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

表征核小体核心颗粒结构和动力学的计算方法

基本信息

批准号：
10442803
负责人：
Sharon Marie Loverde
金额：
$ 49.44万
依托单位：
COLLEGE OF STATEN ISLAND
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10442803
关键词：
Affect Amino Acids Base Sequence Binding Biological Assay Biophysics Caliber Characteristics Charge Chicago Chromatin Chromatin Fiber Chromatin Structure Chromosomes Cities Collaborations Complex Computing Methodologies DNA DNA Packaging DNA Sequence DNA-Binding Proteins Development Disease Event Experimental Designs Faculty Free Energy Genes Genetic Transcription Goals Grant Histones Investigation Island Laboratories Malignant Neoplasms Memorial Sloan-Kettering Cancer Center Mentors Metaphase Methodology Methods Modification Molecular Mutation NMR Spectroscopy New York New York City Nucleic Acids Nucleosome Core Particle Nucleosomes Oncogenic Pathway interactions Polymerase Positioning Attribute Post-Translational Modification Site Post-Translational Protein Processing Protein Dynamics Protein Region Proteins Reaction Recording of previous events Research Role Sampling Structure Students Tail Talents Techniques Testing Time Universities Virus Work career chromatin remodeling college computerized tools dimer epigenetic marker helicase histone modification human disease innovation insight macromolecular assembly member models and simulation molecular dynamics molecular modeling oncohistone programs rational design solid state nuclear magnetic resonance transcription factor undergraduate student

项目摘要

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

核小体核心粒子（NCP）是染色质的基本构建块，这是一个紧凑的包装DNA的动态结构。 NCP由一个带正电荷的组蛋白八聚体核心组成被带负电荷的核小体DNA包围，围绕核心包裹约1.7倍。有染色质组织中的许多级别结构，从NCP周围的DNA包装到直径约30 nm的紧凑型染色质纤维与中期染色体中的染色质纤维，直径〜1.5 µm。 DNA结合蛋白（例如转录因子和染色质重塑）需要结合核小体DNA。为了进行转录，核小体DNA需要完全解开或部分来自Hisstone核心。修改Hisstone核心，通常称为翻译后修改（PTM），可以通过结构的修改和 NCP的动力学。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，染色质成分中的突变，例如 NCP也被发现通常与癌症等疾病有关。创新的方面提案是分子动力学中自由能法的发展，以表征复杂反应分层蛋白核酸组件中的坐标。 PI将开发新的计算方法/反应坐标用于自由能法，验证与局部的原子力场合作者，并开发进一步的方法来预测单氨基酸突变对核小体的影响稳定。我们期望这些计算调查的结果可以增加对实验投资对基本染色质结构的合理设计。 PI的实验室将利用分子动力学中的先进采样方法来表征核小体核心的稳定性粒子。核酸序列，PTM和致癌突变对稳定的作用将得到阐明。组蛋白尾巴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稳定性的影响的新方法。结果将由MSKCC的合作者测试。在这项提出的工作的过程可用于表征核酸和蛋白质中的相互作用其他大分子组件，例如病毒