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Hydroxylamine-induced oxidation of ferrous nitrobindins. J Biol Inorg Chem 2022; 27:443-453. [PMID: 35543759 DOI: 10.1007/s00775-022-01940-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/21/2022] [Indexed: 12/19/2022]
Abstract
Hemoglobin and myoglobin are generally taken as molecular models of all-α-helical heme-proteins. On the other hand, nitrophorins and nitrobindins (Nb), which are arranged in 8 and 10 β-strands, respectively, represent the molecular models of all-β-barrel heme-proteins. Here, kinetics of the hydroxylamine- (HA-) mediated oxidation of ferrous Mycobacterium tuberculosis, Arabidopsis thaliana, and Homo sapiens nitrobindins (Mt-Nb(II), At-Nb(II), and Hs-Nb(II), respectively), at pH 7.0 and 20.0 °C, are reported. Of note, HA displays antibacterial properties and is a good candidate for the treatment and/or prevention of reactive nitrogen species- (RNS-) linked aging-related pathologies, such as macular degeneration. Under anaerobic conditions, mixing the Mt-Nb(II), At-Nb(II), and Hs-Nb(II) solutions with the HA solutions brings about absorbance spectral changes reflecting the formation of the ferric derivative (i.e., Mt-Nb(III), At-Nb(III), and Hs-Nb(III), respectively). Values of the second order rate constant for the HA-mediated oxidation of Mt-Nb(II), At-Nb(II), and Hs-Nb(II) are 1.1 × 104 M-1 s-1, 6.5 × 104 M-1 s-1, and 2.2 × 104 M-1 s-1, respectively. Moreover, the HA:Nb(II) stoichiometry is 1:2 as reported for ferrous deoxygenated and carbonylated all-α-helical heme-proteins. A comparative look of the HA reduction kinetics by several ferrous heme-proteins suggests that an important role might be played by residues (such as His or Tyr) in the proximity of the heme-Fe atom either coordinating it or not. In this respect, Nbs seem to exploit somewhat different structural aspects, indicating that redox mechanisms for the heme-Fe(II)-to-heme-Fe(III) conversion might differ between all-α-helical and all-β-barrel heme-proteins.
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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Das AK, Meuwly M. Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated Hemoglobin N. Angew Chem Int Ed Engl 2018; 57:3509-3513. [PMID: 29356324 DOI: 10.1002/anie.201711445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Indexed: 11/06/2022]
Abstract
The conversion of nitric oxide (NO) into nitrate (NO3- ) by dioxygenation protects cells from lethal NO. Starting from NO-bound heme, the first step in converting NO into benign NO3- is the ligand exchange reaction FeNO+O2 →FeO2 +NO, which is still poorly understood at a molecular level. For wild-type (WT) truncated hemoglobin N (trHbN) and its Y33A mutant, the calculated barriers for the exchange reaction differ by 1.5 kcal mol-1 , compared with 1.7 kcal mol-1 from experiment. It is directly confirmed that the ligand exchange reaction is rate-limiting in trHbN and that entropic contributions account for 75 % of the difference between the WT and the mutant. Residues Tyr 33, Phe 46, Val 80, His 81, and Gln 82 surrounding the active site are expected to control the reaction path. By comparison with electronic structure calculations, the transition state separating the two ligand-bound states was assigned to a 2 A state.
