1
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Ferreira MR, Morgado L, Salgueiro CA. Periplasmic electron transfer network in Geobacter sulfurreducens revealed by biomolecular interaction studies. Protein Sci 2024; 33:e5082. [PMID: 38935664 PMCID: PMC11210610 DOI: 10.1002/pro.5082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
Multiheme cytochromes located in different compartments are crucial for extracellular electron transfer in the bacterium Geobacter sulfurreducens to drive important environmental processes and biotechnological applications. Recent studies have unveiled that for particular sets of electron terminal acceptors, discrete respiratory pathways selectively recruit specific cytochromes from both the inner and outer membranes. However, such specificity was not observed for the abundant periplasmic cytochromes, namely the triheme cytochrome family PpcA-E. In this work, the distinctive NMR spectroscopic signatures of these proteins in different redox states were explored to monitor pairwise interactions and electron transfer reactions between each pair of cytochromes. The results showed that the five proteins interact transiently and can exchange electrons between each other revealing intra-promiscuity within the members of this family. This discovery is discussed in the light of the establishment of an effective electron transfer network by this pool of cytochromes. This network is advantageous to the bacteria as it enables the maintenance of the functional working potential redox range within the cells.
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Affiliation(s)
- Marisa R. Ferreira
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
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2
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Portela PC, Shipps CC, Shen C, Srikanth V, Salgueiro CA, Malvankar NS. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nat Commun 2024; 15:2434. [PMID: 38509081 PMCID: PMC10954620 DOI: 10.1038/s41467-024-46192-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
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Affiliation(s)
- Pilar C Portela
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catharine C Shipps
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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3
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Portela PC, Morgado L, Silva MA, Denkhaus L, Einsle O, Salgueiro CA. Exploring oxidative stress pathways in Geobacter sulfurreducens: the redox network between MacA peroxidase and triheme periplasmic cytochromes. Front Microbiol 2023; 14:1253114. [PMID: 37860142 PMCID: PMC10582990 DOI: 10.3389/fmicb.2023.1253114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
The recent reclassification of the strict anaerobe Geobacter sulfurreducens bacterium as aerotolerant brought attention for oxidative stress protection pathways. Although the electron transfer pathways for oxygen detoxification are not well established, evidence was obtained for the formation of a redox complex between the periplasmic triheme cytochrome PpcA and the diheme cytochrome peroxidase MacA. In the latter, the reduction of the high-potential heme triggers a conformational change that displaces the axial histidine of the low-potential heme with peroxidase activity. More recently, a possible involvement of the triheme periplasmic cytochrome family (PpcA-E) in the protection from oxidative stress in G. sulfurreducens was suggested. To evaluate this hypothesis, we investigated the electron transfer reaction and the biomolecular interaction between each PpcA-E cytochrome and MacA. Using a newly developed method that relies on the different NMR spectral signatures of the heme proteins, we directly monitored the electron transfer reaction from reduced PpcA-E cytochromes to oxidized MacA. The results obtained showed a complete electron transfer from the cytochromes to the high-potential heme of MacA. This highlights PpcA-E cytochromes' efficient role in providing the necessary reducing power to mitigate oxidative stress situations, hence contributing to a better knowledge of oxidative stress protection pathways in G. sulfurreducens.
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Affiliation(s)
- Pilar C. Portela
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta A. Silva
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Lukas Denkhaus
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
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4
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Calisto F, Todorovic S, Louro RO, Pereira MM. Exploring substrate interaction in respiratory alternative complex III from Rhodothermus marinus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148983. [PMID: 37127243 DOI: 10.1016/j.bbabio.2023.148983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
Rhodothermus marinus is a thermohalophilic organism that has optimized its microaerobic metabolism at 65 °C. We have been exploring its respiratory chain and observed the existence of a quinone:cytochrome c oxidoreductase complex, named Alternative Complex III, structurally different from the bc1 complex. In the present work, we took profit from nanodiscs and liposomes technology to investigate ACIII activity in membrane-mimicking systems. In addition, we studied the interaction of ACIII with menaquinone, its potential electron acceptors (HiPIP and cytochrome c) and the caa3 oxygen reductase.
