Each horizontal panel shows an initial position and selected perturbation locations (left), the disrupted structure after a perturbation (center), and the subsequent structural repair (right). In all panels, green represents a flexible region of the protein or the fold tree and a yellow point indicates where a specific φ/ψ angle change occurs.
A: For a rigid-body move, domain A (blue) is kept fixed while domain B (red) samples the conformational space around A, causing the linkers to break. The linkers are repaired using a combination of three-residue fragment insertions and CCD loop closure. The fold tree shows a fixed jump connecting the two parts of domain A in black and the flexible jump connecting domains A and B in green. Both the linkers are flexible so that they can be repaired.
B: For a loop-building move, one linker (green) is built by inserting a three-residue fragment at the point shown in yellow. The insertion of a fragment breaks the linker, and CCD is used to reclose the linker. In the fold tree, only the linker that is being repaired is flexible.
C: For an insertion-flop move, small φ/ψ angle movements are made in one linker (yellow) while allowing the other linker to break. The broken linker is then rebuilt. This “flops” around the insertion domain. In the fold tree, only one jump is used to hold the host domain together.

Rmsd is calculated over all C_α atoms of the protein. (•) Decoy structures.

(A) Signal processing protein (1owq, C_α rmsd = 0.70Å). (B) Hypothetical protein TM0936 (1p1m, C_α rmsd = 0.64Å). (C) Flavocytochrome C3 (1qjd, C_α rmsd = 0.70Å). (D) NADPH-dependent oxidoreductase (1vj1, C_α rmsd = 0.60Å). The native structures are in dark shades with the host domain in blue, insert domain in red, linkers in orange. Structures were superimposed using only the host domain coordinates.

Native structure and best scoring decoy structures for leucyl-tRNA synthetase (1h3n) and C-terminal binding protein 3 (1hku) with the host domain in blue, insert domain in red, and linkers in orange, with the native structure in darker shades. (A) The best scoring decoy structure for leucyl-tRNA synthetase creates a more compact structure than the native structure (B). (C) In the best scoring decoy structure for C-terminal binding protein 3, more contacts occur when the insert domain is rotated 180° from the native structure (D).

A domain insertion protein consists of two domains, A (blue) and B (red). (A) Primary structure; (B) Tertiary structure. The two 11-residue linkers connecting A to B are orange.

Rmsd is calculated over all C_α atoms of the protein. (•) Decoy structures, ( ) refined native structure (using high resolution algorithm).

Rmsd is calculated over all C_α atoms of the protein. (•) Decoy structures, ( ) refined native structure (using high resolution algorithm), ( ) ten refined structures for the lowest rmsd structure from the low-resolution search (only shown for cases where the lowest-rmsd structure from the low-resolution search provides a high-resolution final prediction that is closer to the native structure and lower in energy than any of the refined structures from the ten top-scoring low-resolution decoys.)

Left: Score vs. rmsd over all C_α atoms of the insert domain after superimposing the host domain; Right: Score vs. rmsd over C_α atoms of only the linker residues after superimposing the linkers.

(A) Low-resolution mode; (B) Details of the loop-building algorithm for low-resolution mode; (C) High-resolution mode.