1
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Hagen WR. Very Low-Frequency Broadband Electron Paramagnetic Resonance Spectroscopy of Metalloproteins. J Phys Chem A 2021; 125:3208-3218. [PMID: 33848159 PMCID: PMC8154605 DOI: 10.1021/acs.jpca.1c01217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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A previously developed
spectrometer for broadband electron paramagnetic
resonance (EPR) spectroscopy of dilute randomly oriented systems has
been considerably modified to extend the frequency reach down to the
hundred MHz range and to boost concentration sensitivity by 1 to 2
orders of magnitude. The instrument is now suitable for the study
of biological systems in particular metalloproteins. As a proof of
concept, examples from the class of low-spin ferric hemoproteins are
studied in terms of frequency-dependent changes in their EPR spectra.
Mono-heme cytochrome c EPR is determined by g-strain
over a wide frequency range, whereas a combination of unresolved ligand
hyperfine interaction and concentration-dependent intermolecular dipolar
interaction becomes dominant at very low frequencies. In the four
heme containing cytochrome c3, g-strain
combines with intramolecular dipolar interaction over the full-studied
frequency range of 0.23–12.0 GHz. It is concluded that the
point-dipole approach is inappropriate to describe magnetic interactions
between low-spin ferric heme systems and that a body of literature
on redox interactions in multi-heme proteins will be affected by this
conclusion.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
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2
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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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3
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Kryachko Y, Hemmingsen SM. The Role of Localized Acidity Generation in Microbially Influenced Corrosion. Curr Microbiol 2017; 74:870-876. [PMID: 28444419 DOI: 10.1007/s00284-017-1254-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/13/2017] [Indexed: 10/19/2022]
Abstract
Microbially influenced corrosion is of great industrial concern. Microbial coupling of metal oxidation to sulfate-, nitrate-, nitrite-, or CO2-reduction is proton-mediated, and some sulfate-reducing prokaryotes are capable of regulating extracellular pH. The analysis of the corrosive processes catalyzed by nitrate reducing bacteria and methanogenic archaea indicates that these microorganisms may be capable of regulating extracellular pH as well. It is proposed that nutrient limitation at metal-biofilm interfaces may induce activation of enzymatic proton-producing/proton-secreting functions in respiratory and methanogenic microorganisms to make them capable of using Fe0 as the electron donor. This can be further verified through experiments involving measurements of ion and gas concentrations at metal-biofilm interfaces, microscopy, and transcriptomics analyses.
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Affiliation(s)
- Yuriy Kryachko
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Sean M Hemmingsen
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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4
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Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS. A stable genetic polymorphism underpinning microbial syntrophy. THE ISME JOURNAL 2016; 10:2844-2853. [PMID: 27258948 PMCID: PMC5042321 DOI: 10.1038/ismej.2016.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.
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Affiliation(s)
- Tobias Großkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Simone Zenobi
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Mark Alston
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Leighton Folkes
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - David Swarbreck
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
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5
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Almeida RM, Dell'Acqua S, Krippahl L, Moura JJG, Pauleta SR. Predicting Protein-Protein Interactions Using BiGGER: Case Studies. Molecules 2016; 21:E1037. [PMID: 27517887 PMCID: PMC6274584 DOI: 10.3390/molecules21081037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 11/29/2022] Open
Abstract
The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.