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Affiliation(s)
- Filipa Calisto
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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5
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. Enhancing the population of the encounter complex affects protein complex formation efficiency. FEBS J 2021; 289:535-548. [PMID: 34403572 PMCID: PMC9293183 DOI: 10.1111/febs.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Optimal charge distribution is considered to be important for efficient formation of protein complexes. Electrostatic interactions guide encounter complex formation that precedes the formation of an active protein complex. However, disturbing the optimized distribution by introduction of extra charged patches on cytochrome c peroxidase does not lead to a reduction in productive encounters with its partner cytochrome c. To test whether a complex with a high population of encounter complex is more easily affected by suboptimal charge distribution, the interactions of cytochrome c mutant R13A with wild‐type cytochrome c peroxidase and a variant with an additional negative patch were studied. The complex of the peroxidase and cytochrome c R13A was reported to have an encounter state population of 80%, compared to 30% for the wild‐type cytochrome c. NMR analysis confirms the dynamic nature of the interaction and demonstrates that the mutant cytochrome c samples the introduced negative patch. Kinetic experiments show that productive complex formation is fivefold to sevenfold slower at moderate and high ionic strength values for cytochrome c R13A but the association rate is not affected by the additional negative patch on cytochrome c peroxidase, showing that the total charge on the protein surface can compensate for less optimal charge distribution. At low ionic strength (44 mm), the association with the mutant cytochrome c reaches the same high rates as found for wild‐type cytochrome c, approaching the diffusion limit.
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6
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Erv1 and Cytochrome c Mediate Rapid Electron Transfer via A Collision-Type Interaction. J Mol Biol 2021; 433:167045. [PMID: 33971209 DOI: 10.1016/j.jmb.2021.167045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Being essential for oxidative protein folding in the mitochondrial intermembrane space, the mitochondrial disulfide relay relies on the electron transfer (ET) from the sulfhydryl oxidase Erv1 to cytochrome c (Cc). Using solution NMR spectroscopy, we demonstrate that while the yeast Cc-Erv1 system is functionally active, no observable binding of the protein partners takes place. The transient interaction between Erv1 and Cc can be rationalized by molecular modeling, suggesting that a large surface area of Erv1 can sustain a fast ET to Cc via a collision-type mechanism, without the need for a canonical protein complex formation. We suggest that, by preventing the direct ET to molecular oxygen (O2), the collision-type Cc-Erv1 interaction plays a role in protecting the organism against reactive oxygen species.
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7
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Horn V, Jongkees SAK, van Ingen H. Mimicking the Nucleosomal Context in Peptide-Based Binders of a H3K36me Reader Increases Binding Affinity While Altering the Binding Mode. Molecules 2020; 25:molecules25214951. [PMID: 33114657 PMCID: PMC7662849 DOI: 10.3390/molecules25214951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/29/2022] Open
Abstract
Targeting of proteins in the histone modification machinery has emerged as a promising new direction to fight disease. The search for compounds that inhibit proteins that readout histone modification has led to several new epigenetic drugs, mostly for proteins involved in recognition of acetylated lysines. However, this approach proved to be a challenging task for methyllysine readers, which typically feature shallow binding pockets. Moreover, reader proteins of trimethyllysine K36 on the histone H3 (H3K36me3) not only bind the methyllysine but also the nucleosomal DNA. Here, we sought to find peptide-based binders of H3K36me3 reader PSIP1, which relies on DNA interactions to tightly bind H3K36me3 modified nucleosomes. We designed several peptides that mimic the nucleosomal context of H3K36me3 recognition by including negatively charged Glu-rich regions. Using a detailed NMR analysis, we find that addition of negative charges boosts binding affinity up to 50-fold while decreasing binding to the trimethyllysine binding pocket. Since screening and selection of compounds for reader domains is typically based solely on affinity measurements due to their lack of enzymatic activity, our case highlights the need to carefully control for the binding mode, in particular for the challenging case of H3K36me3 readers.
