Interactive Structural Analysis of KH3-4 Didomains of IGF2BPs with Preferred RNA Motif Having mA Through Dynamics Simulation Studies.

mA modification is the most common internal modification of messenger RNA in eukaryotes, and the disorder of mA can trigger cancer progression. The GGACU is considered the most frequent consensus sequence of target transcripts which have a GGAC mA core motif. Newly identified mA 'readers' insulin-like growth factor 2 mRNA-binding proteins modulate gene expression by binding to the mA binding sites of target mRNAs, thereby affecting various cancer-related processes. The dynamic impact of the methylation at mA within the GGAC motif on human IGF2BPs has not been investigated at the structural level. In this study, through in silico analysis, we mapped IGF2BPs binding sites for the GGmAC RNA core motif of target mRNAs. Subsequent molecular dynamics simulation analysis at 400 ns revealed that only the KH4 domain of IGF2BP1, containing the 503GKGG506 motif and its periphery residues, was involved in the interaction with the GGmAC backbone. Meanwhile, the methyl group of mA is accommodated by a shallow hydrophobic cradle formed by hydrophobic residues. Interestingly, in IGF2BP2 and IGF2BP3 complexes, the RNA was observed to shift from the KH4 domain to the KH3 domain in the simulation at 400 ns, indicating a distinct dynamic behavior. This suggests a conformational stabilization upon binding, likely essential for the functional interactions involving the KH3-4 domains. These findings highlight the potential of targeting IGF2BPs' interactions with mA modifications for the development of novel oncological therapies.