The YTHDC1 glutamate-rich domain docks to the ADAR1 Zα Domain, linking the N ⁶ -methyladenosine modification of pre-mRNAs to dsRNA editing

The p150 isoform of the double-stranded RNA editing enzyme ADAR1 binds Z-DNA and Z-RNA through the conserved winged helix-turn-helix Zα domain. Here, we describe an inverse computational design strategy to map protein interactors of Zα. We used RFdiffusion and ProteinMPNN to generate ∼10,000 synthetic binders optimized for the Zα recognition surface, then used their sequences as structural templates for BLASTp searches against the human proteome. Multi-stage screening of ∼1,200 candidate regions from 298 proteins via ColabFold pDockQ identified 79 candidates for high-resolution AlphaFold3 modeling, which revealed the m6A reader YTHDC1 as the top-ranked interactor. AlphaFold3 predicts that a glutamate-rich poly-E disordered region of YTHDC1 (residues 199–254) docks into the basic recognition pocket of Zα through a charge-complementary mechanism that mimics the phosphate backbone of Z-RNA. Microsecond molecular dynamics simulations confirmed stability of the binary ADAR1p150–YTHDC1 complex, with the Zα–poly-E interface maintaining RMSD below 3 Å throughout. Ternary complex simulations showed that dsRNA acts as a co-anchoring scaffold stabilizing simultaneous engagement of both proteins in a catalytically dormant conformation. YTHDC1 localizes to transcription-associated YT bodies where nascent RNAs undergo m6A modification and negative supercoiling promotes Z-DNA formation, suggesting that YTHDC1 recruits ADAR1p150 to promote editing of intron-containing substrates prior to splicing.