1
|
Raes A, Ninakanti R, Van den Bergh L, Borah R, Van Doorslaer S, Verbruggen SW. Black titania by sonochemistry: A critical evaluation of existing methods. Ultrason Sonochem 2023; 100:106601. [PMID: 37722246 PMCID: PMC10518725 DOI: 10.1016/j.ultsonch.2023.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
In the field of photocatalysis, the fabrication of black titania is a booming topic, as it offers a system with improved solar light harvesting properties and increased overall efficiency. The darkening of white TiO2 powders can be ascribed to surface hydroxylation, oxygen vacancies, Ti3+ centres, or a combination thereof. A handful of studies suggests these defects can be conveniently introduced by acoustic cavitation, generated during sonochemical treatment of pristine TiO2 powders. In reproducing these studies, P25 TiO2 samples were ultrasonicated for various hours with a power density of 8000 W/L, resulting in powders that indeed became gradually darker with increasing sonication time. However, HAADF-STEM revealed that extensive erosion of the sonotrode tip took place and contaminated the samples, which appeared to be the primary reason for the observed colour change. This was confirmed by UV-Vis DRS and DRIFTS, that showed no significant alteration of the catalyst surface after sonication. EPR measurements showed that only an insignificant fraction of Ti3+ centres were produced, far less than in a TiO2 sample that was chemically reduced with NaBH4. No evidence of the presence oxygen vacancies could be found. The enhanced photocatalytic activities of ultrasonicated materials reported in literature can therefore not be ascribed to the synthesis of actual black (defected) TiO2, but rather to specific changes in morphology as a result of acoustic cavitation. Also, this study underlines the importance of considering probe erosion in sonochemical catalyst synthesis, which is an unavoidable side effect that can have an important impact on the catalyst appearance, properties and performance.
Collapse
Affiliation(s)
- Arno Raes
- Sustainable Energy, Air & Water Technology (DuEL), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Rajeshreddy Ninakanti
- Sustainable Energy, Air & Water Technology (DuEL), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lore Van den Bergh
- Laboratory of Physics and BioMedical Physics (BIMEF), University of Antwerp, B-2610 Wilrijk, Belgium; Laboratory of Adsorption and Catalysis (LADCA), University of Antwerp, B-2610 Wilrijk, Belgium
| | - Rituraj Borah
- Sustainable Energy, Air & Water Technology (DuEL), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sabine Van Doorslaer
- Laboratory of Physics and BioMedical Physics (BIMEF), University of Antwerp, B-2610 Wilrijk, Belgium
| | - Sammy W Verbruggen
- Sustainable Energy, Air & Water Technology (DuEL), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| |
Collapse
|
2
|
Ren P, Zhang T, Jain N, Ching HYV, Jaworski A, Barcaro G, Monti S, Silvestre-Albero J, Celorrio V, Chouhan L, Rokicińska A, Debroye E, Kuśtrowski P, Van Doorslaer S, Van Aert S, Bals S, Das S. An Atomically Dispersed Mn-Photocatalyst for Generating Hydrogen Peroxide from Seawater via the Water Oxidation Reaction (WOR). J Am Chem Soc 2023. [PMID: 37487055 DOI: 10.1021/jacs.3c03785] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
In this work, we have fabricated an aryl amino-substituted graphitic carbon nitride (g-C3N4) catalyst with atomically dispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibited excellent reactivity, obtaining up to 2230 μM H2O2 in 7 h from alkaline water and up to 1800 μM from seawater under identical conditions. More importantly, the catalyst was quickly recovered for subsequent reuse without appreciable loss in performance. Interestingly, unlike the usual two-electron oxygen reduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction (WOR) process in which both the direct and indirect WOR processes occurred; namely, photoinduced h+ directly oxidized H2O to H2O2 via a one-step 2e- WOR, and photoinduced h+ first oxidized a hydroxide (OH-) ion to generate a hydroxy radical (•OH), and H2O2 was formed indirectly by the combination of two •OH. We have characterized the material, at the catalytic sites, at the atomic level using electron paramagnetic resonance, X-ray absorption near edge structure, extended X-ray absorption fine structure, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, magic-angle spinning solid-state NMR spectroscopy, and multiscale molecular modeling, combining classical reactive molecular dynamics simulations and quantum chemistry calculations.
Collapse
Affiliation(s)
- Peng Ren
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Tong Zhang
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Noopur Jain
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - H Y Vincent Ching
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Giovanni Barcaro
- CNR-IPCF, Institute for Chemical and Physical Processes, Area della Ricerca, Pisa I-56124, Italy
| | - Susanna Monti
- CNR-ICCOM, Institute of Chemistry of Organometallic Compounds, Area della Ricerca, Pisa I-56124, Italy
| | | | - Veronica Celorrio
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Lata Chouhan
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Anna Rokicińska
- Department of Chemical Technology, Jagiellonian University, Krakow 30-387, Poland
| | - Elke Debroye
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Piotr Kuśtrowski
- Department of Chemical Technology, Jagiellonian University, Krakow 30-387, Poland
| | | | - Sandra Van Aert
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - Sara Bals
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - Shoubhik Das
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| |
Collapse
|
3
|
Van Brempt N, Sgammato R, Beirinckx Q, Hammerschmid D, Sobott F, Dewilde S, Moens L, Herrebout W, Johannessen C, Van Doorslaer S. The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans. Biochim Biophys Acta Proteins Proteom 2023; 1871:140913. [PMID: 37004900 DOI: 10.1016/j.bbapap.2023.140913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.
Collapse
Affiliation(s)
- Niels Van Brempt
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Roberta Sgammato
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Quinten Beirinckx
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Frank Sobott
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | | | | |
Collapse
|
4
|
Sgammato R, Van Brempt N, Aerts R, Van Doorslaer S, Dewilde S, Herrebout W, Johannessen C. Interaction of nitrite with ferric protoglobin from Methanosarcina acetivorans - an interesting model for spectroscopic studies of the haem-ligand interaction. Dalton Trans 2023; 52:2976-2987. [PMID: 36651272 DOI: 10.1039/d2dt03252j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin belonging to the same lineage of the globin superfamily as globin-coupled sensors. A putative role in the scavenging of reactive nitrogen and oxygen species has been suggested as a possible adaptation mechanism of the host organism to different gaseous environments in the course of evolution. A combination of optical absorption, electronic circular dichroism (ECD), resonance Raman (rRaman), and electron paramagnetic resonance (EPR) reveal the unusual in vitro reaction of ferric MaPgb with nitrite. In contrast to other globins, a large excess of nitrite did not induce the formation of a nitriglobin form in MaPgb. Surprisingly, the addition of nitrite in mildly acidic pH led to the formation of a stable nitric-oxide ligated ferric form of the protein (MaPgb-NO). Furthermore, the 300-700 nm ECD spectrum of ferric MaPgb is for the first time reported and discussed, showing strong differences in the Soret and Q ellipticity compared to ferric myoglobin, in line with the unusually strongly ruffled haem group of MaPgb and the related quantum-mechanical admixture of the S = 5/2 and S = 3/2 state of its ferric form. The Soret and Q ellipticity change strongly upon formation of MaPgb-NO, revealing a significant effect of the nitric-oxide ligation on the haem group and pocket. The related changes in the asymmetric pyrrole half-ring stretching vibration modes observed in the rRaman spectra give experimental support to earlier theoretical models, in which an important role of the in-plane breathing modes of the haem was predicted for the stabilization of the binding of diatomic gases to MaPgb.
Collapse
Affiliation(s)
- Roberta Sgammato
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Niels Van Brempt
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.,Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Roy Aerts
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Sabine Van Doorslaer
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Sylvia Dewilde
- Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Wouter Herrebout
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Christian Johannessen
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| |
Collapse
|
5
|
Gys N, Pawlak B, Marcoen K, Reekmans G, Velasco LF, An R, Wyns K, Baert K, Zhang K, Lufungula LL, Piras A, Siemons L, Michielsen B, Van Doorslaer S, Blockhuys F, Hauffman T, Adriaensens P, Mullens S, Meynen V. Self-Induced and Progressive Photo-Oxidation of Organophosphonic Acid Grafted Titanium Dioxide. Chempluschem 2023; 88:e202200441. [PMID: 36802130 DOI: 10.1002/cplu.202200441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/21/2023]
Abstract
While synthesis-properties-performance correlations are being studied for organophosphonic acid grafted TiO2 , their stability and the impact of the exposure conditions on possible changes in the interfacial surface chemistry remain unexplored. Here, the impact of different ageing conditions on the evolution of the surface properties of propyl- and 3-aminopropylphosphonic acid grafted mesoporous TiO2 over a period of 2 years is reported, using solid-state 31 P and 13 C NMR, ToF-SIMS and EPR as main techniques. In humid conditions under ambient light exposure, PA grafted TiO2 surfaces initiate and facilitate photo-induced oxidative reactions, resulting in the formation of phosphate species and degradation of the grafted organic group with a loss of carbon content ranging from 40 to 60 wt %. By revealing its mechanism, solutions were provided to prevent degradation. This work provides valuable insights for the broad community in choosing optimal exposure/storage conditions that extend the lifetime and improve the materials' performance, positively impacting sustainability.
