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

智力优势：染色体DNA的复制是通过一种动态的蛋白质组装完成的，这种蛋白质组装被称为复制体。持续性钳，如增殖细胞核抗原（PCNA）是确保持续复制的复制体的重要组成部分。滑动夹也作为多功能支架在招聘细胞周期控制和DNA修复蛋白，并参与几乎每一个方面的DNA代谢。它们非凡的环形结构使它们能够在拓扑学上环绕DNA并沿着DNA滑动。为了实现它们的各种功能，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，通过夹钳加载器的作用，持续加工性夹钳在DNA引物-模板连接处打开并重新密封。该项目旨在描述持续加工性夹钳打开的详细机制，确定夹钳装载机的作用，并描述夹钳装载循环每个步骤中ATP的利用情况。 原子模型的中间体在循环中将被构建来描述构象转变导致钳打开和重新闭合。该项目将实现一个统一的分子水平上的描述的钳加载过程，并提供洞察钳相关的活动及其在基因组的复制和基因组保真度的调节的重要作用。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机制的认识，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程序，以创建一个多学科的研究和教育计划，这是有趣的和具有挑战性的各级学生。特别是，学生将被介绍给理论方法，分子建模算法和高性能计算（HPC）架构的广泛武器库。课程创新将涉及为格鲁吉亚州立大学（GSU）的研究生级计算化学课程开发一个新模块（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到STEM领域的有效工具，重点是将来自弱势背景的学生带到GSU校园。研究和教育目标是紧密结合的，教育计划延伸到更广泛的社区，目标是将化学，生物学和计算整合到整个课程中，积极促进多样性，并鼓励各级学生对科学的兴趣：从高中生到高级研究生。

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.