1
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Hammerstad M, Rugtveit AK, Dahlen S, Andersen HK, Hersleth HP. Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Antioxidants (Basel) 2023; 12:1224. [PMID: 37371954 DOI: 10.3390/antiox12061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. Bacillus cereus (Bc) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. Bc FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The Bc IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Anne Kristine Rugtveit
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Sondov Dahlen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hilde Kristin Andersen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
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2
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Zhao X, Zhao Y, Gou M, Liu CJ. Tissue-preferential recruitment of electron transfer chains for cytochrome P450-catalyzed phenolic biosynthesis. SCIENCE ADVANCES 2023; 9:eade4389. [PMID: 36630494 PMCID: PMC9833660 DOI: 10.1126/sciadv.ade4389] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Cytochrome P450 system consists of P450 monooxygenase and redox pattern(s). While the importance of monooxygenases in plant metabolism is well documented, the metabolic roles of the related redox components have been largely overlooked. Here, we show that distinct electron transfer chains are recruited in phenylpropanoid-monolignol P450 systems to support the synthesis and distribution of different classes of phenolics in different plant tissues. While Arabidopsis cinnamate 4-hydroxylase adopts conventional NADPH-cytochrome P450 oxidoreductase (CPR) electron transfer chain for its para-hydroxylation reaction, ferulate 5-hydroxylase uses both NADPH-CPR-cytochrome b5 (CB5) and NADH-cytochrome b5 reductase-CB5 chains to support benzene ring 5-hydroxylation, in which the former route is primarily recruited in the stem for syringyl lignin synthesis, while the latter dominates in the syntheses of 5-hydroxylated phenolics in seeds and seed coat suberin. Our study unveils an additional layer of complexity and versatility of P450 system that the plants evolved for diversifying phenolic repertoires.
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3
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Almeida FCL, Sanches K, Caruso IP, Melo FA. NMR Relaxation Dispersion Experiments to Study Phosphopeptide Recognition by SH2 Domains: The Grb2-SH2-Phosphopeptide Encounter Complex. Methods Mol Biol 2023; 2705:135-151. [PMID: 37668973 DOI: 10.1007/978-1-0716-3393-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Protein interactions are at the essence of life. Proteins evolved not to have stable structures, but rather to be specialized in participating in a network of interactions. Every interaction involving proteins comprises the formation of an encounter complex, which may have two outcomes: (i) the dissociation or (ii) the formation of the final specific complex. Here, we present a methodology to characterize the encounter complex of the Grb2-SH2 domain with a phosphopeptide. This method can be generalized to other protein partners. It consists of the measurement of 15N CPMG relaxation dispersion (RD) profiles of the protein in the free state, which describes the residues that are in conformational exchange. We then acquire the dispersion profiles of the protein at a semisaturated concentration of the ligand. At this condition, the chemical exchange between the free and bound state leads to the observation of dispersion profiles in residues that are not in conformational exchange in the free state. This is due to fuzzy interactions that are typical of the encounter complexes. The transient "touching" of the ligand in the protein partner generates these new relaxation dispersion profiles. For the Grb2-SH2 domain, we observed a wider surface at SH2 for the encounter complex than the phosphopeptide (pY) binding site, which might explain the molecular recognition of remote phosphotyrosine. The Grb2-SH2-pY encounter complex is dominated by electrostatic interactions, which contribute to the fuzziness of the complex, but also have contribution of hydrophobic interactions.
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Affiliation(s)
- Fabio C L Almeida
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, Australia
| | - Icaro P Caruso
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
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4
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Teixeira LR, Fernandes TM, Silva MA, Morgado L, Salgueiro CA. Characterization of a Novel Cytochrome Involved in
Geobacter sulfurreducens’
Electron Harvesting Pathways. Chemistry 2022; 28:e202202333. [DOI: 10.1002/chem.202202333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Liliana R. Teixeira
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Tomás M. Fernandes
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Marta A. Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
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5
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Günzel A, Engelbrecht V, Happe T. Changing the tracks: screening for electron transfer proteins to support hydrogen production. J Biol Inorg Chem 2022; 27:631-640. [PMID: 36038787 PMCID: PMC9569306 DOI: 10.1007/s00775-022-01956-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Abstract Ferredoxins are essential electron transferring proteins in organisms. Twelve plant-type ferredoxins in the green alga Chlamydomonas reinhardtii determine the fate of electrons, generated in multiple metabolic processes. The two hydrogenases HydA1 and HydA2 of. C. reinhardtii compete for electrons from the photosynthetic ferredoxin PetF, which is the first stromal mediator of the high-energy electrons derived from the absorption of light energy at the photosystems. While being involved in many chloroplast-located metabolic pathways, PetF shows the highest affinity for ferredoxin-NADP+ oxidoreductase (FNR), not for the hydrogenases. Aiming to identify other potential electron donors for the hydrogenases, we screened as yet uncharacterized ferredoxins Fdx7, 8, 10 and 11 for their capability to reduce the hydrogenases. Comparing the performance of the Fdx in presence and absence of competitor FNR, we show that Fdx7 has a higher affinity for HydA1 than for FNR. Additionally, we show that synthetic FeS-cluster-binding maquettes, which can be reduced by NADPH alone, can also be used to reduce the hydrogenases. Our findings pave the way for the creation of tailored electron donors to redirect electrons to enzymes of interest. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00775-022-01956-1.
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Affiliation(s)
- Alexander Günzel
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany.
