Theoretical Modeling of Protein-Driven Chromosomal Dynamics and Biological Function

该研究项目旨在加强理论和模拟方法的使用，以解决具有基础和实际影响的关键生物学问题。该项目中使用的模型来自聚合物和软材料物理学领域，并为涉及活细胞和生物体的问题注入了新的物理概念和理解。体外和体内实验测量的参与将为定量理论在实际生物学问题中的实施提供指导。该计划的结果将通过出版物、会议和模拟工具的在线存储库以及描述、新闻稿和教育工具广泛传播，供广泛的科学界和公众使用。PI的实验室是培养能够解决生命系统中各种基础和应用问题的定量生物学家的理想环境，实验室对多样性和教育发展的承诺使该小组的校友为学术和工业研究做出了重大贡献。该项目为正在接受儿童癌症和其他疾病治疗的高中生开发和实施实验室科学和工程教学模块。该项目在露西尔·帕卡德儿童医院的医院学院进行试点，项目负责人邀请斯坦福大学的本科生和研究生来开发该项目，为学生提供了一个令人兴奋的机会，通过更广泛的接触来丰富他们的教育经验。目前正在努力在全国范围内广泛传播这一方案，作为医院-学校教育的一般实验室科学课程。原核和真核细胞都有一个艰巨的任务，即紧凑地包装它们巨大的基因组，同时保持基因调控控制和染色体DNA以稳健的方式复制和分离的能力。活细胞内的染色体DNA被许多蛋白质操纵和访问，这些蛋白质在整个细胞周期中执行许多功能。染色体DNA的物理操作是其功能的核心，实现预测和解释染色体组织和动力学的基本定量框架将有助于我们对生命系统的理解。本研究计划旨在研究原核细胞中涉及染色体DNA的三个主要生物学过程：调节、分离和组织。这些努力被描述为三个互补的重点，这些重点建立了对影响染色体组织和动力学的蛋白质协调功能的基本物理见解。在推力1中，PI解决了DNA超卷曲对基因调控的影响。本研究的重点是两种典型的调节蛋白（Lac阻遏蛋白和ë阻遏蛋白），它们是调节蛋白在多个位点参与DNA形成调节复合物的例子。细胞对超卷曲的控制引起基因调控的重大变化，这一推力将直接解决拓扑异构酶和调控蛋白如何协调其功能。推力2旨在通过ParABS系统的高度保守的原核分离装置解决DNA的分离问题。这个系统的神秘功能不同于运动蛋白或细胞骨架蛋白，因为它没有明显的发力功能。这些努力将旨在解决染色体动力学中的时间相关性如何导致ParABS系统的燃烧桥机制中的定向运动。在Thrust 3中，PI将解决RNA聚合酶和凝缩蛋白在决定染色体组织中的相互作用。RNA聚合酶产生的活性力沿着DNA取代蛋白质，这些非平衡过程对染色体组织的影响将在这篇文章中得到解决，为细胞内有组织结构域的形成和维持提供新的物理见解。该项目由物理系的生命系统物理学项目和分子与细胞生物科学系的遗传机制集群共同支持。

This research project aims to enhance the use of theoretical and simulation approaches to address critical biological problems that have both fundamental and practical impact. The models used in this project draw from the fields of polymer and soft-materials physics and infuse novel physical concepts and understanding into problems involving living cells and organisms. The engagement of both in vitro and in vivo experimental measurements will provide guidance on the implementation of quantitative theory into practical biological problems. Results from this program will be widely disseminated through publications, conferences, and an online repository of simulation tools as well as descriptions, press releases, and educational tools for use by the broad scientific community and the general public. The lab of the PI is an ideal environment for training quantitative biologists who are capable of tackling a diverse range of fundamental and applied problems in living systems, and the lab's commitment to diversity and educational development has led to alumni of the group who are making major contributions to both academic and industrial research. This program develops and implements laboratory science and engineering teaching modules for the education of high school students who are being treated for childhood cancer and other illnesses. This program is piloted at the Hospital School at the Lucile Packard Children's Hospital, and the PI engages undergraduate and graduate students at Stanford to develop the program, resulting in an exciting opportunity for students to enrich their educational experience with broader outreach. Ongoing efforts aim to broadly disseminate this program nationally as a general laboratory science curriculum for hospital-school education.Prokaryotic and eukaryotic cells have the daunting task of compactly packaging their immense genome while simultaneously maintaining gene regulatory control and the ability for chromosomal DNA to be replicated and segregated in a robust manner. Chromosomal DNA within living cells is manipulated and accessed by a host of proteins that perform numerous functions that are orchestrated throughout the cellcycle. The physical manipulation of chromosomal DNA is central to its function, and achieving a fundamental quantitative framework for predicting and interpreting chromosomal organization and dynamics would be instrumental to our understanding of living systems. This research program aims to tackle three major biological processes involving chromosomal DNA in prokaryotic cells: regulation, segregation, and organization. These efforts are delineated into three complementary thrusts that establish fundamental physical insight into the orchestrated function of proteins that influence chromosomal organization and dynamics. In Thrust 1, the PI addresses the impact of DNA supercoiling on gene regulation. This effort focuses on two prototypical regulatory proteins (Lac repressor and ë repressor) that serve as examples of regulatory proteins that engage DNA at multiple sites to form a regulatory complex. Cellular control of supercoiling elicits major changes in gene regulation, and this thrust will directly address how topoisomerases and regulatory proteins orchestrate their function. Thrust 2 aims to address segregation of DNA through the ParABS system's highly conserved prokaryotic segregation apparatus. The mysterious function of this system is unlike motor or cytoskeletal proteins in that there is no obvious force generating function. The efforts will aim to resolve how temporal correlations in chromosomal dynamics result in directed motion in a burning-bridge mechanism for the ParABS system. In Thrust 3, the PI will tackle the interplay between RNA polymerase and condensin in dictating chromosomal organization. Active forces generated by RNA polymerase displace proteins along DNA, and the resulting impact of these nonequilibrium processes on chromosomal organization will be addressed in this thrust, providing new physical insight into the formation and maintenance of organized domains within the cell.This project is being jointly supported by the Physics of Living Systems program in the Division of Physics and the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences.