Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States.
Department of Biochemistry, Duke University , Durham, North Carolina 27710, United States.
J Am Chem Soc. 2018 Feb 28;140(8):2853-2861. doi: 10.1021/jacs.7b11926. Epub 2018 Feb 13.
Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.
光驱动的极端微生物光解酶 DNA 修复对于理解地球上生命的早期发展具有重要意义。黄素腺嘌呤二核苷酸修复 DNA 损伤的机制是一个争论的主题，主要在中温物种中进行了研究。特别是，腺嘌呤在修复过程中的作用还不太清楚。我们使用分子对接、分子动力学模拟、电子结构计算和电子隧穿途径分析，研究了在四种在不同温度下茁壮成长的光解酶中腺嘌呤在 DNA 修复中的作用。我们的结果表明，在研究的四种酶中的三种（一种中温酶和两种极端微生物酶）中，腺嘌呤对黄素和要修复的环丁烷嘧啶二聚体损伤之间的电子偶联的贡献是显著的。我们的分析表明，嗜热和超嗜热光解酶在结构上进化，以在其操作的高温下保留腺嘌呤的功能位置（从而保留其催化功能）。水分子可以与腺嘌呤竞争，以建立电子转移修复过程中最强的耦合途径，但腺嘌呤的贡献仍然很大。本研究还调和了先前关于腺嘌呤在中温电子转移修复反应中作用的似乎矛盾的结论，表明腺嘌呤介导的超交换如何受到构象门控。
