Decoding Hairpin Structure Stability in Lin28-mediated Repression

Lin28 protein is well-known for its role in inhibiting biogenesis of micro-RNAs (miRNAs) that belong to the let-7 family. The Lin28 and let-7 axis is associated with several types of cancer. It is imperative to understand the underlying mechanism to treat these cancer in a more efficient way. In this study, we employed all-atom molecular dynamics simulation as research tool to investigate the interaction formed between Lin28 and precursor element of let-7d, one of the 12 members of the let-7 family. By constructing systems of intact sequence length of preE-let-7d, our simulations suggest that both the loop region of hairpin structure and GGAG sequence can form stable interactions with the CSD and ZKD region of the protein, respectively. The system with 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 simulations results coincide well with experimental observations. Based on both simulation results and statistical analysis from two databases, we hypothesized that two factors, namely, interaction between terminal nucleotides and 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 lights on strategies for design sequences to regulate the interactions formed between proteins and hairpin structures.