Nam, SeungyoonRyu, HyojungSon, Won-joonKim, Yon HuiKim, Kyung TaeBalch, CurtNephew, Kenneth P.Lee, Jinhyuk2015-09-282015-09-282014-10-17Nam, S., Ryu, H., Son, W., Kim, Y. H., Kim, K. T., Balch, C., … Lee, J. (2014). Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications. PLoS ONE, 9(10), e109745. http://doi.org/10.1371/journal.pone.0109745https://hdl.handle.net/1805/7064RNA interference (RNAi), mediated by small non-coding RNAs (e.g., miRNAs, siRNAs), influences diverse cellular functions. Highly complementary miRNA-target RNA (or siRNA-target RNA) duplexes are recognized by an Argonaute family protein (Ago2), and recent observations indicate that the concentration of Mg2+ ions influences miRNA targeting of specific mRNAs, thereby modulating miRNA-mRNA networks. In the present report, we studied the thermodynamic effects of differential [Mg2+] on slicing (RNA silencing cycle) through molecular dynamics simulation analysis, and its subsequent statistical analysis. Those analyses revealed different structural conformations of the RNA duplex in Ago2, depending on Mg2+ concentration. We also demonstrate that cation effects on Ago2 structural flexibility are critical to its catalytic/functional activity, with low [Mg2+] favoring greater Ago2 flexibility (e.g., greater entropy) and less miRNA/mRNA duplex stability, thus favoring slicing. The latter finding was supported by a negative correlation between expression of an Mg2+ influx channel, TRPM7, and one miRNA’s (miR-378) ability to downregulate its mRNA target, TMEM245. These results imply that thermodynamics could be applied to siRNA-based therapeutic strategies, using highly complementary binding targets, because Ago2 is also involved in RNAi slicing by exogenous siRNAs. However, the efficacy of a siRNA-based approach will differ, to some extent, based on the Mg2+ concentration even within the same disease type; therefore, different siRNA-based approaches might be considered for patient-to-patient needs.en-USAttribution 3.0 United StatesSmall interfering RNAsMicroRNAsBiochemical simulationsRNA inteferenceEntropyRNA structureMolecular dynamicsBiophysical simulationsArticle