The so-called peroxidatic cysteines and selenocysteines in proteins reduce hydroperoxides through a dual attack to the peroxide bond in a two-step mechanism. First, a proton dislocation from the thiol/selenol to a close residue of the enzymatic pocket occurs. Then, a nucleophilic attack of the anionic cysteine/selenocysteine to one O atom takes place, while the proton is shuttled back to the second O atom, promoting the formation of a water molecule. In this computational study, we use a molecular model of GPx to demonstrate that the enzymatic environment significantly lowers the barrier of the latter SN2 step. Particularly, in our Se-based model the energy barriers for the two steps are 29.82 and 2.83 kcal mol−1, both higher than the corresponding barriers computed in the enzymatic cluster, i. e., 21.60 and null, respectively. Our results, obtained at SMD-B3LYP-D3(BJ)/6-311+G(d,p), cc-pVTZ//B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ level of theory, show that the mechanistic details can be well reproduced using an oversimplified model, but the energetics is definitively more favorable in the GPx active site. In addition, we pinpoint the role of the chalcogen in the peroxide reduction process, rooting the advantages of the presence of selenium in its acidic and nucleophilic properties.
Bibliographical noteFunding Information:
This work was financially supported by Università degli Studi di Padova (P‐DiSC (BIRD2018‐UNIPD) project MADS (Modeling Antioxidant Drugs: Design and Development of computer‐aided molecular Systems), P.I. L.O.. All the calculations were carried out on Galileo (CINECA: Casalecchio di Reno, Italy) thanks to the ISCRA Grant REBEL2 (REdox state role in Bio‐inspired ELementary reactions 2), P.I.: L.O.. M.D.T. is grateful to Fondazione CARIPARO for financial support (PhD grant). F.M.B. thanks the Netherlands Organization for Scientific Research (NWO) for financial support. 3
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- activation strain model
- density functional theory
- glutathione peroxidase
- reaction mechanisms