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6
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Antunes JMA, Silva MA, Salgueiro CA, Morgado L. Electron Flow From the Inner Membrane Towards the Cell Exterior in Geobacter sulfurreducens: Biochemical Characterization of Cytochrome CbcL. Front Microbiol 2022; 13:898015. [PMID: 35620088 PMCID: PMC9129911 DOI: 10.3389/fmicb.2022.898015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Exoelectrogenic microorganisms are in the spotlight due to their unique respiratory mechanisms and potential applications in distinct biotechnological fields, including bioremediation, bioenergy production and microbial electrosynthesis. These applications rely on the capability of these microorganisms to perform extracellular electron transfer, a mechanism that allows the bacteria to transfer electrons to the cell’s exterior by establishing functional interfaces between different multiheme cytochromes at the inner membrane, periplasmic space, and outer membrane. The multiheme cytochrome CbcL from Geobacter sulfurreducens is associated to the inner membrane and plays an essential role in the transfer of electrons to final electron acceptors with a low redox potential, as Fe(III) oxides and electrodes poised at −100 mV. CbcL has a transmembranar di-heme b-type cytochrome domain with six helices, linked to a periplasmic cytochrome domain with nine c-type heme groups. The complementary usage of ultraviolet-visible, circular dichroism and nuclear magnetic resonance permitted the structural and functional characterization of CbcL’s periplasmic domain. The protein was found to have a high percentage of disordered regions and its nine hemes are low-spin and all coordinated by two histidine residues. The apparent midpoint reduction potential of the CbcL periplasmic domain was determined, suggesting a thermodynamically favorable transfer of electrons to the putative redox partner in the periplasm − the triheme cytochrome PpcA. The establishment of a redox complex between the two proteins was confirmed by probing the electron transfer reaction and the molecular interactions between CbcL and PpcA. The results obtained show for the first time how electrons are injected into the periplasm of Geobacter sulfurreducens for subsequent transfer to the cell’s exterior.
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Affiliation(s)
- Jorge M A Antunes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Marta A Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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7
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Morgado L, Salgueiro CA. Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes. Metallomics 2022; 14:6539350. [DOI: 10.1093/mtomcs/mfac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Cytochromes are electron transfer proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electron outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and elucidate the stepwise electron transfer along the respiratory paths. However, investigating direct electron transfer events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. NMR spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor electron transfer within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of electron transfer between c-type cytochromes, using as model a triheme periplasmic cytochrome (PpcA) and a membrane associated monoheme cytochrome (OmcF) from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional electron transfer within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory electron transfer chains.
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Affiliation(s)
- Leonor Morgado
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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8
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Structural and functional insights of GSU0105, a unique multiheme cytochrome from G. sulfurreducens. Biophys J 2021; 120:5395-5407. [PMID: 34688593 DOI: 10.1016/j.bpj.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Geobacter sulfurreducens possesses over 100 cytochromes that assure an effective electron transfer to the cell exterior. The most abundant group of cytochromes in this microorganism is the PpcA family, composed of five periplasmic triheme cytochromes with high structural homology and identical heme coordination (His-His). GSU0105 is a periplasmic triheme cytochrome synthetized by G. sulfurreducens in Fe(III)-reducing conditions but is not present in cultures grown on fumarate. This cytochrome has a low sequence identity with the PpcA family cytochromes and a different heme coordination, based on the analysis of its amino acid sequence. In this work, amino acid sequence analysis, site-directed mutagenesis, and complementary biophysical techniques, including ultraviolet-visible, circular dichroism, electron paramagnetic resonance, and nuclear magnetic resonance spectroscopies, were used to characterize GSU0105. The cytochrome has a low percentage of secondary structural elements, with features of α-helices and β-sheets. Nuclear magnetic resonance shows that the protein contains three low-spin hemes (Fe(II), S = 0) in the reduced state. Electron paramagnetic resonance shows that, in the oxidized state, one of the hemes becomes high-spin (Fe(III), S = 5/2), whereas the two others remain low-spin (Fe(III), S = 1/2). The data obtained also indicate that the heme groups have distinct axial coordination. The apparent midpoint reduction potential of GSU0105 (-154 mV) is pH independent in the physiological range. However, the pH modulates the reduction potential of the heme that undergoes the low- to high-spin interconversion. The reduction potential values of cytochrome GSU0105 are more distinct compared to those of the PpcA family members, providing the protein with a larger functional working redox potential range. Overall, the results obtained, together with an amino acid sequence analysis of different multiheme cytochrome families, indicate that GSU0105 is a member of a new group of triheme cytochromes.
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9
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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10
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Adams EM, Lampret O, König B, Happe T, Havenith M. Solvent dynamics play a decisive role in the complex formation of biologically relevant redox proteins. Phys Chem Chem Phys 2020; 22:7451-7459. [PMID: 32215444 DOI: 10.1039/d0cp00267d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer processes between proteins are vital in many biological systems. Yet, the role of the solvent in influencing these redox reactions remains largely unknown. In this study, terahertz-time domain spectroscopy (THz-TDS) is used to probe the collective hydration dynamics of flavoenzyme ferredoxin-NADP+-reductase (FNR), electron transfer protein ferredoxin-1 (PetF), and the transient complex that results from their interaction. Results reveal changes in the sub-picosecond hydration dynamics that are dependent upon the surface electrostatic properties of the individual proteins and the transient complex. Retarded solvent dynamics of 8-9 ps are observed for FNR, PetF, and the FNR:PetF transient complex. Binding of the FNR:PetF complex to the substrate NADP+ results in bulk-like solvent dynamics of 7 ps, showing that formation of the ternary complex is entropically favored. Our THz measurements reveal that the electrostatic interaction of the protein surface with water results in charge sensitive changes in the solvent dynamics. Complex formation between the positively charged FNR:NADP+ pre-complex and the negatively charged PetF is not only entropically favored, but in addition the solvent reorganization into more bulk-like water assists the molecular recognition process. The change in hydration dynamics observed here suggests that the interaction with the solvent plays a significant role in mediating electron transfer processes between proteins.
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Affiliation(s)
- Ellen M Adams
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
| | - Oliver Lampret
- AG Photobiotechnologie, Ruhr Universität Bochum, 44801 Bochum, Germany
| | - Benedikt König
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
| | - Thomas Happe
- AG Photobiotechnologie, Ruhr Universität Bochum, 44801 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
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11
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Blake RC, White RA. In situ absorbance measurements: a new means to study respiratory electron transfer in chemolithotrophic microorganisms. Adv Microb Physiol 2020; 76:81-127. [PMID: 32408948 DOI: 10.1016/bs.ampbs.2020.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Absorbance measurements on intact chemolithotrophic microorganisms that respire aerobically on soluble iron are described that used a novel integrating cavity absorption meter to eliminate the effects of light scattering on the experimental results. Steady state kinetic measurements on ferric iron production by intact cells revealed that the Michaelis Menten equation described the initial rates of product formation for at least 8 different chemolithotrophic microorganisms in 6 phyla distributed equally among the archaea and the Gram negative and Gram positive eubacteria. Cell-monitored turnover measurements during aerobic respiration on soluble iron by the same 12 intact microorganisms revealed six different patterns of iron-dependent absorbance changes, suggesting that there may be at least six different sets of prosthetic groups and biomolecules that can accomplish aerobic respiration on soluble iron. Detailed kinetic studies revealed that the 3-component iron respiratory chain of Acidithiobacillus ferrooxidans functioned as an ensemble with a single macroscopic rate constant when the iron-reduced proteins were oxidized in the presence of excess molecular oxygen. The principal member of this 3-component system was a cupredoxin called rusticyanin that was present in the periplasm of At. ferrooxidans at an approximate concentration of 350 mg/mL, an observation that provides new insights into the crowded environments in the periplasms of Gram negative eubacteria that conduct electrons across their periplasm. The ability to conduct direct spectrophotometric measurements under noninvasive physiological conditions represents a new and powerful approach to examine the rates and extents of biological events in situ without disrupting the complexity of the live cellular environment.