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Affiliation(s)
- Velten Horn
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502 Leiden, The Netherlands;
| | - Seino A. K. Jongkees
- Chemical Biology and Drug Discovery Group, Utrecht University, P.O. Box 80082 Utrecht, The Netherlands;
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502 Leiden, The Netherlands;
- NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-30-253-9934
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8
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020; 59:23239-23243. [PMID: 32827196 PMCID: PMC7756542 DOI: 10.1002/anie.202010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Thijmen La Haye
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands.,Present address: University of Delft, TNW Applied Sciences, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anneloes Blok
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Monika Timmer
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
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9
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome
c
Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonella Di Savino
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Johannes M. Foerster
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Thijmen La Haye
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
- Present address: University of Delft TNW Applied Sciences Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Anneloes Blok
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Monika Timmer
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - G. Matthias Ullmann
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Marcellus Ubbink
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
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10
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van Son M, Schilder JT, Di Savino A, Blok A, Ubbink M, Huber M. The Transient Complex of Cytochrome c and Cytochrome c Peroxidase: Insights into the Encounter Complex from Multifrequency EPR and NMR Spectroscopy. Chemphyschem 2020; 21:1060-1069. [PMID: 32301564 PMCID: PMC7317791 DOI: 10.1002/cphc.201901160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/03/2020] [Indexed: 12/31/2022]
Abstract
We present a novel approach to study transient protein‐protein complexes with standard, 9 GHz, and high‐field, 95 GHz, electron paramagnetic resonance (EPR) and paramagnetic NMR at ambient temperatures and in solution. We apply it to the complex of yeast mitochondrial iso‐1‐cytochrome c (Cc) with cytochrome c peroxidase (CcP) with the spin label [1‐oxyl‐2,2,5,5‐tetramethyl‐Δ3‐pyrroline‐3‐methyl)‐methanethiosulfonate] attached at position 81 of Cc (SL−Cc). A dissociation constant KD of 20±4×10−6 M (EPR and NMR) and an equal amount of stereo‐specific and encounter complex (NMR) are found. The EPR spectrum of the fully bound complex reveals that the encounter complex has a significant population (60 %) that shares important features, such as the Cc‐interaction surface, with the stereo‐specific complex.
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Affiliation(s)
- Martin van Son
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden (The, Netherlands
| | - Jesika T Schilder
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Antonella Di Savino
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Martina Huber
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden (The, Netherlands
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11
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Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR. Sci Rep 2017; 7:16462. [PMID: 29184123 PMCID: PMC5705603 DOI: 10.1038/s41598-017-16755-x] [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: 07/14/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
Bacteria utilize thermotaxis signal transduction proteins, including CheA, and CheY, to switch the direction of the cell movement. However, the thermally responsive machinery enabling warm-seeking behavior has not been identified. Here we examined the effects of temperature on the structure and dynamics of the full-length CheA and CheY complex, by NMR. Our studies revealed that the CheA-CheY complex exists in equilibrium between multiple states, including one state that is preferable for the autophosphorylation of CheA, and another state that is preferable for the phosphotransfer from CheA to CheY. With increasing temperature, the equilibrium shifts toward the latter state. The temperature-dependent population shift of the dynamic domain arrangement of the CheA-CheY complex induced changes in the concentrations of phosphorylated CheY that are comparable to those induced by chemical attractants or repellents. Therefore, the dynamic domain arrangement of the CheA-CheY complex functions as the primary thermally responsive machinery in warm-seeking behavior.
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12
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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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13
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Zhang N, An L, Li J, Liu Z, Yao L. Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment. J Am Chem Soc 2017; 139:647-654. [DOI: 10.1021/jacs.6b11058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ning Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jingwen Li
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Liu
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
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14
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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15
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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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16
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The low-affinity complex of cytochrome c and its peroxidase. Nat Commun 2015; 6:7073. [PMID: 25944250 PMCID: PMC4432590 DOI: 10.1038/ncomms8073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023] Open
Abstract
The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. The redox activity of cytochrome c in complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
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17
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Huang R, Zhang M, Rwere F, Waskell L, Ramamoorthy A. Kinetic and structural characterization of the interaction between the FMN binding domain of cytochrome P450 reductase and cytochrome c. J Biol Chem 2014; 290:4843-4855. [PMID: 25512382 DOI: 10.1074/jbc.m114.582700] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450 reductase (CPR) is a diflavin enzyme that transfers electrons to many protein partners. Electron transfer from CPR to cyt c has been extensively used as a model reaction to assess the redox activity of CPR. CPR is composed of multiple domains, among which the FMN binding domain (FBD) is the direct electron donor to cyt c. Here, electron transfer and complex formation between FBD and cyt c are investigated. Electron transfer from FBD to cyt c occurs at distinct rates that are dependent on the redox states of FBD. When compared with full-length CPR, FBD reduces cyt c at a higher rate in both the semiquinone and hydroquinone states. The NMR titration experiments reveal the formation of dynamic complexes between FBD and cyt c on a fast exchange time scale. Chemical shift mapping identified residues of FBD involved in the binding interface with cyt c, most of which are located in proximity to the solvent-exposed edge of the FMN cofactor along with other residues distributed around the surface of FBD. The structural model of the FBD-cyt c complex indicates two possible orientations of complex formation. The major complex structure shows a salt bridge formation between Glu-213/Glu-214 of FBD and Lys-87 of cyt c, which may be essential for the formation of the complex, and a predicted electron transfer pathway mediated by Lys-13 of cyt c. The findings provide insights into the function of CPR and CPR-cyt c interaction on a structural basis.