Collapse
Affiliation(s)
- Nick Gys
- Sustainable Materials, Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400, Mol, Belgium.,Laboratory of Adsorption and Catalysis (LADCA), Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.,Present address: Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy (cMACS), KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium.,Research Group Electrochemical and Surface Engineering (SURF), Vrije Universiteit Brussel, Pleinlaan, Leuven, 2, 1050, Brussels, Belgium
| | - Bram Pawlak
- Analytical and Circular Chemistry (ACC), Institute for Materials Research (IMO), Hasselt University, Agoralaan 1, 3590, Diepenbeek, Belgium
| | - Kristof Marcoen
- Research Group Electrochemical and Surface Engineering (SURF), Department Materials and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Gunter Reekmans
- Analytical and Circular Chemistry (ACC), Institute for Materials Research (IMO), Hasselt University, Agoralaan 1, 3590, Diepenbeek, Belgium
| | - Leticia F Velasco
- Department of Chemistry, Royal Military Academy, Renaissancelaan 30, 1000, Brussels, Belgium
| | - Rui An
- Laboratory of Adsorption and Catalysis (LADCA), Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kenny Wyns
- Sustainable Materials, Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400, Mol, Belgium
| | - Kitty Baert
- Research Group Electrochemical and Surface Engineering (SURF), Department Materials and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kaimin Zhang
- Laboratory of Adsorption and Catalysis (LADCA), Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Léon Luntadila Lufungula
- Structural Chemistry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Alessandra Piras
- Laboratory of Applied Materials Chemistry, Unit of Nanomaterials Chemistry, Department of Chemistry, Namur University, Rue de Bruxelles 61, 5000, Namur, Belgium.,Design and Synthesis of Inorganic Nanomaterials (DESINe), Institute for Materials Research (IMO-IMOMEC), Hasselt University, Agoralaan 1, 3590, Diepenbeek, Belgium
| | - Laurens Siemons
- Structural Chemistry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Present address: Institute for Applied Chromatography (IAC), SGS Belgium NV, Polderdijkweg 16, 2030, Antwerp, Belgium
| | - Bart Michielsen
- Sustainable Materials, Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400, Mol, Belgium
| | - Sabine Van Doorslaer
- Laboratory of Biophysics and BioMedical Physics (BIMEF), Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Frank Blockhuys
- Structural Chemistry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Tom Hauffman
- Research Group Electrochemical and Surface Engineering (SURF), Department Materials and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Peter Adriaensens
- Analytical and Circular Chemistry (ACC), Institute for Materials Research (IMO), Hasselt University, Agoralaan 1, 3590, Diepenbeek, Belgium
| | - Steven Mullens
- Sustainable Materials, Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400, Mol, Belgium
| | - Vera Meynen
- Sustainable Materials, Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400, Mol, Belgium.,Laboratory of Adsorption and Catalysis (LADCA), Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| |
Collapse
|
6
|
Schmidt D, Falb N, Serra I, Bellei M, Pfanzagl V, Hofbauer S, Van Doorslaer S, Battistuzzi G, Furtmüller PG, Obinger C. Compound I Formation and Reactivity in Dimeric Chlorite Dismutase: Impact of pH and the Dynamics of the Catalytic Arginine. Biochemistry 2023; 62:835-850. [PMID: 36706455 PMCID: PMC9910045 DOI: 10.1021/acs.biochem.2c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Indexed: 01/28/2023]
Abstract
The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Many questions about the molecular reaction mechanism of this iron protein have remained unanswered, including the electronic nature of the catalytically relevant oxoiron(IV) intermediate and its interaction with the distal, flexible, and catalytically active arginine. Here, we have investigated the dimeric Cld from Cyanothece sp. PCC7425 (CCld) and two variants having the catalytic arginine R127 (i) hydrogen-bonded to glutamine Q74 (wild-type CCld), (ii) arrested in a salt bridge with a glutamate (Q74E), or (iii) being fully flexible (Q74V). Presented stopped-flow spectroscopic studies demonstrate the initial and transient appearance of Compound I in the reaction between CCld and chlorite at pH 5.0 and 7.0 and the dominance of spectral features of an oxoiron(IV) species (418, 528, and 551 nm) during most of the chlorite degradation period at neutral and alkaline pH. Arresting the R127 in a salt bridge delays chlorite decomposition, whereas increased flexibility accelerates the reaction. The dynamics of R127 does not affect the formation of Compound I mediated by hypochlorite but has an influence on Compound I stability, which decreases rapidly with increasing pH. The decrease in activity is accompanied by the formation of protein-based amino acid radicals. Compound I is demonstrated to oxidize iodide, chlorite, and serotonin but not hypochlorite. Serotonin is able to dampen oxidative damage and inactivation of CCld at neutral and alkaline pH. Presented data are discussed with respect to the molecular mechanism of Cld and the pronounced pH dependence of chlorite degradation.
Collapse
Affiliation(s)
- Daniel Schmidt
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Nikolaus Falb
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Ilenia Serra
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2000Antwerp, Belgium
| | - Marzia Bellei
- Department
of Life Sciences, University of Modena and
Reggio Emilia, 41100Modena, Italy
| | - Vera Pfanzagl
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Stefan Hofbauer
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Sabine Van Doorslaer
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2000Antwerp, Belgium
| | - Gianantonio Battistuzzi
- Department
of Chemistry and Geology, University of
Modena and Reggio Emilia, 41100Modena, Italy
| | - Paul G. Furtmüller
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Christian Obinger
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| |
Collapse
|
7
|
Zhang T, Vanderghinste J, Guidetti A, Doorslaer SV, Barcaro G, Monti S, Das S. Pi‐Pi Stacking Complex Induces Three‐Component Coupling Reactions to Synthesize Functionalized Amines. Angew Chem Int Ed Engl 2022; 61:e202212083. [DOI: 10.1002/anie.202212083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tong Zhang
- Universiteit Antwerpen Chemistry BELGIUM
| | | | | | | | - Giovanni Barcaro
- IPCF-CNR UOS di Pisa: Istituto per i Processi Chimico-Fisici Consiglio Nazionale delle Ricerche Unita Organizzativa di Supporto di Pisa Chemistry ITALY
| | - Susanna Monti
- ICCOM CNR: Istituto di Chimica dei Composti Organo Metallici Consiglio Nazionale delle Ricerche Chemistry ITALY
| | - Shoubhik Das
- Universiteit Antwerpen Gronenborgerlaan 171 2600 Antwerp BELGIUM
| |
Collapse
|
8
|
Zhang T, Vanderghinste J, Guidetti A, Doorslaer SV, Barcaro G, Monti S, Das S. Pi‐Pi Stacking Complex Induces Three‐Component Coupling Reactions to Synthesize Functionalized Amines. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tong Zhang
- Universiteit Antwerpen Chemistry BELGIUM
| | | | | | | | - Giovanni Barcaro
- IPCF-CNR UOS di Pisa: Istituto per i Processi Chimico-Fisici Consiglio Nazionale delle Ricerche Unita Organizzativa di Supporto di Pisa Chemistry ITALY
| | - Susanna Monti
- ICCOM CNR: Istituto di Chimica dei Composti Organo Metallici Consiglio Nazionale delle Ricerche Chemistry ITALY
| | - Shoubhik Das
- Universiteit Antwerpen Gronenborgerlaan 171 2600 Antwerp BELGIUM
| |
Collapse
|
9
|
Neven L, Barich H, Ching HYV, Khan SU, Colomier C, Patel HH, Gorun SM, Verbruggen S, Van Doorslaer S, De Wael K. Correlation between the Fluorination Degree of Perfluorinated Zinc Phthalocyanines, Their Singlet Oxygen Generation Ability, and Their Photoelectrochemical Response for Phenol Sensing. Anal Chem 2022; 94:5221-5230. [PMID: 35316027 DOI: 10.1021/acs.analchem.1c04357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron-withdrawing perfluoroalkyl peripheral groups grafted on phthalocyanine (Pc) macrocycles improve their single-site isolation, solubility, and resistance to self-oxidation, all beneficial features for catalytic applications. A high degree of fluorination also enhances the reducibility of Pcs and could alter their singlet oxygen (1O2) photoproduction. The ethanol/toluene 20:80 vol % solvent mixture was found to dissolve perfluorinated FnPcZn complexes, n = 16, 52, and 64, and minimize the aggregation of the sterically unencumbered F16PcZn. The 1O2 production ability of FnPcZn complexes was examined using 9,10-dimethylanthracene (DMA) and 2,2,6,6-tetramethylpiperidine (TEMP) in combination with UV-vis and electron paramagnetic resonance (EPR) spectroscopy, respectively. While the photoreduction of F52PcZn and F64PcZn in the presence of redox-active TEMP lowered 1O2 production, DMA was a suitable 1O2 trap for ranking the complexes. The solution reactivity was complemented by solid-state studies via the construction of photoelectrochemical sensors based on TiO2-supported FnPcZn, FnPcZn|TiO2. Phenol photo-oxidation by 1O2, followed by its electrochemical reduction, defines a redox cycle, the 1O2 production having been found to depend on the value of n and structural features of the supported complexes. Consistent with solution studies, F52PcZn was found to be the most efficient 1O2 generator. The insights on reactivity testing and structural-activity relationships obtained may be useful for designing efficient and robust sensors and for other 1O2-related applications of FnPcZn.
Collapse
Affiliation(s)
- Liselotte Neven
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,BIMEF Research Group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Hanan Barich
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - H Y Vincent Ching
- BIMEF Research Group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Shahid U Khan
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,DuEL Research Group, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Christopher Colomier
- Department of Chemistry and Biochemistry and the Centre for Functional Materials, Seton Hall University, 400 South Orange Ave, New Jersey 07079, United States
| | - Hemantbhai H Patel
- Department of Chemistry and Biochemistry and the Centre for Functional Materials, Seton Hall University, 400 South Orange Ave, New Jersey 07079, United States
| | - Sergiu M Gorun
- Department of Chemistry and Biochemistry and the Centre for Functional Materials, Seton Hall University, 400 South Orange Ave, New Jersey 07079, United States
| | - Sammy Verbruggen
- DuEL Research Group, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sabine Van Doorslaer
- BIMEF Research Group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Karolien De Wael
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| |
Collapse
|
10
|
Gopakumar A, Ren P, Chen J, Manzolli Rodrigues BV, Vincent Ching HY, Jaworski A, Doorslaer SV, Rokicińska A, Kuśtrowski P, Barcaro G, Monti S, Slabon A, Das S. Lignin-Supported Heterogeneous Photocatalyst for the Direct Generation of H 2O 2 from Seawater. J Am Chem Soc 2022; 144:2603-2613. [PMID: 35129333 DOI: 10.1021/jacs.1c10786] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The development of smart and sustainable photocatalysts is in high priority for the synthesis of H2O2 because the global demand for H2O2 is sharply rising. Currently, the global market share for H2O2 is around 4 billion US$ and is expected to grow by about 5.2 billion US$ by 2026. Traditional synthesis of H2O2 via the anthraquinone method is associated with the generation of substantial chemical waste as well as the requirement of a high energy input. In this respect, the oxidative transformation of pure water is a sustainable solution to meet the global demand. In fact, several photocatalysts have been developed to achieve this chemistry. However, 97% of the water on our planet is seawater, and it contains 3.0-5.0% of salts. The presence of salts in water deactivates the existing photocatalysts, and therefore, the existing photocatalysts have rarely shown reactivity toward seawater. Considering this, a sustainable heterogeneous photocatalyst, derived from hydrolysis lignin, has been developed, showing an excellent reactivity toward generating H2O2 directly from seawater under air. In fact, in the presence of this catalyst, we have been able to achieve 4085 μM of H2O2. Expediently, the catalyst has shown longer durability and can be recycled more than five times to generate H2O2 from seawater. Finally, full characterizations of this smart photocatalyst and a detailed mechanism have been proposed on the basis of the experimental evidence and multiscale/level calculations.