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Affiliation(s)
- Robert C Blake
- College of Pharmacy, Xavier University of Louisiana, New Orleans, United States
| | - Richard A White
- Department of Plant Pathology, Washington State University, Pullman, WA, United States; RAW Molecular Systems (RMS) LLC, Spokane, WA, United States; Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
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12
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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13
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Strohmaier SJ, Huang W, Baek JM, Hunter DJB, Gillam EMJ. Rational evolution of the cofactor-binding site of cytochrome P450 reductase yields variants with increased activity towards specific cytochrome P450 enzymes. FEBS J 2019; 286:4473-4493. [PMID: 31276316 DOI: 10.1111/febs.14982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
NADPH-cytochrome P450 reductase (CPR) is the natural redox partner of microsomal cytochrome P450 enzymes. CPR shows a stringent preference for NADPH over the less expensive cofactor, NADH, economically limiting its use as a biocatalyst. The complexity of cofactor-linked CPR protein dynamics and the incomplete understanding of the interaction of CPR with both cofactors and electron acceptors present challenges for the successful rational engineering of a CPR with enhanced activity with NADH. Here, we report a rational evolution approach to enhance the activity of CPR with NADH, in which mutations were introduced into the NADPH-binding flavin adenine dinucleotide (FAD) domain. Multiple CPR mutants that used NADH more effectively than the wild-type CPR in the reduction of the surrogate electron acceptor, cytochrome c were found. However, most were inactive in supporting P450 activity, arguing against the use of cytochrome c as a surrogate electron acceptor. Unexpectedly, several mutants showed significantly improved activity towards CYP2C9 (mutant 1-014) and/or CYP2A6 (mutants 1-014, 1-015, 1-053 and 1-077) using NADPH, even though the mutations were introduced at locations remote from the putative CPR-P450 interaction face. Therefore, mutations at sites in the FAD domain of CPR may be promising future engineering targets to enhance P450-mediated substrate turnover. ENZYMES: NADPH-cytochrome P450 reductase - EC 1.6.2.4; cytochrome P450 - EC 1.14.14.1.
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Affiliation(s)
- Silja J Strohmaier
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Weiliang Huang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jong-Min Baek
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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14
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Ramos S, Basom EJ, Thielges MC. Conformational Change Induced by Putidaredoxin Binding to Ferrous CO-ligated Cytochrome P450cam Characterized by 2D IR Spectroscopy. Front Mol Biosci 2018; 5:94. [PMID: 30483514 PMCID: PMC6243089 DOI: 10.3389/fmolb.2018.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 11/16/2022] Open
Abstract
The importance of conformational dynamics to protein function is now well-appreciated. An outstanding question is whether they are involved in the effector role played by putidaredoxin (Pdx) in its reduction of the O2 complex of cytochrome P450cam (P450cam), an archetypical member of the cytochrome P450 superfamily. Recent studies have reported that binding of Pdx induces a conformational change from a closed to an open state of ferric P450cam, but a similar conformational change does not appear to occur for the ferrous, CO-ligated enzyme. To better understand the effector role of Pdx when binding the ferrous, CO-ligated P450cam, we applied 2D IR spectroscopy to compare the conformations and dynamics of the wild-type (wt) enzyme in the absence and presence of Pdx, as well as of L358P P450cam (L358P), which has served as a putative model for the Pdx complex. The CO vibrations of the Pdx complex and L358P report population of two conformational states in which the CO experiences distinct environments. The dynamics among the CO frequencies indicate that the energy landscape of substates within one conformation are reflective of the closed state of P450cam, and for the other conformation, differ from the free wt enzyme, but are equivalent between the Pdx complex and L358P. The two states co-populated by the Pdx complex are postulated to reflect a loosely bound encounter complex and a more tightly bound state, as is commonly observed for the dynamic complexes of redox partners. Significantly, this study shows that the binding of Pdx to ferrous, CO-ligated P450cam does perturb the conformational ensemble in a way that might underlie the effector role of Pdx.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, United States
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15
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Molecular mechanism of metabolic NAD(P)H-dependent electron-transfer systems: The role of redox cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:233-258. [PMID: 30419202 DOI: 10.1016/j.bbabio.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
NAD(P)H-dependent electron-transfer (ET) systems require three functional components: a flavin-containing NAD(P)H-dehydrogenase, one-electron carrier and metal-containing redox center. In principle, these ET systems consist of one-, two- and three-components, and the electron flux from pyridine nucleotide cofactors, NADPH or NADH to final electron acceptor follows a linear pathway: NAD(P)H → flavin → one-electron carrier → metal containing redox center. In each step ET is primarily controlled by one- and two-electron midpoint reduction potentials of protein-bound redox cofactors in which the redox-linked conformational changes during the catalytic cycle are required for the domain-domain interactions. These interactions play an effective ET reactions in the multi-component ET systems. The microsomal and mitochondrial cytochrome P450 (cyt P450) ET systems, nitric oxide synthase (NOS) isozymes, cytochrome b5 (cyt b5) ET systems and methionine synthase (MS) ET system include a combination of multi-domain, and their organizations display similarities as well as differences in their components. However, these ET systems are sharing of a similar mechanism. More recent structural information obtained by X-ray and cryo-electron microscopy (cryo-EM) analysis provides more detail for the mechanisms associated with multi-domain ET systems. Therefore, this review summarizes the roles of redox cofactors in the metabolic ET systems on the basis of one-electron redox potentials. In final Section, evolutionary aspects of NAD(P)H-dependent multi-domain ET systems will be discussed.