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Affiliation(s)
- Rui Huang
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Meng Zhang
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Freeborn Rwere
- Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and.
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18
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Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014; 281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Navraj S. Pannu
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
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19
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Merloni A, Dobrovolska O, Zambelli B, Agostini F, Bazzani M, Musiani F, Ciurli S. Molecular landscape of the interaction between the urease accessory proteins UreE and UreG. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1662-74. [PMID: 24982029 DOI: 10.1016/j.bbapap.2014.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/12/2014] [Accepted: 06/19/2014] [Indexed: 01/07/2023]
Abstract
Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9μM; Kd2=1.7±0.3μM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed.
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Affiliation(s)
- Anna Merloni
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Olena Dobrovolska
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Federico Agostini
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Micaela Bazzani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.
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20
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Paquete CM, Fonseca BM, Cruz DR, Pereira TM, Pacheco I, Soares CM, Louro RO. Exploring the molecular mechanisms of electron shuttling across the microbe/metal space. Front Microbiol 2014; 5:318. [PMID: 25018753 PMCID: PMC4073285 DOI: 10.3389/fmicb.2014.00318] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 06/10/2014] [Indexed: 11/27/2022] Open
Abstract
Dissimilatory metal reducing organisms play key roles in the biogeochemical cycle of metals as well as in the durability of submerged and buried metallic structures. The molecular mechanisms that support electron transfer across the microbe-metal interface in these organisms remain poorly explored. It is known that outer membrane proteins, in particular multiheme cytochromes, are essential for this type of metabolism, being responsible for direct and indirect, via electron shuttles, interaction with the insoluble electron acceptors. Soluble electron shuttles such as flavins, phenazines, and humic acids are known to enhance extracellular electron transfer. In this work, this phenomenon was explored. All known outer membrane decaheme cytochromes from Shewanella oneidensis MR-1 with known metal terminal reductase activity and a undecaheme cytochrome from Shewanella sp. HRCR-6 were expressed and purified. Their interactions with soluble electron shuttles were studied using stopped-flow kinetics, NMR spectroscopy, and molecular simulations. The results show that despite the structural similarities, expected from the available structural data and sequence homology, the detailed characteristics of their interactions with soluble electron shuttles are different. MtrC and OmcA appear to interact with a variety of different electron shuttles in the close vicinity of some of their hemes, and with affinities that are biologically relevant for the concentrations typical found in the medium for this type of compounds. All data support a view of a distant interaction between the hemes of MtrF and the electron shuttles. For UndA a clear structural characterization was achieved for the interaction with AQDS a humic acid analog. These results provide guidance for future work of the manipulation of these proteins toward modulation of their role in metal attachment and reduction.
