HIV-1 replication requires binding to occur between Transactivation Response Element (TAR) RNA and the TAT protein. This TARTAT binding depends on the conformation of TAR, and therapeutic development has attempted to exploit this dynamic behavior. Here we simulate TAR dynamics in the context of mutations inhibiting TAR binding. We find that two tertiary elements, the apical loop and the bulge, can interact directly, and this interaction may be linked to the affinity of TAR for TAT.
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This work was supported by the 2020 Science Programme (EPSRC Cross Discipline Interface Programme, EP/I017909/1) to C.M.D and the Agency for Science, Technology and Research (A*STAR) Joint Council Office (JCO) Career Development Award (project number 15302FG145) to A.Y.L.S.