Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE.
Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE.
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酶工程的自由基稳定能：解决自由基酶 QueE 的底物范围。
DOI：
10.1021/acs.jcim.9b00017
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发表时间：
2019
影响因子：
5.6
通讯作者：
Suess CJ
中科院分区：
文献类型：
--
作者：
Suess CJ
自由基酶的催化反应机制和配置文件的实验评估可能是非常具有挑战性的，由于中间体的反应性质和辅因子，如铁-硫簇的敏感性。在这里，我们提出了一种酶导向的计算方法，用于评估热力学反应曲线和筛选自由基稳定能量（RSE），用于评估自由基酶中的催化转化率。我们已经应用了这种新的筛选方法的radicalS-腺苷甲硫酮酶7-羧基-7-脱氮鸟嘌呤合酶（QueE），详细的分子动力学（MD）分析，阐明了两个特定的酶残基和绑定的Mg 2+，Ca 2+，或Na+的作用。MD模拟提供了统计方法的基础，以采样不同的构象结果。在M06-2X/6-31+G* 理论水平的RSE计算提供了基于酶的能量的最具计算成本效益的评估，通过使用半经验方法的初始分类来促进。分子间相互作用对RSE的影响是明确建立的，并应用到潜在的替代底物的评估（侧重于自由基时钟型重排）提出了一个选择的碳取代的类似物，将反应提供环丙基carbinyl自由基中间体的候选人QueE催化营业额。
Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron–sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radicalS-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.