8-氧鸟嘌呤的 DNA 变形偶联识别：人类 DNA 糖基化酶的构象动力学门控,Journal of the American Chemical Society

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8-氧鸟嘌呤的 DNA 变形偶联识别：人类 DNA 糖基化酶的构象动力学门控
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2017-02-08 , DOI: 10.1021/jacs.6b11433
Haoquan Li , Anton V. Endutkin _{1,

2} , Christina Bergonzo , Lin Fu ₃ , Arthur Grollman , Dmitry O. Zharkov _{1,

2} , Carlos Simmerling

Affiliation

8-氧鸟嘌呤 (8-oxoG) 是一种在氧化应激下产生的诱变 DNA 损伤，与其前体鸟嘌呤仅通过两个取代（O8 和 H7）不同。人 8-oxoguanine 糖基化酶 1 (OGG1) 可以通过挤压和切除定位和去除 8-oxoG。迄今为止，仍不清楚 OGG1 如何有效地将 8-oxoG 与大量未损坏的 DNA 碱基区分开来。我们最近表明甲酰胺嘧啶-DNA糖基化酶（Fpg）是OGG1的一种细菌功能类似物，可以通过稳定几种中间状态来选择性地促进oxoG的外翻，令人感兴趣的是OGG1是否也在病灶识别中采用了类似的机制。在这里，我们使用分子动力学模拟来探索 OGG1 沿碱基外翻途径区分 8-oxoG 和鸟嘌呤的机制。MD 结果表明糖基化酶对 DNA 的扭结起着重要作用，它以一种有助于碱基外翻过程中损伤识别的方式定位 DNA 磷酸盐。通过对硫代磷酸酯底物类似物的实验酶测定验证了计算预测。我们的模拟表明，OGG1 不仅在活性位点，而且在碱基外翻的早期阶段利用它们的化学差异来区分 8-oxoG 和 G，尽管缺乏结构同源性，但这种机制在 Fpg 中至少部分保守。这种相似性还表明，通过多个门控步骤识别病变可能是 DNA 修复中的一个共同主题。我们的结果为酶如何利用动力学和 DNA 构象变化来探测 DNA 损伤中存在的化学修饰提供了新的见解。

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DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase

8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine-DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition. Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base-eversion pathway. The MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite a lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions.

更新日期：2017-02-08

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