Collapse
Affiliation(s)
- Aswin Gopakumar
- Department of Chemistry, Universiteit Antwerpen, Antwerp 2020, Belgium
| | - Peng Ren
- Department of Chemistry, Universiteit Antwerpen, Antwerp 2020, Belgium
| | - Jianhong Chen
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | | | - H Y Vincent Ching
- Department of Chemistry, Universiteit Antwerpen, Wilrijk 2610, Belgium
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | | | - Anna Rokicińska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków 30-387, Poland
| | - Piotr Kuśtrowski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków 30-387, Poland
| | - Giovanni Barcaro
- CNR-IPCF, Institute for Chemical and Physical Processes, Area della Ricerca, via Moruzzi 1, Pisa I-56124, Italy
| | - Susanna Monti
- CNR-ICCOM, Institute of Chemistry of Organometallic Compounds, Area della Ricerca, via Moruzzi 1, Pisa I-56124, Italy
| | - Adam Slabon
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Shoubhik Das
- Department of Chemistry, Universiteit Antwerpen, Antwerp 2020, Belgium
| |
Collapse
|
11
|
Thiruvottriyur Shanmugam S, Van Echelpoel R, Boeye G, Eliaerts J, Samanipour M, Ching HYV, Florea A, Van Doorslaer S, Van Durme F, Samyn N, Parrilla M, De Wael K. Towards Developing a Screening Strategy for Ecstasy: Revealing the Electrochemical Profile. ChemElectroChem 2021. [DOI: 10.1002/celc.202101198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Saranya Thiruvottriyur Shanmugam
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Robin Van Echelpoel
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Griet Boeye
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Joy Eliaerts
- National Institute for Criminalistics and Criminology (NICC) Vilvoordsesteenweg 100 1120 Brussels Belgium
| | - Mohammad Samanipour
- Laboratory of Biophysics and Biomedical Physics University of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - H. Y. Vincent Ching
- Laboratory of Biophysics and Biomedical Physics University of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Anca Florea
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Sabine Van Doorslaer
- Laboratory of Biophysics and Biomedical Physics University of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Filip Van Durme
- National Institute for Criminalistics and Criminology (NICC) Vilvoordsesteenweg 100 1120 Brussels Belgium
| | - Nele Samyn
- National Institute for Criminalistics and Criminology (NICC) Vilvoordsesteenweg 100 1120 Brussels Belgium
| | - Marc Parrilla
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Karolien De Wael
- A-Sense Lab Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
- NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium
| |
Collapse
|
12
|
Neukermans S, Samanipour M, Vincent Ching HY, Hereijgers J, Van Doorslaer S, Hubin A, Breugelmans T. Corrigendum: A Versatile
In‐Situ
Electron Paramagnetic Resonance Spectro‐electrochemical Approach for Electrocatalyst Research. ChemElectroChem 2021. [DOI: 10.1002/celc.202101599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
13
|
Serra I, Schmidt D, Pfanzagl V, Mlynek G, Hofbauer S, Djinović-Carugo K, Furtmüller PG, García-Rubio I, Van Doorslaer S, Obinger C. Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase. J Inorg Biochem 2021; 227:111689. [PMID: 34922158 DOI: 10.1016/j.jinorgbio.2021.111689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023]
Abstract
Chlorite dismutases (Clds) are heme b containing oxidoreductases able to decompose chlorite to chloride and molecular oxygen. This work analyses the impact of the distal, flexible and catalytic arginine on the binding of anionic angulate ligands like nitrite and the substrate chlorite. Dimeric Cld from Cyanothece sp. PCC7425 was used as a model enzyme. We have investigated wild-type CCld having the distal catalytic R127 hydrogen-bonded to glutamine Q74 and variants with R127 (i) being arrested in a salt-bridge with a glutamate (Q74E), (ii) being fully flexible (Q74V) or (iii) substituted by either alanine (R127A) or lysine (R127K). We present the electronic and spectral signatures of the high-spin ferric proteins and the corresponding low-spin nitrite complexes elucidated by UV-visible, circular dichroism and electron paramagnetic resonance spectroscopies. Furthermore, we demonstrate the impact of the dynamics of R127 on the thermal stability of the respective nitrite adducts and present the X-ray crystal structures of the nitrite complexes of wild-type CCld and the variants Q74V, Q74E and R127A. In addition, the molecular dynamics (MD) and the binding modi of nitrite and chlorite to the ferric wild-type enzyme and the mutant proteins and the interaction of the oxoanions with R127 have been analysed by MD simulations. The findings are discussed with respect to the role(s) of R127 in ligand and chlorite binding and substrate degradation.
Collapse
Affiliation(s)
- Ilenia Serra
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Daniel Schmidt
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Georg Mlynek
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, A-1190 Vienna, Austria; Department of Structural and Computational Biology, Max Perutz Laboratories, A-1030, Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Laboratories, A-1030, Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 5, SI-1000 Ljubljana, Slovenia
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Inés García-Rubio
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009 Zaragoza, Spain; Centro Universitario de la Defensa, 50090 Zaragoza, Spain
| | | | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
| |
Collapse
|
14
|
Nys K, Pfanzagl V, Roefs J, Obinger C, Van Doorslaer S. In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase-The Interplay of Key Amino Acids, pH, Buffer and Glycerol. Int J Mol Sci 2021; 22:ijms22189849. [PMID: 34576013 PMCID: PMC8468270 DOI: 10.3390/ijms22189849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) have gained interest for their ability to oxidize anthraquinone-derived dyes and lignin model compounds. Spectroscopic techniques, such as electron paramagnetic resonance and optical absorption spectroscopy, provide main tools to study how the enzymatic function is linked to the heme-pocket architecture, provided the experimental conditions are carefully chosen. Here, these techniques are used to investigate the effect of active site perturbations on the structure of ferric P-class DyP from Klebsiella pneumoniae (KpDyP) and three variants of the main distal residues (D143A, R232A and D143A/R232A). Arg-232 is found to be important for maintaining the heme distal architecture and essential to facilitate an alkaline transition. The latter is promoted in absence of Asp-143. Furthermore, the non-innocent effect of the buffer choice and addition of the cryoprotectant glycerol is shown. However, while unavoidable or indiscriminate experimental conditions are pitfalls, careful comparison of the effects of different exogenous molecules on the electronic structure and spin state of the heme iron contains information about the inherent flexibility of the heme pocket. The interplay between structural flexibility, key amino acids, pH, temperature, buffer and glycerol during in vitro spectroscopic studies is discussed with respect to the poor peroxidase activity of bacterial P-class DyPs.
Collapse
Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
| | - Vera Pfanzagl
- Division of Biochemistry, Department of Chemistry, BOKU—University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (V.P.); (C.O.)
| | - Jeroen Roefs
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
| | - Christian Obinger
- Division of Biochemistry, Department of Chemistry, BOKU—University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (V.P.); (C.O.)
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
- Correspondence: ; Tel.: +32-3-265-2461
| |
Collapse
|
15
|
Bunda S, May NV, Bonczidai-Kelemen D, Udvardy A, Ching HYV, Nys K, Samanipour M, Van Doorslaer S, Joó F, Lihi N. Copper(II) Complexes of Sulfonated Salan Ligands: Thermodynamic and Spectroscopic Features and Applications for Catalysis of the Henry Reaction. Inorg Chem 2021; 60:11259-11272. [PMID: 34251196 DOI: 10.1021/acs.inorgchem.1c01264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper(II) complexes formed with sulfonated salan ligands (HSS) have been synthesized, and their coordination chemistry has been characterized using pH-potentiometry and spectroscopic methods [UV-vis, electron paramagnetic resonance (EPR), and electron-electron double resonance (ELDOR)-detected NMR (EDNMR)] in aqueous solution. Several bridging moieties between the two salicylamine functions were introduced, e.g., ethyl (HSS), propyl (PrHSS), butyl (BuHSS), cyclohexyl (cis-CyHSS, trans-CyHSS), and diphenyl (dPhHSS). All of the investigated ligands feature excellent copper(II) binding ability via the formation of a (O-,N,N,O-) chelate system. The results indicated that the cyclohexyl moiety significantly enhances the stability of the copper(II) complexes. EPR studies revealed that the arrangement of the coordinated donor atoms is more symmetrical around the copper(II) center and similar for HSS, BuHSS, CyHSS, and dPhHSS, respectively, and a higher rhombicity of the g tensor was detected for PrHSS. The copper(II) complexes of the sulfosalan ligands were isolated in solid form also and showed moderate catalytic activity in the Henry (nitroaldol) reaction of aldehydes and nitromethane. The best yield for nitroaldol production was obtained for copper(II) complexes of PrHSS and BuHSS, although their metal binding ability is moderate compared to that of the cyclohexyl counterparts. However, these complexes possess larger spin density on the nitrogen nuclei than that for the other cases, which alters their catalytic activity.
