Human nitrobindin: the first example of an all‐β‐barrel ferric heme‐protein that catalyzes peroxynitrite detoxification

G, De Simone; Masi, Alessandra di; Polticelli, Fabio; Ascenzi, Paolo

doi:10.1002/2211-5463.12534

Cited by 21 publications

(25 citation statements)

References 66 publications

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“…Ferric Arabidopsis thaliana Nb has been hypothesized to transport and to release NO at the infection site after wounding and pathogenic infections; then, NO may reduce O 2 to the superoxide radical, increasing pathogen burden [ 10 ]. Moreover, ferric Mycobacterium tuberculosis and Homo sapiens Nbs ( Mt -Nb(III) and Hs -Nb(III), respectively) have been reported to selectively bind NO and to catalyze peroxynitrite scavenging, protecting both organisms from peroxynitrite-mediated nitration [ 13 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins

Masi

Ciaccio

et al. 2020

IJMS

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Ferric nitrobindins (Nbs) selectively bind NO and catalyze the conversion of peroxynitrite to nitrate. In this study, we show that NO scavenging occurs through the reductive nitrosylation of ferric Mycobacterium tuberculosis and Homo sapiens nitrobindins (Mt-Nb(III) and Hs-Nb(III), respectively). The conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is a monophasic process, suggesting that over the explored NO concentration range (between 2.5 × 10−5 and 1.0 × 10−3 M), NO binding is lost in the mixing time (i.e., NOkon ≥ 1.0 × 106 M−1 s−1). The pseudo-first-order rate constant for the reductive nitrosylation of Mt-Nb(III) and Hs-Nb(III) (i.e., k) is not linearly dependent on the NO concentration but tends to level off, with a rate-limiting step (i.e., klim) whose values increase linearly with [OH−]. This indicates that the conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is limited by the OH−-based catalysis. From the dependence of klim on [OH−], the values of the second-order rate constant kOH− for the reductive nitrosylation of Mt-Nb(III)-NO and Hs-Nb(III)-NO were obtained (4.9 (±0.5) × 103 M−1 s−1 and 6.9 (±0.8) × 103 M−1 s−1, respectively). This process leads to the inactivation of two NO molecules: one being converted to HNO2 and another being tightly bound to the ferrous heme-Fe(II) atom.

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Section: Introductionmentioning

confidence: 99%

NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins

Masi

Ciaccio

et al. 2020

IJMS

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“…The concentration of peroxynitrite was determined spectrophotometrically at 302 nm (ε = 1.705 × 10 3 M −1 cm −1 ) [ 12 ]. L-tyrosine (obtained from Merck KGaA, Darmstadt, Germany) was dissolved in 5.0 × 10 −2 M Bis-Tris propane buffer, at pH 7.0 and 22.0 °C; the final L-tyrosine concentration was 1.0 × 10 −4 M [ 25 , 30 , 36 , 39 ]. All the other chemicals were purchased from Merck KGaA (Darmstadt, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…In the presence of CO 2 , peroxynitrite isomerization by Dr -Nb(III) and apo- Dr -Nb was investigated by adding NaHCO 3 (final concentration, 5.0 × 10 −1 M) to the Dr -Nb(III) and apo- Dr -Nb solutions; this NaHCO 3 concentration corresponds to different concentrations of CO 2 , HCO 3 − , and CO 3 2- depending on pH. After the addition of NaHCO 3 , the Dr -Nb(III) and apo- Dr -Nb solutions were allowed to equilibrate for at least 5 min; then, the pH was readjusted to the desired pH if needed [ 25 , 27 , 28 , 30 , 36 , 39 ].…”

Section: Methodsmentioning

confidence: 99%

“…This compound further decays (via homolysis of the O–O bond), yielding the reactive species trioxocarbonate ●− (CO 3 ●− ) and ● NO 2 (3% to 35%), which then proceed towards CO 2 and NO 3 − (or by direct yielding of NO 3 − and CO 2 (65% to 90%) [ 9 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ]). As a whole, the complexity of the peroxynitrite inactivation mechanism can be sketched, as is shown in Scheme 1 [ 13 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ], where Dr -Nb(III) represents the contribution of heme proteins.…”