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Affiliation(s)
- Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Bruno M Fonseca
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Davide R Cruz
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Tiago M Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Isabel Pacheco
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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21
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Martínez-Fábregas J, Díaz-Moreno I, González-Arzola K, Janocha S, Navarro JA, Hervás M, Bernhardt R, Velázquez-Campoy A, Díaz-Quintana A, De la Rosa MA. Structural and functional analysis of novel human cytochrome C targets in apoptosis. Mol Cell Proteomics 2014; 13:1439-56. [PMID: 24643968 DOI: 10.1074/mcp.m113.034322] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Since the first description of apoptosis four decades ago, great efforts have been made to elucidate, both in vivo and in vitro, the molecular mechanisms involved in its regulation. Although the role of cytochrome c during apoptosis is well established, relatively little is known about its participation in signaling pathways in vivo due to its essential role during respiration. To obtain a better understanding of the role of cytochrome c in the onset of apoptosis, we used a proteomic approach based on affinity chromatography with cytochrome c as bait in this study. In this approach, novel cytochrome c interaction partners were identified whose in vivo interaction and cellular localization were facilitated through bimolecular fluorescence complementation. Modeling of the complex interface between cytochrome c and its counterparts indicated the involvement of the surface surrounding the heme crevice of cytochrome c, in agreement with the vast majority of known redox adducts of cytochrome c. However, in contrast to the high turnover rate of the mitochondrial cytochrome c redox adducts, those occurring under apoptosis led to the formation of stable nucleo-cytoplasmic ensembles, as inferred mainly from surface plasmon resonance and nuclear magnetic resonance measurements, which permitted us to corroborate the formation of such complexes in vitro. The results obtained suggest that human cytochrome c interacts with pro-survival, anti-apoptotic proteins following its release into the cytoplasm. Thus, cytochrome c may interfere with cell survival pathways and unlock apoptosis in order to prevent the spatial and temporal coexistence of antagonist signals.
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Affiliation(s)
- Jonathan Martínez-Fábregas
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Katiuska González-Arzola
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Simon Janocha
- §Institut für Biochemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany
| | - José A Navarro
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Manuel Hervás
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Rita Bernhardt
- §Institut für Biochemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany
| | - Adrián Velázquez-Campoy
- ¶Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint-Unit IQFR-CSIC-BIFI, Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain, and Fundacion ARAID, Government of Aragon, Zaragoza, Spain
| | - Antonio Díaz-Quintana
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Miguel A De la Rosa
- From the ‡Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain;
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22
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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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23
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Williamson MP. Using chemical shift perturbation to characterise ligand binding. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 73:1-16. [PMID: 23962882 DOI: 10.1016/j.pnmrs.2013.02.001] [Citation(s) in RCA: 939] [Impact Index Per Article: 85.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 02/12/2013] [Accepted: 02/18/2013] [Indexed: 05/05/2023]
Abstract
Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by simultaneous fitting of many measured shift changes, or more simply by adding substoichiometric amounts of ligand. The chemical shift changes can be used as restraints for docking ligand onto protein. By use of quantitative calculations of ligand-induced chemical shift changes, it is becoming possible to determine not just the position but also the orientation of ligands.
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Affiliation(s)
- Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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24
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Guan JY, Keizers PHJ, Liu WM, Löhr F, Skinner SP, Heeneman EA, Schwalbe H, Ubbink M, Siegal G. Small-molecule binding sites on proteins established by paramagnetic NMR spectroscopy. J Am Chem Soc 2013; 135:5859-68. [PMID: 23509882 DOI: 10.1021/ja401323m] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the three-dimensional structure of a small molecule-protein complex with weak affinity can be a significant challenge. We present a paramagnetic NMR method to determine intermolecular structure restraints based on pseudocontact shifts (PCSs). Since the ligand must be in fast exchange between free and bound states and the fraction bound can be as low as a few percent, the method is ideal for ligands with high micromolar to millimolar dissociation constants. Paramagnetic tags are attached, one at a time, in a well-defined way via two arms at several sites on the protein surface. The ligand PCSs were measured from simple 1D (1)H spectra and used as docking restraints. An independent confirmation of the complex structure was carried out using intermolecular NOEs. The results show that structures derived from these two approaches are similar. The best results are obtained if the magnetic susceptibility tensors of the tags are known, but it is demonstrated that with two-armed probes, the magnetic susceptibility tensor can be predicted with sufficient accuracy to provide a low-resolution model of the ligand orientation and the location of the binding site in the absence of isotope-labeled protein. This approach can facilitate fragment-based drug discovery in obtaining structural information on the initial fragment hits.
