CAREER: The Effects of Post-translational Modifications and Histone Variants on Chromatin Fiber Dynamics

在动植物中，DNA被包装并保持在染色质纤维中。这些结构由核小体组成，核小体由包裹在称为组蛋白的蛋白质周围的核酸分子组成。染色质重塑因子改变核小体，从而调节染色质纤维的整体结构和稳定性，并调节基因表达。在这个项目中，两类主要的染色质重塑因子的影响将通过最先进的计算机模拟来解决。这些研究将揭示细胞调节染色体结构和动态的物理基础，以及这如何影响基因表达的重要过程。该项目还将使整个教育系统的学生接触到尖端的生物物理学研究。将开发超越传统科学界限的入门和高级课程，本科生、博士后和博士后将接受实践培训。该项目将增加来自代表不足群体的学生对研究的参与，教育未来的初中和高中教师，并为下一代科学家提供培训。真核生物将它们的遗传密码包装在染色质纤维中并保持其遗传密码。这些结构的基本单位是核小体，它是一个由八种组蛋白组成的复合体，包裹着大约147个碱基对的DNA。通过改变核小体的生化特性，细胞调节染色质的结构和稳定性，从而影响基因表达。发生这种情况的两个主要机制是组蛋白残基的翻译后修饰和用组蛋白变体取代规范的组蛋白。这些染色质重塑因子对核小体结构和稳定性的影响已被广泛研究。然而，直到最近几年才变得明显，染色质表现出显著的构象动力学，其中的细节，以及重塑因素如何影响它们，仍然难以捉摸。该项目的目标是确定翻译后修饰和组蛋白变体如何影响核小体内和核小体间的动力学，作为调节基因表达的一种手段。该项目将测试染色质重塑因子通过产生局部扰动来发挥作用的假设，这些局部扰动通过变构网络传播，从而诱导核小体和染色质纤维的整体变化。为此，将进行生物分子模拟以研究(1)动态热点的翻译后修饰的局部效应如何影响全球结构和动力学，以及(2)组蛋白变体的效应如何通过核小体间动力学网络传播到染色质纤维。这将通过全原子和粗粒分子动力学模拟来完成，并将利用传统的、增强的采样和自由能方法。这项工作将与在核磁共振光谱学和小角X射线散射领域工作的实验员密切合作进行，他们的结果将有助于了解、验证和指导未来模拟的发展。该项目将极大地扩展核小体功能与其构象动力学密切相关的新兴范式，并提供对自然调节多组分蛋白质/DNA系统的机制的见解。

In plants and animals, DNA is packaged and maintained in chromatin fibers. These structures are comprised of nucleosomes, which are made up of nucleic acid molecules wrapped around proteins called histones. Chromatin remodeling factors alter the nucleosome, thereby regulating the overall structure and stability of chromatin fibers, and modulating gene expression. In this project, the effects of two major classes of chromatin remodeling factors will be addressed with state-of-the-art computer simulations. These studies will reveal the physical basis by which cells modulate the structure and dynamics of chromosomes, and how this affects the vital process of gene expression. This project will also expose students throughout the educational system to cutting-edge biophysics research. Introductory and advanced courses will be developed that transcend traditional scientific boundaries and undergraduate and pre-and post-doctoral students will receive hands-on training. This project will increase participation in research for students from underrepresented groups, educate future middle and high school teachers, and provide training to the next generation of scientists. Eukaryotes package and maintain their genetic code in chromatin fibers. The fundamental unit of these structures is the nucleosome, a complex of eight histone proteins that wrap ~147 base pairs of DNA. By altering the biochemical properties of the nucleosome, the cell regulates the structure and stability of chromatin and thus influences gene expression. Two of the primary mechanisms by which this occurs are post-translational modifications of histone residues and replacement of canonical histones with histone variants. The effects of these chromatin remodeling factors on the structures and stabilities of nucleosomes have been extensively studied. However, it is only in recent years that it has become evident that chromatin exhibits significant conformational dynamics, the details of which, and how remodeling factors influences them, remain elusive. The goal of this project is to determine how post-translational modifications and histone variants affect intra- and inter-nucleosome dynamics as a means of regulating gene expression. This project will test the hypothesis that chromatin remodeling factors function by creating local perturbations that propagate through allosteric networks to induce global changes in nucleosomes and chromatin fibers. To do this, biomolecular simulations will be performed to address (1) how the local effects of post-translational modifications at dynamic hotspots influence global structures and dynamics, and (2) how the effects of histone variants propagate through inter-nucleosomal dynamical networks into chromatin fibers. This will be done with all-atom and coarse-grain molecular dynamics simulations, and will utilize conventional, enhanced sampling, and free energy methods. This work will be performed in close collaboration with experimentalists working in the fields of nuclear magnetic resonance spectroscopy and small angle X-ray scattering, whose results will help inform, validate, and guide the development of future simulations. This project will significantly expand emerging paradigm that nucleosome functions are closely related to their conformational dynamics and provide insights into the mechanism by which nature modulates multicomponent protein/DNA systems.