Barlas Ayşe Berçin, Karaca Ezgi
Omics and Computational Biology Program, Izmir Biomedicine and Genome Center, Izmir, Türkiye.
Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye.
Commun Biol. 2025 Aug 13;8(1):1217. doi: 10.1038/s42003-025-08606-7.
DNMT3A and DNMT3B are closely related DNA methyltransferases that catalyze de novo CpG methylation and have distinct preferences for flanking sequences. Despite sharing 91% sequence similarity within their catalytic domains, these paralogs show non-overlapping genomic targeting and divergent biological roles. To uncover the mechanistic basis of this specificity, we performed 16µs of all-atom molecular dynamics simulations on DNMT3A and DNMT3B complexes bound to CpG substrates with varied +2 flanking bases (i.e., CGX). To resolve their base- and shape-readout mechanisms at atomistic detail, we introduced a Comparative Dynamics Analysis (CDA) framework. Our CDA approach revealed that DNMT3A relies on a rigid, sequence-specific hydrogen bonding network and shape-constrained electrostatic anchoring, whereas DNMT3B employs a more flexible and distributed interface, allowing broader substrate tolerance. This represents the first systematic analysis of shape readout in DNMT3 enzymes and demonstrates how flanking sequence specificity is dynamically encoded by two nearly identical proteins. Our findings not only clarify how closely related DNA-modifying enzymes diverge in recognition strategies, but also lay the foundation for future efforts to engineer paralog-specific protein-DNA interactions.
DNMT3A和DNMT3B是密切相关的DNA甲基转移酶，它们催化从头CpG甲基化，并且对侧翼序列有不同的偏好。尽管它们的催化结构域内有91%的序列相似性，但这些旁系同源物显示出不重叠的基因组靶向和不同的生物学作用。为了揭示这种特异性的机制基础，我们对与具有不同+2侧翼碱基（即CGX）的CpG底物结合的DNMT3A和DNMT3B复合物进行了16微秒的全原子分子动力学模拟。为了在原子细节上解析它们的碱基和形状读出机制，我们引入了一种比较动力学分析（CDA）框架。我们的CDA方法表明，DNMT3A依赖于一个刚性的、序列特异性的氢键网络和形状受限的静电锚定，而DNMT3B采用了一个更灵活和分布更广的界面，从而允许更广泛的底物耐受性。这代表了对DNMT3酶中形状读出的首次系统分析，并展示了侧翼序列特异性是如何由两个几乎相同的蛋白质动态编码的。我们的发现不仅阐明了密切相关的DNA修饰酶在识别策略上是如何不同的，而且为未来设计旁系同源物特异性蛋白质-DNA相互作用的努力奠定了基础。