Collapse
Affiliation(s)
- Szilvia Bunda
- Department of Physical Chemistry, University of Debrecen, Debrecen H-4032, Hungary.,Doctoral School of Chemistry, University of Debrecen, Debrecen H-4032, Hungary
| | - Nóra V May
- Centre for Structural Science, Research Centre for Natural Sciences, Budapest H-1519, Hungary
| | - Dóra Bonczidai-Kelemen
- Doctoral School of Chemistry, University of Debrecen, Debrecen H-4032, Hungary.,Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen H-4032, Hungary
| | - Antal Udvardy
- Department of Physical Chemistry, University of Debrecen, Debrecen H-4032, Hungary
| | - H Y Vincent Ching
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, Antwerpen B-2610, Belgium
| | - Kevin Nys
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, Antwerpen B-2610, Belgium
| | - Mohammad Samanipour
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, Antwerpen B-2610, Belgium
| | - Sabine Van Doorslaer
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, Antwerpen B-2610, Belgium
| | - Ferenc Joó
- Department of Physical Chemistry, University of Debrecen, Debrecen H-4032, Hungary.,MTA-DE Redox and Homogeneous Reaction Mechanisms Research Group, University of Debrecen, Debrecen H-4032, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen H-4032, Hungary.,MTA-DE Redox and Homogeneous Reaction Mechanisms Research Group, University of Debrecen, Debrecen H-4032, Hungary
| |
Collapse
|
16
|
Nys K, Furtmüller PG, Obinger C, Van Doorslaer S, Pfanzagl V. On the Track of Long-Range Electron Transfer in B-Type Dye-Decolorizing Peroxidases: Identification of a Tyrosyl Radical by Computational Prediction and Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2021; 60:1226-1241. [PMID: 33784066 PMCID: PMC8154254 DOI: 10.1021/acs.biochem.1c00129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic activity of dye-decolorizing peroxidases (DyPs) toward bulky substrates, including anthraquinone dyes, phenolic lignin model compounds, or 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), is in strong contrast to their sterically restrictive active site. In two of the three known subfamilies (A- and C/D-type DyPs), catalytic protein radicals at surface-exposed sites, which are connected to the heme cofactor by electron transfer path(s), have been identified. So far in B-type DyPs, there has been no evidence for protein radical formation after activation by hydrogen peroxide. Interestingly, B-type Klebsiella pneumoniae dye-decolorizing peroxidase (KpDyP) displays a persistent organic radical in the resting state composed of two species that can be distinguished by W-band electron spin echo electron paramagnetic resonance (EPR) spectroscopy. Here, on the basis of a comprehensive mutational and EPR study of computationally predicted tyrosine and tryptophan variants of KpDyP, we demonstrate the formation of tyrosyl radicals (Y247 and Y92) and a radical-stabilizing Y-W dyad between Y247 and W18 in KpDyP, which are unique to enterobacterial B-type DyPs. Y247 is connected to Y92 by a hydrogen bonding network, is solvent accessible in simulations, and is involved in ABTS oxidation. This suggests the existence of long-range electron path(s) in B-type DyPs. The mechanistic and physiological relevance of the reaction mechanism of B-type DyPs is discussed.
Collapse
Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Paul Georg Furtmüller
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| |
Collapse
|
17
|
Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
Collapse
Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
Collapse
Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| |
Collapse
|
18
|
Schmidt D, Serra I, Mlynek G, Pfanzagl V, Hofbauer S, Furtmüller PG, Djinović-Carugo K, Van Doorslaer S, Obinger C. Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis. Biochemistry 2021; 60:621-634. [PMID: 33586945 PMCID: PMC7931450 DOI: 10.1021/acs.biochem.0c00910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Chlorite dismutases
(Clds) are heme b-containing
oxidoreductases that can decompose chlorite to chloride and molecular
oxygen. They are divided in two clades that differ in oligomerization,
subunit architecture, and the hydrogen-bonding network of the distal
catalytic arginine, which is proposed to switch between two conformations
during turnover. To understand the impact of the conformational dynamics
of this basic amino acid on heme coordination, structure, and catalysis,
Cld from Cyanothece sp. PCC7425 was used as a model
enzyme. As typical for a clade 2 Cld, its distal arginine 127 is hydrogen-bonded
to glutamine 74. The latter has been exchanged with either glutamate
(Q74E) to arrest R127 in a salt bridge or valine (Q74V) that mirrors
the setting in clade 1 Clds. We present the X-ray crystal structures
of Q74V and Q74E and demonstrate the pH-induced changes in the environment
and coordination of the heme iron by ultraviolet–visible, circular
dichroism, and electron paramagnetic resonance spectroscopies as well
as differential scanning calorimetry. The conformational dynamics
of R127 is shown to have a significant role in heme coordination during
the alkaline transition and in the thermal stability of the heme cavity,
whereas its impact on the catalytic efficiency of chlorite degradation
is relatively small. The findings are discussed with respect to (i)
the flexible loop connecting the N-terminal and C-terminal ferredoxin-like
domains, which differs in clade 1 and clade 2 Clds and carries Q74
in clade 2 proteins, and (ii) the proposed role(s) of the arginine
in catalysis.
Collapse
Affiliation(s)
- Daniel Schmidt
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Ilenia Serra
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 5, SI-1000 Ljubljana, Slovenia
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| |
Collapse
|
19
|
den Hartog S, Samanipour M, Ching HV, Van Doorslaer S, Breugelmans T, Hubin A, Ustarroz J. Reactive oxygen species formation at Pt nanoparticles revisited by electron paramagnetic resonance and electrochemical analysis. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2020.106878] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
20
|
Neukermans S, Samanipour M, Vincent Ching HY, Hereijgers J, Van Doorslaer S, Hubin A, Breugelmans T. A Versatile
In‐Situ
Electron Paramagnetic Resonance Spectro‐electrochemical Approach for Electrocatalyst Research. ChemElectroChem 2020. [DOI: 10.1002/celc.202001193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sander Neukermans
- Research Group Applied Electrochemistry & Catalysis (ELCAT) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
| | - Mohammad Samanipour
- Department of Chemistry Research Group Biophysics and Biomedical Physics (BIMEF) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
| | - H. Y. Vincent Ching
- Research Group Applied Electrochemistry & Catalysis (ELCAT) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
- Department of Chemistry Research Group Biophysics and Biomedical Physics (BIMEF) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
| | - Jonas Hereijgers
- Research Group Applied Electrochemistry & Catalysis (ELCAT) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
| | - Sabine Van Doorslaer
- Department of Chemistry Research Group Biophysics and Biomedical Physics (BIMEF) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
| | - Annick Hubin
- Research Group of Electrochemical and Surface Engineering (SURF) Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium
| | - Tom Breugelmans
- Research Group Applied Electrochemistry & Catalysis (ELCAT) University of Antwerp Universiteitsplein 1 Wilrijk 2610 Belgium
- Separation & Conversion Technologies Vlaams Instituut voor Technologisch onderzoek (VITO) Boeretang 200, 2400 Mol Belgium
| |
Collapse
|
21
|
Gadde K, Mampuys P, Guidetti A, Ching HYV, Herrebout WA, Van Doorslaer S, Abbaspour Tehrani K, Maes BUW. Thiosulfonylation of Unactivated Alkenes with Visible-Light Organic Photocatalysis. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02159] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Karthik Gadde
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Pieter Mampuys
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Andrea Guidetti
- Biophysics and Biomedical Physics (BIMEF), Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - H. Y. Vincent Ching
- Biophysics and Biomedical Physics (BIMEF), Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Wouter A. Herrebout
- Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics (BIMEF), Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Kourosch Abbaspour Tehrani
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Bert U. W. Maes
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| |
Collapse
|
22
|
Nys K, Cuypers B, Berghmans H, Hammerschmid D, Moens L, Dewilde S, Van Doorslaer S. Surprising differences in the respiratory protein of insects: A spectroscopic study of haemoglobin from the European honeybee and the malaria mosquito. Biochim Biophys Acta Proteins Proteom 2020; 1868:140413. [PMID: 32179182 DOI: 10.1016/j.bbapap.2020.140413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
Only recently it was discovered that haemoglobin (Hb) belongs to the standard gene repertoire of insects, although their tracheal system is used for respiration. A classical oxygen-carrying function of Hb is only obvious for hexapods living in hypoxic environments. In other insect species, including the common fruit fly Drosophila melanogaster, the physiological role of Hb is yet unclear. Here, we study recombinant haemoglobin from the European honeybee Apis mellifera (Ame) and the malaria mosquito Anopheles gambiae (Aga). Spectroscopic evidence shows that both proteins can be classified as hexacoordinate Hbs with a strong affinity for the distal histidine. AgaHb1 is proposed to play a role in oxygen transport or sensing based on its multimeric state, slow autoxidation, and small but significant amount of five-coordinated haem in the deoxy ferrous form. AmeHb appears to behave more like vertebrate neuroglobin with a complex function given its diversified distribution in the genome.
Collapse
Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium.
| | - Bert Cuypers
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Herald Berghmans
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Dietmar Hammerschmid
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Luc Moens
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Sylvia Dewilde
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | | |
Collapse
|
23
|
Rahemi V, Trashin S, Hafideddine Z, Van Doorslaer S, Meynen V, Gorton L, De Wael K. Amperometric Flow-Injection Analysis of Phenols Induced by Reactive Oxygen Species Generated under Daylight Irradiation of Titania Impregnated with Horseradish Peroxidase. Anal Chem 2020; 92:3643-3649. [PMID: 31985211 DOI: 10.1021/acs.analchem.9b04617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Titanium dioxide (TiO2) is a unique material for biosensing applications due to its capability of hosting enzymes. For the first time, we show that TiO2 can accumulate reactive oxygen species (ROS) under daylight irradiation and can support the catalytic cycle of horseradish peroxidase (HRP) without the need of H2O2 to be present in the solution. Phenolic compounds, such as hydroquinone (HQ) and 4-aminophenol (4-AP), were detected amperometrically in flow-injection analysis (FIA) mode via the use of an electrode modified with TiO2 impregnated with HRP. In contrast to the conventional detection scheme, no H2O2 was added to the analyte solution. Basically, the inherited ability of TiO2 to generate reactive oxygen species is used as a strategy to avoid adding H2O2 in the solution during the detection of phenolic compounds. Electron paramagnetic resonance (EPR) spectroscopy indicates the presence of ROS on titania which, in interaction with HRP, initiate the electrocatalysis toward phenolic compounds. The amperometric response to 4-AP was linear in the concentration range between 0.05 and 2 μM. The sensitivity was 0.51 A M-1 cm-2, and the limit of detection (LOD) 26 nM. The proposed sensor design opens new opportunities for the detection of phenolic traces by HRP-based electrochemical biosensors, yet in a more straightforward and sensitive way following green chemistry principles of avoiding the use of reactive and harmful chemical, such as H2O2.
