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Messias A, Capece L, De Simone G, Coletta M, Ascenzi P, Estrin DA. Mechanism of Peroxynitrite Interaction with Ferric M. tuberculosis Nitrobindin: A Computational Study. Inorg Chem 2024; 63:9907-9918. [PMID: 38754069 DOI: 10.1021/acs.inorgchem.4c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme proteins present along the evolutionary ladder. They display a highly solvent-exposed ferric heme group with the iron atom being coordinated by the proximal His residue and a water molecule at the distal position. Ferric nitrobindins (Nb(III)) play a role in the conversion of toxic peroxynitrite (ONOO-) to harmless nitrate, with the value of the second-order rate constant being similar to those of most heme proteins. The value of the second-order rate constant of Nbs increases as the pH decreases; this suggests that Nb(III) preferentially reacts with peroxynitrous acid (ONOOH), although ONOO- is more nucleophilic. In this work, we shed light on the molecular basis of the ONOO- and ONOOH reactivity of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) by dissecting the ligand migration toward the active site, the water molecule release, and the ligand binding process by computer simulations. Classical molecular dynamics simulations were performed by employing a steered molecular dynamics approach and the Jarzynski equality to obtain ligand migration free energy profiles for both ONOO- and ONOOH. Our results indicate that ONOO- and ONOOH migration is almost unhindered, consistent with the exposed metal center of Mt-Nb(III). To further analyze the ligand binding process, we computed potential energy profiles for the displacement of the Fe(III)-coordinated water molecule using a hybrid QM/MM scheme at the DFT level and a nudged elastic band approach. These results indicate that ONOO- exhibits a much larger barrier for ligand displacement than ONOOH, suggesting that water displacement is assisted by protonation of the leaving group by the incoming ONOOH.
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Affiliation(s)
- Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Luciana Capece
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, I-00146 Roma, Italy
| | - Massimo Coletta
- IRCCS Fondazione Bietti, Via Santo Stefano Rotondo, 6, 00184 Roma, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, I-00146 Roma, Italy
- Accademia Nazionale dei Lincei, Via della Lungara, 10, 00165 Roma, Italy
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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Di Rocco G, Bernini F, Battistuzzi G, Ranieri A, Bortolotti CA, Borsari M, Sola M. Hydrogen peroxide induces heme degradation and protein aggregation in human neuroglobin: roles of the disulfide bridge and hydrogen-bonding in the distal heme cavity. FEBS J 2023; 290:148-161. [PMID: 35866372 PMCID: PMC10087938 DOI: 10.1111/febs.16581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 01/14/2023]
Abstract
In the present study, human neuroglobin (hNgb) was found to undergo H2 O2 -induced breakdown of the heme center at a much slower rate than other globins, namely in the timescale of hours against minutes. We investigated how the rate of the process is affected by the Cys46/Cys55 disulfide bond and the network of non-covalent interactions in the distal heme side involving Tyr44, Lys67, the His64 heme iron axial ligand and the heme propionate-7. The rate is increased by the Tyr44 to Ala and Phe mutations; however the rate is lowered by Lys67 to Ala swapping. The absence of the disulfide bridge slows down the reaction further. Therefore, the disulfide bond-controlled accessibility of the heme site and the residues at position 44 and 67 affect the activation barrier of the reaction. Wild-type and mutated species form β-amyloid aggregates in the presence of H2 O2 producing globular structures. Furthermore, the C46A/C55A, Y44A, Y44F and Y44F/C46A/C55A variants yield potentially harmful fibrils. Finally, the nucleation and growth kinetics for the aggregation of the amyloid structures can be successfully described by the Finke-Watzky model.
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Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Fabrizio Bernini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Antonio Ranieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | | | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Marco Sola
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
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De Simone G, Coletta A, di Masi A, Coletta M, Ascenzi P. The Balancing of Peroxynitrite Detoxification between Ferric Heme-Proteins and CO2: The Case of Zebrafish Nitrobindin. Antioxidants (Basel) 2022; 11:antiox11101932. [PMID: 36290653 PMCID: PMC9599043 DOI: 10.3390/antiox11101932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
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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Affiliation(s)
| | - Andrea Coletta
- Dipartimento di Scienze, Università Roma Tre, 00146 Roma, Italy
| | | | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy
- Correspondence: (M.C.); (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, 00146 Roma, Italy
- Correspondence: (M.C.); (P.A.)
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Badenhorst R, Kadambar VK, Bellare M, Melman A, Katz E, Smutok O. Electrochemically produced local pH changes stimulating (bio)molecule release from pH-switchable electrode-immobilized avidin-biotin systems. Phys Chem Chem Phys 2022; 24:6410-6414. [PMID: 35234792 DOI: 10.1039/d2cp00689h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Immobilized avidin-biotin complexes were used to release biotinylated (bio)molecules upon producing local pH changes near an electrode surface by electrochemical reactions. The nitro-avidin complex with biotin was dissociated by increasing local pH with electrochemical O2 reduction. The avidin complex with iminobiotin was split by decreasing local pH with electrochemical oxidation of ascorbate. Both studied systems were releasing molecule cargo species in response to small electrical potentials (-0.4 V or 0.2 V for the O2 reduction or ascorbate oxidation, respectively) applied on the modified electrodes.
