Ionic competition in protein-nucleic acid interactions

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With this award, Dr. Junji Iwahara from University of Texas Medical Branch (UTMB) at Galveston is supported to investigate ionic interactions of proteins and nucleic acids. These proteins and nucleic acids form ion pairs that involve strong electrostatic interactions between positively and negatively charged groups. Ion pairs are important for biological molecular functions; however, it is not well understood how the macromolecular ion pairs are influenced by free ions in solution. The project team is using light-based methods (nuclear magnetic resonance (NMR) spectroscopy) to study the interplay between free ions and macromolecular ion pairs at protein-DNA interfaces. Because ion pairs are important for many specific molecular association processes, deeper knowledge of the ion pairs at molecular interfaces facilitate development of synthetic compounds in the agricultural, pharmaceutical, and biotechnological industries. This project enables high school students to participate in the interdisciplinary research in the investigator's laboratory. Tours of the NMR facilities are offered to all high school students in UTMB's summer research program. The overall goal in this research project is to understand competition between free ions and macromolecular ion pairs at an atomic level in a biological system. In particular, the project aims at understanding the relationship of the ionic competition to the molecular properties of protein-nucleic acid complexes. In forming intermolecular ion pairs, the charged moieties of protein side-chains and DNA phosphate groups compete with free cations (e.g. potassium ions) and anions (e.g. chloride ions) in solution. The research team is studying the ionic competition at molecular interfaces in the DNA complexes of the homeodomain DNA binding protein HoxD9 and the methyl-CpG-binding domain of MeCP2. NMR spectroscopy is used to study the influence of ionic competition at an atomic level. Isothermal titration calorimetry and stopped-flow fluorescence spectroscopy are used to study the influence of ionic competition on the thermodynamic and kinetic properties of the complexes at a molecular level. This research project is integrating biophysical methods with mutagenesis, to delineate the ionic competition and its role in the protein-nucleic acid interactions.This project is jointly funded by the Chemistry of Life Processes Program in the Division of Chemistry and the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences.