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Polaczek J, Kieca K, Oszajca M, Impert O, Katafias A, Chatterjee D, Ćoćić D, Puchta R, Stochel G, Hubbard CD, van Eldik R. A Personal Account on Inorganic Reaction Mechanisms. CHEM REC 2023:e202300278. [PMID: 37821418 DOI: 10.1002/tcr.202300278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/22/2023] [Indexed: 10/13/2023]
Abstract
The presented Review is focused on the latest research in the field of inorganic chemistry performed by the van Eldik group and his collaborators. The first part of the manuscript concentrates on the interaction of nitric oxide and its derivatives with biologically important compounds. We summarized mechanistic information on the interaction between model porphyrin systems (microperoxidase) and NO as well as the recent studies on the formation of nitrosylcobalamin (CblNO). The following sections cover the characterization of the Ru(II)/Ru(III) mixed-valence ion-pair complexes, including Ru(II)/Ru(III)(edta) complexes. The last part concerns the latest mechanistic information on the DFT techniques applications. Each section presents the most important results with the mechanistic interpretations.
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Affiliation(s)
- Justyna Polaczek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Konrad Kieca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Kraków, 30-348, Krakow, Poland
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Olga Impert
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Torun, Poland
| | - Anna Katafias
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Torun, Poland
| | - Debabrata Chatterjee
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Torun, Poland
- Vice-Chancellor's Research Group, Zoology Department, University of Burdwan, Burdwan, 713104, India
| | - Dušan Ćoćić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, P. O. Box 60, 34000, Kragujevac, Serbia
| | - Ralph Puchta
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058, Erlangen, Germany
- Central Institute for Scientific Computing (CISC), University of Erlangen-Nuremberg, Martensstr. 5a, 91058, Erlangen, Germany
- Computer Chemistry Center, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Nägelsbachstr. 25, 91052, Erlangen, Germany
| | - Grażyna Stochel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Colin D Hubbard
- Department of Chemistry, University of New Hampshire, Durham, 03824, USA
| | - Rudi van Eldik
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058, Erlangen, Germany
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Torun, Poland
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Abstract
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Previously, we have
demonstrated native mass spectrometry imaging
(native MSI) in which the spatial distribution of proteins maintained
in their native-like, folded conformations was determined using liquid
extraction surface analysis (LESA). While providing an excellent testbed
for proof of principle, the spatial resolution of LESA is currently
limited for imaging primarily by the physical size of the sampling
pipette tip. Here, we report the adoption of nanospray-desorption
electrospray ionization (nano-DESI) for native MSI, delivering substantial
improvements in resolution versus native LESA MSI. In addition, native
nano-DESI may be used for location-targeted top–down proteomics
analysis directly from tissue. Proteins, including a homodimeric complex
not previously detected by native MSI, were identified through a combination
of collisional activation, high-resolution MS and proton transfer
charge reduction.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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Mathura S, Sannasy D, de Sousa AS, Perry CB, Navizet I, Marques HM. The preparation of N-acetyl-Co(III)-microperoxidase-8 (NAcCoMP8) and its ligand substitution reactions: A comparison with aquacobalamin (vitamin B12a). J Inorg Biochem 2013; 123:66-79. [DOI: 10.1016/j.jinorgbio.2013.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 12/01/2022]
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Merkley ED, Anderson BJ, Park J, Belchik SM, Shi L, Monroe ME, Smith RD, Lipton MS. Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching. J Proteome Res 2012; 11:6147-58. [PMID: 23082897 DOI: 10.1021/pr3007914] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiheme c-type cytochromes (proteins with covalently attached heme c moieties) play important roles in extracellular metal respiration in dissimilatory metal-reducing bacteria. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of c-type cytochromes is hindered by the presence of multiple heme groups, since the heme c modified peptides are typically not observed or, if observed, not identified. Using a recently reported histidine affinity chromatography (HAC) procedure, we enriched heme c tryptic peptides from purified bovine heart cytochrome c, two bacterial decaheme cytochromes, and subjected these samples to LC-MS/MS analysis. Enriched bovine cytochrome c samples yielded 3- to 6-fold more confident peptide-spectrum matches to heme c containing peptides than unenriched digests. In unenriched digests of the decaheme cytochrome MtoA from Sideroxydans lithotrophicus ES-1, heme c peptides for 4 of the 10 expected sites were observed by LC-MS/MS; following HAC fractionation, peptides covering 9 out of 10 sites were obtained. Heme c peptide spiked into E. coli lysates at mass ratios as low as 1×10(-4) was detected with good signal-to-noise after HAC and LC-MS/MS analysis. In addition to HAC, we have developed a proteomics database search strategy that takes into account the unique physicochemical properties of heme c peptides. The results suggest that accounting for the double thioether link between heme c and peptide, and the use of the labile heme fragment as a reporter ion, can improve database searching results. The combination of affinity chromatography and heme-specific informatics yielded increases in the number of peptide-spectrum matches of 20-100-fold for bovine cytochrome c.
