Wang Qianqian, Li Lanlan, Wang Xiaoting, Liu Huanxiang, Yao Xiaojun
School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
J Mol Model. 2014 Nov;20(11):2500. doi: 10.1007/s00894-014-2500-5. Epub 2014 Oct 26.
The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 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 hZαADAR1 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 hZαADAR1, 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 hZαADAR1 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 hZαADAR1 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 hZαADAR1 is conformation-specific rather than sequence-specific. Additionally, by analyzing the conformational changes of hZαADAR1, we found that the binding of Z-DNA could effectively stabilize hZαADAR1 protein. Our study can provide some valuable information for better understanding the binding mechanism between hZαADAR1 or even other Z-DNA-binding protein and Z-DNA.
人类双链RNA腺苷脱氨酶I（hZαADAR1）的Z-DNA结合结构域能够特异性识别左手螺旋Z-DNA，这种结构优先出现在嘌呤-嘧啶交替重复序列中，尤其是CG重复序列。hZαADAR1与不同序列背景下的Z-DNA之间的相互作用会影响许多重要的生物学功能，包括基因调控和染色质重塑。因此，全面了解它们的识别机制非常必要。然而，现有的大多数研究针对的是标准的CG重复Z-DNA，而非CG重复序列，并且在原子水平上，hZαADAR1与各种Z-DNA结合的分子基础是否相同仍不清楚。在此，基于最近测定的三种代表性非CG重复Z-DNA（d(CACGTG)2、d(CGTACG)2和d(CGGCCG)2）与hZαADAR1复合物的晶体结构，对每个系统进行了40纳秒的分子动力学模拟以及结合自由能计算。为作比较，还模拟了与hZαADAR1复合的标准CG重复Z-DNA（d(CGCGCG)2）。一致的结果表明，非极性相互作用是蛋白质-DNA结合过程中的驱动力，主要来自α3螺旋的极性相互作用也起到重要作用。确定了五个常见的热点残基，即赖氨酸169、赖氨酸170、天冬酰胺173、精氨酸174和酪氨酸177。氢键分析结合表面电荷分布进一步详细揭示了hZαADAR1与Z-DNA之间的界面信息。所有分析表明，无论Z-DNA序列如何，四种复合物都具有共同的关键特征和相似的结合模式，这表明hZαADAR1对Z-DNA的识别是构象特异性而非序列特异性。此外，通过分析hZαADAR1的构象变化，我们发现Z-DNA的结合能够有效稳定hZαADAR1蛋白。我们的研究可为更好地理解hZαADAR1乃至其他Z-DNA结合蛋白与Z-DNA之间的结合机制提供一些有价值的信息。
