title: Dynamic ensemble view of the conformational landscape of HIV-1 TAR RNA and allosteric recognition.
abstract: RNA conformational dynamics and the resulting structural heterogeneity play an important role in RNA functions, e.g., recognition. Recognition of HIV-1 TAR RNA has been proposed to occur via a conformational capture mechanism. Here, using ultrafast time-resolved fluorescence spectroscopy, we have probed the complexity of the conformational landscape of HIV-1 TAR RNA and monitored the position-dependent changes in the landscape upon binding of a Tat protein-derived peptide and neomycin B. In the ligand-free state, the TAR RNA samples multiple families of conformations with various degrees of base stacking around the three-nucleotide bulge region. Some subpopulations partially resemble those ligand-bound states, but the coaxially stacked state is below the detection limit. When Tat or neomycin B binds, the bulge region as an ensemble undergoes a conformational transition in a position-dependent manner. Tat and neomycin B induce mutually exclusive changes in the TAR RNA underlying the mechanism of allosteric inhibition at an ensemble level with residue-specific details. Time-resolved anisotropy decay measurements revealed picosecond motions of bases in both ligand-free and ligand-bound states. Mutation of a base pair at the bulge--stem junction has differential effects on the conformational distributions of the bulge bases. A dynamic model of the ensemble view of the conformational landscape for HIV-1 TAR RNA is proposed, and the implication of the general mechanism of RNA recognition and its impact on RNA-based therapeutics are discussed.
authors.affiliation: Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, United States.
authors.forename: Jia
authors.initials: J
authors.lastname: Lu
authors.forename: Beena M
authors.initials: BM
authors.lastname: Kadakkuzha
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.forename: Martin
authors.initials: M
authors.lastname: Fan
authors.forename: Xin
authors.initials: X
authors.lastname: Qi
authors.forename: Tianbing
authors.initials: T
authors.lastname: Xia
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D000099253:Trans-Activation Responsive RNA-Binding Protein
chemical_list: D008024:Ligands; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D000099253:Trans-Activation Responsive RNA-Binding Protein