Unraveling binding effects of Cobalt(II)-Sepulchrate with the monooxygenase P450BM-3 heme domain using molecular dynamics simulations

Verma, Rajni and Schwaneberg, Ulrich and Holtmann, Dirk and Roccatano, Danilo (2015) Unraveling binding effects of Cobalt(II)-Sepulchrate with the monooxygenase P450BM-3 heme domain using molecular dynamics simulations. Journal of Chemical Theory and Computation, 12 (1). pp. 353-363. ISSN 1549-9618

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Unraveling binding effects of Cobalt(II)-Sepulchrate with the monooxygenase P450BM-3 heme domain using molecular dynamics simulations
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Abstract

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 enzyme redox center. The interactions of these molecules with enzymes are not elucidated at molecular level yet. Herein, molecular dynamics simulations are performed to understand the binding and ET mechanism of the Cobalt(II)Sepulchrate with the heme domain of cytochrome P450BM-3. The study provides a detailed map of ET mediator binding sites on protein surface that resulted prevalently composed by Asp and Glu amino acids. The Cobalt(II)Sepulchrate do 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.

Keywords:mediated electron transfer, Marcus theory, electron pathways, protein stability, co-solute effect, NotOAChecked
Subjects:C Biological Sciences > C760 Biomolecular Science
F Physical Sciences > F170 Physical Chemistry
Divisions:College of Science > School of Mathematics and Physics
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ID Code:19791
Deposited On:11 Dec 2015 10:48

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