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J Chem Inf Model. 2016 Sep 26;56(9):1746-54. doi: 10.1021/acs.jcim.6b00152. Epub 2016 Aug 17.

Tertiary Element Interaction in HIV-1 TAR.

Author information

1
Department of Computer Science, Oxford University , Parks Road, OX1 3QD Oxford, U.K.
2
Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, Singapore 138671.
3
Department of Statistics, Oxford University , St Giles, OX1 3LB 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.

PMID:
27500460
DOI:
10.1021/acs.jcim.6b00152
[Indexed for MEDLINE]

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