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Abstract
Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
Highlights
Reactive oxygen centers (ROCs) are an important means of metabolizing or oxidizing various polyaromatic hydrocarbons (PAH) [1,2,3,4,5]
As a benchmark for this study, we compare the partial charges obtained on the ROC-Asp-Rieske complex and the individual components with the partial charges commonly used in Amber ff99SB protein force field for the isolated amino acid residues
Whereas the approach was directed to a specific dioxygenase protein involved in oxidizing carbazole at a stereospecific position, the approach is widely applicable to a wide varieties of PAH-related Ox proteins
Summary
Reactive oxygen centers (ROCs) are an important means of metabolizing or oxidizing various polyaromatic hydrocarbons (PAH) [1,2,3,4,5]. The ROC is often coupled to an iron–sulfur center, which is an inorganic electron storage structure that typically is found in the form of a rectangular-shaped [2Fe-2S] complex or a parallelepiped-shaped [4Fe-4S] complex (as seen in some photosynthetic Fdx proteins) [6,7]. This study is directed to oxygenase (Ox) proteins, which contain both a ROC and an iron–sulfur center. Ox is found in the form of a mono-oxygenase (mOx) and a dioxygenase (dOx), depending on whether the oxidized form of the PAH gains one or two oxygens. The Rieske is isolated from the ROC by a dense network of hydrophobic residues requiring transmission either via electron tunneling or proton coupled electron transfer (PCET) [10,11,12,13,14,15] via a collimated network of hydrogen-bonded conjugated residues or aromatic residues
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