Collapse
Affiliation(s)
- Vanoushe Rahemi
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Stanislav Trashin
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Zainab Hafideddine
- BIMEF Laboratory, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.,PPES Research Group, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- BIMEF Laboratory, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Vera Meynen
- Laboratory of Adsorption and Catalysis (LADCA), University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Lo Gorton
- Department of Analytical Chemistry/Biochemistry and Structural Biology, Lund University, PO Box 124, SE-22100 Lund, Sweden
| | - Karolien De Wael
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.,Nanolab Center of Excellence, University of Antwerp, 2610 Wilrijk, Belgium
| |
Collapse
|
24
|
Germani F, Nardini M, De Schutter A, Cuypers B, Berghmans H, Van Hauwaert ML, Bruno S, Mozzarelli A, Moens L, Van Doorslaer S, Bolognesi M, Pesce A, Dewilde S. Structural and Functional Characterization of the Globin-Coupled Sensors of Azotobacter vinelandii and Bordetella pertussis. Antioxid Redox Signal 2020; 32:378-395. [PMID: 31559835 DOI: 10.1089/ars.2018.7690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Structural and functional characterization of the globin-coupled sensors (GCSs) from Azotobacter vinelandii (AvGReg) and Bordetella pertussis (BpeGReg). Results: Ultraviolet/visible and resonance Raman spectroscopies confirm the presence in AvGReg and BpeGReg of a globin domain capable of reversible gaseous ligand binding. In AvGReg, an influence of the transmitter domain on the heme proximal region of the globin domain can be seen, and k'CO is higher than for other GCSs. The O2 binding kinetics suggests the presence of an open and a closed conformation. As for BpeGReg, the fully oxygenated AvGReg show a very high diguanylate cyclase activity. The carbon monoxide rebinding to BpeGReg indicates that intra- and intermolecular interactions influence the ligand binding. The globin domains of both proteins (AvGReg globin domain and BpeGRegGb with cysteines (Cys16, 45, 114, 154) mutated to serines [BpeGReg-Gb*]) share the same GCS fold, a similar proximal but a different distal side structure. They homodimerize through a G-H helical bundle as in other GCSs. However, BpeGReg-Gb* shows also a second dimerization mode. Innovation: This article extends our knowledge on the GCS proteins and contributes to a better understanding of the GCSs role in the formation of bacterial biofilms. Conclusions:AvGReg and BpeGReg conform to the GCS family, share a similar overall structure, but they have different properties in terms of the ligand binding. In particular, AvGReg shows an open and a closed conformation that in the latter form will very tightly bind oxygen. BpeGReg has only one closed conformation. In both proteins, it is the fully oxygenated GCS form that catalyzes the production of the second messenger.
Collapse
Affiliation(s)
- Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | - Amy De Schutter
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | | | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| |
Collapse
|
25
|
Pfanzagl V, Nys K, Bellei M, Michlits H, Mlynek G, Battistuzzi G, Djinovic-Carugo K, Van Doorslaer S, Furtmüller PG, Hofbauer S, Obinger C. Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. J Biol Chem 2018; 293:14823-14838. [PMID: 30072383 PMCID: PMC6153280 DOI: 10.1074/jbc.ra118.004773] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide-dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.
Collapse
Affiliation(s)
- Vera Pfanzagl
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Kevin Nys
- the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Hanna Michlits
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Georg Mlynek
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Gianantonio Battistuzzi
- Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and
| | - Kristina Djinovic-Carugo
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Paul G Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Stefan Hofbauer
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria,
| |
Collapse
|
26
|
De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S. The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor. Redox Biol 2018; 19:1-10. [PMID: 30081385 PMCID: PMC6084017 DOI: 10.1016/j.redox.2018.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 12/12/2022] Open
Abstract
Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Collapse
Affiliation(s)
- Joey De Backer
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Dietmar Hammerschmid
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Carl Mensch
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Zainab Hafideddine
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Naresh Kumar
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Geert van Raemdonck
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sabine Van Doorslaer
- The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Christian Johannessen
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sylvia Dewilde
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
| |
Collapse
|
27
|
Loreto S, Cuypers B, Brokken J, Van Doorslaer S, De Wael K, Meynen V. The effect of the buffer solution on the adsorption and stability of horse heart myoglobin on commercial mesoporous titanium dioxide: a matter of the right choice. Phys Chem Chem Phys 2018; 19:13503-13514. [PMID: 28497146 DOI: 10.1039/c6cp08585g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the numerous studies on the adsorption of different proteins onto mesoporous titanium dioxide and indications on the important role of buffer solutions in bioactivity, a systematic study on the impact of the buffer on the protein incorporation into porous substrates is still lacking. We here studied the interaction between a commercial mesoporous TiO2 and three of the most used buffers for protein incorporation, i.e. HEPES, Tris and phosphate buffer. In addition, this paper analyzes the adsorption of horse heart myoglobin (hhMb) onto commercial mesoporous TiO2 as a model system to test the influence of buffers on the protein incorporation behavior in mesoporous TiO2. N2 sorption analysis, FT-IR and TGA/DTG measurements were used to evaluate the interaction between the buffers and the TiO2 surface, and the effect of such an interaction on hhMb adsorption. Cyclic voltammetry (CV) and electron paramagnetic resonance (EPR) were used to detect changes in the microenvironment surrounding the heme. The three buffers show a completely different interaction with the TiO2 surface, which drastically affects the adsorption of myoglobin as well as its structure and electrochemical activity. Therefore, special attention is required while choosing the buffer medium to avoid misguided evaluation of protein adsorption on mesoporous TiO2.
Collapse
Affiliation(s)
- Stefano Loreto
- Department of Chemistry, University of Antwerp, 2610 Wilrijk, Belgium. and Department of Chemistry, University of Antwerp, 2010 Antwerpen, Belgium
| | - Bert Cuypers
- Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium
| | - Jacotte Brokken
- Department of Chemistry, University of Antwerp, 2610 Wilrijk, Belgium.
| | | | - Karolien De Wael
- Department of Chemistry, University of Antwerp, 2010 Antwerpen, Belgium
| | - Vera Meynen
- Department of Chemistry, University of Antwerp, 2610 Wilrijk, Belgium.
| |
Collapse
|
28
|
Pauwels D, Vincent Ching H, Samanipour M, Neukermans S, Hereijgers J, Van Doorslaer S, De Wael K, Breugelmans T. Identifying intermediates in the reductive intramolecular cyclisation of allyl 2-bromobenzyl ether by an improved electron paramagnetic resonance spectroelectrochemical electrode design combined with density functional theory calculations. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.03.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
29
|
Van Landeghem M, Maes W, Goovaerts E, Van Doorslaer S. Disentangling overlapping high-field EPR spectra of organic radicals: Identification of light-induced polarons in the record fullerene-free solar cell blend PBDB-T:ITIC. J Magn Reson 2018; 288:1-10. [PMID: 29367021 DOI: 10.1016/j.jmr.2018.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 06/07/2023]
Abstract
We present a combined high-field EPR and DFT study of light-induced radicals in the bulk heterojunction blend of PBDB-T:ITIC, currently one of the highest efficiency non-fullerene donor:acceptor combinations in organic photovoltaics. We demonstrate two different approaches for disentangling the strongly overlapping high-field EPR spectra of the positive and negative polarons after charge separation: (1) relaxation-filtered field-swept EPR based on the difference in T1 spin-relaxation times and (2) field-swept EDNMR-induced EPR by exploiting the presence of 14N hyperfine couplings in only one of the radical species, the small molecule acceptor radical. The approach is validated by light-induced EPR spectra on related blends and the spectral assignment is underpinned by DFT computations. The broader applicability of the spectral disentangling methods is discussed.
Collapse
Affiliation(s)
- Melissa Van Landeghem
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
| | - Wouter Maes
- Institute for Materials Research, Design & Synthesis of Organic Semiconductors, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium.
| | - Etienne Goovaerts
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
| | - Sabine Van Doorslaer
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
| |
Collapse
|
30
|
Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
31
|
Van Doorslaer S. Understanding heme proteins with hyperfine spectroscopy. J Magn Reson 2017; 280:79-88. [PMID: 28579104 DOI: 10.1016/j.jmr.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 06/07/2023]
Abstract
Heme proteins are versatile proteins that are involved in a large number of biological processes. Many spectroscopic methods are used to gain insight into the different mechanistic processes governing heme-protein functions. Since many (intermediate) states of heme proteins are paramagnetic, electron paramagnetic resonance (EPR) methods, such as hyperfine spectroscopy, offer unique tools for these investigations. This perspective gives an overview of the use of state-of-the-art hyperfine spectroscopy in heme research, focusing on the advantages, limits and challenges of the different techniques.
Collapse
Affiliation(s)
- Sabine Van Doorslaer
- BIMEF Laboratory, Department of Physics, University of Antwerp, B-2610 Antwerp, Belgium.
| |
Collapse
|
32
|
Motion CL, Cassidy SL, Cruickshank PAS, Hunter RI, Bolton DR, El Mkami H, Van Doorslaer S, Lovett JE, Smith GM. The use of composite pulses for improving DEER signal at 94GHz. J Magn Reson 2017; 278:122-133. [PMID: 28402869 DOI: 10.1016/j.jmr.2017.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/03/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
The sensitivity of pulsed electron paramagnetic resonance (EPR) measurements on broad-line paramagnetic centers is often limited by the available excitation bandwidth. One way to increase excitation bandwidth is through the use of chirp or composite pulses. However, performance can be limited by cavity or detection bandwidth, which in commercial systems is typically 100-200MHz. Here we demonstrate in a 94GHz spectrometer, with >800MHz system bandwidth, an increase in signal and modulation depth in a 4-pulse DEER experiment through use of composite rather than rectangular π pulses. We show that this leads to an increase in sensitivity by a factor of 3, in line with theoretical predictions, although gains are more limited in nitroxide-nitroxide DEER measurements.
