Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S using classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our findings suggest that Y432S induces structural alterations in domains responsible for nucleotide addition and ternary complex stabilization while retaining structural features consistent with possible catalysis in the active site. Calculations of the minimum energy path associated with the reaction mechanism of the wild type (WT) and Y432S Pol κ indicate that, while both enzymes are catalytically competent (in terms of energetics and the active site’s geometries), the cancer mutation results in an endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on nonbonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP^3– over dCTP^4–.

中文翻译：

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Y432S 癌症相关变体对人类 DNA 聚合酶 κ 反应机制的影响


人类 DNA 聚合酶对于遗传信息管理至关重要。它们的功能包括以无与伦比的准确性催化 DNA 链的合成，从而确保人类基因组蓝图的保真度和稳定性。一些与疾病相关的突变及其对 DNA 聚合酶的功能影响已被报道。据报道，一种特殊的聚合酶，人类 DNA 聚合酶 kappa (Pol κ)，容易受到多种癌症相关突变的影响。 Pol κ 中的 Y432S 突变与多种癌症相关，由于其对聚合活性的影响和热稳定性的显着降低而引起人们的关注。在这里，我们使用经典分子动力学 (MD) 和耦合量子力学/分子力学 (QM/MM) 方法，通过计算模拟来研究 Y432S 的功能后果。我们的研究结果表明，Y432S 诱导负责核苷酸添加和三元复合物稳定的结构域发生结构改变，同时保留与活性位点可能的催化作用一致的结构特征。与野生型 (WT) 和 Y432S Pol κ 的反应机制相关的最小能量路径的计算表明，虽然两种酶都具有催化能力（就能量学和活性位点的几何形状而言），但癌症突变会导致吸能酶反应和催化势垒的增加。与第三个镁离子的相互作用以及环境对非键相互作用的影响，特别是涉及关键残基，有助于催化反应过程中WT和突变体之间的动力学和热力学区别。能量学和电子学研究结果表明，与 dCTP ^4– 相比，活性位点残基更有利于与 dCTP ^3– 的催化反应。