title: Tertiary Element Interaction in HIV-1 TAR.
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.
authors: Department of Computer Science, Oxford University , Parks Road, OX1 3QD Oxford, U.K.
authors: Konrad
authors: K
authors: Krawczyk
authors: Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, Singapore 138671.
authors: Adelene Y L
authors: AY
authors: Sim
authors: Department of Statistics, Oxford University , St Giles, OX1 3LB Oxford, U.K.
authors: Bernhard
authors: B
authors: Knapp
authors: Department of Statistics, Oxford University , St Giles, OX1 3LB Oxford, U.K.
authors: Charlotte M
authors: CM
authors: Deane
authors: Department of Computer Science, Oxford University , Parks Road, OX1 3QD Oxford, U.K.
authors: Peter
authors: P
authors: Minary
mesh_terms: D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D020218:Response Elements / Q000235:genetics*; D014779:Virus Replication; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000378:metabolism*
chemical_list: D012367:RNA, Viral; D054322:tat Gene Products, Human Immunodeficiency Virus