Structural and spectroscopic properties of the peroxodiferric intermediate of Ricinus communis soluble Δ9 desaturase

Inorganic Chemistry
Martin SrnecE I Solomon

Abstract

Large-scale quantum and molecular mechanical methods (QM/MM) and QM calculations were carried out on the soluble Δ(9) desaturase (Δ(9)D) to investigate various structural models of the spectroscopically defined peroxodiferric (P) intermediate. This allowed us to formulate a consistent mechanistic picture for the initial stages of the reaction mechanism of Δ(9)D, an important diferrous nonheme iron enzyme that cleaves the C-H bonds in alkane chains resulting in the highly specific insertion of double bonds. The methods (density functional theory (DFT), time-dependent DFT (TD-DFT), QM(DFT)/MM, and TD-DFT with electrostatic embedding) were benchmarked by demonstrating that the known spectroscopic effects and structural perturbation caused by substrate binding to diferrous Δ(9)D can be qualitatively reproduced. We show that structural models whose spectroscopic (absorption, circular dichroism (CD), vibrational and Mössbauer) characteristics correlate best with experimental data for the P intermediate correspond to the μ-1,2-O(2)(2-) binding mode. Coordination of Glu196 to one of the iron centers (Fe(B)) is demonstrated to be flexible, with the monodentate binding providing better agreement with spectroscopic data, and the bidentate...Continue Reading

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Citations

Feb 22, 2012·Journal of Computational Chemistry·Tibor András Rokob, Lubomír Rulíšek
Aug 13, 2015·Journal of the American Chemical Society·Alexandria Deliz Liang, Stephen J Lippard
Jan 22, 2015·Nature·Rahul BanerjeeDenis A Proshlyakov
May 28, 2016·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Tibor András RokobLubomír Rulíšek
May 28, 2016·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Cory J KnootJohn D Lipscomb
Jul 2, 2016·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Nathalie Proos Vedin, Marcus Lundberg
Jul 3, 2016·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Edward I Solomon, Kiyoung Park
May 2, 2017·Journal of the American Chemical Society·Kiyoung ParkEdward I Solomon
Jul 6, 2017·Journal of the American Chemical Society·Anastasia C ManesisHannah S Shafaat
Mar 20, 2018·Natural Product Reports·Anna J KomorJohn D Lipscomb
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Dec 18, 2013·Chemical Communications : Chem Comm·József S PapGábor Speier
May 15, 2020·Journal of the American Chemical Society·Daniel BímMartin Srnec
Apr 13, 2021·Angewandte Chemie·Anirban ChandraKallol Ray

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