Collapse
Affiliation(s)
- Claire L Motion
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - Scott L Cassidy
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - Paul A S Cruickshank
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - Robert I Hunter
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - David R Bolton
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | | | - Janet E Lovett
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom
| | - Graham M Smith
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, United Kingdom.
| |
Collapse
|
33
|
Cuypers B, Vermeylen S, Hammerschmid D, Trashin S, Rahemi V, Konijnenberg A, De Schutter A, Cheng CHC, Giordano D, Verde C, De Wael K, Sobott F, Dewilde S, Van Doorslaer S. Antarctic fish versus human cytoglobins - The same but yet so different. J Inorg Biochem 2017; 173:66-78. [PMID: 28501743 DOI: 10.1016/j.jinorgbio.2017.04.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 03/23/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
Abstract
The cytoglobins of the Antarctic fish Chaenocephalus aceratus and Dissostichus mawsoni have many features in common with human cytoglobin. These cytoglobins are heme proteins in which the ferric and ferrous forms have a characteristic hexacoordination of the heme iron, i.e. axial ligation of two endogenous histidine residues, as confirmed by electron paramagnetic resonance, resonance Raman and optical absorption spectroscopy. The combined spectroscopic analysis revealed only small variations in the heme-pocket structure, in line with the small variations observed for the redox potential. Nevertheless, some striking differences were also discovered. Resonance Raman spectroscopy showed that the stabilization of an exogenous heme ligand, such as CO, occurs differently in human cytoglobin in comparison with Antarctic fish cytoglobins. Furthermore, while it has been extensively reported that human cytoglobin is essentially monomeric and can form an intramolecular disulfide bridge that can influence the ligand binding kinetics, 3D modeling of the Antarctic fish cytoglobins indicates that the cysteine residues are too far apart to form such an intramolecular bridge. Moreover, gel filtration and mass spectrometry reveal the occurrence of non-covalent multimers (up to pentamers) in the Antarctic fish cytoglobins that are formed at low concentrations. Stabilization of these oligomers by disulfide-bridge formation is possible, but not essential. If intermolecular disulfide bridges are formed, they influence the heme-pocket structure, as is shown by EPR measurements.
Collapse
Affiliation(s)
- Bert Cuypers
- BIMEF Laboratory, Department of Physics, University of Antwerp, Belgium
| | - Stijn Vermeylen
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Dietmar Hammerschmid
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium; BAMS Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Stanislav Trashin
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Vanoushe Rahemi
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | | | - Amy De Schutter
- BIMEF Laboratory, Department of Physics, University of Antwerp, Belgium
| | | | - Daniela Giordano
- Institute of Biosciences and BioResources, CNR, Naples, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, CNR, Naples, Italy; Department of Biology, University Roma 3, Rome, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Karolien De Wael
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Frank Sobott
- BAMS Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Sylvia Dewilde
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium
| | | |
Collapse
|
34
|
Calvo-Begueria L, Cuypers B, Van Doorslaer S, Abbruzzetti S, Bruno S, Berghmans H, Dewilde S, Ramos J, Viappiani C, Becana M. Characterization of the Heme Pocket Structure and Ligand Binding Kinetics of Non-symbiotic Hemoglobins from the Model Legume Lotus japonicus. Front Plant Sci 2017; 8:407. [PMID: 28421084 PMCID: PMC5378813 DOI: 10.3389/fpls.2017.00407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 05/04/2023]
Abstract
Plant hemoglobins (Hbs) are found in nodules of legumes and actinorhizal plants but also in non-symbiotic organs of monocots and dicots. Non-symbiotic Hbs (nsHbs) have been classified into two phylogenetic groups. Class 1 nsHbs show an extremely high O2 affinity and are induced by hypoxia and nitric oxide (NO), whereas class 2 nsHbs have moderate O2 affinity and are induced by cold and cytokinins. The functions of nsHbs are still unclear, but some of them rely on the capacity of hemes to bind diatomic ligands and catalyze the NO dioxygenase (NOD) reaction (oxyferrous Hb + NO → ferric Hb + nitrate). Moreover, NO may nitrosylate Cys residues of proteins. It is therefore important to determine the ligand binding properties of the hemes and the role of Cys residues. Here, we have addressed these issues with the two class 1 nsHbs (LjGlb1-1 and LjGlb1-2) and the single class 2 nsHb (LjGlb2) of Lotus japonicus, which is a model legume used to facilitate the transfer of genetic and biochemical information into crops. We have employed carbon monoxide (CO) as a model ligand and resonance Raman, laser flash photolysis, and stopped-flow spectroscopies to unveil major differences in the heme environments and ligand binding kinetics of the three proteins, which suggest non-redundant functions. In the deoxyferrous state, LjGlb1-1 is partially hexacoordinate, whereas LjGlb1-2 shows complete hexacoordination (behaving like class 2 nsHbs) and LjGlb2 is mostly pentacoordinate (unlike other class 2 nsHbs). LjGlb1-1 binds CO very strongly by stabilizing it through hydrogen bonding, but LjGlb1-2 and LjGlb2 show lower CO stabilization. The changes in CO stabilization would explain the different affinities of the three proteins for gaseous ligands. These affinities are determined by the dissociation rates and follow the order LjGlb1-1 > LjGlb1-2 > LjGlb2. Mutations LjGlb1-1 C78S and LjGlb1-2 C79S caused important alterations in protein dynamics and stability, indicating a structural role of those Cys residues, whereas mutation LjGlb1-1 C8S had a smaller effect. The three proteins and their mutant derivatives exhibited similarly high rates of NO consumption, which were due to NOD activity of the hemes and not to nitrosylation of Cys residues.
Collapse
Affiliation(s)
- Laura Calvo-Begueria
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Bert Cuypers
- Department of Physics, University of AntwerpAntwerp, Belgium
| | | | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università degli Studi di ParmaParma, Italy
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle RicerchePisa, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università degli Studi di ParmaParma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of AntwerpAntwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of AntwerpAntwerp, Belgium
| | - Javier Ramos
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Cristiano Viappiani
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle RicerchePisa, Italy
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di ParmaParma, Italy
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| |
Collapse
|
35
|
Moons H, Patel HH, Gorun SM, Doorslaer SV. Electron Paramagnetic Resonance and DFT Analysis of the Effects of Bulky Perfluoroalkyl Substituents on a Vanadyl Perfluoro Phthalocyanine. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/zpch-2016-0827] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
F64PcVO, the vanadyl complex of the perfluoro-isopropyl-substituted perfluorophthalocyanine ligand F64PcH2, exhibits interesting electronic properties compared to related vanadyl phthalocyanine complexes. X- and W-band continuous-wave electron paramagnetic resonance (CW EPR) of undiluted F64PcVO powders illustrate the absence of π-π stacking in these materials due to the bulky substituents. Furthermore, pulsed EPR and electron nuclear double resonance (ENDOR) experiments in combination with density functional theory (DFT) computations were used to determine the principal g values and the 51V, 14N, 1H and 19F hyperfine couplings of a frozen ethanol solution of F64PcVO. The axial ligation of ethanol to vanadium was proven. Axial accessibility of the vanadyl center combined with the high solubility of the complex in different solvents make F64PcVO an interesting molecule for catalytic applications.
Collapse
Affiliation(s)
- Hans Moons
- BIMEF Laboratory, Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Hemantbhai H. Patel
- Department of Chemistry and Biochemistry and Center for Functional Materials, Seton Hall University, South Orange, NJ 07079, United States of America
| | - Sergiu M. Gorun
- Department of Chemistry and Biochemistry and Center for Functional Materials, Seton Hall University, South Orange, NJ 07079, United States of America
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| |
Collapse
|
36
|
Van Doorslaer S, Beirinckx Q, Nys K, Mangiameli MF, Cuypers B, Callens F, Vrielinck H, González JC. EPR and DFT analysis of biologically relevant chromium(V) complexes with d-glucitol and d-glucose. J Inorg Biochem 2016; 162:216-226. [PMID: 27460210 DOI: 10.1016/j.jinorgbio.2016.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
1,2-diolato ligands, such as carbohydrates and glycoproteins, tend to stabilize chromium(V), thus forming important intermediates that have been implicated in the genotoxicity of Cr(VI). Since many years, room-temperature continuous-wave electron paramagnetic resonance (EPR) at X-band microwave frequencies has been used as a standard characterization tool to study chromium(V) intermediates formed during the reduction of Cr(VI) in the presence of biomolecules. In this work, the added value is tested of using a combination of pulsed and high-field EPR techniques with density functional theory computations to unravel the nature of Cr(V) complexes with biologically relevant chelators, such as carbohydrates. The study focuses on the oxidochromium(V) complexes formed during reduction of potassium dichromate with glutathione in the presence of the monosaccharide d-glucose or the polyalcohol d-glucitol. It is shown that although the presence of a multitude of Cr(V) intermediates may hamper a complete structural determination, the combined EPR and DFT approach reveals unambiguously the effect of freezing on the location of the counterions, the gradual replacement of water ligands by the diols, and the preference of Cr(V) to bind certain conformers.
