Functional dynamics in HIV-1 regulatory RNA elements

描述（申请人提供）：构象动力学在许多HIV-1病毒调控RNA元件的功能中起着至关重要的作用。我们的长期目标是阐明这些RNA功能动力学的分子基础，作为合理设计靶向RNA的抗hiv治疗药物的先决条件。本研究的主要假设是，构象动力学在自适应识别中起着重要作用，而自适应识别是transactivation response element （TAR）功能的基础，构象动力学是二聚化起始位点（DIS）功能的基础。这一假设得到以下观察结果的支持，(i)通过经历不同的结构变化，TAR可以混合结合不相关的化合物，（ii）降低TAR构象柔韧性的化合物抑制其功能，（iii） DIS可以自发地经历其功能所需的大量二级结构转变，（iv） DIS的结构动力学与其经历这些转变的速度直接相关。本提案的总体目标是发展核磁共振方法来阐明构象灵活性在TAR和DIS功能中的作用，并将这种理解应用于针对TAR和DIS的抗hiv治疗药物的合理设计。具体目标是：发展和应用核磁共振方法来阐明构象动力学在TAR自适应识别中的作用。结果将用于检查TAR是否可以动态进入蛋白质结合状态。2. 阐明结构动力学在DIS结构异构化中的作用。结果将用于检查DIS是否可以访问动态结构异构化的独特构象。3. 阐明RNA柔韧性在氨基糖苷识别中的作用。结果将用于检验静电相互作用在阻止RNA全局运动中起主要作用的假设，以及不同的氨基糖苷可以结合相同RNA靶标的不同构象表现。

DESCRIPTION (provided by applicant): Conformational dynamics plays an essential role in the functions of many HIV-1 viral regulatory RNA elements. Our long term goal is to elucidate the molecular basis for functional dynamics in these RNAs as a prerequisite for rationally designing anti-HIV therapeutics targeting RNA. The main hypothesis in this proposal is that conformational dynamics plays an essential role in adpative recognition underlying the function of the transactivation response element (TAR) and structural isomerization underlying the function of the dimerization initiation site (DIS). This hypothesis is supported by the following observations, (i) TAR can promiscuously bind unrelated compounds by undergoing distinct structural changes, (ii) Compounds that diminish TAR's conformational flexibility inhibit its function, (iii) The DIS can spontanously undergo large secondary structural transitions needed for its function, (iv) Structural dynamics in DIS has been directly correlated with the rate at which it undergoes these transitions. The overall objective of this proposal is to develop NMR methods for elucidating the role of conformational flexibility in the functions of TAR and DIS and to apply this understanding in the rational design of anti-HIV therapeutics targeting TAR and DIS. The specific aims are to: 1. Develop and apply NMR methods to elucidate the role of conformational dynamics in TAR adaptive recognition. Results will be used to examine if TAR can dynamically access protein bound states. 2. Elucidate the role of structural dynamics in the DIS structural isomerization. Results will be used to examine if DIS can access conformations uniquely poised for structural isomerization dynamically. 3. Elucidate the role of RNA flexibility in aminoglycoside recognition. Results will be used to examine the hypothesis that electrostatic interactions play a primary role in arresting RNA global motions and that different aminoglycosides can bind different conformational manifestations of the same RNA target.