Understanding the recognition mechanisms of Zα domain of human editing enzyme ADAR1 (hZα_ADAR1) and various Z-DNAs from molecular dynamics simulation

The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZα_ADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZα_ADAR1 and Z-DNAs in different sequence contexts can affect many important biological functions including gene regulation and chromatin remodeling. Therefore it is of great necessity to fully understand their recognition mechanisms. However, most existing studies are aimed at the standard CG-repeat Z-DNA rather than the non-CG-repeats, and whether the molecular basis of hZα_ADAR1 binding to various Z-DNAs are identical or not is still unclear on the atomic level. Here, based on the recently determined crystal structures of three representative non-CG-repeat Z-DNAs (d(CACGTG)₂, d(CGTACG)₂ and d(CGGCCG)₂) in complex with hZα_ADAR1, 40 ns molecular dynamics simulation together with binding free energy calculation were performed for each system. For comparison, the standard CG-repeat Z-DNA (d(CGCGCG)₂) complexed with hZα_ADAR1 was also simulated. The consistent results demonstrate that nonpolar interaction is the driving force during the protein-DNA binding process, and that polar interaction mainly from helix α3 also provides important contributions. Five common hot-spot residues were identified, namely Lys169, Lys170, Asn173, Arg174 and Tyr177. Hydrogen bond analysis coupled with surface charge distribution further reveal the interfacial information between hZα_ADAR1 and Z-DNA in detail. All of the analysis illustrate that four complexes share the common key features and the similar binding modes irrespective of Z-DNA sequences, suggesting that Z-DNA recognition by hZα_ADAR1 is conformation-specific rather than sequence-specific. Additionally, by analyzing the conformational changes of hZα_ADAR1, we found that the binding of Z-DNA could effectively stabilize hZα_ADAR1 protein. Our study can provide some valuable information for better understanding the binding mechanism between hZα_ADAR1 or even other Z-DNA-binding protein and Z-DNA.