Khalilian M Hossein, DiLabio Gino A
Department of Chemistry, The University of British Columbia 3247 University Way Kelowna British Columbia V1V 1V7 Canada
Chem Sci. 2024 Jun 10;15(30):11865-11874. doi: 10.1039/d4sc01785d. eCollection 2024 Jul 31.
Radicals are highly reactive, short-lived chemical species that normally react indiscriminately with biological materials, and yet, nature has evolved thousands of enzymes that employ radicals to catalyze thermodynamically challenging chemistry. How these enzymes harness highly reactive radical intermediates to steer the catalysis to the correct outcome is a topic of intense investigation. Here, the results of detailed QM/MM calculations on archetype radical B-enzymes are presented that provide new insights into how these enzymes control the reactivity of radicals within their active sites. The catalytic cycle in B-enzymes is initiated through the formation of the 5'-deoxyadenosyl (Ado˙) moiety, a primary carbon-centred radical, which must migrate up to 8 Å to reach the target substrate to engage in the next step of the catalytic process, a hydrogen atom abstraction. Our calculations reveal that Ado˙ within the protein environment exhibits an unusual non-Aufbau electronic structure in which the singly occupied molecular orbital is lower in energy than the doubly occupied orbitals, an uncommon phenomenon known as SOMO-HOMO inversion (SHI). We find that the magnitude of SHI in the initially formed Ado˙ is larger compared to when the Ado˙ is near the intended substrate, leading to the former being relatively less reactive. The modulation of the SHI originates from Coulombic interactions of a quantum nature between a negative charge on a conserved glutamate residue and the spin on the Ado˙. Our findings support a novel hypothesis that these enzymes utilize this quantum Coulombic effect as a means of maintaining exquisite control over the chemistry of highly reactive radical intermediates in enzyme active sites.
自由基是高反应性、短寿命的化学物种，通常会不加区分地与生物材料发生反应，然而，自然界已经进化出数千种利用自由基来催化热力学上具有挑战性的化学反应的酶。这些酶如何利用高反应性的自由基中间体将催化作用导向正确的结果是一个深入研究的课题。在此，我们展示了对典型自由基B-酶进行详细量子力学/分子力学（QM/MM）计算的结果，这些结果为这些酶如何控制其活性位点内自由基的反应性提供了新的见解。B-酶中的催化循环是通过形成5'-脱氧腺苷（Ado˙）部分启动的，这是一种以碳为中心的初级自由基，它必须迁移多达8埃才能到达目标底物，从而进入催化过程的下一步——氢原子提取。我们的计算表明，蛋白质环境中的Ado˙呈现出一种不寻常的非奥弗贝格电子结构，其中单占据分子轨道的能量低于双占据轨道，这是一种罕见的现象，称为单占据分子轨道-最高占据分子轨道反转（SHI）。我们发现，与Ado˙靠近目标底物时相比，最初形成的Ado˙中的SHI幅度更大，导致前者的反应性相对较低。SHI的调节源于保守谷氨酸残基上的负电荷与Ado˙上的自旋之间的量子性质的库仑相互作用。我们的研究结果支持了一种新的假设，即这些酶利用这种量子库仑效应作为一种手段，对酶活性位点中高反应性自由基中间体的化学反应进行精确控制。