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Affiliation(s)
- Rui M Almeida
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
| | - Simone Dell'Acqua
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
| | - Ludwig Krippahl
- CENTRIA, Departamento de Informática, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
| | - José J G Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
| | - Sofia R Pauleta
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
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6
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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7
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de Poulpiquet A, Ranava D, Monsalve K, Giudici-Orticoni MT, Lojou E. Biohydrogen for a New Generation of H2/O2Biofuel Cells: A Sustainable Energy Perspective. ChemElectroChem 2014. [DOI: 10.1002/celc.201402249] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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8
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Reconstitution of supramolecular organization involved in energy metabolism at electrochemical interfaces for biosensing and bioenergy production. Anal Bioanal Chem 2013; 406:1011-27. [DOI: 10.1007/s00216-013-7465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/01/2013] [Accepted: 10/25/2013] [Indexed: 12/26/2022]
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10
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Quintas PO, Oliveira MS, Catarino T, Turner DL. Electron transfer between multihaem cytochromes c3 from Desulfovibrio africanus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:502-6. [DOI: 10.1016/j.bbabio.2013.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/16/2013] [Accepted: 01/24/2013] [Indexed: 11/26/2022]
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11
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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12
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Grein F, Ramos AR, Venceslau SS, Pereira IAC. Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:145-60. [PMID: 22982583 DOI: 10.1016/j.bbabio.2012.09.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron-sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Fabian Grein
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
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13
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Fonseca BM, Paquete CM, Salgueiro CA, Louro RO. The role of intramolecular interactions in the functional control of multiheme cytochromes c. FEBS Lett 2011; 586:504-9. [PMID: 21856299 DOI: 10.1016/j.febslet.2011.08.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
Abstract
Detailed thermodynamic and structural data measured in soluble monomeric multiheme cytochromes c provided the basis to investigate the functional significance of interactions between redox co-factors. The steep decay of intramolecular interactions with distance means that close proximity of the redox centers is necessary to modulate the intrinsic reduction potentials in a significant way. This ensures selection of specific populations during redox activity in addition to maintaining fast intramolecular electron transfer. Therefore, intramolecular interactions between redox co-factors play an important role in establishing the biological function of the protein by controlling how electrons flow through and are distributed among the co-factors.
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Affiliation(s)
- Bruno M Fonseca
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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14
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Homotropic and heterotropic interactions in cytochromes c
3
from sulphate reducing bacteria. FEBS Lett 2011; 586:494-503. [DOI: 10.1016/j.febslet.2011.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/04/2011] [Indexed: 11/23/2022]
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15
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Pereira IAC, Ramos AR, Grein F, Marques MC, da Silva SM, Venceslau SS. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2011; 2:69. [PMID: 21747791 PMCID: PMC3119410 DOI: 10.3389/fmicb.2011.00069] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/25/2011] [Indexed: 11/13/2022] Open
Abstract
The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H(+)-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H(2), formate, pyruvate, NAD(P)H, β-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.
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Affiliation(s)
- Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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16
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Rüdiger O, Gutiérrez-Sánchez C, Olea D, Pereira I, Vélez M, Fernández V, De Lacey A. Enzymatic Anodes for Hydrogen Fuel Cells based on Covalent Attachment of Ni-Fe Hydrogenases and Direct Electron Transfer to SAM-Modified Gold Electrodes. ELECTROANAL 2010. [DOI: 10.1002/elan.200880002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Devred F, Barbier P, Lafitte D, Landrieu I, Lippens G, Peyrot V. Microtubule and MAPs: thermodynamics of complex formation by AUC, ITC, fluorescence, and NMR. Methods Cell Biol 2010; 95:449-80. [PMID: 20466148 DOI: 10.1016/s0091-679x(10)95023-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Microtubules are implicated in many essential cellular processes such as architecture, cell division, and intracellular traffic, due to their dynamic instability. This dynamicity is tightly regulated by microtubule-associated proteins (MAPs), such as tau and stathmin. Despite extensive studies motivated by their central role in physiological functions and pathological role in neurodegenerative diseases and cancer, the precise mechanisms of tau and stathmin binding to tubulin and their consequences on microtubule stability are still not fully understood. One of the most crucial points missing is a quantitative thermodynamic description of their interaction with tubulin/microtubules and of the tubulin complexes formed upon these interactions. In this chapter, we will focus on the use of analytical ultracentrifugation, isothermal titration calorimetry, and nuclear magnetic resonance-three powerful and complementary techniques in the field of MAP-tubulin/microtubule interactions, in addition to the spectrometric techniques and co-sedimentation approach. We will present the limits of these techniques to study this particular interaction and precautions that need to be taken during MAPs preparation. Understanding the molecular mechanisms that govern MAPs action on microtubular network will not only shed new light on the role of this crucial family of protein in the biology of the cell, but also hopefully open new paths to increase the therapeutic efficiency of microtubule-targeting drugs in cancers therapies and neurodegeneratives diseases prevention.
