Local and global effects of Mg2+ on Ago and miRNA-target interactions

Three magnesium ions (Mg(2+)), named Mg1 (in Mid domain), Mg2 and Mg3 (both in PIWI domain), located at the small RNA binding domain of Argonaute (Ago) protein, are important for sequence-specific miRNA-target interactions. Such conjunction between the Ago protein and miRNA raises the question: How do Mg(2+) ions participate in the recognition process of miRNA by Ago or its target. Furthermore, it is still unclear whether the Mg(2+) ions contribute to the local or global stability of the miRNA complex. In this work, we have performed a series of 16 independent molecular dynamic simulations (MD) to characterize the functions of Mg(2+), hydration patterns and the conformational events involved in the miRNA-target interactions. The cross correlation analysis shows that Mg1 and Mg2 significantly enhance a locally cooperated movement of the PAZ, PIWI and Mid domains with the average correlation coefficient of ∼0.65, producing an "open-closed" motion (rotation Angle, 46.5°) between the PAZ and PIWI domains. Binding of Mg3 can globally stabilize the whole Ago protein with the average RMSD of ∼0.34 Å, compared with the systems in absence of Mg3 (average RMSD = ∼0.43 Å). Three structural water molecules surrounding the Mg(2+)-binding regions also stabilize these ions, thus facilitating the recognition of miRNA to its target. In addition, the thermodynamic analysis also verifies the positive contribution of all three Mg(2+) to the binding of miRNA to Ago, as well as the importance Mg2 plays in the cleavage of the miRNA targets.