Interactive Structural Analysis of KH3-4 Didomains of IGF2BPs with Preferred RNA Motif Having m⁶A Through Dynamics...

m⁶A modification is the most common internal modification of messenger RNA in eukaryotes, and the disorder of m⁶A can trigger cancer progression. The GGACU is considered the most frequent consensus sequence of target transcripts which have a GGAC m⁶A core motif. Newly identified m⁶A 'readers' insulin-like growth factor 2 mRNA-binding proteins modulate gene expression by binding to the m⁶A binding sites of target mRNAs, thereby affecting various cancer-related processes. The dynamic impact of the methylation at m⁶A 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 GGm⁶AC 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 GGm⁶AC backbone. Meanwhile, the methyl group of m⁶A 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 m⁶A modifications for the development of novel oncological therapies.