X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch.
X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch.
复制标题
X 射线晶体学研究 TPP 核糖开关的构象变化。
DOI：
10.1007/978-1-0716-2687-0_14
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Serganov,Alexander
中科院分区：
文献类型：
--
作者：
Nuthanakanti,Ashok;Ariza-Mateos,Ascensión;Serganov,Alexander
构象重排是核糖开关功能的关键。这些调控mRNA区域使用进化上保守的传感结构域特异性结合细胞代谢物，并通过携带基因表达信号的相邻下游表达平台调节基因表达。这种调节是通过两种不同的、相互排斥的构象的配体依赖性形成来实现的，这两种构象涉及相同的RNA区域。虽然X射线晶体学无法可视化这种戏剧性的构象重排的动力学，但这种方法对于理解稳定传感结构域和驱动表达平台折叠的RNA-配体相互作用至关重要。X射线晶体学可以揭示区分同源和非同源配体所必需的RNA的局部变化。本章描述了硫胺素焦磷酸核糖开关RNA的制备及其与不同配体的结晶，导致RNA中具有局部构象变化的结构。这些结构可以帮助获得对小分子特异性结合所必需的RNA的动力学信息，并有可能使用这些信息来开发设计师核糖开关配体系统。
Conformational rearrangements are key to the function of riboswitches. These regulatory mRNA regions specifically bind to cellular metabolites using evolutionarily conserved sensing domains and modulate gene expression via adjacent downstream expression platforms, which carry gene expression signals. The regulation is achieved through the ligand-dependent formation of two alternative and mutually exclusive conformations involving the same RNA region. While X-ray crystallography cannot visualize dynamics of such dramatic conformational rearrangements, this method is pivotal to understand RNA–ligand interaction that stabilize the sensing domain and drive folding of the expression platform. X-ray crystallography can reveal local changes in RNA necessary for discriminating cognate and noncognate ligands. This chapter describes preparation of thiamine pyrophosphate riboswitch RNAs and its crystallization with different ligands, resulting in structures with local conformational changes in RNA. These structures can help to derive information on the dynamics of the RNA essential for specific binding to small molecules, with potential for using this information for developing designer riboswitch–ligand systems.