Dynamics of DNA scanning and recognition by proteins

Protein-DNA interactions are crucial for life. Dysfunction of DNA-binding proteins often causes human diseases because these proteins are vital for cells to regulate gene expression and to maintain genomic integrity. Therefore, a deep understanding of protein-DNA interactions is biomedically important. In the past decades, knowledge about three-dimensional structures of protein-DNA complexes has tremendously increased, largely due to methodological advances in structural biology. However, structure information alone is not sufficient to truly understand protein-DNA interactions because they are inherently dynamic. The overall objective in this project is to deepen our understanding of dynamic aspects of molecular processes whereby DNA-binding proteins scan DNA and recognize their targets. Using unique and powerful nuclear magnetic resonance (NMR) methods along with various other biophysical methods, the research team of this project will investigate the dynamics of protein-DNA interactions at molecular, sub-molecular, and atomic levels. At a molecular level, the research team will examine how DNA-binding proteins overcome traps and obstacles that impede the search process whereby the proteins find targets on DNA. The dynamics involving intrinsically disordered regions (IDRs) and transient microscopic dissociation/re-association will be investigated using NMR and stopped-flow fluorescence methods. At a sub-molecular level, the research team will study the mechanisms whereby IDRs exert strong influences on DNA-binding proteins. Recently, the research team has developed a unique NMR method to directly determine local electrostatic potentials for each residue of biomolecules without any use of structural information. The research team will take full advantage of this method in conjunction with other methods and investigate dynamic long-range communications between IDRs and the DNA-binding domains as well as the electrostatic impacts of post-translational modifications in IDRs. At an atomic level, the research team will investigate the dynamic behavior of various counterions around DNA and proteins using special hardware for diffusion NMR spectroscopy. This information is important because the release of counterions makes a major entropic contribution to the binding free energy for protein-DNA association. This project will illuminate the dynamic aspects of protein-DNA interactions and will help develop therapeutic strategies for human diseases caused by dysfunction of DNA-binding proteins.