Issue 30, 2024

Elucidation of factors shaping reactivity of 5′-deoxyadenosyl – a prominent organic radical in biology

Abstract

This study investigates the factors modulating the reactivity of 5′-deoxyadenosyl (5′dAdo˙) radical, a potent hydrogen atom abstractor that forms in the active sites of radical SAM enzymes and that otherwise undergoes 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. With that we reveal that HAA efficiency of 5′dAdo˙ is due to (i) the in situ formation of 5′dAdo˙ in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5′dAdo˙ complex formation, and (ii) the prevention of the conformational changes associated with self-decay by a tight active-site cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5′dAdo˙. Thus, we performed an analysis of in-water HAA performed by 5′dAdo˙ based on a three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. To this aim, we took advantage of 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 reactions 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 a 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 presumably 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.

Graphical abstract: Elucidation of factors shaping reactivity of 5′-deoxyadenosyl – a prominent organic radical in biology

Supplementary files

Article information

Article type
Paper
Submitted
26 Apr. 2024
Accepted
05 Jūl. 2024
First published
08 Jūl. 2024
This article is Open Access
Creative Commons BY license

Phys. Chem. Chem. Phys., 2024,26, 20280-20295

Elucidation of factors shaping reactivity of 5′-deoxyadenosyl – a prominent organic radical in biology

Z. Wojdyla, M. Maldonado-Domínguez, P. Bharadwaz, M. Culka and M. Srnec, Phys. Chem. Chem. Phys., 2024, 26, 20280 DOI: 10.1039/D4CP01725K

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