Literature DB >> 25313991

Reactivity of the binuclear non-heme iron active site of Δ⁹ desaturase studied by large-scale multireference ab initio calculations.

Jakub Chalupský1, Tibor András Rokob, Yuki Kurashige, Takeshi Yanai, Edward I Solomon, Lubomír Rulíšek, Martin Srnec.   

Abstract

The results of density matrix renormalization group complete active space self-consistent field (DMRG-CASSCF) and second-order perturbation theory (DMRG-CASPT2) calculations are presented on various structural alternatives for the O-O and first C-H activating step of the catalytic cycle of the binuclear nonheme iron enzyme Δ(9) desaturase. This enzyme is capable of inserting a double bond into an alkyl chain by double hydrogen (H) atom abstraction using molecular O2. The reaction step studied here is presumably associated with the highest activation barrier along the full pathway; therefore, its quantitative assessment is of key importance to the understanding of the catalysis. The DMRG approach allows unprecedentedly large active spaces for the explicit correlation of electrons in the large part of the chemically important valence space, which is apparently conditio sine qua non for obtaining well-converged reaction energetics. The derived reaction mechanism involves protonation of the previously characterized 1,2-μ peroxy Fe(III)Fe(III) (P) intermediate to a 1,1-μ hydroperoxy species, which abstracts an H atom from the C10 site of the substrate. An Fe(IV)-oxo unit is generated concomitantly, supposedly capable of the second H atom abstraction from C9. In addition, several popular DFT functionals were compared to the computed DMRG-CASPT2 data. Notably, many of these show a preference for heterolytic C-H cleavage, erroneously predicting substrate hydroxylation. This study shows that, despite its limitations, DMRG-CASPT2 is a significant methodological advancement toward the accurate computational treatment of complex bioinorganic systems, such as those with the highly open-shell diiron active sites.

Entities:  

Mesh:

Substances:

Year:  2014        PMID: 25313991     DOI: 10.1021/ja506934k

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  10 in total

Review 1.  Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes.

Authors:  Andrew J Jasniewski; Lawrence Que
Journal:  Chem Rev       Date:  2018-02-05       Impact factor: 60.622

Review 2.  Mono- and binuclear non-heme iron chemistry from a theoretical perspective.

Authors:  Tibor András Rokob; Jakub Chalupský; Daniel Bím; Prokopis C Andrikopoulos; Martin Srnec; Lubomír Rulíšek
Journal:  J Biol Inorg Chem       Date:  2016-05-26       Impact factor: 3.358

Review 3.  Protein effects in non-heme iron enzyme catalysis: insights from multiscale models.

Authors:  Nathalie Proos Vedin; Marcus Lundberg
Journal:  J Biol Inorg Chem       Date:  2016-06-30       Impact factor: 3.358

4.  Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase.

Authors:  Daniel Bím; Jakub Chalupský; Martin Culka; Edward I Solomon; Lubomír Rulíšek; Martin Srnec
Journal:  J Am Chem Soc       Date:  2020-05-29       Impact factor: 15.419

5.  Castor Stearoyl-ACP Desaturase Can Synthesize a Vicinal Diol by Dioxygenase Chemistry.

Authors:  Edward J Whittle; Yuanheng Cai; Jantana Keereetaweep; Jin Chai; Peter H Buist; John Shanklin
Journal:  Plant Physiol       Date:  2019-12-05       Impact factor: 8.340

6.  Substrate-Triggered μ-Peroxodiiron(III) Intermediate in the 4-Chloro-l-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate.

Authors:  Molly J McBride; Mrutyunjay A Nair; Debangsu Sil; Jeffrey W Slater; Monica E Neugebauer; Michelle C Y Chang; Amie K Boal; Carsten Krebs; J Martin Bollinger
Journal:  Biochemistry       Date:  2022-04-05       Impact factor: 3.321

Review 7.  Structure/function correlations over binuclear non-heme iron active sites.

Authors:  Edward I Solomon; Kiyoung Park
Journal:  J Biol Inorg Chem       Date:  2016-07-01       Impact factor: 3.358

8.  A Peroxodiiron(III/III) Intermediate Mediating Both N-Hydroxylation Steps in Biosynthesis of the N-Nitrosourea Pharmacophore of Streptozotocin by the Multi-domain Metalloenzyme SznF.

Authors:  Molly J McBride; Debangsu Sil; Tai L Ng; Anne Marie Crooke; Grace E Kenney; Christina R Tysoe; Bo Zhang; Emily P Balskus; Amie K Boal; Carsten Krebs; J Martin Bollinger
Journal:  J Am Chem Soc       Date:  2020-06-24       Impact factor: 15.419

9.  Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis.

Authors:  Michal Tupec; Martin Culka; Aleš Machara; Stanislav Macháček; Daniel Bím; Aleš Svatoš; Lubomír Rulíšek; Iva Pichová
Journal:  Comput Struct Biotechnol J       Date:  2022-03-14       Impact factor: 7.271

10.  Orbital entanglement and CASSCF analysis of the Ru-NO bond in a Ruthenium nitrosyl complex.

Authors:  Leon Freitag; Stefan Knecht; Sebastian F Keller; Mickaël G Delcey; Francesco Aquilante; Thomas Bondo Pedersen; Roland Lindh; Markus Reiher; Leticia González
Journal:  Phys Chem Chem Phys       Date:  2015-03-13       Impact factor: 3.676

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.