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Affiliation(s)
- Ronaldo Badenhorst
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | | | - Madhura Bellare
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
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Ferric nitrosylated myoglobin catalyzes peroxynitrite scavenging. J Biol Inorg Chem 2020; 25:361-370. [PMID: 32172452 DOI: 10.1007/s00775-020-01767-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/13/2020] [Indexed: 01/12/2023]
Abstract
Myoglobin (Mb), generally taken as the molecular model of monomeric globular heme-proteins, is devoted: (i) to act as an intracellular oxygen reservoir, (ii) to transport oxygen from the sarcolemma to the mitochondria of vertebrate heart and red muscle cells, and (iii) to act as a scavenger of nitrogen and oxygen reactive species protecting mitochondrial respiration. Here, the first evidence of ·NO inhibition of ferric Mb- (Mb(III)) mediated detoxification of peroxynitrite is reported, at pH 7.2 and 20.0 °C. ·NO binds to Mb(III) with a simple equilibrium; the value of the second-order rate constant for Mb(III) nitrosylation (i.e., ·NOkon) is (6.8 ± 0.7) × 104 M-1 s-1 and the value of the first-order rate constant for Mb(III)-NO denitrosylation (i.e., ·NOkoff) is 3.1 ± 0.3 s-1. The calculated value of the dissociation equilibrium constant for Mb(III)-NO complex formation (i.e., ·NOkoff/·NOkon = (4.6 ± 0.7) × 10-5 M) is virtually the same as that directly measured (i.e., ·NOK = (3.8 ± 0.5) × 10-5 M). In the absence of ·NO, Mb(III) catalyzes the conversion of peroxynitrite to NO3-, the value of the second-order rate constant (i.e., Pkon) being (1.9 ± 0.2) × 104 M-1 s-1. However, in the presence of ·NO, Mb(III)-mediated detoxification of peroxynitrite is only partially inhibited, underlying the possibility that also Mb(III)-NO is able to catalyze the peroxynitrite isomerization, though with a reduced rate (Pkon* = (2.8 ± 0.3) × 103 M-1 s-1). These data expand the multiple roles of ·NO in modulating heme-protein actions, envisaging a delicate balancing between peroxynitrite and ·NO, which is modulated through the relative amount of Mb(III) and Mb(III)-NO.
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Abstract
In this study, we reported on a novel mimetic peroxidase, deuterohemin–Ala–His–Glu, (Dh–A–H–E). The kinetic parameters of Dh–A–H–E suggested that it was a mimetic peroxidase and followed the ping–pong mechanism. Compared to horseradish peroxidase, Dh–A–H–E exhibited excellent stability when tested at different pH and temperatures, and using different organic solvents. Based on our above results, a new method using Dh–A–H–E has successfully been developed for the fast and quantitative detection of trace amounts of glucose.
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De Simone G, di Masi A, Polticelli F, Ascenzi P. Human nitrobindin: the first example of an all-β-barrel ferric heme-protein that catalyzes peroxynitrite detoxification. FEBS Open Bio 2018; 8:2002-2010. [PMID: 30524950 PMCID: PMC6275384 DOI: 10.1002/2211-5463.12534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/29/2018] [Accepted: 09/26/2018] [Indexed: 11/12/2022] Open
Abstract
Nitrobindins (Nbs), constituting a heme‐protein family spanning from bacteria to Homo sapiens, display an all‐β‐barrel structural organization. Human Nb has been described as a domain of the nuclear protein named THAP4, whose physiological function is still unknown. We report the first evidence of the heme‐Fe(III)‐based detoxification of peroxynitrite by the all‐β‐barrel C‐terminal Nb‐like domain of THAP4. Ferric human Nb (Nb(III)) catalyzes the conversion of peroxynitrite to NO3− and impairs the nitration of free l‐tyrosine. The rate of human Nb(III)‐mediated scavenging of peroxynitrite is similar to those of all‐α‐helical horse heart and sperm whale myoglobin and human hemoglobin, generally taken as the prototypes of all‐α‐helical heme‐proteins. The heme‐Fe(III) reactivity of all‐β‐barrel human Nb(III) and all‐α‐helical prototypical heme‐proteins possibly reflects the out‐to‐in‐plane transition of the heme‐Fe(III)‐atom preceding peroxynitrite binding. Human Nb(III) not only catalyzes the detoxification of peroxynitrite but also binds NO, possibly representing a target of reactive nitrogen species.
