Structural biology of chromatin in vitro and in cells

体外和细胞内染色质的结构生物学

• 批准号: 10190974
• 负责人: Galia Debelouchina
• 金额: $ 37.04万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10190974
• 关键词: Acetylation; Age; Biological; Biology; Cell Differentiation process; Cell Nucleus; Cells; Chemicals; Chromatin; Chromatin Structure; Complex; DNA; DNA Packaging; DNA Sequence; Data; Development; Disease; Environment; Five-Year Plans; Gene Silencing; Heterochromatin; Human body; In Vitro; Investigation; Laboratories; Light; Liquid substance; Malignant Neoplasms; Methodology; Methylation; Modification; Molecular; NMR Spectroscopy; Normal Cell; Nuclear Magnetic Resonance; Output; Phase; Polymers; Post-Translational Protein Processing; Process; Protein Dynamics; Proteins; Resolution; Signal Transduction; Stress; Structure; Technology; Therapeutic Agents; Translating; base; biological systems; biophysical properties; design; genetic information; insight; meter; protein complex; protein structure; solid state nuclear magnetic resonance; structural biology; tool

Project Summary The laboratory led by PI Galia Debelouchina has the following objectives: 1) The development of structural biology methodology to study complex and dynamic biological assemblies in vitro, and 2) The extension of these methodologies for structural biology investigations in the cellular environment. Our methodology development combines solid-state nuclear magnetic resonance (NMR) spectroscopy with state-of-the-art chemical biology tools for the comprehensive description of biological systems both in vitro and in cells. We use these technologies to investigate chromatin, a complex protein-DNA polymer responsible for the packaging of genetic information in the nucleus. Over the next five years, we plan to focus on the following projects: 1) The influence of protein post-translational modifications on chromatin structure and dynamics. Modifications such as methylation and acetylation have profound effects on the compaction of the chromatin polymer and the accessibility of the packaged DNA. We plan to investigate the molecular mechanisms of chromatin compaction and decompaction imparted by these modifications at atomic resolution using solid-state NMR spectroscopy. We expect that this study will provide unique insights into the biophysical properties of the chromatin polymer and how they can be translated into functional biological outputs. 2) The molecular basis of heterochromatin formation. Heterochromatin compartments are associated with gene silencing and repetitive DNA sequences, and their formation is a vital step in cell differentiation and development. Recent hypotheses indicate that they are formed through liquid-liquid phase separation. We plan to investigate the interactions that promote phase separation and to provide the first molecular description of this process. 3) Development of NMR-based tools for structural biology in cells. Here, we plan to focus on the design and implementation of a strategy to target a specific protein in the cellular milieu and to increase its NMR signals selectively over the cellular background. Ultimately, we aim to develop a selective and sensitive NMR methodology that will allow us to record relevant structural data of endogenous amounts of cellular proteins. Such tools will provide the unprecedented opportunity to build an atomic resolution picture of the cellular milieu and to investigate changes in protein structure and dynamics as we stress, age or treat cells with therapeutic agents.

项目概要 PI Galia Debelouchina 领导的实验室有以下目标： 1) 结构材料的开发 体外研究复杂和动态生物组装的生物学方法，以及 2) 的扩展 这些用于细胞环境中结构生物学研究的方法。我们的方法论 开发将固态核磁共振 (NMR) 光谱与最先进的技术相结合 用于全面描述体外和细胞内生物系统的化学生物学工具。我们 使用这些技术来研究染色质，这是一种复杂的蛋白质-DNA 聚合物，负责 细胞核中遗传信息的包装。未来五年，我们计划重点做好以下工作 项目：1）蛋白质翻译后修饰对染色质结构和动力学的影响。 甲基化和乙酰化等修饰对染色质的压缩具有深远的影响 聚合物和包装 DNA 的可及性。我们计划研究其分子机制 使用固态在原子分辨率下由这些修饰引起的染色质压缩和解压缩 核磁共振波谱。我们期望这项研究将为生物物理特性提供独特的见解。 染色质聚合物以及它们如何转化为功能性生物输出。 2）分子基础 异染色质形成。异染色质区室与基因沉默和重复相关 DNA序列及其形成是细胞分化和发育的重要步骤。最近的假设 表明它们是通过液-液相分离形成的。我们计划调查以下相互作用 促进相分离并提供该过程的第一个分子描述。 3）开发 基于 NMR 的细胞结构生物学工具。在这里，我们计划重点关注一个 策略针对细胞环境中的特定蛋白质并选择性地增加其 NMR 信号 细胞背景。最终，我们的目标是开发一种选择性且灵敏的 NMR 方法，该方法将允许 我们记录内源性细胞蛋白质数量的相关结构数据。此类工具将提供 构建细胞环境的原子分辨率图像并进行研究的前所未有的机会 当我们对细胞施加压力、老化或用治疗剂治疗时，蛋白质结构和动力学会发生变化。