Decoding Hairpin Structure Stability in Lin28-Mediated Repression

The Lin28 protein is well known for its role in inhibiting the biogenesis of microRNAs (miRNAs) that belong to the let-7 family. The Lin28 and let-7 axes are associated with several types of cancers. It is imperative to understand the underlying mechanism to treat these cancers in a more efficient way. In this study, we employed all-atom molecular dynamics simulation as a research tool to investigate the interaction formed between Lin28 and the precursor element of let-7d, one of the 12 members of the let-7 family. By constructing systems of an intact sequence length of preE-let-7d, our simulations suggest that both the loop region of the hairpin structure and the GGAG sequence can form stable interactions with the cold shock domain (CSD) and zinc knuckle domain (ZKD) regions of the protein, respectively. The system, by deleting the nucleotides GGAG at the 3' terminal, indicates that the loop region is more responsible for its ability in bypassing the binding and repression of Lin28. Additionally, using let-7c-2, which can bypass Lin28 regulation, as a template, we constructed systems with mutated loop region sequences in miRNAs and tested their stabilities. Our simulation results coincide well with experimental observations. Based on both simulation results and statistical analysis from two databases, we hypothesized that two factors, namely, the interaction between terminal nucleotides and the ring tension originating from the middle nucleotides, can significantly influence their stabilities. Systems combining strong and weak terminal interactions with large and small ring tensions were recruited to validate our hypothesis. Our findings offer a new perspective and shed light on strategies for designing sequences to regulate the interactions formed between proteins and hairpin structures.