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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Theoretical study of the human DNA repair protein HOGG1 activity
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Theoretical study of the human DNA repair protein HOGG1 activity

机译：人类DNA修复蛋白HOGG1活性的理论研究

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We have examined the role of the catalytic lysine (Lys 249) in breaking the glycosidic bond of 8-oxoguanine in the enzyme human 8-oxoguanine DNA glycosylase. Until quite recently it has been assumed that this lysine acts as a nucleophile in ail S(N)2 type of reaction after being activated through a donation of a proton to a strictly conserved aspartate, also located in the active site. However, evidence from crystallographic, as well as biochemical studies, questions this assumption mainly because the lysine is not ideally positioned for such an attack. In addition, the catalytic activity is preserved even after that aspartate is mutated to a residue not accepting protons, but still keeping the interactions in the active site. In this study, we have investigated several different reaction mechanisms to discover plausible ways where the lysine could assist in breaking the glycosidic bond. We use hybrid density functional theory to characterize both associative and dissociative pathways. We find that the smallest energetical barrier involves an S(N)1 type of mechanism where the lysine electrostatically stabilizes the dissociating base and then donates a proton with a very small barrier and then finally attacks the sugar ring to create the covalently bound protein-DNA intermediate complex. The S(N)2 mechanism also has a lower barrier than the "spontaneous" bond breaking but considerably above that of the S(N)1 reaction. However, in current conditions, the reactants placed in a conformation posed for an S(N)2 reaction is substantially more stable than if posed for the S(N)1 reaction, indicating that the active site has to bind stronger to the latter in order to achieve a full catalytic effect. An analysis of the polarization of the transition states shows that the polarization is largest for the S(N)1 reaction, indicating that this path will gain most by being placed in a prepolarized active site. These findings give further support to the hypothesis that a dissociative mechanism may be the preferred mode of action for this type of enzymes.
机译：我们已经检查了赖氨酸催化酶（Lys 249）在破坏人类8-氧鸟嘌呤DNA糖基化酶中8-氧鸟嘌呤的糖苷键中的作用。直到最近，人们一直认为该赖氨酸在通过质子捐赠给也位于活性位点的严格保守的天冬氨酸而被激活后，在所有S（N）2型反应中充当亲核试剂。但是，晶体学和生化研究的证据对该假设提出了质疑，主要是因为赖氨酸的位置不理想。另外，即使在天冬氨酸突变为不接受质子但仍将相互作用保持在活性位点的残基后，仍保留了催化活性。在这项研究中，我们研究了几种不同的反应机制，以发现赖氨酸可能有助于破坏糖苷键的合理方式。我们使用混合密度泛函理论来表征缔合和解离途径。我们发现最小的能量屏障涉及一种S（N）1类型的机制，其中赖氨酸静电稳定离解碱基，然后以非常小的屏障提供质子，然后最终攻击糖环以创建共价结合的蛋白质-DNA中间复合体。与“自发”键断裂相比，S（N）2机理还具有较低的势垒，但远高于S（N）1反应的势垒。然而，在当前条件下，以S（N）2反应构成的构象的反应物比S（N）1反应构成的稳定得多，这表明活性位点必须在S（N）1反应中更强地结合为了达到充分的催化作用。对过渡态极化的分析表明，对于S（N）1反应，极化最大，这表明该路径通过放置在预极化的活性位中将获得最大收益。这些发现进一步支持了以下假设：解离机制可能是此类酶的首选作用方式。

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