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.