Stimulation of N−glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair
Stimulation of N−glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair
复制标题
DOI：
10.1007/s00894-014-2168-x
复制
发表时间：
2014-03
影响因子：
2.2
通讯作者：
Zeqin Chen;Xiaoqiang Liu;Ying Xue
中科院分区：
文献类型：
--
作者：
Zeqin Chen;Xiaoqiang Liu;Ying Xue
胸腺嘧啶乙二醇（Tg）是一种毒性氧化DNA损伤，优先被内切核酸酶III（Endo III）去除。为了研究Endo III的糖基化酶活性，在本理论研究中基于BHandHLYP/6 − 311 ++ G（d，p）理论水平考察了脱氧胸苷二醇（dTg）中的N −糖苷转移机制。有两种有争议的机制，即，位移和内环机制。对于每种机理，建立了三种反应模型，包括直接反应模型、局部微水化模型和质子化模型。计算结果表明：（i）三种反应模型都倾向于置换反应，而不是内环反应：（ii）局部微水合反应模型考虑了离散的质子转移，降低了活化能，但仍有较大的活化能;（三）O4 '-质子化内环模型可以有效地促进赖氨酸残基的亲核攻击，并且应该是亲核赖氨酸以外的氨基酸残基负责打开糖环;（iv）O2 −质子化置换模型有利于离去基团（Tg）的稳定，因此是dTg的N −糖苷转移的首选机制，其活化能为17.7 kcal mol − 1，与实验估计的19.0 kcal mol − 1非常一致。因此，核碱基的质子化在预测优选的糖基化酶机制中起着重要作用。我们的研究结果可以为将来Endo III的大规模酶模拟提出适当的机制，并提供有关酶催化反应中可能包含的重要残基的更多基本信息。图脱氧胸苷二醇中的N-糖苷转移
Thymine glycol (Tg), a toxic oxidative DNA lesion, is preferentially removed by endonuclease III (Endo III). To investigate the glycosylase activity of Endo III, the N−glycoside transfer mechanism in deoxythymidine glycol (dTg) is examined in this theoretical study based on the BHandHLYP/6−311++G(d,p) level of theory. Two controversial mechanisms were characterized, i.e., the displacement and endocyclic mechanisms. For each mechanism, three types of reaction models were established, including the direct reaction, local microhydration and protonated models. The calculated results indicate that (i) all three reaction models favor the displacement mechanism more than the endocyclic mechanism; (ii) the local microhydration model allows for discrete proton transfer and contributes to the reduction of activation energies, nevertheless, large activation energies are still involved; (iii) the O4′−protonated endocyclic model can efficiently promote the nucleophilic attack of lysine residue and an amino acid residue other than the nucleophilic lysine should be responsible for the opening of the sugar ring; (iv) the O2−protonated displacement model facilitates the leaving group (Tg) stabilization and therefore is the preferred mechanism for the N−glycoside transfer of dTg, whose activation energy of 17.7 kcal mol−1is in good agreement with the experimental estimate of 19.0 kcal mol−1. As a result, the protonation of nucleobase plays a significant role in predicting the preferred glycosylase mechanism. Our findings can propose appropriate mechanisms for future large−scale enzymatic modeling of Endo III and provide more fundamental information about the important residues that may be included in the enzyme−catalyzed reactions.FigureN−glycoside transfer in deoxythymidine glycol