Fundamental Studies of RNA Folding

描述（由申请人提供）：该计划项目资助汇集了七名主要研究人员，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，所有这些都由一个中心假设联系在一起：RNA折叠可以被理解，并最终从还原论的角度预测。在结构和分子生物学的早期，RNA看起来像一个简单的信使。在过去的20年里，我们已经证明了RNA的多种生物、化学和物理作用，但我们对它的机制的理解仍然有限。对RNA物理行为的深入研究将使我们能够全面描述基因表达及其控制。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合理的RNA工程，并最终促进靶向或涉及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气氛，并使用综合的实验-计算反馈回路来理解静电，这是影响RNA行为和相互作用的最大和最普遍的力。项目2的重点是螺旋-连接-螺旋基序，RNA三级结构的构建模块。我们将开发和应用新的实验和分析方法来充分描述这些元素的构象合奏。项目3确定了RNA在未折叠、折叠和中间状态下的构象集合，并定义了这些状态之间转换的能量学。我们将比较P4-P6 RNA和RNA/蛋白质复合物的行为与根据其元素性质预测的行为，如项目2所述。因此，我们直接测试的假设，复杂的RNA的能量学和行为可以理解从“他们的部分的总和”，一个假设，如果真的，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框架的基础上，现在解决RNA折叠动力学，测试定量预测和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，化学和生物学行为的基本性质和行为，并催化从描述性到定量预测性理解RNA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.