Effect of HIV-1 subtype-specific Tat protein polymorphisms on Tat-TAR interaction
Fig 3
The Tat-TAR interaction analysis of significant subtypes.
The figure (right) shows amino acids of the Tat protein binding to RNA nucleotides, the positions of interacting residues, and the types of interactions (hydrophobic, pi-cation, hydrogen bonds, and salt bridges). The left panel shows the Tat-TAR interaction, with the Tat protein in red and the TAR element in green. Only subtypes with the highest (A and B) and lowest (C and D) binding affinity in docking/MDS are shown. Yellow shaded boxes show common amino acids among subtypes that were involved in Tat-TAR interaction. The Tat-TAR poses were generated in Discovery Studio v21.1.0.20298 (https://discover.3ds.com/discovery-studio-visualizer-download), while interactions were drawn using MS PowerPoint.