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Affiliation(s)
- François Devred
- CRO2, U911 Inserm, Aix-Marseille Université, 27 Bd Jean Moulin, 13385 Marseille cedex 05, France
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18
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Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:222-32. [PMID: 19857457 DOI: 10.1016/j.bbabio.2009.10.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/16/2009] [Accepted: 10/20/2009] [Indexed: 11/23/2022]
Abstract
Periplasmic cytochromes c(7) are important in electron transfer pathway(s) in Fe(III) respiration by Geobacter sulfurreducens. The genome of G. sulfurreducens encodes a family of five 10-kDa, three-heme cytochromes c(7). The sequence identity between the five proteins (designated PpcA, PpcB, PpcC, PpcD, and PpcE) varies between 45% and 77%. Here, we report the high-resolution structures of PpcC, PpcD, and PpcE determined by X-ray diffraction. This new information made it possible to compare the sequences and structures of the entire family. The triheme cores are largely conserved but are not identical. We observed changes, due to different crystal packing, in the relative positions of the hemes between two molecules in the crystal. The overall protein fold of the cytochromes is similar. The structure of PpcD differs most from that of the other homologs, which is not obvious from the sequence comparisons of the family. Interestingly, PpcD is the only cytochrome c(7) within the family that has higher abundance when G. sulfurreducens is grown on insoluble Fe(III) oxide compared to ferric citrate. The structures have the highest degree of conservation around "heme IV"; the protein surface around this heme is positively charged in all of the proteins, and therefore all cytochromes c(7) could interact with similar molecules involving this region. The structures and surface characteristics of the proteins near the other two hemes, "heme I" and "heme III", differ within the family. The above observations suggest that each of the five cytochromes c(7) could interact with its own redox partner via an interface involving the regions of heme I and/or heme III; this provides a possible rationalization for the existence of five similar proteins in G. sulfurreducens.
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Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol 2009; 11:1038-55. [PMID: 19187283 PMCID: PMC2702500 DOI: 10.1111/j.1462-2920.2008.01825.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 10/25/2008] [Indexed: 01/23/2023]
Abstract
Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
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Affiliation(s)
- Axel W Strittmatter
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Heiko Liesegang
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Ralf Rabus
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University OldenburgCarl-von-Ossietzky Str. 9-11, D-26111 Oldenburg, Germany
| | - Iwona Decker
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Judith Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Sönke Andres
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Anke Henne
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Wolfgang Florian Fricke
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rosa Martinez-Arias
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Daniela Bartels
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Lutz Krause
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität BielefeldD-33594 Bielefeld, Germany
| | - Hans-Peter Klenk
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7 B, D-38124 Braunschweig, Germany
| | - Michael Richter
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Margarete Schüler
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | | | - Anke Meyerdierks
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
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20
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Cordas CM, Moura I, Moura JJG. Direct electrochemical study of the multiple redox centers of hydrogenase from Desulfovibrio gigas. Bioelectrochemistry 2008; 74:83-9. [PMID: 18632311 DOI: 10.1016/j.bioelechem.2008.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 04/10/2008] [Accepted: 04/12/2008] [Indexed: 11/28/2022]
Abstract
Direct electrochemical response was first time observed for the redox centers of Desulfovibrio gigas [NiFe]-Hase, in non-turnover conditions, by cyclic voltammetry, in solution at glassy carbon electrode. The activation of the enzyme was achieved by reduction with H(2) and by electrochemical control and electrocatalytic activity was observed. The inactivation of the [NiFe]-Hase was also attained through potential control. All electrochemical data was obtained in the absence of enzyme inhibitors. The results are discussed in the context of the proposed mechanism currently accepted for activation/inactivation of [NiFe]-Hases.