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Affiliation(s)
- Eric D Merkley
- Pacific Northwest National Laboratories, Richland, Washington 99352, United States
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Bechara C, Bolbach G, Bazzaco P, Sharma KS, Durand G, Popot JL, Zito F, Sagan S. MALDI-TOF mass spectrometry analysis of amphipol-trapped membrane proteins. Anal Chem 2012; 84:6128-35. [PMID: 22703540 DOI: 10.1021/ac301035r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphipols (APols) are amphipathic polymers with the ability to substitute detergents to keep membrane proteins (MPs) soluble and functional in aqueous solutions. APols also protect MPs against denaturation. Here, we have examined the ability of APol-trapped MPs to be analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For that purpose, we have used ionic and nonionic APols and as model proteins (i) the transmembrane domain of Escherichia coli outer membrane protein A, a β-barrel, eubacterial MP, (ii) Halobacterium salinarum bacteriorhodopsin, an α-helical archaebacterial MP with a single cofactor, and (iii, iv) two eukaryotic MP complexes comprising multiple subunits and many cofactors, cytochrome b(6)f from the chloroplast of the green alga Chlamydomonas reinhardtii and cytochrome bc(1) from beef heart mitochondria. We show that these MP/APol complexes can be readily analyzed by MALDI-TOF-MS; most of the subunits and some lipids and cofactors were identified. APols alone, even ionic ones, had no deleterious effects on MS signals and were not detected in mass spectra. Thus, the combination of MP stabilization by APols and MS analyses provides an interesting new approach to investigating supramolecular interactions in biological membranes.
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Affiliation(s)
- Chérine Bechara
- Université Pierre et Marie Curie (UPMC Université Paris 06), Laboratoire des BioMolécules (LBM), Paris, France
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Haselberg R, de Jong GJ, Somsen GW. Capillary electrophoresis–mass spectrometry of intact basic proteins using Polybrene–dextran sulfate–Polybrene-coated capillaries: System optimization and performance. Anal Chim Acta 2010; 678:128-34. [DOI: 10.1016/j.aca.2010.08.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/23/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
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Cirpus IEY, de Been M, den Camp HJMO, Strous M, Le Paslier D, Kuenen GJ, Jetten MSM. A new soluble 10 kDa monoheme cytochromec-552 from the anammox bacteriumCandidatus“Kuenenia stuttgartiensis”. FEMS Microbiol Lett 2006; 252:273-8. [PMID: 16216446 DOI: 10.1016/j.femsle.2005.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Revised: 08/29/2005] [Accepted: 09/04/2005] [Indexed: 11/28/2022] Open
Abstract
The chemolithoautotrophic anammox bacterium Candidatus "Kuenenia stuttgartiensis" grows anaerobically using ammonium as electron donor for nitrite reduction. More than 10% of the proteins in cell extracts of "K. stuttgartiensis" consist of c-type heme proteins. A 10kDa soluble cytochrome c was purified from cell extracts using ultracentrifugation and anion exchange chromatography. The UV/Vis spectrum of the reduced cytochrome showed the gamma, beta and alpha absorption maxima at 419, 522 and 552nm, respectively. The N-terminal amino acid sequence and peptide fragments of the tryptic digest of the protein were used to identify the corresponding gene. Analysis of the gene product showed that the protein was preceded by a 30 amino acids long leader sequence and that it belonged to the low-spin class ID cytochrome c. The CXXCH motive was located at the N-terminal site of the protein. The gene organization of the cytochrome showed some resemblance to cytochrome c clusters of unknown function in the genome of Nitrosomonas europaea and Geobacter sulfurreducens PCA.
