Mapping allosteric rewiring in viral RNA: Sequence-encoded control of protein binding mechanisms

RNA recognition by proteins is governed not only by static structure but also by allostery encoded within non-local dynamic motifs. In this study, we systematically identify allosteric communication hubs in RNA and map multiple residue-connected pathways, revealing how these networks are rewired upon mutation and protein binding. To capture these effects under physiological salt conditions, we performed extensive atomistic simulations of TAR RNA, both in its apo and Tat-protein bound states, across three immunodeficiency virus variants, BIV, HIV-1, and HIV-2. Allosterically coupled sites were identified using contact-based principal-component analysis, and communication pathways were traced through a graph-network-based algorithm. Two distant motifs-the bulge and the apical loop-emerge as allosteric switches and information hubs: the bulge engages Tat, while the loop interacts with another protein partner, Cyc-T1, both essential for transcriptional activation and antiviral targeting. We find that HIV-2 TAR, with strong loop-bulge coupling and high self-integrity, favors conformational selection and exhibits lower Tat-binding affinity reported in early experiments. In contrast, a single C24 insertion in HIV-1 TAR reconfigures communication pathways, enabling an induced fit mechanism with enhanced affinity. The study not only elucidates an allosteric rewiring between the loop and bulge but also highlights how this communication is dynamically reconfigured upon protein binding. Tat association at the bulge reorganizes and reorients loop residues, thereby promoting the subsequent recruitment of Cyc-T1. This work overall underscores how sequence (even a single mutation)-encoded RNA allostery can modulate not only a protein's binding mechanism and affinity but also influence downstream molecular events within transcriptional signaling cascades.