Fig 1.
Tat protein sequence alignment for the nine HIV-1 subtypes.
A) The Tat protein sequence alignment, with conserved, semi-conservative, and non-conservative sites highlighted in red, yellow, and white, respectively, while the polymorphisms are shown in black font. The alignment figure was prepared using the ESPript3 tool (https://espript.ibcp.fr/ESPript/ESPript/) [40]. B) The nature of amino acids in each subtype: green = hydrophobic, blue = polar, red = basic, yellow = acidic, purple = special (Glycine and proline, due to unique physicochemical properties that influence protein structure and function). The figure was generated in MS Excel.
Fig 2.
Secondary structure assessment of the Tat protein from nine HIV-1 subtypes.
The figure shows the changes in the secondary structure of HIV-1 Tat protein sequences from nine subtypes at polymorphic sites. Key: gray = C (coil), pink = H (helix). The figure was generated in MS PowerPoint.
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.
Table 1.
Contribution of different energy components of various subtype-specific Tat and TAR complexes over 200 ns MDS and amino acids involved in Tat-TAR interactions obtained after docking using HDOCK tools. Underlined amino acids are common amino acids between subtypes.
Fig 4.
The figure shows A) binding energy per frame and B) RMSD of the backbone atoms with respect to the initial structure of the Tat protein from different subtypes. Key: CRF01_AE (black), CRF02_AG (red), A (blue), A1 (cyan), A3 (magenta), A6 (yellow), B (navy), C (wine), and D (pink) in complex with TAR RNA over 200 ns MDS. The figures were generated using OriginPro (OriginLab, Northampton, MA, USA; https://www.originlab.com/).
Table 2.
Subtype-specific Tat polymorphisms in sequences from different HIV-1 clinical stages. Polymorphisms (observed in the study) are shown relative to subtype consensus sequences and were identified by aligning clinical sequences with subtype-specific consensus sequences.