Figure 4.

The designability landscape of a simple α/β motif. (A) The fragment was initially excised from PDB entry 2KL8 (residues 18–24 and 33–35) and idealized (to avoid bias in searching) by superimposing perfectly repeating α-helix ( φ/ψ angles of −57°/−47°, respectively) and β-strand ( φ/ψ angles of −135°/135°, respectively) elements onto the corresponding segments (total backbone-RMSD upon superposition was 0.25 Å; ideal version shown). The principal axis of the helix served to define the Z-axis (shown as a gray tube), with Δφ defined by rotating the helix around Z and ΔZ defined by translating the strand relative to the helix in the Z-direction. ΔR was defined as translations along the axis connecting the centroids of the helix and the strand (in the original structure). Positive directions of change are indicated with arrows for all three variables. (B) The number of matches within 0.5 Å in terms of both CA- and full-backbone RMSD, as a function of ΔR and Δφ. ΔZ is optimized for largest number of matches for each point, with the corresponding values shown in (C). (D) Structures and sequence logos corresponding to the two apparent maxima in the designability landscape (left) and the structure closest to the original motif (corresponding to ΔR = 0, Δφ = 0, and ΔZ = 0; right). Images in (B) and (C) are generated via cubic interpolation of the raw counts.