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Affiliation(s)
- Irina E Y Cirpus
- Kluyver Laboratory for Biotechnology, Delft University of Technology, The Netherlands
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Dallacosta C, Casella L, Monzani E. Modified Microperoxidases Exhibit Different Reactivity Towards Phenolic Substrates. Chembiochem 2004; 5:1692-9. [PMID: 15532028 DOI: 10.1002/cbic.200400175] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The reactivity of several microperoxidase derivatives with different distal-site environments has been studied. The distal-site environments of these heme peptides include a positively charged one, an uncharged environment, two bulky and doubly or triply positively charged ones, and one containing aromatic apolar residues. The reactivity in the catalytic oxidation of two representative phenols, carrying opposite charges, by hydrogen peroxide has been investigated. This allows the determination of the binding constants and of the electron-transfer rate from the phenol to the catalyst in the substrate/microperoxidase complex. The electron-transfer rates scarcely depend on the redox and charge properties of the phenol, but depend strongly on the microperoxidase. Information on the disposition of the substrate in the adducts with the microperoxidases has been obtained through determination of the paramagnetic contribution to the 1H NMR relaxation rates of the protons of the bound substrates. The data show that the electron-transfer rate drops when the substrate binds too far away from the iron and that the phenols bind to microperoxidases at similar distances to those observed with peroxidases. While the reaction rate of microperoxidases with peroxide is significantly smaller than that of the enzymes, the efficiency in the one-electron oxidation of phenolic substrates is almost comparable. Interestingly, the oxyferryl form of the triply positively charged microperoxidases shows a reactivity larger than that exhibited by horseradish peroxidase.
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Affiliation(s)
- Corrado Dallacosta
- Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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Chuang WJ, Chang YD, Jeng WY. Kinetic and structural studies of N-acetyl-microperoxidase-5 and -microperoxidase-8. J Inorg Biochem 1999. [DOI: 10.1016/s0162-0134(99)00038-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Carraway AD, McCollum MG, Peterson J. Characterization of N-Acetylated Heme Undecapeptide and Some of Its Derivatives in Aqueous Media: Monomeric Model Systems for Hemoproteins. Inorg Chem 1996; 35:6885-6891. [PMID: 11666857 DOI: 10.1021/ic960434o] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The heme undecapeptide of cytochrome c has been converted to a bis(N-acetylated) derivative by reaction with acetic anhydride. The structure of the product has been confirmed by liquid secondary-ion mass spectrometry. As anticipated, the N-acetylated molecule exhibits much less tendency to aggregate in aqueous solution than its heme undecapeptide precursor. Around neutral pH, one axial ligand on the heme iron is provided by the same histidine residue as in the native cytochrome. The other axial ligand can be varied by the addition of exogenous donor species to produce a range of hemoprotein model compounds exhibiting mixed axial ligation. Contrary to the findings of Othman et al. [Biochemistry 1994, 33, 15437-15448] concerning heme octapeptide, the N-acetylated undecapeptide showed no tendency to bind more than one exogenous ligand per heme. At concentrations approaching millimolar and in the absence of exogenous ligands, the N-acetylated molecule may either be monodispersed, exhibiting a characteristic high-spin (S = (5)/(2)) ferric heme electron paramagnetic resonance (EPR) signal, or exist in an EPR-silent and presumably aggregated form. Interestingly, the system displays a novel dependence on the buffer with regard to which of these two forms is present in a given sample. There is no evidence in any of the spectra for the existence of an intermediate-spin (S = (3)/(2)) ferric heme as suggested by Wang and Van Wart [J. Phys. Chem. 1989, 93, 7925-7931] to be present in aqueous solutions of N-acetylated heme octapeptide. Also, in contrast to another earlier report concerning the underivatized undecapeptide [Clore et al. Inorg. Chim. Acta 1981, 56, 143-148], the N-acetylated molecule showed no evidence of catalase activity. In fact, the heme chromophore was surprisingly unstable in the presence of hydrogen peroxide.
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Affiliation(s)
- Angela D. Carraway
- Departments of Chemistry and Chemical Engineering, The University of Alabama, Tuscaloosa, Alabama 35487-0336
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Mathew S, Peterson J, de Gaulejac B, Vicente N, Denis M, Bonaventura J, Pearce LL. Manganese and “pinnaglobin” in Pinna nobilis. Comp Biochem Physiol B Biochem Mol Biol 1996. [DOI: 10.1016/0305-0491(95)02077-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Carraway AD, Povlock SL, Houston ML, Johnston DS, Peterson J. Monomeric ferric heme peptide derivatives: model systems for hemoproteins. J Inorg Biochem 1995; 60:267-76. [PMID: 8530922 DOI: 10.1016/0162-0134(95)00026-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Electron paramagnetic resonance spectra of a number of ferric heme peptide derivatives, in aqueous-detergent and various aqueous-alcohol solvent mixtures, have been obtained using samples in the concentration range 0.1-1.0 mM. Some of these were clearly monomeric, homogeneous, mixed-ligand adducts, entirely suitable for use as model systems for hemoprotein spectroscopic studies. As anticipated, the measured EPR parameters were largely independent of solvent environment. Surprisingly, micellar preparations of ferric heme undecapeptide in mildly alkaline solution showed no evidence for the formation of a hydroxide adduct, contrary to a previous report [S. Mazumdar, O. K. Medhi and S. Mitra, Inorg. Chem. 30 700 (1991)].
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Affiliation(s)
- A D Carraway
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336, USA
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