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

在植物和动物中，DNA被包装并保存在染色质纤维中。这些结构由核小体组成，核小体由包裹在组蛋白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，两个主要类别的染色质重塑因子的影响将与国家的最先进的计算机模拟解决。这些研究将揭示细胞调节染色体结构和动力学的物理基础，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最前沿的生物物理学研究。将开发超越传统科学界限的入门和高级课程，本科生和博士前和博士后学生将接受实践培训。该项目将增加代表性不足群体的学生参与研究，教育未来的初中和高中教师，并为下一代科学家提供培训。真核生物在染色质纤维中包装和维持它们的遗传密码。这些结构的基本单位是核小体，核小体是由8个组蛋白组成的复合物，它们包裹着约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替换经典组蛋白。 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，它只是在最近几年才变得明显，染色质表现出显着的构象动力学，其中的细节，以及重塑因子如何影响它们，仍然难以捉摸。本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。本项目将检验染色质重塑因子通过产生局部扰动，通过变构网络传播，诱导核小体和染色质纤维的全局变化来发挥作用的假设。为此，将进行生物分子模拟以解决（1）动态热点处的翻译后修饰的局部效应如何影响全局结构和动态，以及（2）组蛋白变体的效应如何通过核小体间动态网络传播到染色质纤维中。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。这项工作将与核磁共振光谱和小角度X射线散射领域的实验人员密切合作，其结果将有助于为未来模拟的发展提供信息，验证和指导。该项目将显著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.