<i>Ab initio</i> HIV-1 Tat–TAR interactions study using hybrid scoring-enhanced molecular modeling across subtypes

The role of the HIV-1 Tat protein in viral transcription is linked to variations among subtypes. However, research on Tat-TAR RNA interactions has largely focused on subtypes B and C, leaving the binding dynamics of other subtypes insufficiently explored. In this study, we employed a hybrid scoring-enhanced molecular modeling approach to systematically investigate the interactions between Tat exon 1 from nine major HIV-1 subtypes (A, B, C, D, F, G, H, J, and K) and TAR RNA. The hybrid scoring strategy captures complex interaction patterns and tackles the inherent challenges in assessing RNA-protein interactions. Our findings reveal a highly conserved interaction region (residues 48-58) within Tat's Arg-rich basic domain, which is essential for TAR binding. While the core binding mechanism remains consistent across subtypes, sequence and structural flexibility variations impact binding stability and energetics. Subtypes A, B, and D exhibited the strongest binding affinities and structural compactness, with subtype B demonstrating the highest stability, potentially correlating with its reported clinical severity. In contrast, subtypes G, H, J, and K showed increased flexibility and weaker binding, which may affect transcriptional efficiency. This study enhances the understanding of Tat-TAR interactions across HIV-1 subtypes and introduces a hybrid scoring approach that could serve as a valuable framework for future RNA-protein interaction studies. Substitution of the residue R57 led to decreased binding affinity to TAR, consistent with previous experimental observations. These insights may guide the development of subtype-adapted antiviral strategies.