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

基因调控和 DNA 修复中分子机器的高级计算模型

• 批准号: 10358509
• 负责人: Ivaylo Nikolaev Ivanov
• 金额: $ 47.42万
• 依托单位: GEORGIA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10358509
• 关键词: Aging; Biochemical Pathway; Cancer Etiology; Cells; Cockayne Syndrome; Complex; Computer Models; Coupled; Cryoelectron Microscopy; DNA; DNA Polymerase I; DNA Polymerase II; DNA Polymerase III; DNA Repair; DNA-Directed RNA Polymerase; Data; Defect; Development; Disease; Etiology; Foundations; Gene Expression; Gene Expression Regulation; Genetic Code; Genetic Diseases; Genetic Transcription; Genomic DNA; Goals; Hereditary Disease; Knowledge; Life; Malignant Neoplasms; Modeling; Molecular; Molecular Machines; Mutation; Nature; Process; Proteins; RNA; Regulation; Regulator Genes; Repair Complex; Science; Structure; Systems Biology; Transcription Factor TFIID; Transcriptional Regulation; Trichothiodystrophy; Work; Xeroderma Pigmentosum; cell growth; cell repository; disease phenotype; effective therapy; environmental change; experimental group; gene function; gene repair; human disease; insight; promoter; response; success; transcription factor TFIIH

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.

项目总结/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-动态生物分子机器， 将遗传密码转录成RNA。转录是一个复杂且高度调控的过程， 生长、分化、发展和对环境变化的所有反应。重要的是， 协调基因表达和修复的途径错综复杂地交织在一起。因此，在这方面， 许多人类疾病的起源可追溯到基因调节或DNA修复的缺陷。了解 作为基因表达和转录偶联DNA修复（TCR）基础的分子水平机制是 生物医学科学的巨大挑战。实现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。在最初的研究中，我们的实验 我们将计算模型与冷冻电子显微镜数据相结合， 来自所有三类RNA聚合酶（Pol I、Pol II和Pol III）。这些结构捕获了处于多种功能状态的PIC，涵盖了从启动子识别到启动子激活的路径。 形成一个熟练的延伸复合体。这些结果为整合提供了前所未有的机会。 建模连接实验观察到的状态，描绘DNA重塑的早期阶段， 转录和揭示转录调控的关键机制。具体来说，我们将利用 计算和结构系统生物学方法，以1）确定Pol I、II和III转录 机器识别并打开启动子DNA; 2）检查转录因子TFIID如何与 启动子DNA并作为组装PIC的平台;以及3）揭示两个启动子的关键功能。 识别的TCR主协调子、转录因子IIH（TFIIH）和Cockayne综合征B蛋白（CS B）。 我们的工作将受益于与世界级实验小组的协同合作互动， 验证和扩展我们的模型。计算和冷冻EM的并行进展将产生关键的见解， 基因调控复合物的结构、动力学和功能，同时与遗传疾病直接相关 表型因此，该项目的成功将产生重大影响-无论是在了解癌症的病因学， 和遗传性遗传疾病，并提供一个结构框架，以设计有效的治疗方法。