Probing Na+-Induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings:: New insights into the role of counterions and electrostatic interactions in adaptive recognition
Probing Na+-Induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings:: New insights into the role of counterions and electrostatic interactions in adaptive recognition
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DOI：
10.1021/bi700335n
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发表时间：
2007-06-05
期刊：
影响因子：
2.9
通讯作者：
Al-Hashimi, Hashim M.
中科院分区：
文献类型：
--
作者：
Casiano-Negroni, Anette;Sun, Xiaoyan;Al-Hashimi, Hashim M.
许多调控RNA在识别蛋白质和配体时发生结构上的巨大变化，但这种变化发生的机制仍然知之甚少。使用NMR残余偶极耦合（RDC），我们的特点是Na+诱导的变化的结构和动力学的凸起含有HIV-1反式激活反应元件（TAR）RNA，反映了变化引起的小分子携带不同数量的阳离子基团。将Na+浓度从25 mM增加到320 mM导致平均螺旋间弯曲角（从46度到22度）、螺旋间扭转角（从66度到-18度）和螺旋间柔性（通过内部广义有序度从0.56增加到0.74来测量）的连续减小。观察到类似的构象变化与Mg 2+，表明非特异性静电相互作用驱动的构象转变，虽然结果也表明，Na+和Mg 2+可能与TAR在不同的模式。过渡可以合理化的基础上的人口加权平均的两个合奏，包括一个静电松弛的弯曲和灵活的TAR构象，是弱相关的抗衡离子和全球刚性同轴构象，具有较强的静电势和协会与抗衡离子。由小分子稳定的TAR螺旋间取向落在金属诱导的构象途径周围，表明抗衡离子可能有助于使TAR构象易于被靶向识别。我们的研究结果强调了RNA构象动力学对环境条件的复杂敏感性，并证明了使用NMR RDC检测细微构象变化的能力。
Many regulatory RNAs undergo large changes in structure upon recognition of proteins and ligands, but the mechanism by which this occurs remains poorly understood. Using NMR residual dipolar coupling (RDCs), we characterized Na+-induced changes in the structure and dynamics of the bulge-containing HIV-1 transactivation response element (TAR) RNA that mirrors changes induced by small molecules bearing a different number of cationic groups. Increasing the Na+ concentration from 25 to 320 mM led to a continuous reduction in the average inter-helical bend angle (from 46 degrees to 22 degrees), inter-helical twist angle (from 66 degrees to -18 degrees), and inter-helix flexibility (as measured by an increase in the internal generalized degree of order from 0.56 to 0.74). Similar conformational changes were observed with Mg2+, indicating that nonspecific electrostatic interactions drive the conformational transition, although results also suggest that Na+ and Mg2+ may associate with TAR in distinct modes. The transition can be rationalized on the basis of a population-weighted average of two ensembles comprising an electrostatically relaxed bent and flexible TAR conformation that is weakly associated with counterions and a globally rigid coaxial conformation that has stronger electrostatic potential and association with counterions. The TAR inter-helical orientations that are stabilized by small molecules fall around the metal-induced conformational pathway, indicating that counterions may help predispose the TAR conformation for target recognition. Our results underscore the intricate sensitivity of RNA conformational dynamics to environmental conditions and demonstrate the ability to detect subtle conformational changes using NMR RDCs.