CAREER: Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Loaders

智力优势：染色体DNA的复制是通过一种名为复制体的动态蛋白质组装完成的。增殖细胞核抗原(增殖细胞核抗原)等过程性钳夹是复制体的重要组成部分，确保了过程性复制。滑动夹在细胞周期控制和DNA修复蛋白的招募中也起到了多功能的支架作用，几乎参与了DNA新陈代谢的各个方面。它们非凡的环形结构使它们能够在拓扑上环绕DNA并沿着DNA滑动。为了实现不同的功能，夹子必须在稳定性和打开能力之间取得微妙的平衡，以便加载到DNA上。在涉及ATP结合和水解的循环中，通过钳夹加载器的作用，在DNA引物-模板连接处，加工性钳子被打开和重新密封。该项目旨在描述可加工夹具打开的详细机制，确定夹具装载器的作用，并描述在夹具装夹周期的每个步骤中ATP的利用情况。将构建循环中中间体的原子模型，以描述导致夹具打开和重合的构象转变。这个项目将实现对钳位加载过程的统一的分子水平的描述，并提供对钳位相关活动及其在基因组复制和基因组保真度调节中的重要作用的洞察。更广泛的影响：该项目将极大地影响我们对控制遗传完整性的生物学机制的了解，并对生物技术、环境和生物能源研究产生广泛影响。该项目融合了新的方法和新颖的应用，以创建一个多学科的研究和教育计划，对所有水平的学生来说都是有趣和具有挑战性的。特别是，将向学生介绍广泛的理论方法、分子建模算法和高性能计算(HPC)体系结构。课程改革将涉及为佐治亚州立大学(GSU)的研究生计算化学课程开发一个新的模块(高级采样、QM/MM和AIMD方法)，并为GSU的计算化学中心引入高级建模研讨会。此外，分子可视化将被用作吸引高中生进入STEM领域的有效工具，重点是将弱势背景的学生带到格拉斯哥州立大学校园。研究和教育目标紧密相连，教育计划接触到更广泛的社区，目标是将化学、生物和计算整合到整个课程中，积极促进多样性，鼓励各级学生--从高中生到高级研究生--对科学的兴趣。

Intellectual Merit: Replication of chromosomal DNA is accomplished by a dynamic protein assembly termed the replisome. Processivity clamps such as Proliferating Cell Nuclear Antigen (PCNA) are important constituents of the replisome that ensure processive replication. Sliding clamps also act as versatile scaffolds in the recruitment of cell-cycle control and DNA repair proteins and are engaged in almost every aspect of DNA metabolism. Their remarkable ring-shaped architecture allows them to topologically encircle and slide along DNA. To fulfill their varied functions, the clamps have to strike a delicate balance between stability and the ability to open in order to be loaded onto DNA. Processivity clamps are opened and resealed at DNA primer-template junctions by the action of a clamp loader in a cycle involving ATP binding and hydrolysis. The project aims to delineate the detailed mechanisms for processivity clamp opening, determine the role of the clamp loader and describe the utilization of ATP during each step of the clamp loading cycle. Atomistic models for the intermediates in the cycle will be constructed to describe the conformational transitions leading to clamp opening and reclosing. This project will achieve a unified molecular-level description of the clamp loading processes and provide insight into clamp-associated activities and their essential roles in duplication of the genome and the regulation of genome fidelity. Broader Impact: This project will substantially impact our knowledge of the biological mechanisms controlling genetic integrity with broad implications for biotechnology, environmental and bioenergy research. The project blends new methodologies and novel applications to create a multidisciplinary research and education program that is interesting and challenging for students of all levels. In particular, students will be introduced to a broad arsenal of theoretical methods, molecular modeling algorithms and High Performance Computing (HPC) architectures. Curricular innovation would involve development of a new module (advanced sampling, QM/MM and AIMD methods) for a graduate-level Computational Chemistry class at Georgia State University (GSU) and the introduction of Advanced Modeling seminars for the computational chemistry center at GSU. Additionally, molecular visualization will be used as an effective tool in attracting high school students to STEM fields with an emphasis on bringing students from disadvantaged backgrounds to the GSU campus. The research and educational objectives are tightly coupled and the educational plan reaches out to a broader community, with goals to integrate chemistry, biology and computation across the curriculum, actively promote diversity and encourage interest in science among students at all levels: from high school students to advanced graduate students.