title: Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition.
abstract: Experimental studies have uncovered a variety of microRNA (miRNA)-target duplex structures that include perfect, imperfect and seedless duplexes. However, non-canonical binding modes from imperfect/seedless duplexes are not well predicted by computational approaches, which rely primarily on sequence and secondary structural features, nor have their tertiary structures been characterized because solved structures to date are limited to near perfect, straight duplexes in Argonautes (Agos). Here, we use structural modeling to examine the role of Ago dynamics in assembling viable eukaryotic miRNA-induced silencing complexes (miRISCs). We show that combinations of low-frequency, global modes of motion of Ago domains are required to accommodate RNA duplexes in model human and C. elegans Ago structures. Models of viable miRISCs imply that Ago adopts variable conformations at distinct target sites that generate distorted, imperfect miRNA-target duplexes. Ago's ability to accommodate a duplex is dependent on the region where structural distortions occur: distortions in solvent-exposed seed and 3'-end regions are less likely to produce steric clashes than those in the central duplex region. Energetic analyses of assembled miRISCs indicate that target recognition is also driven by favorable Ago-duplex interactions. Such structural insights into Ago loading and target recognition mechanisms may provide a more accurate assessment of miRNA function.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA hhg3@nyu.edu.
authors.forename: Hin Hark
authors.initials: HH
authors.lastname: Gan
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA New York University Abu Dhabi, Abu Dhabi, UAE kcg1@nyu.edu.
authors.forename: Kristin C
authors.initials: KC
authors.lastname: Gunsalus
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry; D017173:Caenorhabditis elegans / Q000235:genetics; D005656:Fungal Proteins / Q000737:chemistry; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D034743:RNA-Induced Silencing Complex / Q000737:chemistry* / Q000378:metabolism; D016963:Thermus thermophilus
chemical_list: D060565:Argonaute Proteins; D001426:Bacterial Proteins; D005656:Fungal Proteins; D035683:MicroRNAs; D034743:RNA-Induced Silencing Complex