title: Mg2+ effect on argonaute and RNA duplex by molecular dynamics and bioinformatics implications.
abstract: RNA 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.
authors.affiliation: Cancer Genomics Branch, National Cancer Center, Goyang, Kyunggi-do, Korea.
authors.forename: Seungyoon
authors.initials: S
authors.lastname: Nam
authors.affiliation: Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Bioinformatics, University of Sciences and Technology, Daejeon, Korea.
authors.forename: Hyojung
authors.initials: H
authors.lastname: Ryu
authors.affiliation: Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America.
authors.forename: Won-joon
authors.initials: WJ
authors.lastname: Son
authors.affiliation: Next Therapeutics Branch, National Cancer Center, Goyang, Kyunggi-do, Korea.
authors.forename: Yon Hui
authors.initials: YH
authors.lastname: Kim
authors.affiliation: Molecular Epidemiology Branch, National Cancer Center, Goyang, Kyunggi-do, Korea.
authors.forename: Kyung Tae
authors.initials: KT
authors.lastname: Kim
authors.affiliation: Bioscience Advising, Indianapolis, Indiana, United States of America.
authors.forename: Curt
authors.initials: C
authors.lastname: Balch
authors.affiliation: Medical Science Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America.
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
authors.affiliation: Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Bioinformatics, University of Sciences and Technology, Daejeon, Korea.
authors.forename: Jinhyuk
authors.initials: J
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D060565:Argonaute Proteins / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D006801:Humans; D008274:Magnesium / Q000737:chemistry / Q000494:pharmacology*; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000187:drug effects
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; D035683:MicroRNAs; D008274:Magnesium