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19. Building the backbone with ideal geometry

19.1 Overview

Some problems, such as dihedral angle minimization or loop stitching (see below), require rebuilding the backbone with ideal geometry. However, due to non-ideal bond geometries, simply using the phi, psi, and omega angles extracted from the experimental pdb structure results in structures that deviate significantly from the original structure. Therefore, it is necessary to adjust the backbone dihedral angles so that the coordinates of atoms in the rebuilt structure are similar to their coordinates in the non-ideal structure. The changes in the dihedral angles required for this are quite small.

JOBTYPE ideal_backbone_geometry uses Powell minimization to minimize the rmsd between starting and rebuilt backbone heavy atom coordinates.

19.2 Example - grafting and stitching of backbone fragments

All the backbone dihedrals are rebuilt and permitted to move. However, there may be cases when the exact coordinates of a subset of backbone residues are ambiguous, while the coordinates of other positions do matter. For example, if a structure was missing residues due to poor electron density or lack of NOEs in that region, it may be of interest to fill it in. Candidate coordinates from another structure may be aligned to the "stumps" preceding and following the missing region. Since perfect alignments at both ends may not be possible, the structure of the grafted region may need to be adjusted to match the stumps of the target protein.

An example of this procedure is in examples/backbone_graft_stitch/. In this example, the basal-activity structure of sos is missing residues 654-675. The structure of sos in an alternative, hyperactive conformation, has these positions. The missing residues may be transplanted from the hyperactive structure to the basal-activity structure. First, extract the residues to be grafted from the hyperactive structure, including one or two residues up- and downstream of the missing residues (loop_653_676.pdb). Next, align this to the basal structure stumps (residues 653 and 676; align_loop_653_676.input), using the alignment functionality. Modify the output structure (aligned_loop_653_676.pdb) so that the coordinates for the stump residues are replaced with those from the basal structure (transplanted_loop_653_676.pdb).

Since this results in unreasonable bond geometry, the backbone needs to be rebuilt, and the torsions adjusted. However, since we don't actually know the coordinates of the missing residues, and since we do know the coordinates of the stumps, it is may be better to use just the stump coordinates as an objective function for adjusting backbone torsions. The may be defined in two ways. Since the template (transplanted_loop_653_676.pdb) includes only the stump residues and the transplanted residues, the scoring may be restricted only to the specified stump residues (653 and 676; stitch_loop_653_676_include.input):
START
...
JOBTYPE ideal_backbone_geometry
...
END
INCLUDE
653S
676S
END
For this, the rmsd scoring is restricted only to the backbone atoms of residues 653 and 676.

Alternatively, one may exclude the transplanted residues from being scored (stitch_loop_653_676_exclude.input):
START
...
JOBTYPE ideal_backbone_geometry
...
END
EXCLUDE
654S
655S
...
674S
675S
END
For this, the rmsd scoring excludes the backbone atoms of residues 654-675.

Both definitions yield the same structure (stitch_loop_653_676_include.pdb and stitch_loop_653_676_exclude.pdb respectively). This structure can be inserted into the basal sos structure (basal_sos_stitched_loop_653_676.pdb).

Adjusting the grafted positions in order to relieve clashes with the atoms from the actual structure is discussed below.

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