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Affiliation(s)
- Akshaya Kumar Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
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Kinetische Analyse und strukturelle Interpretation der kompetitiven Ligandenbindung für Denitrifikation in gekürztem Hämoglobin N. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ascenzi P, Ciaccio C, Gasperi T, Pesce A, Caporaso L, Coletta M. Hydroxylamine-induced oxidation of ferrous carbonylated truncated hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni is limited by carbon monoxide dissociation. J Biol Inorg Chem 2017. [PMID: 28646425 DOI: 10.1007/s00775-017-1476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydroxylamine (HA) is an oxidant of ferrous globins and its action has been reported to be inhibited by CO, even though this mechanism has not been clarified. Here, kinetics of the HA-mediated oxidation of ferrous carbonylated Mycobacterium tuberculosis truncated hemoglobin N and O (Mt-trHbN(II)-CO and Mt-trHbO(II)-CO, respectively) and Campylobacter jejuni truncated hemoglobin P (Cj-trHbP(II)-CO), at pH 7.2 and 20.0 °C, are reported. Mixing Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO solution with the HA solution brings about absorption spectral changes reflecting the disappearance of the ferrous carbonylated derivatives with the concomitant formation of the ferric species. HA oxidizes irreversibly Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO with the 1:2 stoichiometry. The dissociation of CO turns out to be the rate-limiting step for the oxidation of Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO by HA. Values of the second-order rate constant for HA-mediated oxidation of Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO range between 8.8 × 104 and 8.6 × 107 M-1 s-1, reflecting different structural features of the heme distal pocket. This study (1) demonstrates that the inhibitory effect of CO is linked to the dissociation of this ligand, giving a functional basis to previous studies, (2) represents the first comparative investigation of the oxidation of ferrous carbonylated bacterial 2/2 globins belonging to the N, O, and P groups by HA, (3) casts light on the correlation between kinetics of HA-mediated oxidation and carbonylation of globins, and (4) focuses on structural determinants modulating the HA-induced oxidation process.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, 00146, Rome, Italy.
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", 00133, Rome, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, 70126, Bari, Italy
| | - Tecla Gasperi
- Department of Sciences, Roma Tre University, 00146, Rome, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, 16146, Genoa, Italy
| | - Lucia Caporaso
- Department of Mathematics and Physics, Roma Tre University, 00146, Rome, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", 00133, Rome, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, 70126, Bari, Italy
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Cazade PA, Berezovska G, Meuwly M. Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks. Biochim Biophys Acta Gen Subj 2014; 1850:996-1005. [PMID: 25224733 DOI: 10.1016/j.bbagen.2014.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. METHODS All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. RESULTS Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. CONCLUSIONS Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. GENERAL SIGNIFICANCE Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland
| | - Ganna Berezovska
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland; Department of Chemistry, Brown University, Providence/RI, USA.
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Abstract
Small size globins that have been defined as 'truncated haemoglobins' or as '2/2 haemoglobins' have increasingly been discovered in microorganisms since the early 1990s. Analysis of amino acid sequences allowed to distinguish three groups that collect proteins with specific and common structural properties. All three groups display 3D structures that are based on four main α-helices, which are a subset of the conventional eight-helices globin fold. Specific features, such as the presence of protein matrix tunnels that are held to promote diffusion of functional ligands to/from the haem, distinguish members of the three groups. Haem distal sites vary for their accessibility, local structures, polarity, and ligand stabilization mechanisms, suggesting functional roles that are related to O2/NO chemistry. In a few cases, such activities have been proven in vitro and in vivo through deletion mutants. The issue of 2/2 haemoglobin varied biological functions throughout the three groups remains however fully open.
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Abstract
The genus Mycobacterium is comprised of Gram-positive bacteria occupying a wide range of natural habitats and includes species that range from severe intracellular pathogens to economically useful and harmless microbes. The recent upsurge in the availability of microbial genome data has shown that genes encoding haemoglobin-like proteins are ubiquitous among Mycobacteria and that multiple haemoglobins (Hbs) of different classes may be present in pathogenic and non-pathogenic species. The occurrence of truncated haemoglobins (trHbs) and flavohaemoglobins (flavoHbs) showing distinct haem active site structures and ligand-binding properties suggests that these Hbs may be playing diverse functions in the cellular metabolism of Mycobacteria. TrHbs and flavoHbs from some of the severe human pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae have been studied recently and their roles in effective detoxification of reactive nitrogen and oxygen species, electron cycling, modulation of redox state of the cell and facilitation of aerobic respiration have been proposed. This multiplicity in the function of Hbs may aid these pathogens to cope with various environmental stresses and survive during their intracellular regime. This chapter provides recent updates on genomic, structural and functional aspects of Mycobacterial Hbs to address their role in Mycobacteria.
