Fig. 4
From: CirPred, the first structure modeling and linker design system for circularly permuted proteins
Modeling of proteins with 3D domain swapping phenomenon induced by CP. The structures of a the native βB2-crystallin (PDB 1blbC) and b the engineered CPM87 βB2-crystallin (PDB 1bd7A; CP site on the native crystallin: Glu87) have both been solved by X-ray crystallography. This pair of circular permutants is also an example of the 3D domain-swapping phenomenon. Since this crystallin had a two-fold rotational symmetric structure and the CP site was at the middle of the subunit, conventional comparative modeling methods might be able to construct the full model of the CPM by mimicking the template structure, such as c the model of CPM87 βB2-crystallin constructed by SWISS-MODEL using a as the template. However, the conformation of the models constructed by conventional methods was very different from that of the actual CPM structure, as shown by d the superimposition between b and c. Interestingly, e the model of CPM87 βB2-crystallin constructed by CirPred was highly similar to the actual CPM conformation, as shown by f the superimposition between b and e