Dataset of "Elucidation of factors shaping reactivity of 5'-deoxyadenosyl – a prominent organic radical in biology"

This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo•) radical, a potent hydrogen atom abstractor, present in the active sites of radical SAM enzymes, but otherwise undergoing a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo• in aqueous solution and in two enzymatic microenvironments and reveal that HAA efficiency of 5'dAdo• depends on (i) formation of 5'dAdo• in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo• complex formation, (ii) hindering the conformational change associated with self-decay by performing the reaction in a tight cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5'dAdo•. We performed an analysis of HAA performed by 5'dAdo• based on the three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. The study is based on the straightforward relationship between the off-diagonal thermodynamic effects and the electronic-structure descriptor – the redistribution of charge between the reactants during the reaction. It allows to access HAA-competent redox and acidobasic properties of 5'dAdo• that are otherwise unavailable due to its instability upon one-electron reduction and protonation. The results show that all reactions feature a favourable thermodynamic driving force and tunneling, the latter of which lowers systematically barriers by ~2 kcal mol-1. In addition, most of the reaction experience a favourable off-diagonal thermodynamic contribution. In HAA reactions, 5'dAdo• acts as a weak oxidant as well as a base, also 5'dAdo•-promoted HAA reactions proceed with quite low degree of asynchronicity of proton and electron transfer. Finally, the study elucidates the crucial and dual role of asynchronicity. It directly lowers the barrier as a part of the off-diagonal thermodynamic contribution, but also indirectly increases the non-thermodynamic part of the barrier by controlling the adiabatic coupling between proton and electron transfer. The latter signals that the reaction proceeds as a hydrogen atom transfer rather than a proton-coupled electron transfer.本研究探究了调控5'-脱氧腺苷自由基(5'dAdo•)反应活性的因素。5'-脱氧腺苷自由基是一种强效氢原子提取剂，存在于自由基SAM酶的活性位点中，但在水溶液中会发生快速自衰变。本研究对比了水溶液及两种酶微环境中，自由基SAM酶天然底物与5'dAdo•之间的氢原子提取(HAA)反应，揭示了5'dAdo•的HAA效率取决于两点：(i) 5'dAdo•与底物形成预有序复合物，该过程可削弱底物与5'dAdo•复合物形成带来的不利效应；(ii) 在紧密空腔中进行反应，从而阻碍与自衰变相关的构象变化。不过，酶空腔对5'dAdo•的HAA活性并无显著影响。本研究基于三组分热力学模型对5'dAdo•介导的HAA反应进行了分析，该模型纳入了反应自由能的对角效应，以及异步性与受挫的非对角效应。本研究依托非对角热力学效应与电子结构描述符——反应过程中反应物间的电荷再分布——之间的直接关联，得以获取5'dAdo•具备HAA活性所需的氧化还原与酸碱性质，而由于该自由基在单电子还原及质子化后不稳定，这类性质此前无法被直接观测。研究结果表明，所有反应均具备有利的热力学驱动力，且存在隧穿效应，后者可使反应能垒系统性降低约2千卡每摩尔。此外，多数反应还存在有利的非对角热力学贡献。在HAA反应中，5'dAdo•兼具弱氧化剂与碱的双重属性，且5'dAdo•介导的HAA反应中，质子与电子转移的异步性程度较低。本研究最终阐明了异步性的关键双重作用：一方面，作为非对角热力学贡献的一部分，异步性可直接降低反应能垒；另一方面，通过调控质子与电子转移间的绝热耦合，异步性又会间接提升能垒的非热力学部分。这一结果表明，该反应以氢原子转移而非质子耦合电子转移的路径进行。