Collapse
Affiliation(s)
- Sabine Van Doorslaer
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Quinten Beirinckx
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kevin Nys
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - María Florencia Mangiameli
- Universidad National de Rosario, Departamento de Químico Física - Área Química General, Facultad de Ciencias Bioquímicas y Farmacéuticas, IQUIR-CONICET, Suipacha 531, Rosario, Santa Fe, Argentina.
| | - Bert Cuypers
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Freddy Callens
- Ghent University, Dept. of Solid State Sciences, Krijgslaan 281-S1, B-9000 Ghent, Belgium.
| | - Henk Vrielinck
- Ghent University, Dept. of Solid State Sciences, Krijgslaan 281-S1, B-9000 Ghent, Belgium.
| | - Juan Carlos González
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium; Universidad National de Rosario, Departamento de Químico Física - Área Química General, Facultad de Ciencias Bioquímicas y Farmacéuticas, IQUIR-CONICET, Suipacha 531, Rosario, Santa Fe, Argentina.
| |
Collapse
|
37
|
Mampuys P, Zhu Y, Sergeyev S, Ruijter E, Orru RVA, Van Doorslaer S, Maes BUW. Iodide-Catalyzed Synthesis of Secondary Thiocarbamates from Isocyanides and Thiosulfonates. Org Lett 2016; 18:2808-11. [DOI: 10.1021/acs.orglett.6b01023] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pieter Mampuys
- Organic
Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| | - Yanping Zhu
- Organic
Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| | - Sergey Sergeyev
- Organic
Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| | - Eelco Ruijter
- Department
of Chemistry and Pharmaceutical Sciences and Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Romano V. A. Orru
- Department
of Chemistry and Pharmaceutical Sciences and Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Sabine Van Doorslaer
- Biophysics
and Biomedical Physics (BIMEF), Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Bert U. W. Maes
- Organic
Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| |
Collapse
|
38
|
Kusakovskij J, Caretti I, Van Doorslaer S, Callens F, Vrielinck H. Fourth stable radical species in X-irradiated solid-state sucrose. Phys Chem Chem Phys 2016; 18:10983-91. [PMID: 27044055 DOI: 10.1039/c6cp01118g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
High-energy radiation produces radicals in crystalline sucrose. As such, sucrose is considered as a relevant model system for studying radiation damage to the sugar units of DNA. Many of these radicals are stable, detectable at room temperature with electron paramagnetic resonance (EPR) and their concentration is proportional to the absorbed dose in a considerable range. This makes sucrose also an interesting system for dosimetry. Dose assessment protocols rely on measurements of the total intensity of the EPR powder spectrum, so it is likely that they could be further improved if the composite nature of the spectrum was understood completely. Recently, it was shown that the three known stable radicals can only account for the central part of the spectrum and that features in the wings remain unidentified. In this work, we show, based on the analysis of the powder EPR patterns recorded at three microwave frequencies, that the contribution of one more species is sufficient to explain the entire spectrum. The determination of the spin Hamiltonian parameters is corroborated by a Q-band (34 GHz) single crystal electron-nuclear double resonance (ENDOR) analysis. The chemical structure of the fourth species is explored by analysis of the determined g and four (1)H hyperfine (HF) tensors, and verified using density functional theory (DFT) calculations. The ENDOR spectrum of the largest HF interaction of the fourth species was exploited to isolate the radical's absorption-like EPR spectrum from a multicomponent powder pattern.
Collapse
Affiliation(s)
- Jevgenij Kusakovskij
- Ghent University, Department of Solid State Sciences, Krijgslaan 281-S1, 9000 Ghent, Belgium.
| | - Ignacio Caretti
- Antwerp University, Department of Physics, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Antwerp University, Department of Physics, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Freddy Callens
- Ghent University, Department of Solid State Sciences, Krijgslaan 281-S1, 9000 Ghent, Belgium.
| | - Henk Vrielinck
- Ghent University, Department of Solid State Sciences, Krijgslaan 281-S1, 9000 Ghent, Belgium.
| |
Collapse
|
39
|
Motion C, Lovett JE, Bell S, Cassidy SL, Cruickshank PAS, Bolton DR, Hunter RI, El Mkami H, Van Doorslaer S, Smith GM. DEER Sensitivity between Iron Centers and Nitroxides in Heme-Containing Proteins Improves Dramatically Using Broadband, High-Field EPR. J Phys Chem Lett 2016; 7:1411-5. [PMID: 27035368 PMCID: PMC4863198 DOI: 10.1021/acs.jpclett.6b00456] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 05/22/2023]
Abstract
This work demonstrates the feasibility of making sensitive nanometer distance measurements between Fe(III) heme centers and nitroxide spin labels in proteins using the double electron-electron resonance (DEER) pulsed EPR technique at 94 GHz. Techniques to measure accurately long distances in many classes of heme proteins using DEER are currently strongly limited by sensitivity. In this paper we demonstrate sensitivity gains of more than 30 times compared with previous lower frequency (X-band) DEER measurements on both human neuroglobin and sperm whale myoglobin. This is achieved by taking advantage of recent instrumental advances, employing wideband excitation techniques based on composite pulses and exploiting more favorable relaxation properties of low-spin Fe(III) in high magnetic fields. This gain in sensitivity potentially allows the DEER technique to be routinely used as a sensitive probe of structure and conformation in the large number of heme and many other metalloproteins.
Collapse
Affiliation(s)
- Claire
L. Motion
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Janet E. Lovett
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Stacey Bell
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Scott L. Cassidy
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Paul A. S. Cruickshank
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - David R. Bolton
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Robert I. Hunter
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | | | - Graham M. Smith
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| |
Collapse
|
40
|
Sterckx H, De Houwer J, Mensch C, Caretti I, Tehrani KA, Herrebout WA, Van Doorslaer S, Maes BUW. Mechanism of the Cu II-catalyzed benzylic oxygenation of (aryl)(heteroaryl)methanes with oxygen. Chem Sci 2016; 7:346-357. [PMID: 29861987 PMCID: PMC5952523 DOI: 10.1039/c5sc03530a] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 12/24/2022] Open
Abstract
A mechanistic study of the copper-catalyzed oxidation of the methylene group of aryl(di)azinylmethanes was performed. Initial reaction rates were measured making use of in situ IR reaction monitoring and a kinetic analysis of the reaction was executed. The reaction proved to be first order in oxygen concentration. For substrate and acid concentration, saturation kinetics due to O2 mass transfer limitation were observed. The occurrence of mass transfer limitation was further confirmed by examining the effect of the stirring rate on the initial reaction rate. Interestingly, the effect of the concentration of the catalyst on the rate shows that higher loadings result in a maximal initial rate, followed initially by a steady decrease and subsequently a rate plateau when the concentration is increased further. Mass transfer limitation and increased concentration of dinuclear catalytically active species rationalizes this hitherto unprecedented rate behavior. Continuous-wave and pulsed electron paramagnetic resonance methods were used to characterize the catalytic species present in the solution during the reaction and confirmed the presence of both mono- and dinuclear copper species. Analysis of a diverse substrate scope points towards imine-enamine tautomerization as a crucial process in the oxidation reaction. DFT calculations of these equilibrium constants (pKeq) provided us with a qualitative tool to predict whether or not a substrate is viable for oxidation under the reaction conditions developed.
Collapse
Affiliation(s)
- Hans Sterckx
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , B-2020 Antwerp , Belgium .
| | - Johan De Houwer
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , B-2020 Antwerp , Belgium .
| | - Carl Mensch
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , B-2020 Antwerp , Belgium .
| | - Ignacio Caretti
- Department of Physics , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | | | - Wouter A Herrebout
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , B-2020 Antwerp , Belgium .
| | - Sabine Van Doorslaer
- Department of Physics , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Bert U W Maes
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , B-2020 Antwerp , Belgium .
| |
Collapse
|
41
|
Nevjestić I, Depauw H, Leus K, Kalendra V, Caretti I, Jeschke G, Van Doorslaer S, Callens F, Van Der Voort P, Vrielinck H. Back Cover: Multi-frequency (S, X, Q and W-band) EPR and ENDOR Study of Vanadium(IV) Incorporation in the Aluminium Metal-Organic Framework MIL-53 (ChemPhysChem 14/2015). Chemphyschem 2015. [DOI: 10.1002/cphc.201500778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
42
|
De Schutter A, Correia HD, Freire DM, Rivas MG, Rizzi A, Santos-Silva T, González PJ, Van Doorslaer S. Ligand Binding to Chlorite Dismutase from Magnetospirillum sp. J Phys Chem B 2015; 119:13859-69. [PMID: 26287794 DOI: 10.1021/acs.jpcb.5b04141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms. Addition of an axial ligand, such as azide or imidazole, removes this heterogeneity almost entirely. This is in line with the two high resolution crystal structures of MaCld obtained in the presence of azide and thiocyanate that show the coordination of the ligands to the heme iron. The crystal structure of the MaCld-azide complex reveals a single well-defined orientation of the azide molecule in the heme pocket. EPR shows, however, a pH-dependent heme structure, probably due to acid-base transitions of the surrounding amino-acid residues stabilizing azide. For the azide and imidazole complex of MaCld, the hyperfine and nuclear quadrupole interactions with the close-by (14)N and (1)H nuclei are determined using pulsed EPR. These values are compared to the corresponding data for the low-spin forms observed in the ferric wild-type MaCld and to existing EPR data on azide and imidazole complexes of other heme proteins.
Collapse
Affiliation(s)
- Amy De Schutter
- BIMEF Laboratory, Department of Physics, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Hugo D Correia
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Diana M Freire
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - María G Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Alberto Rizzi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Teresa Santos-Silva
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Physics, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk, Belgium
| |
Collapse
|
43
|
Nevjestić I, Depauw H, Leus K, Kalendra V, Caretti I, Jeschke G, Van Doorslaer S, Callens F, Van Der Voort P, Vrielinck H. Multi-frequency (S, X, Q and W-band) EPR and ENDOR Study of Vanadium(IV) Incorporation in the Aluminium Metal-Organic Framework MIL-53. Chemphyschem 2015; 16:2968-73. [DOI: 10.1002/cphc.201500522] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Indexed: 11/10/2022]
|
44
|
Caretti I, Keulemans M, Verbruggen SW, Lenaerts S, Van Doorslaer S. Light-Induced Processes in Plasmonic Gold/TiO2 Photocatalysts Studied by Electron Paramagnetic Resonance. Top Catal 2015. [DOI: 10.1007/s11244-015-0419-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
45
|
Freire DM, Rivas MG, Dias AM, Lopes AT, Costa C, Santos-Silva T, Van Doorslaer S, González PJ. The homopentameric chlorite dismutase from Magnetospirillum sp. J Inorg Biochem 2015. [PMID: 26218477 DOI: 10.1016/j.jinorgbio.2015.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chlorite dismutase (Cld) is a b-type heme containing enzyme that catalyzes the reduction of chlorite into chloride plus dioxygen. This enzyme has gained attention because it can be used in the development of bioremediation processes, biosensors, and controlled dioxygen production. In the present work, Cld was purified from Magnetospirillum sp. cells cultured anaerobically with acetate/perchlorate until stationary phase. Biochemical, spectroscopic and X-ray crystallography methods showed that Cld from Magnetospirillum sp. is a ~140 kDa homopentamer comprising ~27.8 kDa monomers. Preliminary X-ray crystallography studies confirmed the quaternary structure and the presence of one b-type heme per monomer. The EPR spectroscopic signature of the as-purified Cld samples is affected by the buffer composition used during the purification. Potassium phosphate buffer is the only buffer that affected neither the spectral nor the kinetic properties of Cld. Kinetic studies in solution revealed that Cld from Magnetospirillum sp. decomposes chlorite at high turnover rates with optimal pH6.0. A temperature below 10 °C is required to avoid enzyme inactivation due to cofactor bleaching during turnover, and to achieve full substrate consumption. Cld kinetic parameters were not affected when kinetic assays were performed in the presence of air or under argon atmosphere, but chloride is a weak mixed inhibitor that modifies the EPR signal of as-prepared samples.
