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Barbosa C, Rodrigues CF, Lončar N, Martins LO, Todorovic S, Silveira CM. Spectroelectrochemistry for determination of the redox potential in heme enzymes: Dye-decolorizing peroxidases. BBA ADVANCES 2023; 5:100112. [PMID: 38235374 PMCID: PMC10792693 DOI: 10.1016/j.bbadva.2023.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-containing enzymes that are structurally unrelated to other peroxidases. Some DyPs show high potential for applications in biotechnology, which critically depends on the stability and redox potential (E°') of the enzyme. Here we provide a comparative analysis of UV-Vis- and surface-enhanced resonance Raman-based spectroelectrochemical methods for determination of the E°' of DyPs from two different organisms, and their variants generated targeting E°' upshift. We show that substituting the highly conserved Arginine in the distal side of the heme pocket by hydrophobic amino acid residues impacts the heme architecture and redox potential of DyPs from the two organisms in a very distinct manner. We demonstrate the advantages and drawbacks of the used spectroelectrochemical approaches, which is relevant for other heme proteins that contain multiple heme centers or spin populations.
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Affiliation(s)
- Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Nikola Lončar
- Gecco Biotech, Nijenborgh 4, Groningen 9747AG, the Netherlands
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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3
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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4
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Silveira CM, Zuccarello L, Barbosa C, Caserta G, Zebger I, Hildebrandt P, Todorovic S. Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies. Molecules 2021; 26:4852. [PMID: 34443440 PMCID: PMC8398457 DOI: 10.3390/molecules26164852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.
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Affiliation(s)
- Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Giorgio Caserta
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Ingo Zebger
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Peter Hildebrandt
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
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5
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Zuccarello L, Barbosa C, Galdino E, Lončar N, Silveira CM, Fraaije MW, Todorovic S. SERR Spectroelectrochemistry as a Guide for Rational Design of DyP-Based Bioelectronics Devices. Int J Mol Sci 2021; 22:7998. [PMID: 34360763 PMCID: PMC8348443 DOI: 10.3390/ijms22157998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Immobilised dye-decolorizing peroxidases (DyPs) are promising biocatalysts for the development of biotechnological devices such as biosensors for the detection of H2O2. To this end, these enzymes have to preserve native, solution properties upon immobilisation on the electrode surface. In this work, DyPs from Cellulomonas bogoriensis (CboDyP), Streptomyces coelicolor (ScoDyP) and Thermobifida fusca (TfuDyP) are immobilised on biocompatible silver electrodes functionalized with alkanethiols. Their structural, redox and catalytic properties upon immobilisation are evaluated by surface-enhanced resonance Raman (SERR) spectroelectrochemistry and cyclic voltammetry. Among the studied electrode/DyP constructs, only CboDyP shows preserved native structure upon attachment to the electrode. However, a comparison of the redox potentials of the enzyme in solution and immobilised states reveals a large discrepancy, and the enzyme shows no electrocatalytic activity in the presence of H2O2. While some immobilised DyPs outperform existing peroxidase-based biosensors, others fail to fulfil the essential requirements that guarantee their applicability in the immobilised state. The capacity of SERR spectroelectrochemistry for fast screening of the performance of immobilised heme enzymes places it in the front-line of experimental approaches that can advance the search for promising DyP candidates.
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Affiliation(s)
- Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Edilson Galdino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Nikola Lončar
- Gecco Biotech, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Marco W. Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
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6
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Abstract
Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability.
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Kaiser J, Castellano M, Gnandt D, Koslowski T. Monte Carlo simulation and thermodynamic integration applied to protein charge transfer. J Comput Chem 2020; 41:1105-1115. [PMID: 31981372 DOI: 10.1002/jcc.26155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/29/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022]
Abstract
We introduce a combination of Monte Carlo simulation and thermodynamic integration methods to address a model problem in free energy computations, electron transfer in proteins. The feasibility of this approach is tested using the ferredoxin protein from Clostridium acidurici. The results are compared to numerical solutions of the Poisson-Boltzmann equation and data from recent molecular dynamics simulations on charge transfer in a protein complex, the NrfHA nitrite reductase of Desulfovibrio vulgaris. Despite the conceptual and computational simplicity of the Monte Carlo approach, the data agree well with those obtained by other methods. A link to experiments is established via the cytochrome subunit of the bacterial photosynthetic reaction center of Rhodopseudomonas viridis.
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Affiliation(s)
- Jan Kaiser
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - Mike Castellano
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
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8
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Barbosa C, Silveira CM, Silva D, Brissos V, Hildebrandt P, Martins LO, Todorovic S. Immobilized dye-decolorizing peroxidase (DyP) and directed evolution variants for hydrogen peroxide biosensing. Biosens Bioelectron 2020; 153:112055. [PMID: 32056659 DOI: 10.1016/j.bios.2020.112055] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 02/07/2023]
Abstract
Immobilized dye-decolorizing peroxidase from Pseudomonas putida MET94 (PpDyP) and three variants generated by directed evolution (DE) are studied aiming at the design of a biosensor for H2O2 detection. Structural properties of the enzymes in solution and immobilized state are addressed by resonance Raman (RR) and surface enhanced RR (SERR) spectroscopy, and the electrocatalytic properties are analyzed by electrochemistry. The wild-type (wt) and 29E4 variant (with E188K and H125Y mutations) represent excellent candidates for development of H2O2 biosensors, since they exhibit a good dynamic response range (1-200 μM H2O2), short response times (2 s) and a superior sensitivity (1.3-1.4 A⋅M-1⋅cm-2) for H2O2, as well as selectivity and long term stability. In contrast to the solution state, 6E10 (with E188K, A142V and H125Y mutations) and 25F6 (with E188K, A142V, H125Y and G129D mutations) variants display much lower activity and are inhibited by high concentrations of H2O2 upon adsorption on an electrode. In terms of sensitivity, the bioelectrodes employing wt PpDyP and 29E4 variant outperform HRP based counterparts reported in the literature by 1-4 orders of magnitude. We propose the development of wt or 29E4 PpDyP based biosensor as a valuable alternative to devices that rely on peroxidases.