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16
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Gudim I, Hammerstad M, Lofstad M, Hersleth HP. The Characterization of Different Flavodoxin Reductase-Flavodoxin (FNR-Fld) Interactions Reveals an Efficient FNR-Fld Redox Pair and Identifies a Novel FNR Subclass. Biochemistry 2018; 57:5427-5436. [DOI: 10.1021/acs.biochem.8b00674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ingvild Gudim
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Oslo 0316, Norway
| | - Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Oslo 0316, Norway
| | - Marie Lofstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Oslo 0316, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Oslo 0316, Norway
- Department of Chemistry, Section for Chemical Life Sciences, University of Oslo, Oslo 0316, Norway
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17
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Dantas JM, Ferreira MR, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:619-630. [PMID: 29777686 DOI: 10.1016/j.bbabio.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 01/17/2023]
Abstract
The bacterium Geobacter sulfurreducens can transfer electrons to quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH2QDS) can also be used as energy source by G. sulfurreducens. Such bidirectional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bifunctional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH2QDS. Using stopped-flow kinetic measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13C,15N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1H heme methyl signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens.
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Affiliation(s)
- Joana M Dantas
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Marisa R Ferreira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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18
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Nathanael JG, Gamon LF, Cordes M, Rablen PR, Bally T, Fromm KM, Giese B, Wille U. Amide Neighbouring-Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer. Chembiochem 2018; 19:922-926. [PMID: 29460322 DOI: 10.1002/cbic.201800098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Indexed: 12/27/2022]
Abstract
In nature, proteins serve as media for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides. The considerably increased susceptibility of the aromatic ring to oxidation is caused by the lone pairs of neighbouring amide carbonyl groups, which stabilise the Phe radical cation. This neighbouring-amide-group effect helps improve understanding of the mechanism of extracellular electron transfer through conductive protein filaments (pili) of anaerobic bacteria during mineral respiration.
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Affiliation(s)
- Joses G Nathanael
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Luke F Gamon
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Meike Cordes
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Paul R Rablen
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA, 19081-1397, USA
| | - Thomas Bally
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700, Fribourg, Switzerland
| | - Katharina M Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700, Fribourg, Switzerland
| | - Bernd Giese
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700, Fribourg, Switzerland
| | - Uta Wille
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
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19
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Freeman SL, Martel A, Devos JM, Basran J, Raven EL, Roberts GCK. Solution structure of the cytochrome P450 reductase-cytochrome c complex determined by neutron scattering. J Biol Chem 2018; 293:5210-5219. [PMID: 29475945 PMCID: PMC5892573 DOI: 10.1074/jbc.ra118.001941] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/20/2018] [Indexed: 01/22/2023] Open
Abstract
Electron transfer in all living organisms critically relies on formation of complexes between the proteins involved. The function of these complexes requires specificity of the interaction to allow for selective electron transfer but also a fast turnover of the complex, and they are therefore often transient in nature, making them challenging to study. Here, using small-angle neutron scattering with contrast matching with deuterated protein, we report the solution structure of the electron transfer complex between cytochrome P450 reductase (CPR) and its electron transfer partner cytochrome c This is the first reported solution structure of a complex between CPR and an electron transfer partner. The structure shows that the interprotein interface includes residues from both the FMN- and FAD-binding domains of CPR. In addition, the FMN is close to the heme of cytochrome c but distant from the FAD, indicating that domain movement is required between the electron transfer steps in the catalytic cycle of CPR. In summary, our results reveal key details of the CPR catalytic mechanism, including interactions of two domains of the reductase with cytochrome c and motions of these domains relative to one another. These findings shed light on interprotein electron transfer in this system and illustrate a powerful approach for studying solution structures of protein-protein complexes.
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Affiliation(s)
- Samuel L Freeman
- From the Departments of Chemistry and.,Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom and
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Juliette M Devos
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Jaswir Basran
- From the Departments of Chemistry and.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom and.,Molecular and Cell Biology and
| | - Emma L Raven
- From the Departments of Chemistry and .,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom and
| | - Gordon C K Roberts
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom and .,Molecular and Cell Biology and
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20
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Lee CY, Reuillard B, Sokol KP, Laftsoglou T, Lockwood CWJ, Rowe SF, Hwang ET, Fontecilla-Camps JC, Jeuken LJC, Butt JN, Reisner E. A decahaem cytochrome as an electron conduit in protein-enzyme redox processes. Chem Commun (Camb) 2018; 52:7390-3. [PMID: 27193068 DOI: 10.1039/c6cc02721k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The decahaem cytochrome MtrC from Shewanella oneidensis MR-1 was employed as a protein electron conduit between a porous indium tin oxide electrode and redox enzymes. Using a hydrogenase and a fumarate reductase, MtrC was shown as a suitable and efficient diode to shuttle electrons to and from the electrode with the MtrC redox activity regulating the direction of the enzymatic reactions.
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Affiliation(s)
- Chong-Yong Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Bertrand Reuillard
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Katarzyna P Sokol
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Theodoros Laftsoglou
- School of Biomedical Sciences and the Astbury Centre, University of Leeds, Leeds, LS2 9JT, UK.
| | - Colin W J Lockwood
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Sam F Rowe
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Ee Taek Hwang
- School of Biomedical Sciences and the Astbury Centre, University of Leeds, Leeds, LS2 9JT, UK.
| | - Juan C Fontecilla-Camps
- Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 38044 Grenoble, France
| | - Lars J C Jeuken
- School of Biomedical Sciences and the Astbury Centre, University of Leeds, Leeds, LS2 9JT, UK.
