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成分，染色质是一种致密的 包装DNA的动态结构。NCP由一个带正电的组蛋白八聚体核心组成， 被带负电荷的核小体DNA包围，核小体DNA被核心包裹约1.7倍。确实有 染色质组织中的许多层次的结构，从围绕NCP的DNA包装到 中期染色体上直径约30 nm的致密染色质纤维到致密的染色质纤维。 直径~1.5微米。转录因子和染色质重构体等DNA结合蛋白需要结合 核小体DNA。因此，为了进行转录，核小体DNA需要完全展开或 部分来自组蛋白核心。组蛋白核心的修饰，通常被称为翻译后 修饰(PTM)，可以允许更容易地通过结构和 全国大会党的动态。组蛋白或DNA的共价修饰通常控制基因活性和 它们是最重要的表观遗传标记。此外，染色质成分的突变，如 NCP，也被发现与癌症等疾病有关。它的创新之处在于 建议发展分子动力学中的自由能方法来表征复杂反应。 在分级蛋白质-核酸组装中的坐标。PI将开发新的计算 在自由能方法中使用的方法/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一氨基酸突变对核小体的影响 稳定性。我们预计，这些计算调查的结果可以增加对 染色质基本结构实验研究的合理设计。私家侦探的实验室 利用先进的分子动力学取样方法表征核小体核心的稳定性 粒子。核酸序列、PTM和致癌突变对稳定性的作用将被阐明。 组蛋白尾部的力场将通过与当地合作者的核磁共振研究进行比较来验证。 将开发新的方法来预测致癌突变对NCP稳定性的影响。结果将 由MSKCC的合作者进行测试。计算力领域和方法是在 这项拟议的工作可以用来描述核酸和蛋白质之间的相互作用。 其他大分子组件，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