EXPLORATION OF METAL-ION BINDING-SITES IN RNA FOLDS BY BROWNIAN-DYNAMICS SIMULATIONS

Background: Metal ions participate in the three-dimensional folding of RNA and provide active centers in catalytic RNA molecules. The positi ons of metal ions are known for a few RNA structures determined by X-r ay crystallography. In addition to the crystallographically identified sites, solution studies point to many more metal ion binding sites ar ound structured RNAs. Metal ions are also present in RNA structures de termined by nuclear magnetic resonance (NMR) spectroscopy, but the pos itions of the ions are usually not revealed. Results: A novel method f or predicting metal ion binding sites in RNA folds has been successful ly applied to a number of different RNA structures. The method is base d on Brownian-dynamics simulations of cations diffusing under the infl uence of random Brownian motion within the electrostatic field generat ed by the static three-dimensional fold of an RNA molecule. In test ru ns, the crystallographic positions of Mg2+ ions were reproduced with d eviations between 0.3 and 2.7 Angstrom for several RNA molecules for w hich X-ray structures are available. In addition to the crystallograph ically identified metal ions, more binding sites for cations were reve aled: for example, tRNAs were shown to bind more than ten Mg2+ ions in solution. Predictions for metal ion binding sites in four NMR structu res of RNA molecules are discussed. Conclusions: The successful reprod uction of experimentally observed metal ion binding sites demonstrates the efficiency of the prediction method. A promising application of t he method is the prediction of cation-binding sites in RNA solution st ructures, determined by NMR.