Dynamic Ensemble View of the Conformational Landscape of HIV-1 TAR RNA and Allosteric Recognition
Dynamic Ensemble View of the Conformational Landscape of HIV-1 TAR RNA and Allosteric Recognition
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DOI：
10.1021/bi200495d
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发表时间：
2011-06-07
期刊：
影响因子：
2.9
通讯作者：
Xia, Tianbing
中科院分区：
文献类型：
--
作者：
Lu, Jia;Kadakkuzha, Beena M.;Xia, Tianbing
RNA构象动力学和由此产生的结构异质性在RNA功能中起着重要作用，例如识别。HIV-1 TAR RNA的识别被认为是通过构象捕获机制发生的。在这里，我们使用超快时间分辨荧光光谱，探测了HIV-1 TAR RNA构象景观的复杂性，并监测了Tat蛋白衍生肽与新霉素b结合后的位置依赖性景观变化。在无配体状态下，TAR RNA在三核苷酸突起区周围具有不同程度的碱基堆积的多个构象家族。一些亚种群部分类似于这些配体结合态，但同轴堆叠态低于检测极限。当Tat或新霉素B结合时，凸起区域作为一个整体以位置依赖的方式经历构象转变。Tat和新霉素B诱导了TAR RNA中互斥的变化，这是在具有残基特异性细节的整体水平上的变构抑制机制的基础。时间分辨各向异性衰变测量揭示了在无配体和配体束缚状态下碱的皮秒运动。凸起-茎交界处的一个碱基对突变对凸起碱基的构象分布有不同的影响。提出了HIV-1 TAR RNA构象景观的整体动态模型，并讨论了RNA识别的一般机制及其对基于RNA的治疗方法的影响。
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.