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Affiliation(s)
- Jia-Ying Guan
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands
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25
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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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26
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Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1. Biochem J 2012; 449:101-8. [DOI: 10.1042/bj20121467] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular electron transfer is the key metabolic trait that enables some bacteria to play a significant role in the biogeochemical cycling of metals and in bioelectrochemical devices such as microbial fuel cells. In Shewanella oneidensis MR-1, electrons generated in the cytoplasm by catabolic processes must cross the periplasmic space to reach terminal oxidoreductases found at the cell surface. Lack of knowledge on how these electrons flow across the periplasmic space is one of the unresolved issues related with extracellular electron transfer. Using NMR to probe protein–protein interactions, kinetic measurements of electron transfer and electrostatic calculations, we were able to identify protein partners and their docking sites, and determine the dissociation constants. The results showed that both STC (small tetrahaem cytochrome c) and FccA (flavocytochrome c) interact with their redox partners, CymA and MtrA, through a single haem, avoiding the establishment of stable redox complexes capable of spanning the periplasmic space. Furthermore, we verified that the most abundant periplasmic cytochromes STC, FccA and ScyA (monohaem cytochrome c5) do not interact with each other and this is likely to be the consequence of negative surface charges in these proteins. This reveals the co-existence of two non-mixing redox pathways that lead to extracellular electron transfer in S. oneidensis MR-1 established through transient protein interactions.
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27
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Shan J, Zhang X, Bao J, Cassell R, Zheng JJ. Synthesis of potent dishevelled PDZ domain inhibitors guided by virtual screening and NMR studies. Chem Biol Drug Des 2012; 79:376-83. [PMID: 22172211 DOI: 10.1111/j.1747-0285.2011.01295.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dishevelled (Dvl) PDZ domains transduce Wnt signals from the membrane-bound receptor Frizzled to the downstream. As abnormal Wnt signaling has been implicated in tumorigenesis, the Dvl PDZ domain is a potential target for small-molecule inhibitors that block Wnt signaling at the Dvl level. We expanded our in silico search to examine the chemical space near previously developed PDZ binders and identified nine additional compounds bind to the Dvl PDZ. We then performed a quantitative structure-activity relationship (QSAR) analysis of these compounds and combined these results with structural studies of the PDZ domain in complex with the compounds to design and synthesize a group of new, further optimized compounds. Two rounds of synthesis and testing yielded a total of six compounds that have greatly improved binding affinity to the Dvl PDZ domain and most potent ones competitively displace Dapper peptide from the PDZ domain. In addition to providing more potent Dvl PDZ domain inhibitors, this study demonstrates that virtual screening and structural studies can be powerful tools in guiding the chemical synthesis hit-to-lead optimization stage during the drug discovery process.
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Affiliation(s)
- Jufang Shan
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Shan J, Zheng JJ. Virtual ligand screening combined with NMR to identify Dvl PDZ domain inhibitors targeting the Wnt signaling. Methods Mol Biol 2012; 928:17-28. [PMID: 22956130 PMCID: PMC3964848 DOI: 10.1007/978-1-62703-008-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Virtual ligand screening is a powerful technique to identify potential hits of targets and to increase hit rates. Here, we describe how we used this technique combined with NMR (15)N HSQC experiments to obtain small molecules that bind to the PDZ domain of Dvl targeting the Wnt signaling pathway.
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Cytochrome c signalosome in mitochondria. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1301-15. [DOI: 10.1007/s00249-011-0774-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/12/2011] [Accepted: 10/21/2011] [Indexed: 10/15/2022]
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Lederer F. Another look at the interaction between mitochondrial cytochrome c and flavocytochrome b (2). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1283-99. [PMID: 21503671 DOI: 10.1007/s00249-011-0697-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/28/2011] [Accepted: 03/16/2011] [Indexed: 11/29/2022]
Abstract
Yeast flavocytochrome b (2) tranfers reducing equivalents from lactate to oxygen via cytochrome c and cytochrome c oxidase. The enzyme catalytic cycle includes FMN reduction by lactate and reoxidation by intramolecular electron transfer to heme b (2). Each subunit of the soluble tetrameric enzyme consists of an N terminal b (5)-like heme-binding domain and a C terminal flavodehydrogenase. In the crystal structure, FMN and heme are face to face, and appear to be in a suitable orientation and at a suitable distance for exchanging electrons. But in one subunit out of two, the heme domain is disordered and invisible. This raises a central question: is this mobility required for interaction with the physiological acceptor cytochrome c, which only receives electrons from the heme and not from the FMN? The present review summarizes the results of the variety of methods used over the years that shed light on the interactions between the flavin and heme domains and between the enzyme and cytochrome c. The conclusion is that one should consider the interaction between the flavin and heme domains as a transient one, and that the cytochrome c and the flavin domain docking areas on the heme b (2) domain must overlap at least in part. The heme domain mobility is an essential component of the flavocytochrome b (2) functioning. In this respect, the enzyme bears similarity to a variety of redox enzyme systems, in particular those in which a cytochrome b (5)-like domain is fused to proteins carrying other redox functions.
