Microenvironment analysis and identification of magnesium binding sites in RNA.
Interactions with magnesium (Mg2+) ions are essential for RNA folding and function. The locations and function of bound Mg2+ 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 Mg2+ binding in RNA, but characteristics of all the binding sites remain unclear. We therefore investigated the Mg2+ binding capabilities of these RNA systems using a computational approach to identify and further characterize their Mg2+ 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 Mg2+ 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 Mg2+ binding sites. We note their potential function and believe they deserve experimental follow-up.
Banatao
D Rey
DR
Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, CA 94305, USA.
Altman
Russ B
RB
Klein
Teri E
TE
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D023281:Genomics / Q000379:methods; D007438:Introns; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013768:Tetrahymena / Q000235:genetics
D012338:RNA, Ribosomal, 23S; D012313:RNA; D008274:Magnesium