Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA.
Acta Biochim Biophys Sin (Shanghai). 2022 May 25;54(6):796-806. doi: 10.3724/abbs.2022050.
DNA glycosylase, as one member of DNA repair machineries, plays an essential role in correcting mismatched/damaged DNA nucleotides by cleaving the N-glycosidic bond between the sugar and target nucleobase through the base excision repair (BER) pathways. Efficient corrections of these DNA lesions are critical for maintaining genome integrity and preventing premature aging and cancers. The target-site searching/recognition mechanisms and the subsequent conformational dynamics of DNA glycosylase, however, remain challenging to be characterized using experimental techniques. In this review, we summarize our recent studies of sequential structural changes of thymine DNA glycosylase (TDG) during the DNA repair process, achieved mostly by molecular dynamics (MD) simulations. Computational simulations allow us to reveal atomic-level structural dynamics of TDG as it approaches the target-site, and pinpoint the key structural elements responsible for regulating the translocation of TDG along DNA. Subsequently, upon locating the lesions, TDG adopts a base-flipping mechanism to extrude the mispaired nucleobase into the enzyme active-site. The constructed kinetic network model elucidates six metastable states during the base-extrusion process and suggests an active role of TDG in flipping the intrahelical nucleobase. Finally, the molecular mechanism of product release dynamics after catalysis is also summarized. Taken together, we highlight to what extent the computational simulations advance our knowledge and understanding of the molecular mechanism underlying the conformational dynamics of TDG, as well as the limitations of current theoretical work.
DNA 糖苷酶作为 DNA 修复机制的成员之一，通过碱基切除修复 (BER) 途径在糖和靶核碱基之间的 N-糖苷键处切割，从而在纠正错配/受损的 DNA 核苷酸方面发挥着重要作用。这些 DNA 损伤的有效修复对于维持基因组完整性、防止过早衰老和癌症至关重要。然而，使用实验技术来表征靶位点搜索/识别机制和随后的 DNA 糖苷酶构象动力学仍然具有挑战性。在这篇综述中，我们总结了我们最近使用分子动力学 (MD) 模拟研究胸腺嘧啶 DNA 糖苷酶 (TDG) 在 DNA 修复过程中的顺序结构变化的研究。计算模拟使我们能够揭示 TDG 在接近靶位点时的原子级结构动力学，并确定负责调节 TDG 在 DNA 上易位的关键结构元素。随后，在定位损伤后，TDG 采用碱基翻转机制将错配的核碱基逐出酶活性部位。构建的动力学网络模型阐明了碱基逐出过程中的六个亚稳态，并表明 TDG 在翻转螺旋内核碱基方面具有积极作用。最后，还总结了催化后产物释放动力学的分子机制。总之，我们强调了计算模拟在多大程度上推进了我们对 TDG 构象动力学的分子机制的认识和理解，以及当前理论工作的局限性。
