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Journal articles on the topic 'Nitrobindin'

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Author: Grafiati

Published: 11 March 2023

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1

Sauer, Daniel F., Malte Wittwer, Ulrich Markel, Alexander Minges, Markus Spiertz, Johannes Schiffels, Mehdi D. Davari, Georg Groth, Jun Okuda, and Ulrich Schwaneberg. "Chemogenetic engineering of nitrobindin toward an artificial epoxygenase." Catalysis Science & Technology 11, no. 13 (2021): 4491–99. http://dx.doi.org/10.1039/d1cy00609f.

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Chemogenetic engineering turned the heme protein nitrobindin into an artificial epoxygenase: MnPPIX was introduced and subsequent protein engineering increased the activity in the epoxidation of styrene derivatives by overall 7-fold.

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2

De Simone, Giovanna, Paolo Ascenzi, and Fabio Polticelli. "Nitrobindin: An Ubiquitous Family of Allβ-Barrel Heme-proteins." IUBMB Life 68, no. 6 (April 15, 2016): 423–28. http://dx.doi.org/10.1002/iub.1500.

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3

De Simone, Giovanna, Andrea Coletta, Alessandra di Masi, Massimo Coletta, and Paolo Ascenzi. "The Balancing of Peroxynitrite Detoxification between Ferric Heme-Proteins and CO2: The Case of Zebrafish Nitrobindin." Antioxidants 11, no. 10 (September 28, 2022): 1932. http://dx.doi.org/10.3390/antiox11101932.

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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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4

Grimm, Alexander R., Daniel F. Sauer, Tino Polen, Leilei Zhu, Takashi Hayashi, Jun Okuda, and Ulrich Schwaneberg. "A Whole CellE. coliDisplay Platform for Artificial Metalloenzymes: Poly(phenylacetylene) Production with a Rhodium–Nitrobindin Metalloprotein." ACS Catalysis 8, no. 3 (February 21, 2018): 2611–14. http://dx.doi.org/10.1021/acscatal.7b04369.

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5

De Simone, Giovanna, Alessandra di Masi, Fabio Polticelli, and Paolo Ascenzi. "Human nitrobindin: the first example of an all‐β‐barrel ferric heme‐protein that catalyzes peroxynitrite detoxification." FEBS Open Bio 8, no. 12 (November 9, 2018): 2002–10. http://dx.doi.org/10.1002/2211-5463.12534.

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6

De Simone, Giovanna, Paolo Ascenzi, Alessandra di Masi, and Fabio Polticelli. "Nitrophorins and nitrobindins: structure and function." Biomolecular Concepts 8, no. 2 (May 24, 2017): 105–18. http://dx.doi.org/10.1515/bmc-2017-0013.

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AbstractClassical all α-helical globins are present in all living organisms and are ordered in three lineages: (i) flavohemoglobins and single domain globins, (ii) protoglobins and globin coupled sensors and (iii) truncated hemoglobins, displaying the 3/3 or the 2/2 all α-helical fold. However, over the last two decades, all β-barrel and mixed α-helical-β-barrel heme-proteins displaying heme-based functional properties (e.g. ligand binding, transport and sensing) closely similar to those of all α-helical globins have been reported. Monomeric nitrophorins (NPs) and α1-microglobulin (α1-m), belonging to the lipocalin superfamily and nitrobindins (Nbs) represent prototypical heme-proteins displaying the all β-barrel and mixed α-helical-β-barrel folds. NPs are confined to the Reduviidae and Cimicidae families of Heteroptera, whereas α1-m and Nbs constitute heme-protein families spanning bacteria to Homo sapiens. The structural organization and the reactivity of the stable ferric solvent-exposed heme-Fe atom suggest that NPs and Nbs are devoted to NO transport, storage and sensing, whereas Hs-α1-m participates in heme metabolism. Here, the structural and functional properties of NPs and Nbs are reviewed in parallel with those of sperm whale myoglobin, which is generally taken as the prototype of monomeric globins.

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7

De Simone, Giovanna, Alessandra di Masi, Paola Fattibene, Chiara Ciaccio, Carlos Platas-Iglesias, Massimo Coletta, Alessandra Pesce, and Paolo Ascenzi. "Oxygen-mediated oxidation of ferrous nitrosylated nitrobindins." Journal of Inorganic Biochemistry 224 (November 2021): 111579. http://dx.doi.org/10.1016/j.jinorgbio.2021.111579.

