Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

中文翻译：

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AGT 对甲基诱导的 DNA 损伤修复机制的结构见解


甲基化引起的DNA碱基配对损伤是癌症的主要原因之一。 O6-烷基鸟嘌呤-DNA 烷基转移酶 (AGT) 被认为是甲基化 DNA 的去甲基化剂。仍然缺乏 AGT-DNA 复合物热力学性质的结构研究。在本报告中，我们模拟了 AGT-DNA 相互作用的两种催化状态和 AGT-DNA 共价复合物，并使用分子动力学 (MD) 模拟探索了结构特征。我们利用伞式采样方法研究了两种不同AGT-DNA催化状态下相互作用自由能的变化，一种是DNA中甲基化的GUA，另一种是AGT中甲基化的CYS145。这些非共价复合物代表修复前和修复后复合物。因此，我们的研究涵盖了 AGT 和受损（甲基化）DNA 碱基的识别、复合物形成和分离过程。我们相信，使用氨基酸和核苷酸修饰以及蛋白质-DNA 共价键参数将允许研究 DNA 修复机制以及探索针对各种功能状态的 AGT-DNA 复合物的癌症治疗方法作为通过稳定复合体进行的探索。