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Affiliation(s)
- Cristina M Cordas
- REQUIMTE - Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2859-516 Monte de Caparica, Portugal
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21
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Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 2007; 107:4273-303. [PMID: 17850165 DOI: 10.1021/cr050195z] [Citation(s) in RCA: 998] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juan C Fontecilla-Camps
- Laboratoire de Cristallographie et Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel, CEA, CNRS, Universitè Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.
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22
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Key role of the anchoring PEI layer on the electrochemistry of redox proteins at carbon electrodes. Electrochim Acta 2007. [DOI: 10.1016/j.electacta.2007.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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De Lacey AL, Fernandez VM, Rousset M, Cammack R. Activation and Inactivation of Hydrogenase Function and the Catalytic Cycle: Spectroelectrochemical Studies. Chem Rev 2007; 107:4304-30. [PMID: 17715982 DOI: 10.1021/cr0501947] [Citation(s) in RCA: 364] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio L De Lacey
- Instituto de CatAlisis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
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24
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Paquete CM, Turner DL, Louro RO, Xavier AV, Catarino T. Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1169-79. [PMID: 17692816 DOI: 10.1016/j.bbabio.2007.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 06/25/2007] [Indexed: 11/27/2022]
Abstract
The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.
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Affiliation(s)
- Catarina M Paquete
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, 2780-156 Oeiras, Portugal
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25
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Paquete CM, Pereira PM, Catarino T, Turner DL, Louro RO, Xavier AV. Functional properties of type I and type II cytochromes c3 from Desulfovibrio africanus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:178-88. [PMID: 17316553 DOI: 10.1016/j.bbabio.2007.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/09/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
Type I cytochrome c(3) is a key protein in the bioenergetic metabolism of Desulfovibrio spp., mediating electron transfer between periplasmic hydrogenase and multihaem cytochromes associated with membrane bound complexes, such as type II cytochrome c(3). This work presents the NMR assignment of the haem substituents in type I cytochrome c(3) isolated from Desulfovibrio africanus and the thermodynamic and kinetic characterisation of type I and type II cytochromes c(3) belonging to the same organism. It is shown that the redox properties of the two proteins allow electrons to be transferred between them in the physiologically relevant direction with the release of energised protons close to the membrane where they can be used by the ATP synthase.
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Affiliation(s)
- Catarina M Paquete
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, 2780-156 Oeiras, Portugal
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26
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Iida S, Asakura N, Tabata K, Okura I, Kamachi T. Incorporation of Unnatural Amino Acids into Cytochrome c3 and Specific Viologen Binding to the Unnatural Amino Acid. Chembiochem 2006; 7:1853-5. [PMID: 17131373 DOI: 10.1002/cbic.200600347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shin Iida
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama 226-8501, Japan
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27
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Pereira PM, Teixeira M, Xavier AV, Louro RO, Pereira IAC. The Tmc complex from Desulfovibrio vulgaris hildenborough is involved in transmembrane electron transfer from periplasmic hydrogen oxidation. Biochemistry 2006; 45:10359-67. [PMID: 16922512 DOI: 10.1021/bi0610294] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three membrane-bound redox complexes have been reported in Desulfovibrio spp., whose genes are not found in the genomes of other sulfate reducers such as Desulfotalea psycrophila and Archaeoglobus fulgidus. These complexes contain a periplasmic cytochrome c subunit of the cytochrome c(3) family, and their presence in these organisms probably correlates with the presence of a pool of periplasmic cytochromes c(3), also absent in the two other sulfate reducers. In this work we report the isolation and characterization of the first of such complexes, Tmc from D. vulgaris Hildenborough, which is associated with the tetraheme type II cytochrome c(3). The isolated Tmc complex contains four subunits, including the TpIIc(3) (TmcA), an integral membrane cytochrome b (TmcC), and two cytoplasmically predicted proteins, an iron-sulfur protein (TmcB) and a tryptophan-rich protein (TmcD). Spectroscopic studies indicate the presence of eight hemes c and two hemes b in the complex pointing to an alpha(2)betagammadelta composition (TmcA(2)BCD). EPR analysis reveals the presence of a [4Fe4S](3+) center and up to three other iron-sulfur centers in the cytoplasmic subunit. Nearly full reduction of the redox centers in the Tmc complex could be obtained upon incubation with hydrogenase/TpIc(3), supporting the role of this complex in transmembrane transfer of electrons resulting from periplasmic oxidation of hydrogen.
