Advanced Computational Modeling of Molecular Machines in Gene Regulation and DNA Repair

项目摘要/摘要 基因组DNA是细胞的信息库，编码维持生命所需的无数蛋白质。 为了利用这些信息，细胞依赖于RNA聚合酶--一种动态的生物分子机器，它首先 将遗传密码转录成RNA。转录是一个复杂和高度调控的过程，它控制着细胞 增长、分化、发展和对环境变化的所有反应。重要的是，生物化学 协调基因表达和修复的途径错综复杂。因此， 许多人类疾病的起源可以追溯到基因调控或DNA修复的缺陷。了解 基因表达和转录偶联DNA修复(TCR)的分子水平机制是 生物医学科学领域的重大挑战。这一目标的进展受到了规模、复杂性和 完成转录和TCR的组件的动态性质。在我们的实验的初步研究中 合作者：我们将计算模型与低温电子显微镜数据相结合来确定结构 所有三类RNA聚合酶(Pol I、Pol II和Pol)的转录预起始复合体(PIC) 三)。这些结构捕捉到了覆盖从启动子识别到 形成熟练的伸长复合体。这些结果提供了一个前所未有的机会， 建模以连接实验观察到的状态，描绘早期阶段的DNA重塑 转录，并揭示转录调控的关键机制。具体地说，我们将利用 计算和结构系统生物学方法1)确定Pol I、II和III转录的方式 机器识别和打开启动子DNA；2)检测转录因子TFIID如何与 启动子DNA，并作为组装PIC的平台；以及3)揭示两个 识别TCR主协调子、转录因子IIH(TFIIH)和Cockayne综合征B蛋白(CSB)。 我们的工作将受益于与世界级实验小组的协同协作互动，以告知， 验证并扩展我们的模型。计算和低温电磁的并行进展将产生对 与遗传病直接相关的基因调控复合体的结构、动力学和功能 表型。因此，该项目的成功将对了解癌症的病因产生重大影响 和遗传性遗传疾病，并提供了一个结构框架来设计有效的治疗方法。

PROJECT SUMMARY/ABSTRACT Genomic DNA is the information repository of the cell, encoding the myriad of proteins required to sustain life. To harness this information, cells depend on RNA polymerases - dynamic biomolecular machines that first transcribe the genetic code into RNA. Transcription is a complex and highly regulated process that governs cell growth, differentiation, development and all responses to environmental change. Importantly, the biochemical pathways that orchestrate the expression and repair of genes are intricately intertwined. As a consequence, many human diseases trace their origins to deficiencies in gene regulation or DNA repair. Understanding the molecular-level mechanisms that underlie gene expression and transcription-coupled DNA repair (TCR) is a grand challenge in biomedical science. Progress toward this goal has been hindered by the size, complexity and dynamic nature of the assemblies that accomplish transcription and TCR. In initial studies with our experimental collaborators we combined computational modeling with cryo-electron microscopy data to determine structures of transcription preinitiation complexes (PICs) from all three classes of RNA polymerases (Pol I, Pol II and Pol III). The structures captured the PICs in multiple functional states covering the path from promoter recognition to the formation of a proficient elongation complex. These results offer an unprecedented opportunity for integrative modeling to connect the experimentally observed states, delineate DNA remodeling during the early stages of transcription and uncover the critical mechanisms of transcription regulation. Specifically, we will leverage computational and structural systems biology approaches to 1) determine how the Pol I, II and III transcription machineries recognize and open promoter DNA; 2) examine how the transcription factor TFIID associates with promoter DNA and serves as a platform for assembling the PIC; and 3) uncover the key functions of two recognized TCR master coordinators, transcription factor IIH (TFIIH) and Cockayne Syndrome B protein (CSB). Our work will benefit from synergistic collaborative interactions with world-class experimental groups to inform, validate, and extend our models. Parallel advances in computation and cryo-EM will yield key insights into the structure, dynamics and function of gene regulatory complexes while making direct connection to genetic disease phenotypes. Success of the project will thus have major impacts - both in understanding the etiology of cancers and inherited genetic disorders and in offering a structural framework to devise effective treatments.