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Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM‑3 Heme Domain Using Molecular Dynamics Simulations

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journal contribution
posted on 12.01.2016, 00:00 by Rajni Verma, Ulrich Schwaneberg, Dirk Holtmann, Danilo Roccatano
One of the major limitations to exploit enzymes in industrial processes is their dependence on expensive reduction equivalents like NADPH to drive their catalytic cycle. Soluble electron-transfer (ET) mediators like cobalt­(II) sepulchrate have been proposed as a cost-effective alternative to shuttle electrons between an inexpensive electron source and an enzyme’s redox center. The interactions of these molecules with enzymes have not yet been elucidated at the molecular level. Herein, molecular dynamics simulations are performed to understand the binding and ET mechanism of the cobalt­(II) sepulchrate with the heme domain of cytochrome P450 BM-3. The study provides a detailed map of ET mediator binding sites on the protein surface that are prevalently composed of Asp and Glu amino acids. The cobalt­(II) sepulchrate does not show a preferential binding to these sites. However, among the observed binding sites, only few of them provide efficient ET pathways to heme iron. The results of this study can be used to improve the ET mediator efficiency of the enzyme for possible biotechnological applications.

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