Kinetic/Thermodynamic/Structural studies of RNA folding

描述（由申请人提供）：关联RNA的结构、功能和动力学需要对RNA折叠的结构基础有基本的理解。这个提议的目的是阐明RNA折叠的结构基础，以及核酶在转录过程中如何折叠，这是细胞中折叠行为的模拟。将使用细菌核糖核酸酶P的RNA组分。自2003年以来，已经确定了这种核酶的四种晶体结构，使我们能够在理解这种大型核酶的折叠方面取得根本性的进展。目标1将揭示沿着折叠途径的大RNA的结构测定的折叠中间体的残留水平的分辨率，使用溶液研究/分子建模/低温电子显微镜的综合方法。这是RNA折叠途径的首次研究，将为结构形成的顺序、核心和外围结构之间的相互作用以及引导折叠和调节稳定性的金属离子-RNA相互作用提供前所未有的见解。目标2将比较具有相同核心但不同外围结构的同源RNA之间关键折叠中间体的结构。目标3将确定转录过程中改变折叠的机制，特别是细菌RNA聚合酶引入的显著停顿位点如何影响RNA-蛋白质复合物的折叠和组装。这个广泛的研究计划将揭示RNA折叠的结构基础，以及RNA折叠和RNA聚合酶之间的进化和机制联系。Narrative 核糖核酸（RNA）不仅是蛋白质合成的信使，它们还在折叠成精细结构后调节基因表达方面发挥重要作用。该项目旨在揭示RNA折叠的结构和机制基础，以揭示RNA折叠与功能的关系。

DESCRIPTION (provided by applicant): Correlating structure, function and dynamics of RNA requires fundamental understanding of structural basis in RNA folding. The objectives of this proposal are to elucidate the structural basis of RNA folding and how ribozymes fold during transcription, a mimic of folding behavior in the cell. The RNA component of bacterial ribonuclease P will be used. Four crystal structures of this ribozyme have been determined since 2003, enabling us to make fundamental advances in understanding the folding of this large ribozyme. Aim 1 will reveal the major events along the folding pathway of a large RNA by the structural determination of folding intermediates at the residue-level resolution using an integrated approach of solution studies/molecular modeling/cryo-Electron Microscopy. This first of its kind look at RNA folding pathways will offer unprecedented insights on the order of structure formation, the interplay between core and peripheral structures, and the role of metal ion-RNA interactions that guide folding and modulate stability. Aim 2 will compare structures of key folding intermediates among homologous RNAs that have the same core, but distinct peripheral structures. Aim 3 will identify mechanisms for altering folding during transcription, in particular, how prominent pause sites introduced by bacterial RNA polymerase affects folding and the assembly of a RNA-protein complex. This broad research program will reveal the structural basis of RNA folding, and the evolutionary and mechanistic link between RNA folding and RNA polymerase.Narrative Ribonucleic acids (RNA) are not only messengers for protein synthesis, they also play essential roles in regulating gene expression upon folding into elaborate structures. This project aims to uncover the structural and mechanistic basis of RNA folding in order to reveal relationships of RNA folding and function.