| | - Julea N Butt
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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21
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Sawyer A, Winkler M. Evolution of Chlamydomonas reinhardtii ferredoxins and their interactions with [FeFe]-hydrogenases. PHOTOSYNTHESIS RESEARCH 2017; 134:307-316. [PMID: 28620699 DOI: 10.1007/s11120-017-0409-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/30/2017] [Indexed: 05/10/2023]
Abstract
Ferredoxins are soluble iron sulphur proteins which function as electron donors in a number of metabolic pathways in a broad range of organisms. In photosynthetic organisms, PETF, or ferredoxin 1 (FDX1), is the most studied ferredoxin due to its essential role in photosynthesis, where it transfers electrons from photosystem I to ferredoxin-NADP+ oxidoreductase. However, PETF can also transfer electrons to a large number of other proteins. One important PETF electron acceptor found in green microalgae is the biologically and biotechnologically important [FeFe]-hydrogenase HYDA, which catalyses the production of molecular hydrogen (H2) from protons and electrons. The interaction between PETF and HYDA is of considerable interest, as PETF is the primary electron donor to HYDA and electron supply is one of the main limiting factors for H2 production on a commercial scale. Although there is no three dimensional structure of the PETF-HYDA complex available, protein variants, nuclear magnetic resonance titration studies, molecular dynamics and modelling have provided considerable insight into the residues essential for forming and maintaining the interaction. In this review, we discuss the most recent findings with regard to ferredoxin-HYDA interactions and the evolution of the various Chlamydomonas reinhardtii ferredoxin isoforms. Finally, we provide an outlook on new PETF-based biotechnological approaches for improved H2 production efficiencies.
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Affiliation(s)
- Anne Sawyer
- Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Martin Winkler
- Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44801, Bochum, Germany.
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22
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Gentry KA, Prade E, Barnaba C, Zhang M, Mahajan M, Im SC, Anantharamaiah GM, Nagao S, Waskell L, Ramamoorthy A. Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b 5 and Cytochrome c. Sci Rep 2017; 7:7793. [PMID: 28798301 PMCID: PMC5552742 DOI: 10.1038/s41598-017-08130-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Cytochrome b5 (cytb5) is a membrane protein vital for the regulation of cytochrome P450 (cytP450) metabolism and is capable of electron transfer to many redox partners. Here, using cyt c as a surrogate for cytP450, we report the effect of membrane on the interaction between full-length cytb5 and cyt c for the first time. As shown through stopped-flow kinetic experiments, electron transfer capable cytb5 - cyt c complexes were formed in the presence of bicelles and nanodiscs. Experimentally measured NMR parameters were used to map the cytb5-cyt c binding interface. Our experimental results identify differences in the binding epitope of cytb5 in the presence and absence of membrane. Notably, in the presence of membrane, cytb5 only engaged cyt c at its lower and upper clefts while the membrane-free cytb5 also uses a distal region. Using restraints generated from both cytb5 and cyt c, a complex structure was generated and a potential electron transfer pathway was identified. These results demonstrate the importance of studying protein-protein complex formation in membrane mimetic systems. Our results also demonstrate the successful preparation of novel peptide-based lipid nanodiscs, which are detergent-free and possesses size flexibility, and their use for NMR structural studies of membrane proteins.
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Affiliation(s)
| | - Elke Prade
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlo Barnaba
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mukesh Mahajan
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama, 35294, USA
| | - Satoshi Nagao
- Graduate School of Material Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Bhatt MR, Khatri Y, Rodgers RJ, Martin LL. Role of cytochrome b5 in the modulation of the enzymatic activities of cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1). J Steroid Biochem Mol Biol 2017; 170:2-18. [PMID: 26976652 DOI: 10.1016/j.jsbmb.2016.02.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Cytochrome b5 (cyt b5) is a small hemoprotein that plays a significant role in the modulation of activities of an important steroidogenic enzyme, cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1, CYP17A1). Located in the zona fasciculata and zona reticularis of the adrenal cortex and in the gonads, P450 17A1 catalyzes two different reactions in the steroidogenic pathway; the 17α-hydroxylation and 17,20-lyase, in the endoplasmic reticulum of these respective tissues. The activities of P450 17A1 are regulated by cyt b5 that enhances the 17,20-lyase reaction by promoting the coupling of P450 17A1 and cytochrome P450 reductase (CPR), allosterically. Cyt b5 can also act as an electron donor to enhance the 16-ene-synthase activity of human P450 17A1. In this review, we discuss the many roles of cyt b5 and focus on the modulation of CYP17A1 activities by cyt b5 and the mechanisms involved.
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Affiliation(s)
- Megh Raj Bhatt
- Everest Biotech Pvt. Ltd., Khumaltar, Lalitpur, P.O. Box 21608, Kathmandu 44600, Nepal
| | - Yogan Khatri
- Institute of Biochemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Raymond J Rodgers
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide SA 5005, Australia
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Victoria, Australia.
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24
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Identification of productive and futile encounters in an electron transfer protein complex. Proc Natl Acad Sci U S A 2017; 114:E1840-E1847. [PMID: 28223532 DOI: 10.1073/pnas.1616813114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.
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25
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Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens. Biochem J 2017; 474:797-808. [DOI: 10.1042/bcj20161022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens. The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens.
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Sheu SY, Yang DY. Mechanically Controlled Electron Transfer in a Single-Polypeptide Transistor. Sci Rep 2017; 7:39792. [PMID: 28051140 PMCID: PMC5209712 DOI: 10.1038/srep39792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
Proteins are of interest in nano-bio electronic devices due to their versatile structures, exquisite functionality and specificity. However, quantum transport measurements produce conflicting results due to technical limitations whereby it is difficult to precisely determine molecular orientation, the nature of the moieties, the presence of the surroundings and the temperature; in such circumstances a better understanding of the protein electron transfer (ET) pathway and the mechanism remains a considerable challenge. Here, we report an approach to mechanically drive polypeptide flip-flop motion to achieve a logic gate with ON and OFF states during protein ET. We have calculated the transmission spectra of the peptide-based molecular junctions and observed the hallmarks of electrical current and conductance. The results indicate that peptide ET follows an NC asymmetric process and depends on the amino acid chirality and α-helical handedness. Electron transmission decreases as the number of water molecules increases, and the ET efficiency and its pathway depend on the type of water-bridged H-bonds. Our results provide a rational mechanism for peptide ET and new perspectives on polypeptides as potential candidates in logic nano devices.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences, Institute of Genome Sciences and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
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27
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Feifel SC, Stieger KR, Kapp A, Weber D, Allegrozzi M, Piccioli M, Turano P, Lisdat F. Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix. ACS OMEGA 2016; 1:1058-1066. [PMID: 30023500 PMCID: PMC6044710 DOI: 10.1021/acsomega.6b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/04/2016] [Indexed: 06/08/2023]
Abstract
The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.
