Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets

• Published in: Scientific reports 2012-08, Vol.2 (1), p.569-569, Article 569
• Main Authors: Xia, Zhen, Clark, Peter, Huynh, Tien, Loher, Phillipe, Zhao, Yue, Chen, Huang-Wen, Rigoutsos, Isidore, Zhou, Ruhong
• Format: Article
• Language: English
• Subjects: 631/337/199; 631/337/384; 631/337/505; 631/337/521; Data processing; Humanities and Social Sciences; MicroRNAs - chemistry; MicroRNAs - genetics; miRNA; Molecular Docking Simulation; Molecular Dynamics Simulation; mRNA; multidisciplinary; Mutation; Nucleic Acid Conformation; Nucleic acids; Protein Conformation; Protein Stability; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA-Induced Silencing Complex - chemistry; Science; Simulation; siRNA
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep00569

To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 ‘hinge’ and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs.