Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition.
Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition.
复制标题
作者：
JMJD 2A是一种组蛋白赖氨酸脱甲基酶，其识别H3 K9 me 3和H3 K36 me 3残基并使其脱甲基化，并且在各种癌症中过表达。它利用串联的tudor结构域来促进其自身向组蛋白位点的募集，以中等亲和力识别各种二甲基和三甲基赖氨酸残基。在这项研究中，我们成功地改造了JMJD 2A的tudor结构域，使其特异性结合H4 K20 me 3，亲和力增加了20倍，选择性提高了。为了揭示分子基础，我们对与H4 K20 me 2、H4 K20 me 3和H3 K23 me 3肽结合的人JMJD 2A串联tudor结构域进行了分子动力学和自由能分解分析，以揭示对H4 K20 me 23增强的结合亲和力和选择性重要的残基和构象变化。这些分析揭示了理解染色质阅读器结构域识别组蛋白修饰和提高这些结构域的结合亲和力和选择性的新见解。此外，我们表明JMJD 2A与H4 K20 me 2/3的紧密结合不足以提高CRISPR-CAS 9介导的同源定向修复（HDR）的效率，这表明JMJD 2A与DNA损伤应答之间的复杂关系超出了对H4 K20 me 2/3标记的结合亲和力。
JMJD2A is a histone lysine demethylase which recognizes and demethylates H3K9me3 and H3K36me3 residues and is overexpressed in various cancers. It utilizes a tandem tudor domain to facilitate its own recruitment to histone sites, recognizing various di- and tri-methyl lysine residues with moderate affinity. In this study, we successfully engineered the tudor domain of JMJD2A to specifically bind to H4K20me3 with a 20-fold increase of affinity and improved selectivity. To reveal the molecular basis, we performed molecular dynamics and free energy decomposition analysis on the human JMJD2A tandem tudor domains bound to H4K20me2, H4K20me3, and H3K23me3 peptides to uncover the residues and conformational changes important for the enhanced binding affinity and selectivity toward H4K20me2/3. These analyses revealed new insights into understanding chromatin reader domains recognizing histone modifications and improving binding affinity and selectivity of these domains. Furthermore, we showed that the tight binding of JMJD2A to H4K20me2/3 is not sufficient to improve the efficiency of CRISPR-CAS9 mediated homology directed repair (HDR), suggesting a complicated relationship between JMJD2A and the DNA damage response beyond binding affinity toward the H4K20me2/3 mark.