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Affiliation(s)
| | | | - Fabio Polticelli
- Department of Sciences Roma Tre University Italy.,National Institute of Nuclear Physics Roma Tre Section Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy Roma Tre University Italy
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Reductive nitrosylation of ferric microperoxidase-11. J Biol Inorg Chem 2018; 24:21-29. [PMID: 30390140 DOI: 10.1007/s00775-018-1623-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c, which is considered as a heme-protein model. Here, the reductive nitrosylation of ferric MP11 (MP11(III)) under anaerobic conditions has been investigated between pH 7.4 and 9.2, at T = 20.0 °C. At pH ≤ 7.7, NO binds reversibly to MP11(III) leading to the formation of the MP11(III)-NO complex. However, between pH 8.2 and 9.2, the addition of NO to MP11(III) leads to the formation of ferrous nitrosylated MP11(II) (MP11(II)-NO). In fact, the transient MP11{FeNO}6 species is converted to ferrous deoxygenated MP11 (MP11(II)) by OH-- and H2O-based catalysis, which represents the rate-limiting step of the whole reaction. Then, MP11(II) binds NO very rapidly leading to MP11(II)-NO formation. Over the whole pH range explored, the apparent values of kon, koff, and K (= koff/kon) for MP11(III)(-NO) (de)nitrosylation are essentially pH independent, ranging between 5.8 × 105 M-1 s-1 and 1.6 × 106 M-1 s-1, between 1.9 s-1 and 3.7 s-1, and between 1.4 × 10-6 M and 4.6 × 10-6 M, respectively. Values of the apparent pseudo-first-order rate constant for the MP11{FeNO}6 conversion to MP11(II) (i.e., h) increase linearly with pH; the apparent values [Formula: see text] and [Formula: see text] are 7.2 × 102 M-1 s-1 and 2.5 × 10-4 s-1, respectively. Present data confirm that MP11 is a useful molecular model to highlight the role of the protein matrix on the heme-based reactivity.
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Ascenzi P, Coletta M. Peroxynitrite Detoxification by Human Haptoglobin:Hemoglobin Complexes: A Comparative Study. J Phys Chem B 2018; 122:11100-11107. [DOI: 10.1021/acs.jpcb.8b05340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Via Montpellier 1, I-00133 Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126 Bari, Italy
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Ascenzi P, Pesce A. Peroxynitrite scavenging by Campylobacter jejuni truncated hemoglobin P. J Biol Inorg Chem 2017; 22:1141-1150. [DOI: 10.1007/s00775-017-1490-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
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Prieto T, Santana V, Britto AMM, Araujo-Chaves JC, R Nascimento O, L Nantes-Cardoso I. Structure and Catalysis of Fe(III) and Cu(II) Microperoxidase-11 Interacting with the Positively Charged Interfaces of Lipids. Molecules 2017; 22:molecules22081212. [PMID: 28933729 PMCID: PMC6151982 DOI: 10.3390/molecules22081212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 11/24/2022] Open
Abstract
Numerous applications have been described for microperoxidases (MPs) such as in photoreceptors, sensing, drugs, and hydrogen evolution. The last application was obtained by replacing Fe(III), the native central metal, by cobalt ion and inspired part of the present study. Here, the Fe(III) of MP-11 was replaced by Cu(II) that is also a stable redox state in aerated medium, and the structure and activity of both MPs were modulated by the interaction with the positively charged interfaces of lipids. Comparative spectroscopic characterization of Fe(III) and Cu(II)MP-11 in the studied media demonstrated the presence of high and low spin species with axial distortion. The association of the Fe(III)MP-11 with CTAB and Cu(II)MP-11 with DODAB affected the colloidal stability of the surfactants that was recovered by heating. This result is consistent with hydrophobic interactions of MPs with DODAB vesicles and CTAB micelles. The hydrophobic interactions decreased the heme accessibility to substrates and the Fe(III) MP-11catalytic efficiency. Cu(II)MP-11 challenged by peroxides exhibited a cyclic Cu(II)/Cu(I) interconversion mechanism that is suggestive of a mimetic Cu/ZnSOD (superoxide dismutase) activity against peroxides. Hydrogen peroxide-activated Cu(II)MP-11 converted Amplex Red® to dihydroresofurin. This study opens more possibilities for technological applications of MPs.
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Affiliation(s)
- Tatiana Prieto
- Universidade Federal do ABC, Santo André 09210-170, SP, Brazil.
| | - Vinicius Santana
- Universidade de São Paulo, Instituto de Física de São Carlos, São Carlos 13400-970, SP, Brazil.
| | | | | | - Otaciro R Nascimento
- Universidade de São Paulo, Instituto de Física de São Carlos, São Carlos 13400-970, SP, Brazil.
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Ascenzi P, Sbardella D, Santucci R, Coletta M. Cyanide binding to ferrous and ferric microperoxidase-11. J Biol Inorg Chem 2016; 21:511-22. [DOI: 10.1007/s00775-016-1361-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
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