Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase

Abstract

Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate–Schiff base to the product–Schiff base, which includes the rate-limiting cleavage of the Cα–H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα–H bond involves direct hydride transfer to the topaquinone cofactor—a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction.

Histamine Intolerance: The Current State of the Art

“…The gateway for dietary histamine in the body is the intestinal epithelium. Therefore, although HNMT is also present in the gastrointestinal tract, the more highly expressed DAO plays the major role in protecting the body against exogenous histamine, whether originating from ingested food or generated by the intestinal microbiota [ 24 , 25 , 26 ]. The protective effect of DAO has been demonstrated in animal experimentation models that were administered aminoguanidine for irreversible and selective DAO inhibition, followed by a dose of histamine [ 24 , 27 , 28 ].…”

Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway

“…However, in these cases, the Hamiltonian used to describe the catalytic region is usually simplied, and the size of the QM region is reduced, in order to calculate the energies of very many structures generated by these methods. [20][21][22][23][24][25] Recent state-of-theart studies have already calculated potentials of mean force with high-level hybrid-meta Hamiltonians, even though the size of the QM region is still reduced and the MD time, despite being remarkable, is still smaller than the timescale of many enzyme structural uctuations, due to insurmountable CPU limitations. 26 In these excellent studies, the effects of conformational diversity are accounted for implicitly, through the sampling made in each point along the reaction coordinate, and thus not used to gain understanding of the nature of the uctuations in the interactions that stabilize the transition structures, which is the major purpose of this study and other studies of this kind.…”

Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting Step

“…Furthermore, the EVB methodology was used to tackle selectivity of both isoforms MAO-A and MAO-B towards adrenaline [42], and to elucidate the reactive step of decomposition of serotonin by MAO-A [43]. In addition to MAO enzymes, an EVB study supported by DFT cluster calculations suggests that the hydride transfer mechanism is involved in the function of the DAO enzyme [44]. Apart from EVB methodology, reactions catalyzed by MAO enzymes have been studied by the "traditional" QM/MM approach including DFT methodology in the quantum part [45], or by cluster models treated by DFT [37,46,47].…”