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8

De Simone, Giovanna, Alessandra di Masi, Gian Marco Vita, Fabio Polticelli, Alessandra Pesce, Marco Nardini, Martino Bolognesi, et al. "Mycobacterial and Human Nitrobindins: Structure and Function." Antioxidants & Redox Signaling 33, no. 4 (August 1, 2020): 229–46. http://dx.doi.org/10.1089/ars.2019.7874.

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9

De Simone, Giovanna, Alessandra di Masi, Alessandra Pesce, Martino Bolognesi, Chiara Ciaccio, Lorenzo Tognaccini, Giulietta Smulevich, et al. "Mycobacterial and Human Ferrous Nitrobindins: Spectroscopic and Reactivity Properties." International Journal of Molecular Sciences 22, no. 4 (February 7, 2021): 1674. http://dx.doi.org/10.3390/ijms22041674.

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Structural and functional properties of ferrous Mycobacterium tuberculosis (Mt-Nb) and human (Hs-Nb) nitrobindins (Nbs) were investigated. At pH 7.0 and 25.0 °C, the unliganded Fe(II) species is penta-coordinated and unlike most other hemoproteins no pH-dependence of its coordination was detected over the pH range between 2.2 and 7.0. Further, despite a very open distal side of the heme pocket (as also indicated by the vanishingly small geminate recombination of CO for both Nbs), which exposes the heme pocket to the bulk solvent, their reactivity toward ligands, such as CO and NO, is significantly slower than in most hemoproteins, envisaging either a proximal barrier for ligand binding and/or crowding of H2O molecules in the distal side of the heme pocket which impairs ligand binding to the heme Fe-atom. On the other hand, liganded species display already at pH 7.0 and 25 °C a severe weakening (in the case of CO) and a cleavage (in the case of NO) of the proximal Fe-His bond, suggesting that the ligand-linked movement of the Fe(II) atom onto the heme plane brings about a marked lengthening of the proximal Fe-imidazole bond, eventually leading to its rupture. This structural evidence is accompanied by a marked enhancement of both ligands dissociation rate constants. As a whole, these data clearly indicate that structural–functional relationships in Nbs strongly differ from what observed in mammalian and truncated hemoproteins, suggesting that Nbs play a functional role clearly distinct from other eukaryotic and prokaryotic hemoproteins.

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10

De Simone, Giovanna, Alessandra di Masi, Chiara Ciaccio, Massimo Coletta, and Paolo Ascenzi. "NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins." International Journal of Molecular Sciences 21, no. 24 (December 10, 2020): 9395. http://dx.doi.org/10.3390/ijms21249395.

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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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11

Goodsell, D. S. "Featured System Nitrobindin." Protein Structure Initiative Structural Genomics Knowledgebase, December 1, 2010. http://dx.doi.org/10.3942/psi_sgkb/fm_2010_12.

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12

De Simone, Giovanna, Federico Sebastiani, Giulietta Smulevich, Massimo Coletta, and Paolo Ascenzi. "Nitrosylation of ferric zebrafish nitrobindin: A spectroscopic, kinetic, and thermodynamic study." Journal of Inorganic Biochemistry, September 2022, 111996. http://dx.doi.org/10.1016/j.jinorgbio.2022.111996.

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13

Ascenzi, Paolo, Giovanna De Simone, Paola Fattibene, Federico Sebastiani, Massimo Coletta, and Giulietta Smulevich. "Switching of the Fifth-Coordination Heme-Fe Bond in Ferrous Zebrafish Nitrobindin." SSRN Electronic Journal, 2022. http://dx.doi.org/10.2139/ssrn.4148147.

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14

De Simone, Giovanna, Paola Fattibene, Federico Sebastiani, Giulietta Smulevich, Massimo Coletta, and Paolo Ascenzi. "Dissociation of the proximal His-Fe bond upon NO binding to ferrous zebrafish nitrobindin." Journal of Inorganic Biochemistry, August 2022, 111962. http://dx.doi.org/10.1016/j.jinorgbio.2022.111962.

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15

De Simone, Giovanna, Grazia R. Tundo, Andrea Coletta, Massimo Coletta, and Paolo Ascenzi. "Hydroxylamine-induced oxidation of ferrous nitrobindins." JBIC Journal of Biological Inorganic Chemistry, May 11, 2022. http://dx.doi.org/10.1007/s00775-022-01940-9.

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