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Affiliation(s)
- Sven Christian Feifel
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Kai Ralf Stieger
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Andreas Kapp
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Dennis Weber
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marco Allegrozzi
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Fred Lisdat
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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Ceccon A, Marius Clore G, Tugarinov V. Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit. JOURNAL OF BIOMOLECULAR NMR 2016; 66:1-7. [PMID: 27558624 DOI: 10.1007/s10858-016-0053-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ 2 (app) ) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k ex between the species is fast on the PRE time scale (k ex ≫ Γ2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789-5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd(3+), we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k ex ≫ Γ2) the ratio of the apparent proton to carbon methyl PREs, ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γΗ/γC)(2). However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ2 is comparable in magnitude to k ex) the ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ) ratio provides a reliable measure of the 'true' methyl PREs.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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30
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DeLoid GM, Cohen JM, Pyrgiotakis G, Pirela SV, Pal A, Liu J, Srebric J, Demokritou P. Advanced computational modeling for in vitro nanomaterial dosimetry. Part Fibre Toxicol 2015; 12:32. [PMID: 26497802 PMCID: PMC4619515 DOI: 10.1186/s12989-015-0109-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/12/2015] [Indexed: 12/27/2022] Open
Abstract
Background Accurate and meaningful dose metrics are a basic requirement for in vitro screening to assess potential health risks of engineered nanomaterials (ENMs). Correctly and consistently quantifying what cells “see,” during an in vitro exposure requires standardized preparation of stable ENM suspensions, accurate characterizatoin of agglomerate sizes and effective densities, and predictive modeling of mass transport. Earlier transport models provided a marked improvement over administered concentration or total mass, but included assumptions that could produce sizable inaccuracies, most notably that all particles at the bottom of the well are adsorbed or taken up by cells, which would drive transport downward, resulting in overestimation of deposition. Methods Here we present development, validation and results of two robust computational transport models. Both three-dimensional computational fluid dynamics (CFD) and a newly-developed one-dimensional Distorted Grid (DG) model were used to estimate delivered dose metrics for industry-relevant metal oxide ENMs suspended in culture media. Both models allow simultaneous modeling of full size distributions for polydisperse ENM suspensions, and provide deposition metrics as well as concentration metrics over the extent of the well. The DG model also emulates the biokinetics at the particle-cell interface using a Langmuir isotherm, governed by a user-defined dissociation constant, KD, and allows modeling of ENM dissolution over time. Results Dose metrics predicted by the two models were in remarkably close agreement. The DG model was also validated by quantitative analysis of flash-frozen, cryosectioned columns of ENM suspensions. Results of simulations based on agglomerate size distributions differed substantially from those obtained using mean sizes. The effect of cellular adsorption on delivered dose was negligible for KD values consistent with non-specific binding (> 1 nM), whereas smaller values (≤ 1 nM) typical of specific high-affinity binding resulted in faster and eventual complete deposition of material. Conclusions The advanced models presented provide practical and robust tools for obtaining accurate dose metrics and concentration profiles across the well, for high-throughput screening of ENMs. The DG model allows rapid modeling that accommodates polydispersity, dissolution, and adsorption. Result of adsorption studies suggest that a reflective lower boundary condition is appropriate for modeling most in vitro ENM exposures. Electronic supplementary material The online version of this article (doi:10.1186/s12989-015-0109-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Glen M DeLoid
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.
| | - Joel M Cohen
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Georgios Pyrgiotakis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Sandra V Pirela
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Anoop Pal
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Jiying Liu
- Department of Architectural Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,School of Thermal Engineering, Shandong Jianzhu University, 1000 Fengming Rd, Jinan, China
| | - Jelena Srebric
- Department of Architectural Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.
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31
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Dantas JM, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interaction studies revealed the bifunctional behavior of triheme cytochrome PpcA from Geobacter sulfurreducens toward the redox active analog of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1129-38. [DOI: 10.1016/j.bbabio.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 11/17/2022]
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32
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Larom S, Kallmann D, Saper G, Pinhassi R, Rothschild A, Dotan H, Ankonina G, Schuster G, Adir N. The Photosystem II D1-K238E mutation enhances electrical current production using cyanobacterial thylakoid membranes in a bio-photoelectrochemical cell. PHOTOSYNTHESIS RESEARCH 2015; 126:161-9. [PMID: 25588957 DOI: 10.1007/s11120-015-0075-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 01/02/2015] [Indexed: 05/12/2023]
Abstract
The conversion of solar energy (SEC) to storable chemical energy by photosynthesis has been performed by photosynthetic organisms, including oxygenic cyanobacteria for over 3 billion years. We have previously shown that crude thylakoid membranes from the cyanobacterium Synechocytis sp. PCC 6803 can reduce the electron transfer (ET) protein cytochrome c even in the presence of the PSII inhibitor DCMU. Mutation of lysine 238 of the Photosystem II D1 protein to glutamic acid increased the cytochrome reduction rates, indicating the possible position of this unknown ET pathway. In this contribution, we show that D1-K238E is rather unique, as other mutations to K238, or to other residues in the same vicinity, are not as successful in cytochrome c reduction. This observation indicates the sensitivity of ET reactions to minor changes. As the next step in obtaining useful SEC from biological material, we describe the use of crude Synechocystis membranes in a bio-photovoltaic cell containing an N-acetyl cysteine-modified gold electrode. We show the production of significant current for prolonged time durations, in the presence of DCMU. Surprisingly, the presence of cytochrome c was not found to be necessary for ET to the bio-voltaic cell.
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Affiliation(s)
- Shirley Larom
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Dan Kallmann
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Grand Technion Energy Program, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Faculty of Material Science and Engineering, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Gadiel Saper
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Grand Technion Energy Program, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Faculty of Material Science and Engineering, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Roy Pinhassi
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Grand Technion Energy Program, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Faculty of Material Science and Engineering, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Avner Rothschild
- Faculty of Material Science and Engineering, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Hen Dotan
- Faculty of Material Science and Engineering, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Guy Ankonina
- Photovoltaics Lab, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel
| | - Gadi Schuster
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel.
