A detailed mechanism of the oxidative half-reaction of<scp>d</scp>-amino acid oxidase: another route for flavin oxidation

Kiss, Dániel; Ferenczy, György G.

doi:10.1039/c9ob00975b

Cited by 17 publications

(19 citation statements)

References 71 publications

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“…To demonstrate the current capabilities of our LMP2 method, calculations for even larger systems were carried out for a 565-atom model of bicarbonate in photosystem II (PSII) 63 ( Figure 9 ) and for a 601-atom model of the d -amino acid oxidase (DAAO) 133 ( Figure 4 ).…”

Section: Computational Details and Test Systemsmentioning

confidence: 99%

“…Following the recent mechanistic study of Kiss and Ferenczy, 133 two steps are taken from the DAAO-catalyzed oxidation of d -alanine along the oxidative half-reaction. As illustrated in Figure 5 , the reduced form of the flavin moiety of the flavin adenine dinucleotide (FAD) cofactor is reoxidized by O 2 .…”

Section: Computational Details and Test Systemsmentioning

confidence: 99%

“…The diradical reactant state of Figure 5 results from a single electron transfer from reduced FAD to O 2 , leading finally to the oxidized form of FAD and H 2 O 2 . Models of the corresponding triplet and singlet states of the structures labeled by O1 T and O3 CSS in ref ( 133 ) are provided in the Supporting Information .…”

Section: Computational Details and Test Systemsmentioning

confidence: 99%

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Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

Szabó

Csóka

Kállay

et al. 2021

J. Chem. Theory Comput.

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A linear-scaling local second-order Møller–Plesset (MP2) method is presented for high-spin open-shell molecules based on restricted open-shell (RO) reference functions. The open-shell local MP2 (LMP2) approach inherits the iteration- and redundancy-free formulation and the completely integral-direct, OpenMP-parallel, and memory and disk use economic algorithms of our closed-shell LMP2 implementation. By utilizing restricted local molecular orbitals for the demanding integral transformation step and by introducing a novel long-range spin-polarization approximation, the computational cost of RO-LMP2 approaches that of closed-shell LMP2. Extensive benchmarks were performed for reactions of radicals, ionization potentials, as well as spin-state splittings of carbenes and transition-metal complexes. Compared to the conventional MP2 reference for systems of up to 175 atoms, local errors of at most 0.1 kcal/mol were found, which are well below the intrinsic accuracy of MP2. RO-LMP2 computations are presented for challenging protein models of up to 601 atoms and 11 000 basis functions, which involve either spin states of a complexed iron ion or a highly delocalized singly occupied orbital. The corresponding runtimes of 9–15 h obtained with a single, many-core CPU demonstrate that MP2, as well as spin-scaled MP2 and double-hybrid density functional methods, become widely accessible for open-shell systems of unprecedented size and complexity.

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Section: Computational Details and Test Systemsmentioning

confidence: 99%

Section: Computational Details and Test Systemsmentioning

confidence: 99%

Section: Computational Details and Test Systemsmentioning

confidence: 99%

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Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

Szabó

Csóka

Kállay

et al. 2021

J. Chem. Theory Comput.

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“…A byproduct of FAD-dependent oxidative deamination by DAAO is H 2 O 2 . A detailed mechanism of this reaction is described in [99]. Briefly, DAAO reduces FAD bound to the enzyme to FADHvia hydride transfer from a substrate (an available D-amino acid).…”

Section: Accepted Articlementioning

confidence: 99%

A guide to genetically encoded tools for the study of H₂O₂

et al. 2021

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Cell metabolism heavily relies on the redox reactions that inevitably generate reactive oxygen species (ROS). It is now well established that ROS fluctuations near basal levels coordinate numerous physiological processes in living organisms, thus exhibiting regulatory functions. Hydrogen peroxide, the most long-lived ROS, is a key contributor to ROS-dependent signal transduction in the cell. H 2 O 2 is known to impact various targets in the cell, therefore the question of how H 2 O 2 modulates physiological processes Accepted ArticleThis article is protected by copyright. All rights reserved in a highly specific manner is central in redox biology. To resolve this question, novel genetic tools have recently been created for detecting H 2 O 2 and emulating its generation in living organisms with unmatched spatiotemporal resolution. Here, we review H 2 O 2 -sensitive genetically encoded fluorescent sensors and opto-and chemogenetic tools for controlled H 2 O 2 generation.

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“…( 11) is unusually strong for such light molecule as dioxygen. That is why the Massey's mechanism is so efficient in many enzymes [22][23][24][25][26][27][28][29][30]. The T-S matrix element of SOC operator in enzyme active center described by Eq.…”

Section: Spin-orbit Coupling In Dioxygen Open Shellmentioning

confidence: 99%

"Magnetc Torque in Superoxide Ion is the Main Driving Force of Dioxygen Activation in Aerobic Life"

Минаев

2021

BJSTR

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Dioxygen (O 2 molecule) is a biradical with two unpaired electron spins, while most of organic substances have all electron spins paired; therefore reactions catalysed by oxidases and oxygenases have to involve intersystem crossing (ISC), that is a total spin change in the state multiplicity during bio oxidation. These reactions are strictly forbidden in the ordinary non-relativistic quantum chemistry. In order to overcome this severe quantum prohibition and sovereign limitation of dioxygen-induced metabolism, oxygenation enzymes require usually a redox cofactor or paramagnetic metal cofactor for effective catalysis. The spin-containing metal ions have no formal spin prohibition for reactions with dioxygen. But many oxidative enzymes include the metal-free flavin or pterin cofactors; their catalytic activity in respect to O 2 still remains mysterious in modern biochemistry and medicine. Last decades have shown, that some oxygenases can catalyse dioxygen incorporation into organic substrates even in the absence of any enzymatic cofactor. The intriguing mechanism followed by those cofactor-free enzymes which enable to provide ISC and overcome spin prohibition has been unraveled recently on the ground of common idea about specific magnetic properties of dioxygen open shell. Similar spin-orbit coupling effects are typical for O 2 molecule and for some reactive oxygen species (ROS). These spin-orbit torques are vitally decisive forces for all aerobic life.

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A detailed mechanism of the oxidative half-reaction ofd-amino acid oxidase: another route for flavin oxidation

Abstract: Flavin oxidation by d-amino acid oxidase follows a mechanism not seen in other oxidases.

Cited by 17 publications

References 71 publications

Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

A guide to genetically encoded tools for the study of H₂O₂

"Magnetc Torque in Superoxide Ion is the Main Driving Force of Dioxygen Activation in Aerobic Life"

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A detailed mechanism of the oxidative half-reaction ofd-amino acid oxidase: another route for flavin oxidation

Abstract: Flavin oxidation by d-amino acid oxidase follows a mechanism not seen in other oxidases.

Cited by 17 publications

References 71 publications

Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications

A guide to genetically encoded tools for the study of H2O2

"Magnetc Torque in Superoxide Ion is the Main Driving Force of Dioxygen Activation in Aerobic Life"

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Product

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About

A guide to genetically encoded tools for the study of H₂O₂