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Affiliation(s)
- Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia M Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin, Inbstitut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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9
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Gnandt D, Koslowski T. Long-range electron-electron interaction and charge transfer in protein complexes: a numerical approach. Phys Chem Chem Phys 2019; 21:18595-18604. [PMID: 31414082 DOI: 10.1039/c9cp03141c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
With application to the nitrite reductase hexameric protein complex of Desulfovibrio vulgaris, NrfH2A4, we suggest a strategy to compute the energy landscape of electron transfer in large systems of biochemical interest. For small complexes, the energy of all electronic configurations can be scanned completely on the level of a numerical solution of the Poisson-Boltzmann equation. In contrast, larger systems have to be treated using a pair approximation, which is verified here. Effective Coulomb interactions between neighbouring sites of excess electron localization may become as large as 200 meV, and they depend in a nontrivial manner on the intersite distance. We discuss the implications of strong Coulomb interactions on the thermodynamics and kinetics of charging and decharging a protein complex. Finally, we turn to the effect of embedding the system into a biomembrane.
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Affiliation(s)
- David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany.
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10
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Paquete CM, Rusconi G, Silva AV, Soares R, Louro RO. A brief survey of the "cytochromome". Adv Microb Physiol 2019; 75:69-135. [PMID: 31655743 DOI: 10.1016/bs.ampbs.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.
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11
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Gnandt D, Na S, Koslowski T. Simulating biological charge transfer: Continuum dielectric theory or molecular dynamics? Biophys Chem 2018; 241:1-7. [PMID: 30036762 DOI: 10.1016/j.bpc.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
We study the thermodynamic parameters of Marcus's theory of charge transfer, the driving forces and the reorganization energies, using two widely applied approaches to bioenergetic problems that seem to be radically different: continuum dielectric theory via a numerical solution of Poisson's equation, and the thermodynamic integration approach based upon classical Newtonian molecular dynamics, as perfomed by Na et al., PCCP 19, 18,938 (2017). With application to a nitrite reductase NrfHA protein heterodimer, we obtain an excellent agreement between the respective driving forces with an r.m.s. deviation of 1.7 kcal/mol, and a lower limit to the reorganization energies. The computational methods turn out to be mutually supportive: molecular dynamics can be used to determine the parameters of a dielectric theory computation, which on the other hand can be used to properly rescale the reorganization energies and partition them into aqueous and protein contributions. In addition, we use the electrostatic approach to study the influence of Ca2+ ions on the free energy landscape of charge transfer.
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Affiliation(s)
- David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany.
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12
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Na S, Bauß A, Langenmaier M, Koslowski T. Thermodynamic integration network study of electron transfer: from proteins to aggregates. Phys Chem Chem Phys 2017; 19:18938-18947. [DOI: 10.1039/c7cp03030d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe electron transfer through the NrfHA nitrite reductase using a thermodynamic integration scheme. Driving forces are hardly affected by dimerization, but the transport mechanism only emerges simulating the dimer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Michael Langenmaier
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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13
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Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:924-931. [PMID: 25534748 DOI: 10.1021/es504484m] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause “souring” of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.
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14
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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15
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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16
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McMillan DGG, Marritt SJ, Firer-Sherwood MA, Shi L, Richardson DJ, Evans SD, Elliott SJ, Butt JN, Jeuken LJC. Protein-protein interaction regulates the direction of catalysis and electron transfer in a redox enzyme complex. J Am Chem Soc 2013; 135:10550-6. [PMID: 23799249 PMCID: PMC3823026 DOI: 10.1021/ja405072z] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Protein–protein interactions
are well-known to regulate
enzyme activity in cell signaling and metabolism. Here, we show that
protein–protein interactions regulate the activity of a respiratory-chain
enzyme, CymA, by changing the direction or bias of catalysis. CymA,
a member of the widespread NapC/NirT superfamily, is a menaquinol-7
(MQ-7) dehydrogenase that donates electrons to several distinct terminal
reductases in the versatile respiratory network of Shewanella oneidensis. We report the incorporation
of CymA within solid-supported membranes that mimic the inner membrane
architecture of S. oneidensis. Quartz-crystal
microbalance with dissipation (QCM-D) resolved the formation of a
stable complex between CymA and one of its native redox partners,
flavocytochrome c3 (Fcc3) fumarate reductase.
Cyclic voltammetry revealed that CymA alone could only reduce MQ-7,
while the CymA-Fcc3 complex catalyzed the reaction required
to support anaerobic respiration, the oxidation of MQ-7. We propose
that MQ-7 oxidation in CymA is limited by electron transfer to the
hemes and that complex formation with Fcc3 facilitates
the electron-transfer rate along the heme redox chain. These results
reveal a yet unexplored mechanism by which bacteria can regulate multibranched
respiratory networks through protein–protein interactions.
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Affiliation(s)
- Duncan G G McMillan
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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17
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Contrasting catalytic profiles of multiheme nitrite reductases containing CxxCK heme-binding motifs. J Biol Inorg Chem 2013; 18:655-67. [DOI: 10.1007/s00775-013-1011-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
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18
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Sezer M, Santos A, Kielb P, Pinto T, Martins LO, Todorovic S. Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study. Biochemistry 2013; 52:3074-84. [PMID: 23560556 DOI: 10.1021/bi301630a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.
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Affiliation(s)
- Murat Sezer
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, 2780-157 Oeiras, Portugal
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