CAREER: Chromatin Folding from the Bottom-up

染色质，包装DNA的看似惰性的结构，在调节基因表达中起着积极的作用。已经鉴定了具有不同组蛋白修饰模式和选择性蛋白质可及性的多种染色质状态。该研究将导致这些状态之间的差异的详细结构表征，以揭示染色质结构-功能关系，并阐明基因调控的分子机制。这项研究的见解可以启发新的癌症治疗策略的设计，使用小分子靶向染色质调节剂和调节染色质结构，以恢复正常的基因表达谱。我们研究中的技术创新将引起更广泛的建模社区的极大兴趣。它们可以应用于其他系统的激活过程中发生的时间范围很广。研究中使用的分子模拟技术，当与虚拟现实工具集相结合时，可以产生令人难忘的交互式学习体验的演示。这些示范可以激发学生对化学和分子生物学的兴趣。他们将被纳入一个外展计划，并提交给初中和高中学生在大波士顿地区。该项目旨在研究染色质组织使用近原子力场与隐式溶剂化。力场在描述蛋白质-蛋白质和蛋白质-DNA相互作用方面的准确性将得到系统性的提高。利用先进的采样和自由能计算算法，我们将计算最可能的原纤维结构形成的途径，研究染色质折叠的动力学和机制。将原纤维结构与沿着折叠路径的无序构型之间的稳定性进行比较，可以提供对原位检测30 nm纤维的挑战的深入了解。该研究还将通过表征兼性和组成性异染色质来研究关键蛋白质调节剂对染色质组织的影响。蛋白质/染色质复合物的高分辨率结构可以阐明染色质调节剂如何介导组蛋白标记传播的长距离核小体接触。它们可以进一步揭示相分离如何驱动染色质进入FRAP实验中揭示的浓缩但动态的构象。与实验小组的密切合作也将证明对验证模型准确性和伪造预测至关重要。拟议的研究将显着提高我们的分子决定因素，驱动染色质在体外和原位折叠的理解，并有助于将染色质建模向定量和预测方向发展。该项目由生物科学理事会分子和细胞生物科学部的分子生物物理学和遗传机制集群支持。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Chromatin, the seemingly inert structure that packages the DNA, plays an active role in regulating gene expression. Multiple chromatin states with distinct patterns of histone modifications and selective protein accessibility have been identified. This research will lead to a detailed structural characterization of the differences between these states to reveal the chromatin structure-function relationship and elucidate the molecular mechanisms of gene regulation. Insights from this study could inspire the design of new cancer therapeutic strategies using small molecules to target chromatin regulators and modulate chromatin structure to restore normal gene expression profiles. Technological innovations from our study will be of great interest to the more general modeling community. They can be applied to other systems with activated processes that occur over a wide range of timescales. Molecular simulation techniques used in the research, when combined with virtual reality toolsets, could produce demonstrations for a memorable and interactive learning experience. These demonstrations could inspire students’ interest in chemistry and molecular biology. They will be incorporated into an outreach program and presented to middle school and high school students in the Greater Boston area. The project aims to study the chromatin organization using a near-atomistic force field with implicit solvation. The force field's accuracy in describing protein-protein and protein-DNA interactions will be systematically improved. Using advanced sampling and free energy computation algorithms, we will compute the most probable pathways for fibril structure formation to study the dynamics and mechanism of chromatin folding. Comparing the stability between fibril structures with that of disordered configurations along the folding pathway may provide insight into the challenge of detecting the 30nm fiber in situ. The research will also investigate the impact of key protein regulators on chromatin organization by characterizing both facultative and constitutive heterochromatin. High-resolution structures for protein/chromatin complexes can elucidate how chromatin regulators mediate long-range nucleosomal contacts for histone mark propagation. They can further reveal how phase separation drives chromatin into condensed but dynamic conformations revealed in FRAP experiments. Close collaboration with experimental groups will also prove crucial for validating model accuracy and falsifying predictions. The proposed research will significantly enhance our understanding of the molecular determinants that drive chromatin folding in vitro and situ and help move chromatin modeling towards quantitative and predictive directions. This project is supported by the Molecular Biophysics and Genetic Mechanisms Clusters of the Molecular and Cellular Biosciences Division in the Directorate for Biological Sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.