Tables Turned─Structural Mechanisms of Target-Induced miRNA Destabilization

Argonaute 2 (Ago2) loaded with a microRNA (miRNA) forms an RNA-induced silencing complex (RISC), which targets mRNA through miRNA-mRNA base pairing, leading to translation inhibition or degradation of the target mRNA. However, certain target mRNAs can turn the table by binding to the miRNA-Ago complex with high complementarity, resulting in the destruction of the miRNA itself, and the process is commonly known as target-directed miRNA degradation (TDMD). Highly complementary targets can also promote miRNA destabilization and release from Ago2. However, the dynamic nature of the target-induced effects of miRNA-Ago2 interactions and miRNA dissociation from Ago2 is not well understood. The lack of a complete crystal structure of the complex involved in TDMD has limited computational study of the dynamics of target or miRNA destabilization. In this work, we utilized AlphaFold 3 (AF3) to model the full structures of Ago2-miR-27a-mRNA-target complexes and investigated the dynamics of miRNA-mRNA and miRNA-Ago2 interactions using molecular dynamics simulations. We chose miR-27a because it has not only been extensively investigated for its involvement in cancer biology but it is also a known target for its degradation via TDMD by viral mRNAs such as HVS HSUR1 from Herpesvirus saimiri. We systematically changed the targets from seed-only base pairing (target ATF3) to seed and extensive supplementary base pairing (target HVS HSUR1) to compare the stability of the miRNA-Ago2 complexes. We find that the sequence complementarity in seed, central, and supplementary pairings as well as the structural agility of Ago2 allow for differential stability of miRNA binding, potentially facilitating dissociation under different conditions.