Phylogenetic trees of all-β protein folds with
β-barrel-like architecture. Maximum parsimony was used to reconstruct a
general tree of β-barrel-like folds with different β-sheet
topologies and barrel mimic folds (A) and trees of β-barrel
folds with Greek-key, meander, and complex β-sheet topologies
(B). Barrel mimic folds include architectures such as the
barrel-sandwich hybrid, with two β-sheets in the shape of a half-barrel
packed in a sandwich-like arrangement, and the β-clip, with two-stranded
β-sheets that fold upon themselves. Folds are described by general
characteristics such as barrel architecture [closed (C), partly open (P), or
open barrel (O)], number of strands (n), and shear number
(S), and special features (SF) such as cross-over psi loops (p),
over-side connections (oc), capping by α-helices (c), and internal
pseudo-threefoil symmetry (i). Trees with lengths ranging 659–768 steps
[CI = 0.833–0.941, RI = 0.729–0.904; g1 =
-(0.554–0.904); PTP tests, P = 0.001] were retained after
branch-and-bound or exhaustive searches.