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, 32000, Haifa, Israel.
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33
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Li TF, Painter RG, Ban B, Blake RC. The Multicenter Aerobic Iron Respiratory Chain of Acidithiobacillus ferrooxidans Functions as an Ensemble with a Single Macroscopic Rate Constant. J Biol Chem 2015; 290:18293-303. [PMID: 26041781 PMCID: PMC4513090 DOI: 10.1074/jbc.m115.657551] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
Electron transfer reactions among three prominent colored proteins in intact cells of Acidithiobacillus ferrooxidans were monitored using an integrating cavity absorption meter that permitted the acquisition of accurate absorbance data in suspensions of cells that scattered light. The concentrations of proteins in the periplasmic space were estimated to be 350 and 25 mg/ml for rusticyanin and cytochrome c, respectively; cytochrome a was present as one molecule for every 91 nm(2) in the cytoplasmic membrane. All three proteins were rapidly reduced to the same relative extent when suspensions of live bacteria were mixed with different concentrations of ferrous ions at pH 1.5. The subsequent molecular oxygen-dependent oxidation of the multicenter respiratory chain occurred with a single macroscopic rate constant, regardless of the proteins' in vitro redox potentials or their putative positions in the aerobic iron respiratory chain. The crowded electron transport proteins in the periplasm of the organism constituted an electron conductive medium where the network of protein interactions functioned in a concerted fashion as a single ensemble with a standard reduction potential of 650 mV. The appearance of product ferric ions was correlated with the reduction levels of the periplasmic electron transfer proteins; the limiting first-order catalytic rate constant for aerobic respiration on iron was 7,400 s(-1). The ability to conduct direct spectrophotometric studies under noninvasive physiological conditions represents a new and powerful approach to examine the extent and rates of biological events in situ without disrupting the complexity of the live cellular environment.
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Affiliation(s)
- Ting-Feng Li
- From the College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
| | - Richard G Painter
- From the College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
| | - Bhupal Ban
- From the College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
| | - Robert C Blake
- From the College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
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34
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Alves MN, Neto SE, Alves AS, Fonseca BM, Carrêlo A, Pacheco I, Paquete CM, Soares CM, Louro RO. Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1. Front Microbiol 2015; 6:665. [PMID: 26175726 PMCID: PMC4484225 DOI: 10.3389/fmicb.2015.00665] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/17/2015] [Indexed: 01/14/2023] Open
Abstract
The versatile anaerobic metabolism of the Gram-negative bacterium Shewanella oneidensis MR-1 (SOMR-1) relies on a multitude of redox proteins found in its periplasm. Most are multiheme cytochromes that carry electrons to terminal reductases of insoluble electron acceptors located at the cell surface, or bona fide terminal reductases of soluble electron acceptors. In this study, the interaction network of several multiheme cytochromes was explored by a combination of NMR spectroscopy, activity assays followed by UV-visible spectroscopy and comparison of surface electrostatic potentials. From these data the small tetraheme cytochrome (STC) emerges as the main periplasmic redox shuttle in SOMR-1. It accepts electrons from CymA and distributes them to a number of terminal oxidoreductases involved in the respiration of various compounds. STC is also involved in the electron transfer pathway to reduce nitrite by interaction with the octaheme tetrathionate reductase (OTR), but not with cytochrome c nitrite reductase (ccNiR). In the main pathway leading the metal respiration STC pairs with flavocytochrome c (FccA), the other major periplasmic cytochrome, which provides redundancy in this important pathway. The data reveals that the two proteins compete for the binding site at the surface of MtrA, the decaheme cytochrome inserted on the periplasmic side of the MtrCAB-OmcA outer-membrane complex. However, this is not observed for the MtrA homologues. Indeed, neither STC nor FccA interact with MtrD, the best replacement for MtrA, and only STC is able to interact with the decaheme cytochrome DmsE of the outer-membrane complex DmsEFABGH. Overall, these results shown that STC plays a central role in the anaerobic respiratory metabolism of SOMR-1. Nonetheless, the trans-periplasmic electron transfer chain is functionally resilient as a consequence of redundancies that arise from the presence of alternative pathways that bypass/compete with STC.
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Affiliation(s)
- Mónica N Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Sónia E Neto
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Alexandra S Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Bruno M Fonseca
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Afonso Carrêlo
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Isabel Pacheco
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Catarina M Paquete
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cláudio M Soares
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo O Louro
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase fromChlamydomonas reinhardtii. Chembiochem 2015; 16:1663-9. [DOI: 10.1002/cbic.201500130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/01/2023]
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36
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Khruschev SS, Abaturova AM, Diakonova AN, Fedorov VA, Ustinin DM, Kovalenko IB, Riznichenko GY, Rubin AB. Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Insights into the role of substrates on the interaction between cytochrome b5 and cytochrome P450 2B4 by NMR. Sci Rep 2015; 5:8392. [PMID: 25687717 PMCID: PMC4330534 DOI: 10.1038/srep08392] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/16/2014] [Indexed: 01/08/2023] Open
Abstract
Mammalian cytochrome b5 (cyt b5) is a membrane-bound protein capable of donating an electron to cytochrome P450 (P450) in the P450 catalytic cycle. The interaction between cyt b5 and P450 has been reported to be affected by the substrates of P450; however, the mechanism of substrate modulation on the cyt b5-P450 complex formation is still unknown. In this study, the complexes between full-length rabbit cyt b5 and full-length substrate-free/substrate-bound cytochrome P450 2B4 (CYP2B4) are investigated using NMR techniques. Our findings reveal that the population of complexes is ionic strength dependent, implying the importance of electrostatic interactions in the complex formation process. The observation that the cyt b5-substrate-bound CYP2B4 complex shows a weaker dependence on ionic strength than the cyt b5-substrate-free CYP2B4 complex suggests the presence of a larger fraction of steoreospecific complexes when CYP2B4 is substrate-bound. These results suggest that a CYP2B4 substrate likely promotes specific interactions between cyt b5 and CYP2B4. Residues D65, V66, T70, D71 and A72 are found to be involved in specific interactions between the two proteins due to their weak response to ionic strength change. These findings provide insights into the mechanism underlying substrate modulation on the cyt b5-P450 complexation process.
