Srivastava Amit, Idriss Haitham, Das Gobind, Abedrabbo Sufian, Shamsir Mohd Sahir, Homouz Dirar
Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
School of Public Health, Imperial College of Science, Technology and Medicine, London, UK.
PLoS One. 2025 Mar 12;20(3):e0318614. doi: 10.1371/journal.pone.0318614. eCollection 2025.
DNA polymerase β, a member of the X-family of DNA polymerases, undergoes complex regulations both in vitro and in vivo through various posttranslational modifications, including phosphorylation and methylation. The impact of these modifications varies depending on the specific amino acid undergoing alterations. In vitro, methylation of DNA polymerase β with the enzyme protein arginine methyltransferase 6 (PRMT6) at R83 and R152 enhances polymerase activity by improving DNA binding and processivity. Although these studies have shown that methylation improves DNA binding, the underlying mechanism of enhancement of polymerase activity in terms of structure and dynamics remains poorly understood. To address this gap, we modeled the methylated enzyme/DNA complex and conducted a microsecond-long simulation in the presence of Mg ions. Our results revealed significant structural changes induced by methylating both R83 and R152 sites in the enzyme. Specifically, these changes caused the DNA fragment to move closer to the C- and N-subdomains, forming additional hydrogen bonds. Furthermore, the cross-correlation map demonstrated that methylation enhanced long-range correlations within the domains/subdomains of DNA polymerase β, along with an increase in the linear mutual information value between the domains/subdomains and DNA fragments. The graph connectivity network also illustrated that methylation modulates the information pathway and identifies residues exhibiting long-distance coupling with the methylated sites. Our results provide an atomic-level understanding of the structural transition induced by methylation, shedding light on the mechanisms underlying the methylation-induced enhancement of activity in DNA polymerase β.
DNA聚合酶β是DNA聚合酶X家族的成员之一，在体外和体内通过各种翻译后修饰（包括磷酸化和甲基化）受到复杂的调控。这些修饰的影响因发生改变的特定氨基酸而异。在体外，用蛋白质精氨酸甲基转移酶6（PRMT6）对DNA聚合酶β的R83和R152位点进行甲基化，通过改善DNA结合和持续合成能力来增强聚合酶活性。尽管这些研究表明甲基化改善了DNA结合，但从结构和动力学角度来看，聚合酶活性增强的潜在机制仍知之甚少。为了填补这一空白，我们对甲基化的酶/DNA复合物进行了建模，并在镁离子存在的情况下进行了长达微秒的模拟。我们的结果揭示了酶中R83和R152位点甲基化所诱导的显著结构变化。具体而言，这些变化导致DNA片段向C亚结构域和N亚结构域靠近，形成额外的氢键。此外，交叉相关图表明甲基化增强了DNA聚合酶β各结构域/亚结构域内的长程相关性，同时各结构域/亚结构域与DNA片段之间的线性互信息值也有所增加。图谱连通性网络还表明甲基化调节了信息通路，并识别出与甲基化位点存在长距离耦合的残基。我们的结果提供了对甲基化诱导的结构转变的原子水平理解，揭示了DNA聚合酶β中甲基化诱导活性增强的潜在机制。
