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.