Figure 1. PyMOL22 target renderings (left) and Grishin plots (right) for two two-domain targets:(A) target T1112, a protein involved in the synthesis of an osmolyte involved in thermoadaptation, and (B) target T1124, a methyltransferase MfnG (PDB: 7UX8). Grishin plots are built on the GDT_TS scores for all collected models. The plots suggest evaluating domains together as the angle between the data trend line and the diagonal is small (i.e., the evaluation scores for the combined domains (X-axis) and individual domains (Y-axis) are similar for most groups).
The last target in this category, T1180, is an exception to the splitting rule (section 2.1 ). Even though the Grishin plot advised splitting, we did not proceed with that as the target is a fusion enzyme of two known domains, where the only prediction interest was to model inter-domain orientation.
3.1.3 | Multidomain-targets requiring splitting (20)
For half of the 20 targets that required splitting, the number of EUs was determined by the number of structural domains (no merging was necessary), and for the other half, some domains but not all were joined.
In several cases splitting was required because different chains exhibited different folding patterns.
For example, target T1120, a DNA-binding protein DdrC, is composed of an N-terminal winged helix-turn-helix motif and a C-terminal four-helix bundle, that folds as an asymmetric domain-swapped dimer (Figure 2A)23. Superposition of the two chains revealed the distortion of the long central helix hA in chain A (cyan) into two smaller, non-colinear helices (hB1 and hB2) in chain B (green) and cause a shift in the relative position of the C-terminal domain with regards to the anchor N-terminal domain (Figure 2B). This prompted splitting of the target into two EUs at the break point (residue 125). Such a split is strongly supported by the Grishin plot (Figure 2C).