Specific recognition between YTHDF3 and m⁶ A-modified RNA: An all-atom molecular dynamics simulation study

The YTH domain of YTHDF3 belongs to a class of protein "readers" recognizing the N6-methyladenosine (m⁶ A) modification in mRNA. Although static crystal structure reveals m⁶ A recognition by a conserved aromatic cage, the dynamic process in recognition and importance of aromatic cage residues are not completely clear. Here, molecular dynamics (MD) simulations are performed to explore the issues and negative selectivity of YTHDF3 toward unmethylated substrate. Our results reveal that there exist conformation selectivity and induced-fit in YTHDF3 binding with m⁶ A-modified RNA, where recognition loop and loop6 play important roles in the specific recognition. m⁶ A modification enhances the stability of YTHDF3 in complex with RNA. The methyl group of m⁶ A, like a warhead, enters into the aromatic cage of YTHDF3, where Trp492 anchors the methyl group and constraints m⁶ A, making m⁶ A further stabilized by π-π stacking interactions from Trp438 and Trp497. In addition, the methylation enhances the hydrophobicity of adenosine, facilitating water molecules excluded out of the aromatic cage, which is another reason for the specific recognition and stronger intermolecular interaction. Finally, the comparative analyses of hydrogen bonds and binding free energy between the methylated and unmethylated complexes reveal the physical basis for the preferred recognition of m⁶ A-modified RNA by YTHDF3. This study sheds light on the mechanism by which YTHDF3 specifically recognizes m⁶ A-modified RNA and can provide important information for structure-based drug design.