Helix lengths are represented by numbers within green and red rectangles, strand residues indicated by filled and open boxes: filled boxes represent pleats (the vectors from Cα atom to Cβ atom) coming out of the page and the open boxes represent pleats going into the page. Loops are labeled by the extended ABEGO torsion patterns (see Methods and Supplementary Fig. 1). (middle) Design topologies are illustrated with circles (helices) and triangles (strands) connected by solid lines (loops). (bottom) Design models created from the blueprints (top). The blueprints were created by inserting an αβ or αβ-αβ motif (gray color) into the position immediately before the C-terminal helix in the blueprints we used previously to design four-stranded β-sheet proteins6. The secondary structure lengths and the loop ABEGO patterns are based on the design rules for βαβ-motif described in Fig. S5 and S6 of ref. 9, with the extension of the ABEGO bins. For Rossmann3×3-fold, we experimented with two blueprints, changing the register shift and the length of the fourth strand.
