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Updated: Mar 16, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Tertiary Element Interaction in HIV-1 TAR
Konrad Krawczyk1, Adelene Y L Sim2, Bernhard Knapp3
1Department of Computer Science, Oxford University , Parks Road, OX1 3QD Oxford, U.K.
Abstract:
HIV-1 replication requires binding to occur between Trans-activation Response Element (TAR) RNA and the TAT protein. This TAR-TAT 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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