Computational Methods to Characterize Structure and Dynamics of the Nucleosome Core Particle

核小体核心颗粒 (NCP) 是染色质的基本组成部分，它是一个紧凑的、但 包装 DNA 的动态结构。 NCP 由带正电荷的组蛋白八聚核心组成， 被带负电的核小体 DNA 包围，核小体 DNA 围绕核心缠绕约 1.7 圈。有 染色质组织中的许多层次的结构，从 NCP 周围的 DNA 包装到 直径约 30 nm 的致密染色质纤维到中期染色体中更致密的染色质纤维 直径〜1.5微米。 DNA 结合蛋白（例如转录因子和染色质重塑剂）需要结合 核小体DNA。因此，为了发生转录，核小体 DNA 需要完全解开或 部分来自组蛋白核心。组蛋白核心的修饰，通常称为翻译后修饰 修饰（PTM），可以通过结构修饰更容易地获取核小体 DNA NCP 的动态。组蛋白或 DNA 的共价修饰通常控制基因活性 它们是最重要的表观遗传标记。此外，染色质成分的突变，例如 NCP 也被发现通常与癌症等疾病有关。这方面的创新之处 提案是发展分子动力学中的自由能方法来表征复杂反应 分层蛋白质-核酸组装体中的坐标。 PI 将开发新的计算 用于自由能方法的方法/反应坐标，用局部验证原子力场 合作者，并开发进一步的方法来预测单个氨基酸突变对核小体的影响 稳定性。我们期望这些计算研究的结果可以增加对 基本染色质结构实验研究的合理设计。 PI 实验室将 利用分子动力学中先进的采样方法来表征核小体核心的稳定性 颗粒。将阐明核酸序列、PTM 和致癌突变对稳定性的作用。 组蛋白尾部的力场将通过与当地合作者的 NMR 研究进行比较来验证。 将开发预测致癌突变对 NCP 稳定性影响的新方法。结果将 由 MSKCC 的合作者进行测试。期间开发的计算力场和方法 这项拟议工作的过程可用于表征核酸和蛋白质的相互作用 其他大分子组装体，例如病毒

The nucleosome core particle (NCP) is the basic building block of chromatin, which is a compact, yet dynamic structure that packages DNA. The NCP consists of a positively charged histone octameric core, surrounded by negatively charged nucleosomal DNA which is wrapped ~ 1.7 times around the core. There are many levels of structure in chromatin organization, ranging from the packaging of DNA around the NCP to compact chromatin fibers with diameters ~ 30 nm to denser chromatin fibers in metaphase chromosome with diameters ~ 1.5 µm. DNA binding proteins such as transcription factors and chromatin remodelers need to bind nucleosomal DNA. Thus, in order for transcription to occur, the nucleosomal DNA needs to unwrap fully or partially from the histone core. Modification of the histone core, commonly known as post-translational modification (PTM), can allow for easier access to nucleosomal DNA through modifications in the structure and dynamics of the NCP. Covalent modifications of either histone proteins or DNA often control gene activity and they are the most important epigenetic markers. Furthermore, mutations in chromatin components, such as the NCP, are also found to be commonly involved in diseases such as cancer. The innovative aspect of this proposal is the development of free energy methods in molecular dynamics to characterize complex reaction coordinates in hierarchical protein-nucleic acid assemblies. The PI will develop new computational methods/reaction coordinates to be used in free energy methods, validate atomistic force fields with local collaborators, and develop further methods to predict the impact of single amino acid mutations on nucleosome stability. We expect that the results from these computational investigations can add additional insight into the rational design of experimental investigations into fundamental chromatin structure. The PI’s laboratory will utilize advanced sampling methods in molecular dynamics to characterize the stability of the nucleosome core particle. The role of nucleic acid sequence, PTM, and oncogenic mutations on stability will be elucidated. Force fields for histone tails will be validated through comparison with NMR studies with local collaborators. New methodology to predict the effect of oncogenic mutations on NCP stability will be developed. Results will be tested by collaborators at MSKCC. The computational force fields and methodologies developed during the course of this proposed work could be used to characterize the interactions of nucleic acids and proteins in other macromolecular assemblies, for example, viruses