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Affiliation(s)
- Patrícia M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
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28
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Louro RO. Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c 3. J Biol Inorg Chem 2006; 12:1-10. [PMID: 16964504 DOI: 10.1007/s00775-006-0165-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 08/21/2006] [Indexed: 10/24/2022]
Abstract
Tetrahaem cytochromes c (3) from sulfate-reducing bacteria have revealed exquisite complexity in their ligand binding properties and they couple the cooperative binding of two electrons with the binding of protons. In this review, the molecular mechanisms for these cooperative effects are described, and the functional consequences of these cooperativities are discussed in the context of the general mechanisms of biological energy transduction and the specific physiological metabolism of Desulfovibrio.
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Affiliation(s)
- Ricardo O Louro
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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29
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Yahata N, Ozawa K, Tomimoto Y, Morita K, Komori H, Ogata H, Higuchi Y, Akutsu H. Roles of charged residues in pH-dependent redox properties of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F. Biophysics (Nagoya-shi) 2006; 2:45-56. [PMID: 27857559 PMCID: PMC5036644 DOI: 10.2142/biophysics.2.45] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Accepted: 05/26/2006] [Indexed: 12/01/2022] Open
Abstract
Complicated pH-properties of the tetraheme cytochrome c3 (cyt c3) from Desulfovibrio vulgaris Miyazaki F (DvMF) were examined by the pH titrations of 1H-15N HSQC spectra in the ferric and ferrous states. The redox-linked pKa shift for the propionate group at C13 of heme 1 was observed as the changes of the NH signals around it. This pKa shift is consistent with the redox-linked conformational alteration responsible for the cooperative reduction between hemes 1 and 2. On the other hand, large chemical shift changes caused by the protonation/deprotonation of Glu41 and/or Asp42, and His67 were redox-independent. Nevertheless, these charged residues affect the redox properties of the four hemes. Furthermore, one of interesting charged residues, Glu41, was studied by site-directed mutagenesis. E41K mutation increased the microscopic redox potentials of heme 1 by 46 and 34 mV, and heme 2 by 35 and 30 mV at the first and last reduction steps, respectively. Although global folding in the crystal structure of E41K cyt c3 is similar to that of wild type, local change was observed in 1H NMR spectrum. Glu41 is important to keep the stable conformation in the region between hemes 1 and 2, controlling the redox properties of DvMF cyt c3. In contrast, the kinetic parameters for electron transfer from DvMF [NiFe] hydrogenase were not influenced by E41K mutation. This suggests that the region between hemes 1 and 2 is not involved in the interaction with [NiFe] hydrogenase, and it supports the idea that heme 4 is the exclusive entrance gate to accept the electron in the initial reduction stage.
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Affiliation(s)
- Naoki Yahata
- Institute for Protein Research, Osaka University, Yamadaoka, Suita 565-0871, Japan
| | - Kiyoshi Ozawa
- Faculty of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yusuke Tomimoto
- Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Koto, Kamigori, Hyogo 678-1297, Japan
| | - Kumiko Morita
- Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Koto, Kamigori, Hyogo 678-1297, Japan
| | - Hirofumi Komori
- Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Koto, Kamigori, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideaki Ogata
- Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Koto, Kamigori, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Koto, Kamigori, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, Yamadaoka, Suita 565-0871, Japan
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