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Affiliation(s)
- Florence Lederer
- Laboratoire de Chimie Physique, Université Paris-Sud, Orsay Cedex, France.
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Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J Am Chem Soc 2010; 132:11487-95. [PMID: 20672804 DOI: 10.1021/ja100867c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent experimental studies have confirmed a long-held view that protein complex formation proceeds via a short-lived encounter state. The population of this transient intermediate, stabilized mainly by long-range electrostatic interactions, varies among different complexes. Here we show that the occupancy of the encounter state can be modulated across a broad range by single point mutations of interfacial residues. Using a combination of Monte Carlo simulations and paramagnetic relaxation enhancement NMR spectroscopy, we illustrate that it is possible to both enhance and diminish the binding specificity in an electron transfer complex of yeast cytochrome c (Cc) and cytochrome c peroxidase. The Cc T12A mutation decreases the population of the encounter to 10% as compared with 30% in the wild-type complex. More dramatically, the Cc R13A substitution reverses the relative occupancies of the stereospecific and the encounter forms, with the latter now being the dominant species with the population of 80%. This finding indicates that the encounter state can make a large contribution to the stability of a protein complex. Also, it appears that by adjusting the amount of the encounter through a judicious choice of point mutations, we can remodel the energy landscape of a protein complex and tune its binding specificity.
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Meschi F, Wiertz F, Klauss L, Cavalieri C, Blok A, Ludwig B, Heering HA, Merli A, Rossi GL, Ubbink M. Amicyanin Transfers Electrons from Methylamine Dehydrogenase to Cytochrome c-551i via a Ping-Pong Mechanism, not a Ternary Complex. J Am Chem Soc 2010; 132:14537-45. [DOI: 10.1021/ja105498m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Francesca Meschi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Frank Wiertz
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Linda Klauss
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Chiara Cavalieri
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Anneloes Blok
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Bernd Ludwig
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Hendrik A. Heering
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Angelo Merli
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Gian Luigi Rossi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
| | - Marcellus Ubbink
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, and Institute of Biochemistry, Molecular Genetics Group, and Cluster of Excellence Macromolecular Complexes, Goethe University, D-60438 Frankfurt, Germany
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Xu X, Scanu S, Chung JS, Hirasawa M, Knaff DB, Ubbink M. Structural and functional characterization of the ga-substituted ferredoxin from Synechocystis sp. PCC6803, a mimic of the native protein. Biochemistry 2010; 49:7790-7. [PMID: 20690702 DOI: 10.1021/bi100712g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosynthetic organisms, ferredoxin (Fd) interacts with many proteins, acting as a shuttle for electrons from Photosystem I to a group of enzymes involved in NADP(+) reduction, sulfur and nitrogen assimilation, and the regulation of carbon assimilation. The study of the dynamic interactions between ferredoxin and these enzymes by nuclear magnetic resonance is severely hindered by the paramagnetic [2Fe-2S] cluster of a ferredoxin. To establish whether ferredoxin in which the cluster has been replaced by Ga is a suitable diamagnetic mimic, the solution structure of Synechocystis Ga-substituted ferredoxin has been determined and compared with the structure of the native protein. The ensemble of 10 structures with the lowest energies has an average root-mean-square deviation of 0.30 +/- 0.05 A for backbone atoms and 0.65 +/- 0.04 A for all heavy atoms. Comparison of the NMR structure of GaFd with the crystal structure of the native Fd indicates that the general structural fold found for the native, iron-containing ferredoxin is conserved in GaFd. The ferredoxin contains a single gallium and no inorganic sulfide. The distortion of the metal binding loop caused by the single gallium substitution is small. The binding site on Fd for binding ferredoxin:NADP(+) reductase in solution, determined using GaFd, includes the metal binding loop and its surroundings, consistent with the crystal structures of related complexes. The results provide a structural justification for the use of the gallium-substituted analogue in interaction studies.
