Exploration of functional sites in complex RNA folds and macromolecular assemblies

Structural genomics efforts enable the high-throughput discovery of novel molecular structures and are quickly outpacing traditional biochemical methods for determining the function of those molecules. This flood of structural data has created the need for rapid and automated ways to annotate function to molecular structures. Additionally, the interest in RNA structure and function has increased rapidly within the past several years, as dramatic discoveries have been made about novel biological mechanisms directly involving RNA. The folding, structure, and function of all RNA molecules are dependent on the direct and indirect coordination of magnesium (Mg2+) ions. However, locating Mg2+ binding sites is difficult experimentally and computationally. Thus, in my doctoral research, I have created and applied computational tools to address issues in the identification of functional sites in RNA structures and assemblies. I developed a novel approach, based on a previous method of identifying functional sites in protein structures, for understanding and locating Mg2+ binding sites in RNA. I have developed additional tools for the integrated analysis and visualization of my results with RNA structure. I have also contributed to the development of a generally applicable tool for knowledge modeling and structural modeling of the ribosome, the large assembly of RNA and proteins responsible for protein synthesis in the cell. I have successfully validated this approach on experimentally characterized RNA systems and have demonstrated that it is scalable to the analysis of large RNA assemblies. Most importantly, I have identified novel Mg2+ binding sites that may have important functional roles in RNA catalysis, especially in ribosomal activity. I provided detailed descriptions of these sites that may guide experimentalists in the comprehensive analysis of Mg2+ binding in RNA and the ribosome. My methods and discoveries may serve as tools for rational drug design targeting RNA and its assemblies.