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The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1305-15. [DOI: 10.1016/j.bbabio.2014.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/13/2014] [Accepted: 03/16/2014] [Indexed: 11/23/2022]
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39
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Johansson H, Jensen MR, Gesmar H, Meier S, Vinther JM, Keeler C, Hodsdon ME, Led JJ. Specific and nonspecific interactions in ultraweak protein-protein associations revealed by solvent paramagnetic relaxation enhancements. J Am Chem Soc 2014; 136:10277-86. [PMID: 24969589 PMCID: PMC4111215 DOI: 10.1021/ja503546j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Weak
and transient protein–protein interactions underlie
numerous biological processes. However, the location of the interaction
sites of the specific complexes and the effect of transient, nonspecific
protein–protein interactions often remain elusive. We have
investigated the weak self-association of human growth hormone (hGH, KD = 0.90 ± 0.03 mM) at neutral pH by the
paramagnetic relaxation enhancement (PRE) of the amide protons induced
by the soluble paramagnetic relaxation agent, gadodiamide (Gd(DTPA-BMA)).
Primarily, it was found that the PREs are in agreement with the general
Hwang-Freed model for relaxation by translational diffusion (J. Chem. Phys.1975, 63, 4017–4025),
only if crowding effects on the diffusion in the protein solution
are taken into account. Second, by measuring the PREs of the amide
protons at increasing hGH concentrations and a constant concentration
of the relaxation agent, it is shown that a distinction can be made
between residues that are affected only by transient, nonspecific
protein–protein interactions and residues that are involved
in specific protein–protein associations. Thus, the PREs of
the former residues increase linearly with the hGH concentration in
the entire concentration range because of a reduction of the diffusion
caused by the transient, nonspecific protein–protein interactions,
while the PREs of the latter residues increase only at the lower hGH
concentrations but decrease at the higher concentrations because of
specific protein–protein associations that impede the access
of gadodiamide to the residues of the interaction surface. Finally,
it is found that the ultraweak aggregation of hGH involves several
interaction sites that are located in patches covering a large part
of the protein surface.
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Affiliation(s)
- Helle Johansson
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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40
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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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41
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Schilder J, Löhr F, Schwalbe H, Ubbink M. The cytochrome c peroxidase and cytochrome c encounter complex: the other side of the story. FEBS Lett 2014; 588:1873-8. [PMID: 24726731 DOI: 10.1016/j.febslet.2014.03.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/18/2014] [Accepted: 03/26/2014] [Indexed: 11/18/2022]
Abstract
Formation of an encounter complex is important for efficient protein complex formation. The encounter state consists of an ensemble of orientations of two proteins in the complex. Experimental description of such ensembles inherently suffers from insufficient data availability. We have measured paramagnetic relaxation enhancements (PRE) on cytochrome c peroxidase (CcP) caused by its partner cytochrome c (Cc) carrying a spin label. The data complement earlier PRE data of spin labelled CcP, identifying several new interactions. This work demonstrates the need of obtaining as many independent data sets as possible to achieve the most accurate description of an encounter complex.
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Affiliation(s)
- Jesika Schilder
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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42
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Dantas JM, Morgado L, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:750-60. [PMID: 24530867 DOI: 10.1016/j.bbabio.2014.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 11/25/2022]
Abstract
The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Carlos A Salgueiro
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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43
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Guan JY, Foerster JM, Drijfhout JW, Timmer M, Blok A, Ullmann GM, Ubbink M. An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. Chembiochem 2014; 15:556-66. [DOI: 10.1002/cbic.201300623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Indexed: 12/21/2022]
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44
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Abstract
Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies establishes the parameter by which the energetic efficiency of protein electron transfer is increased relative to the standard expectations, thus minimizing losses of energy to heat. Energetically efficient electron transfer occurs in a chain of conformationally quenched cofactors and is characterized by flattened free energy surfaces, reminiscent of the flat and rugged landscape at the stability basin of a folded protein.
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Affiliation(s)
- Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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45
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Alvarez-Paggi D, Zitare U, Murgida DH. The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1196-207. [PMID: 24502917 DOI: 10.1016/j.bbabio.2014.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 01/06/2023]
Abstract
In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the CuA site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Damian Alvarez-Paggi
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Ulises Zitare
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Daniel H Murgida
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina.
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46
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Van de Water K, van Nuland NAJ, Volkov AN. Transient protein encounters characterized by paramagnetic NMR. Chem Sci 2014. [DOI: 10.1039/c4sc01232a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multiple encounters, sampled by interacting proteins in search of the dominant, functionally active orientation, are visualized by paramagnetic NMR.
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Affiliation(s)
- K. Van de Water
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - N. A. J. van Nuland
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - A. N. Volkov
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
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47
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Schilder J, Ubbink M. Formation of transient protein complexes. Curr Opin Struct Biol 2013; 23:911-8. [PMID: 23932200 DOI: 10.1016/j.sbi.2013.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 01/16/2023]
Abstract
The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron transfer complexes. Here, we describe the current methods for studying and visualizing encounter complexes. We discuss recent developments in mapping the energy landscapes, the role of hydrophobic interactions during encounter complex formation and the discovery of futile encounter complexes. These studies have not only provided insight into encounter complexes of electron transfer proteins, but also opened up new questions and approaches for studying encounter complexes in other weakly associated proteins.
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Affiliation(s)
- Jesika Schilder
- Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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48
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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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49
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Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis. Proc Natl Acad Sci U S A 2013; 110:7136-41. [PMID: 23596212 DOI: 10.1073/pnas.1302378110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins--NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin--form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins. The Ndor1-anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells.
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50
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Hervás M, Bashir Q, Leferink NGH, Ferreira P, Moreno-Beltrán B, Westphal AH, Dίaz-Moreno I, Medina M, de la Rosa MA, Ubbink M, Navarro JA, van Berkel WJH. Communication between L-galactono-1,4-lactone dehydrogenase and cytochromec. FEBS J 2013; 280:1830-40. [DOI: 10.1111/febs.12207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Physics of Complex Systems; University of Zaragoza; Spain
| | - Blas Moreno-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | | | - Irene Dίaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Physics of Complex Systems; University of Zaragoza; Spain
| | - Miguel A. de la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - José A. Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
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