FIGURE 5 . 3D models of influenza virus PA protein and C69
peptide, and selected docking models. A : several C69 peptides
clustered on the PA protein, B : single C69 peptide-PA model
(the interaction area was presented in enlarged circle), C:chemical bounds defined between viral PA and C69 peptide with PDBsum
algorithm.
In the Y2H method, the candidate
interactor protein is synthesized in the cells as fused with the
activation domain (AD) of the yeast GAL4 transcription activator.
Therefore, the 3D models of the C69 peptide fused with GAL4 AD (AD-C69)
(Figure 2) were predicted by I-TASSAR. Two models with higher c-scores
were subjected to docking analysis with the PA protein by ignoring the
AD of the protein. In many interaction patterns, the AD-C69 protein was
found to be clustered in the same area as the C69 peptide (Figure 5) on
the bait PA protein in both docking patterns (Figures 6A and 6C). Figure
6B and 6D show the predicted interaction patterns between a single
AD-C69 protein and viral PA.