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Cazade PA, Meuwly M. Oxygen migration pathways in NO-bound truncated hemoglobin. Chemphyschem 2012; 13:4276-86. [PMID: 23161831 DOI: 10.1002/cphc.201200608] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/28/2012] [Indexed: 11/10/2022]
Abstract
Atomistic simulations of dioxygen (O(2)) dynamics and migration in nitric oxide-bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O(2) ligand is built and analyzed. It is found that channel I is the primary entrance point for O(2) whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O(2) a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O(2) can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O(2) docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a "hub" and free energy barriers between the different metastable states are ≈1.5 kcal mol(-1) which allows facile O(2) migration within the protein.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056, Basel, Switzerland
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Mishra S, Meuwly M. Atomistic Simulation of NO Dioxygenation in Group I Truncated Hemoglobin. J Am Chem Soc 2010; 132:2968-82. [DOI: 10.1021/ja9078144] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
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Ascenzi P, De Marinis E, Visca P, Ciaccio C, Coletta M. Peroxynitrite detoxification by ferryl Mycobacterium leprae truncated hemoglobin O. Biochem Biophys Res Commun 2009; 380:392-6. [DOI: 10.1016/j.bbrc.2009.01.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 01/19/2009] [Indexed: 10/21/2022]
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H2O2 and NO scavenging by Mycobacterium leprae truncated hemoglobin O. Biochem Biophys Res Commun 2008; 373:197-201. [DOI: 10.1016/j.bbrc.2008.05.168] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 11/23/2022]
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Abacavir and warfarin modulate allosterically kinetics of NO dissociation from ferrous nitrosylated human serum heme-albumin. Biochem Biophys Res Commun 2008; 369:686-91. [DOI: 10.1016/j.bbrc.2008.02.077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 02/18/2008] [Indexed: 11/18/2022]
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Thijs L, Vinck E, Bolli A, Trandafir F, Wan X, Hoogewijs D, Coletta M, Fago A, Weber RE, Van Doorslaer S, Ascenzi P, Alam M, Moens L, Dewilde S. Characterization of a globin-coupled oxygen sensor with a gene-regulating function. J Biol Chem 2007; 282:37325-40. [PMID: 17925395 DOI: 10.1074/jbc.m705541200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Globin-coupled sensors (GCSs) are multiple-domain transducers, consisting of a regulatory globin-like heme-binding domain and a linked transducer domain(s). GCSs have been described in both Archaea and bacteria. They are generally assumed to bind O(2) (and perhaps other gaseous ligands) and to transmit a conformational change signal through the transducer domain in response to fluctuating O(2) levels. In this study, the heme-binding domain, AvGReg178, and the full protein, AvGReg of the Azotobacter vinelandii GCS, were cloned, expressed, and purified. After purification, the heme iron of AvGReg178 was found to bind O(2). This form was stable over many hours. In contrast, the predominant presence of a bis-histidine coordinate heme in ferric AvGReg was revealed. Differences in the heme pocket structure were also observed for the deoxygenated ferrous state of these proteins. The spectra showed that the deoxygenated ferrous derivatives of AvGReg178 and AvGReg are characterized by a penta-coordinate and hexa-coordinate heme iron, respectively. O(2) binding isotherms indicate that AvGReg178 and AvGReg show a high affinity for O(2) with P(50) values at 20 degrees C of 0.04 and 0.15 torr, respectively. Kinetics of CO binding indicate that AvGReg178 carbonylation conforms to a monophasic process, comparable with that of myoglobin, whereas AvGReg carbonylation conforms to a three-phasic reaction, as observed for several proteins with bis-histidine heme iron coordination. Besides sensing ligands, in vitro data suggest that AvGReg(178) may have a role in O(2)-mediated NO-detoxification, yielding metAvGReg(178) and nitrate.
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Affiliation(s)
- Liesbet Thijs
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
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