Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions

Giordano, Daniela; Pesce, Alessandra; Vermeylen, Stijn; Abbruzzetti, Stefania; Nardini, M.; Marchesani, Francesco; Berghmans, Herald; Seira, Constantí; Bruno, Stefano; Luque, F. Javier; Prisco, Guido di; Ascenzi, Paolo; Dewilde, Sylvia; Bolognesi, M.; Viappiani, Cristiano; Verde, Cinzia

doi:10.1016/j.csbj.2020.08.007

Cited by 10 publications

(15 citation statements)

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“…Indeed, a heterogeneity in ligand migration pathways was evident in previous biphasic ligand binding kinetics ( 4 , 5 ). However, biphasic kinetics was attributed to a structural heterogeneity in the isolated flavoHbs, rather than to the existence of multiple and dynamic pathways, as recently argued for CO migration in Cygb ( 50 ).…”

Section: Resultsmentioning

confidence: 90%

“…Indeed, the Fe 3+ and O 2 interactions are relatively weak given the large micromolar K 2 values ( Tables 1 and 3 ) relative to the corresponding nanomolar K d values for Fe 2+ O 2 ( Table 5 ). The strictured and segmented LT further suggests potential mechanisms for the controlled storage and influx of O 2 in the NOD function of flavoHb and roles for similar tunnels in other globin-NODs including HbN, the alpha subunit of HbA ( 18 , 61 ), and Cygb ( 10 , 17 , 36 , 37 , 50 ). The failure of O 2 to compete with NO suggests strong discrimination against O 2 entry by the ST.…”

Section: Discussionmentioning

confidence: 95%

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Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin

Gardner

2021

Journal of Biological Chemistry

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The substrates O 2 and NO cooperatively activate the NO dioxygenase function of Escherichia coli flavohemoglobin. Steady-state and transient kinetic measurements support a structure-based mechanistic model in which O 2 and NO movements and conserved amino acids at the E11, G8, E2, E7, B10, and F7 positions within the globin domain control activation. In the cooperative and allosteric mechanism, O 2 migrates to the catalytic heme site via a long hydrophobic tunnel and displaces LeuE11 away from the ferric iron, which forces open a short tunnel to the catalytic site gated by the ValG8/IleE15 pair and LeuE11. NO permeates this tunnel and leverages upon the gating side chains trigger the CD loop to furl, which moves the E and F-helices and switches an electron transfer gate formed by LysF7, GlnE7, and water. This allows FADH 2 to reduce the ferric iron, which forms the stable ferric–superoxide–TyrB10/GlnE7 complex. This complex reacts with internalized NO with a bimolecular rate constant of 10 10 M −1 s −1 forming nitrate, which migrates to the CD loop and unfurls the spring-like structure. To restart the cycle, LeuE11 toggles back to the ferric iron. Actuating electron transfer with O 2 and NO movements averts irreversible NO poisoning and reductive inactivation of the enzyme. Together, structure snapshots and kinetic constants provide glimpses of intermediate conformational states, time scales for motion, and associated energies.

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Section: Resultsmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 95%

Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin

Gardner

2021

Journal of Biological Chemistry

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“…Values of the pseudo-first-order rate constant for peroxynitrite isomerization by Dr -Nb(III) and apo- Dr -Nb (i.e., k obs ) were determined according to Equation (1) [ 13 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 54 , 55 ]: [peroxynitrite] t = [peroxynitrite] i × e − k obs × t …”

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%

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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“…Neuroglobin and cytoglobin were discovered in Antarctic fishes, including the haemoglobin-less channichthyid species, suggesting the evolution of functional innovations to mitigate such oxidative damage. Under experimental conditions, neuroglobin showed oxygen-related functions but its precise role in protection from damage remains unknown (Cuypers et al, 2017, Giordano et al, 2020.…”

Section: (D) Sentinel Species and Communities Warn Of Environmental Changesmentioning

confidence: 99%

Antarctic ecosystems in transition – life between stresses and opportunities

et al. 2020

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Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions

Abstract: Graphical abstract 1 These authors contributed equally as First Author.

Cited by 10 publications

References 84 publications

Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin

Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin

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

Antarctic ecosystems in transition – life between stresses and opportunities

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