Figure 4

Correlations between HIV-1 protein diversity and HIV-human protein interactions, protein disorder and viral particle structures. (A) Plot of polynomial regression between the HIV-1 protein diversity (x-axis) and the number of HIV-human protein interactions (y-axis). The second-order model is \( \mathcal{Y}=8346{\mathcal{X}}^2-1223\mathcal{X}+57.96 \) (adjusted R-squared: 0.82, root-mean-square error: 42.31). (B) Plot of average protein disorder score and average amino acid diversity in HIV-1 proteins. Red circles indicate the number of HIV-human protein interactions at individual viral proteins, for visualization purpose, scaled between 20 and 200 interactions (proteins with fewer than 20 interactions are scaled to the same size as those with 20, proteins with more than 200 interactions are scaled to the same size as those with 200). Average amino acid diversities of HIV-1 proteins are calculated using subtype B sequences (one genomic sequence per patient, Table 1). (C) Clustering of HIV-1 proteins and schematic view of HIV-1 viral particle. On the left, each colored circle represents a viral protein positioned according to the clusters of protein functions. The size of each red circle indicates the number of HIV-human protein interactions involving each HIV-1 protein (see (B)). On the right, the schematic view of mature viral particle is visualized at the bottom with annotations indicated in the inserted figure legend. Above, surface representations show the structures of HIV-1 proteins that are grouped according to their functional roles. Different units in HIV-1 multimeric proteins are indicated with different colors and HIV-1 monomeric proteins are colored pink. HIV-1 protein structures are scaled according to their precise protein sizes for direct comparison. Visualization software: PyMOL V1.5 (http://www.pymol.org/).