Microenvironment analysis and identification of magnesium binding sites in RNA

摘要

Interactions with magnesium (Mg~(2+)) ions are essential for RNA folding and function. The locations and function of bound Mg~(2+) ions are difficult to characterize both experimentally and computationally. In particular, the P456 domain of the Tetrahymena thermophila group I intron, and a 58 nt 23s rRNA from Escherichia coli have been important systems for studying the role of Mg~(2+) binding in RNA, but characteristics of all the binding sites remain unclear. We therefore investigated the Mg~(2+) binding capabilities of these RNA systems using a computational approach to identify and further characterize their Mg~(2+) binding sites. The approach is based on the FEATURE algorithm, reported previously for microenvironment analysis of protein functional sites. We have determined novel physicochemical descriptions of site-bound and diffusely bound Mg~(2+) ions in RNA that are useful for prediction. Electrostatic calculations using the Non-Linear Poisson Boltzmann (NLPB) equation provided further evidence for the locations of site-bound ions. We confirmed the locations of experimentally determined sites and further differentiated between classes of ion binding. We also identified potentially important, high scoring sites in the group I intron that are not currently annotated as Mg~(2+) binding sites. We note their potential function and believe they deserve experimental follow-up.