Collapse
Affiliation(s)
- Diana M Freire
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria G Rivas
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - André M Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana T Lopes
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cristina Costa
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Sabine Van Doorslaer
- Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | - Pablo J González
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina.
| |
Collapse
|
46
|
Tilleman L, Abbruzzetti S, Ciaccio C, De Sanctis G, Nardini M, Pesce A, Desmet F, Moens L, Van Doorslaer S, Bruno S, Bolognesi M, Ascenzi P, Coletta M, Viappiani C, Dewilde S. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans. PLoS One 2015; 10:e0125959. [PMID: 26047471 PMCID: PMC4457829 DOI: 10.1371/journal.pone.0125959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 03/28/2015] [Indexed: 12/02/2022] Open
Abstract
Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity.
Collapse
Affiliation(s)
- Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Giampiero De Sanctis
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Stefano Bruno
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Cristiano Viappiani
- Department of Physics and Earth Sciences, University of Parma, Parma, Italy
- * E-mail: (SD); (CV)
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- * E-mail: (SD); (CV)
| |
Collapse
|
47
|
Maurelli S, Morra E, Van Doorslaer S, Busico V, Chiesa M. EPR investigation of TiCl3 dissolved in polar solvents--implications for the understanding of active Ti(III) species in heterogeneous Ziegler-Natta catalysts. Phys Chem Chem Phys 2015; 16:19625-33. [PMID: 25109263 DOI: 10.1039/c4cp02722a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multi-frequency continuous-wave and pulsed EPR techniques are employed to investigate Ti(III)-chloro complexes obtained by dissolving TiCl3 in anhydrous and hydrated methanol. Two distinctly different species, characterized by different g matrices are observed in the two cases. Hyperfine sublevel correlation (HYSCORE) spectroscopy is found to be a powerful method to identify the type of nuclei surrounding the Ti(3+) ion. For the first time, the hyperfine and nuclear quadrupole data of Ti(III)-bound (35/37)Cl nuclei are reported together with (1)H and (13)C hyperfine data of the coordinated methanol molecules. DFT modelling allows interpreting the measured spin Hamiltonian parameters in terms of microscopic models of the solvated species. The theoretical observable properties (g matrix, (35/37)Cl, (1)H and (13)C hyperfine tensors) are in quantitative agreement with the experiments for two families of complexes: [TiCln(CH3OH)6-n]((3-n)+) (with n ranging from 1 to 3) and [Ti(CH3OH)5(OH)](2+) or [Ti(CH3OH)5(OCH3)](2+). The first complex is observed in anhydrous methanol, while the second type of complex is observed when water is added to the solution, the presence of OH(-) and/or CH3O(-) species being promoted by water hydrolysis. The results obtained for the frozen solutions are critically compared to EPR spectra recorded for a MgCl2-supported Ti-based Ziegler-Natta model catalyst.
Collapse
Affiliation(s)
- Sara Maurelli
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | | | | | | | | |
Collapse
|
48
|
Peys N, Adriaensens P, Van Doorslaer S, Gielis S, Peeters E, De Dobbelaere C, De Gendt S, Hardy A, Van Bael MK. Aqueous citrato-oxovanadate(IV) precursor solutions for VO2: synthesis, spectroscopic investigation and thermal analysis. Dalton Trans 2015; 43:12614-23. [PMID: 25005054 DOI: 10.1039/c4dt01346h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aqueous precursor solution, containing citrato-VO(2+) complexes, is synthesized for the formation of monoclinic VO2. With regard to the decomposition of the VO(2+) complexes towards vanadium oxide formation, it is important to gain insights into the chemical structure and transformations of the precursor during synthesis and thermal treatment. Hence, the conversion of the cyclic [V4O12](4-) ion to the VO(2+) ion in aqueous solution, using oxalic acid as an acidifier and a reducing agent, is studied by (51)Vanadium nuclear magnetic resonance spectroscopy. The citrate complexation of this VO(2+) ion and the differentiation between a solution containing citrato-oxalato-VO(2+) and citrato-VO(2+) complexes are studied by electron paramagnetic resonance and Fourier transform infra-red spectroscopy. In both solutions, the VO(2+) containing complex is mononuclear and has a distorted octahedral geometry with a fourfold R-CO2(-) ligation at the equatorial positions and likely a fifth R-CO2(-) ligation at the axial position. Small differences in the thermal decomposition pathway between the gel containing citrato-oxalato-VO(2+) complexes and the oxalate-free gel containing citrato-VO(2+) complexes are observed between 150 and 200 °C in air and are assigned to the presence of (NH4)2C2O4 in the citrato-oxalato-VO(2+) solution. Both precursor solutions are successfully used for the formation of crystalline vanadium oxide nanostructures on SiO2, after thermal annealing at 500 °C in a 0.1% O2 atmosphere. However, the citrato-oxalato-VO(2+) and the oxalate-free citrato-VO(2+) solution result in the formation of monoclinic V6O13 and monoclinic VO2, respectively.
Collapse
Affiliation(s)
- Nick Peys
- Hasselt University, Institute for Materials Research, Inorganic and Physical Chemistry, Diepenbeek, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Tilleman L, Germani F, De Henau S, Helbo S, Desmet F, Berghmans H, Van Doorslaer S, Hoogewijs D, Schoofs L, Braeckman BP, Moens L, Fago A, Dewilde S. A globin domain in a neuronal transmembrane receptor of Caenorhabditis elegans and Ascaris suum: molecular modeling and functional properties. J Biol Chem 2015; 290:10336-52. [PMID: 25666609 DOI: 10.1074/jbc.m114.576520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 01/12/2023] Open
Abstract
We report the structural and biochemical characterization of GLB-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode Caenorhabditis elegans. This unique chimeric protein is composed of a 7-transmembrane domain (7TM), GLB-33 7TM, typical of a G-protein-coupled receptor, and of a globin domain (GD), GLB-33 GD. Comprehensive sequence similarity searches in the genome of the parasitic nematode, Ascaris suum, revealed a chimeric protein that is similar to a Phe-Met-Arg-Phe-amide neuropeptide receptor. The three-dimensional structures of the separate domains of both species and of the full-length proteins were modeled. The 7TM domains of both proteins appeared very similar, but the globin domain of the A. suum receptor surprisingly seemed to lack several helices, suggesting a novel truncated globin fold. The globin domain of C. elegans GLB-33, however, was very similar to a genuine myoglobin-type molecule. Spectroscopic analysis of the recombinant GLB-33 GD showed that the heme is pentacoordinate when ferrous and in the hydroxide-ligated form when ferric, even at neutral pH. Flash-photolysis experiments showed overall fast biphasic CO rebinding kinetics. In its ferrous deoxy form, GLB-33 GD is capable of reversibly binding O2 with a very high affinity and of reducing nitrite to nitric oxide faster than other globins. Collectively, these properties suggest that the globin domain of GLB-33 may serve as a highly sensitive oxygen sensor and/or as a nitrite reductase. Both properties are potentially able to modulate the neuropeptide sensitivity of the neuronal transmembrane receptor.
Collapse
Affiliation(s)
| | | | - Sasha De Henau
- the Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Signe Helbo
- the Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
| | - Filip Desmet
- Physics, University of Antwerp, 2610 Antwerp, Belgium
| | | | | | - David Hoogewijs
- the Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, 8006 Zürich, Switzerland, Institute of Physiology, University of Duisburg-Essen, D-45147 Essen, Germany, and
| | - Liliane Schoofs
- the Functional Genomics and Proteomics Group, KU Leuven, 3000 Leuven, Belgium
| | - Bart P Braeckman
- the Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Luc Moens
- From the Departments of Biomedical Sciences and
| | - Angela Fago
- the Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
| | | |
Collapse
|
50
|
Lin F, Meng X, Kukueva E, Mertens M, Van Doorslaer S, Bals S, Cool P. New insights into the mesophase transformation of ethane-bridged PMOs by the influence of different counterions under basic conditions. RSC Adv 2015. [DOI: 10.1039/c4ra15849k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The counterions are of crucial importance in determining the mesostructure and morphology of ethane-bridged PMO materials synthesized under basic conditions.
Collapse
Affiliation(s)
- Feng Lin
- Laboratory of Adsorption and Catalysis
- Department of Chemistry
- University of Antwerp
- Wilrijk
- Belgium
| | - Xiangyan Meng
- Laboratory of Adsorption and Catalysis
- Department of Chemistry
- University of Antwerp
- Wilrijk
- Belgium
| | - Elena Kukueva
- EMAT
- Department of Physics
- University of Antwerp
- B-2020 Antwerpen
- Belgium
| | - Myrjam Mertens
- Flemish Institute for Technological Research
- VITO
- Mol
- Belgium
| | | | - Sara Bals
- EMAT
- Department of Physics
- University of Antwerp
- B-2020 Antwerpen
- Belgium
| | - Pegie Cool
- Laboratory of Adsorption and Catalysis
- Department of Chemistry
- University of Antwerp
- Wilrijk
- Belgium
| |
Collapse
|