Fundamental Studies of RNA Folding

描述(由申请者提供)：该计划项目拨款汇集了七名主要研究人员，他们致力于了解RNA分子折叠成其生物活性结构的原理。该提案包括四个项目和一个资源核心，所有这些项目都由一个中心假设联系在一起：RNA折叠可以从简化论者的角度进行理解和最终预测。在结构和分子生物学的早期，RNA看起来就像一个简单的信使。在过去的二十年里，RNA在生物、化学和物理方面发挥了不同的作用，但我们对其机理的理解仍然有限。深入研究RNA的物理行为将有助于全面描述基因的表达及其调控。特别是，预测性和定量的理解将在分子和系统生物学水平上催化理性RNA工程，并最终促进针对或涉及RNA的合理治疗干预。我们的组件项目从简单到复杂。项目1研究围绕简单螺旋的离子大气，并使用集成的实验-计算反馈回路来发展对静电学的理解，静电学是影响RNA行为和相互作用的最大和最一般的力。项目2的重点是螺旋-连接-螺旋基序，即RNA三级结构的构建块。我们将开发和应用新的实验和分析方法来全面描述这些元素的构象系综。项目3确定了RNA在展开、折叠和中间状态下的构象系综，并定义了这些状态之间的跃迁的能量学。我们将比较P4-P6 RNA和RNA/蛋白质复合体的行为与根据其元素的性质预测的行为，如项目2所描述的。因此，我们直接测试了这样一个假设，即复杂RNA的能量学和行为可以根据它们部分的总和来理解，这个假设如果为真，将导致预测RNA折叠和能量学的一般能力。项目4建立在其他项目中开发的还原论框架的基础上，现在解决RNA折叠动力学，测试定量预测，并开发新的系统方法来剖析共转录折叠的影响。总之，这些研究将揭示定义RNA的物理、化学和生物行为的基本属性和行为，并催化对RNA的从描述性到定量预测性理解的转变。

DESCRIPTION (provided by applicant): This Program Project Grant brings together seven principal investigators committed to understanding the principles by which RNA molecules fold into their biologically active structures. The proposal comprises four Projects and a Resource Core, all bound together by a central hypothesis: RNA folding can be understood and eventually predicted from a reductionist perspective. RNA looked like a simple messenger in the early days of structural and molecular biology. The last two decades have demonstrated diverse biological, chemical, and physical roles of RNA, and yet our mechanistic understanding remains limited. Deep investigation of the physical behavior of RNA will enable a full description of gene expression and its control. In particular, a predictive and quantitative understanding will catalyz rational RNA engineering at the molecular and systems biology levels and ultimately facilitate rational therapeutic interventions that target or involve RNA. Our component projects build from simple to complex. Project 1 studies the ion atmosphere that surrounds simple helices and uses an integrated experimental-computational feedback loop to develop an understanding of electrostatics, the largest and most general force influencing the behavior and interactions of RNA. Project 2 focuses on helix-junction-helix motifs, the building blocks of RNA tertiary structure. We will develop and apply novel experimental and analytical approaches to fully describe the conformational ensemble for these elements. Project 3 determines the conformational ensembles of RNAs in their unfolded, folded, and intermediate states and defines the energetics of the transitions between these states. We will compare the behaviors of P4-P6 RNA and RNA/protein complexes to the behavior predicted from the properties of their elements, as delineated from Project 2. We thereby directly test the hypothesis that the energetics and behavior of complex RNAs can be understood from the 'sum of their parts', a hypothesis that if true, will lead to a general ability to predict RNA folding and energetics. Projct 4 builds on the reductionist framework developed in the other projects to now address RNA folding kinetics, testing quantitative predictions and developing novel systematic approaches to dissect the influence of co-transcription folding. Together, these studies will uncover basic properties and behaviors that define the physical, chemical, and biological behavior of RNA and catalyze a transformation from a descriptive to quantitative predictive understanding of RNA.