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Figure 2 | Retrovirology

Figure 2

From: Arginine rich short linear motif of HIV-1 regulatory proteins inhibits Dicer dependent RNA interference

Figure 2

Bioinformatics based functional assessment of HIV-1 ARM. To assess the functional role of viral ARM, molecular interaction networks for HIV-1 Tat and Rev proteins was constructed using HIV-1 interaction database (A). The Tat targeted host proteins are in green colour, Rev targeted in red and common interacting partners in purple. Individual proteins are depicted as nodes and edges represent interactions. The functional assignment of the commonly targeted proteins are according to gene annotation (GO) (molecular function and biological process) and is summarised with top 8 GO term with p value <10-7 along with their cluster frequency as percentage. (B) shows domain profiling of commonly targeted host proteins by ARM is based on correlated domain structures. In the matrix representation, both rows and columns are domains of targeted proteins, “1” and “0” represent the presence or absence of homo or heterotypic domain interaction among them respectively. Single linkage hierarchial clustering (C) based on Euclidean distance gives clusters of domains (domain clubs) as a possible protein context that can be targeted by ARM containing proteins. The red box indicates domain clubs shared by pathways of nucleic acid based on immunity. (D) shows the most represented structural domains in commonly targeted host proteins and RNAi pathway. In both the pie chart, Double-stranded RNA binding motif (DSRM) and P-loop_NTPase (AAA domain) are common and enriched. Based on these domains and the club to which they belong, most probable targets of viral ARM are shown in (E). Refer method for details.

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