To obtain atomic level insight into GSK-3β activation, we first modeled the inactive GSK-3β·ATP and the active GSK-3β(p)·ATP (see Methods).
The same three GPCRs in the inactive conformations were used for modelling the structure of the inactive TSHR TMD (TMD_In).
A previous virtual screen of a DRD3 homology modeled on the inactive β2AR structure predicted ligands with hit rates, novelty, and potency equaling that of the DRD3 crystal structure, confirming the transferability of structural information, at least with high sequence similarity, in the inactive state; in unpublished studies, we have observed the same for the DRD2 and serotonin 5HT2A receptors.
In the model, the inactive conformation "O" corresponds to that of a free Ire1 monomer that has the αC-helix in the inactive, "out" position also observed for other protein kinases.
The same homologous GPCR structures used for modelling the structure of the TSHR TMD were used for modelling the active and inactive conformations of the FSHR and LHR TMDs.
However to compare the models of the inactive and active conformations of the TSHR (as well as FSHR and LHR), the models should be produced based on templates of the inactive and active conformations of the same GPCRs.
Second, we developed DFGmodel, a method based on homology modeling that utilizes a diverse set of DFG-out template structures to generate kinase models in the inactive, DFG-out conformation.
Our model uses the inactive crystal of delta opioid receptor.
The model of the inactive conformation of the TSHR TMD predicts an aromatic interaction between Phe5945.51 and Phe6346.54 at 2.9 Å (Supplementary Table 6, Fig. 3d).
A "homology model" of the inactive conformation of Plk1 was constructed, as the crystal structure in its inactive conformation is unknown.