Section: Introductionmentioning

confidence: 99%

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The Balancing of Peroxynitrite Detoxification between Ferric Heme-Proteins and CO2: The Case of Zebrafish Nitrobindin

Coletta

Masi

et al. 2022

Antioxidants

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Nitrobindins (Nbs) are all-β-barrel heme proteins and are present in prokaryotes and eukaryotes. Although their function(s) is still obscure, Nbs trap NO and inactivate peroxynitrite. Here, the kinetics of peroxynitrite scavenging by ferric Danio rerio Nb (Dr-Nb(III)) in the absence and presence of CO2 is reported. The Dr-Nb(III)-catalyzed scavenging of peroxynitrite is facilitated by a low pH, indicating that the heme protein interacts preferentially with peroxynitrous acid, leading to the formation of nitrate (~91%) and nitrite (~9%). The physiological levels of CO2 dramatically facilitate the spontaneous decay of peroxynitrite, overwhelming the scavenging activity of Dr-Nb(III). The effect of Dr-Nb(III) on the peroxynitrite-induced nitration of L-tyrosine was also investigated. Dr-Nb(III) inhibits the peroxynitrite-mediated nitration of free L-tyrosine, while, in the presence of CO2, Dr-Nb(III) does not impair nitro-L-tyrosine formation. The comparative analysis of the present results with data reported in the literature indicates that, to act as efficient peroxynitrite scavengers in vivo, i.e., in the presence of physiological levels of CO2, the ferric heme protein concentration must be higher than 10−4 M. Thus, only the circulating ferric hemoglobin levels appear to be high enough to efficiently compete with CO2/HCO3− in peroxynitrite inactivation. The present results are of the utmost importance for tissues, like the eye retina in fish, where blood circulation is critical for adaptation to diving conditions.

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“…Epoxide hydrolase 4 (epoxide hydratase 4) is a biotransformation enzyme that catalyses the hydrolysis of arene and aliphatic epoxides to produce water-soluble dihydrodiols [146], converting highly toxic chemical groups to less reactive and easily excluded groups. THAP domaincontaining protein 4 is involved in the detoxification of reactive nitrogen species (RNS) and reactive oxygen species (ROS) [147][148]. S-formylglutathione hydrolase is a kind of serine hydrolase involved in the detoxification of formaldehyde [149].…”

Section: Evolutionary Convergence Triggered By Intracellular Algal Cellsmentioning

confidence: 99%

Full-length transcriptome maps of reef-building coral illuminate the molecular basis of calcification, symbiosis, and circadian genes

Han¹,

Liao

Zhu³

et al. 2022

Preprint

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Background: Reef-building corals are critical species for sustaining coral reefs and are highly threatened by global climate change. However, relevant transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Results: We sequenced the full-length transcriptomes of four common and frequently dominant reef-building corals, including two Robusta clade species, Pocillopora damicornis and Pocillopora verrucosa, and two Complexa clade species, Acropora muricata and Montipora foliosa, using the PacBio Sequel II platform. We obtained information on gene functions, structures and expression profiles. Among them, a comparative analysis of biomineralization-related genes provided insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiote Symbiodiniaceae were also isolated and annotated from the holobiont sequence data; these profiles showed more highly convergent traits related to gene structure and expression level than those of coral hosts. Interestingly, we observed that intracellular algal cells share some evolutionary convergence between intracellular symbiosis in corals and intracellular digestion in amphioxus. Finally, a phylogenetic analysis of key circadian clock genes among 27 evolutionarily representative species indicated that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. Conclusions: Our work overcomes the incompleteness of short-read sequencing and illuminates the molecular basis of calcification, symbiosis, and circadian genes, thus providing a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

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Human nitrobindin: the first example of an all‐β‐barrel ferric heme‐protein that catalyzes peroxynitrite detoxification

Cited by 21 publications

References 66 publications

NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins

NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins

The Balancing of Peroxynitrite Detoxification between Ferric Heme-Proteins and CO2: The Case of Zebrafish Nitrobindin

Full-length transcriptome maps of reef-building coral illuminate the molecular basis of calcification, symbiosis, and circadian genes

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