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Affiliation(s)
- Xingfu Xu
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Keizers PHJ, Mersinli B, Reinle W, Donauer J, Hiruma Y, Hannemann F, Overhand M, Bernhardt R, Ubbink M. A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy. Biochemistry 2010; 49:6846-55. [PMID: 20695524 DOI: 10.1021/bi100598f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lanthanide tags offer the opportunity to retrieve long-range distance information from NMR experiments that can be used to guide protein docking. To determine whether sufficient restraints can be retrieved for proteins with low solubility and availability, Ln tags were applied in the study of the 65 kDa membrane-associated protein complex formed by the electron carrier adrenodoxin and its electron donor, adrenodoxin reductase. The reductase is only monomeric at low concentration, and the paramagnetic iron-sulfur cluster of adrenodoxin broadens many of the resonances of nuclei in the interface. Guided by the paramagnetic restraints obtained using two Ln-tag attachment sites, protein docking yields a cluster of solutions with an rmsd of 3.2 A. The mean structure is close to the crystal structure of the cross-linked complex, with an rmsd of 4.0 A. It is concluded that with the application of Ln tags paramagnetic NMR restraints for structure determination can be retrieved even for difficult, low-concentration protein complexes.
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Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Ewen KM, Kleser M, Bernhardt R. Adrenodoxin: the archetype of vertebrate-type [2Fe-2S] cluster ferredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:111-25. [PMID: 20538075 DOI: 10.1016/j.bbapap.2010.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/15/2022]
Abstract
Adrenodoxin is probably the best characterized member of the vertebrate-type [2Fe-2S]-cluster ferredoxins. It has been in the spotlight of scientific interest for many years due to its essential role in mammalian steroid hormone biosynthesis, where it acts as electron mediator between the NADPH-dependent adrenodoxin reductase and several mitochondrial cytochromes P450. In this review we will focus on the present knowledge about protein-protein recognition in the mitochondrial cytochrome P450 system and the modulation of the electron transfer between Adx and its redox partners, AdR and CYP(s). We also intend to point out the potential biotechnological applications of Adx as a versatile electron donor to different cytochromes P450, both in vitro and in vivo. Finally we will address the comparison between the mammalian cytochrome P450-associated adrenodoxin and ferredoxins involved in iron-sulfur-cluster biosynthesis. Despite their different functions, these proteins display an amazing similarity regarding their primary sequence, tertiary structure and biophysical features.
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Affiliation(s)
- Kerstin Maria Ewen
- Department of Biochemistry, Saarland University, D-66041 Saarbrücken, Germany
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Bashir Q, Volkov AN, Ullmann GM, Ubbink M. Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase. J Am Chem Soc 2010; 132:241-7. [PMID: 19961227 DOI: 10.1021/ja9064574] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We use paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize the ensemble of encounter orientations in the short-lived electron transfer complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). The complete conformational space sampled by the protein molecules during the dynamic part of the interaction was mapped experimentally. The encounter complex was described by an electrostatic ensemble of orientations based on Monte Carlo calculations, considering the protein structures in atomic detail. We demonstrate that this visualization of the encounter complex, in combination with the specific complex, is in excellent agreement with the experimental data. Our results indicate that Cc samples only about 15% of the surface area of CcP, surrounding the specific binding interface. The encounter complex is populated for 30% of the time, representing a mere 0.5 kcal/mol difference in the free energies between the two states. This delicate balance is interpreted to be a consequence of the conflicting requirements of fast electron transfer and high turnover of the complex.
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Affiliation(s)
- Qamar Bashir
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Pepelina TY, Chertkova RV, Dolgikh DA, Kirpichnikov MP. The role of individual lysine residues of horse cytochrome c in the formation of reactive complexes with components of the respiratory chain. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:98-104. [DOI: 10.1134/s1068162010010097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Frago S, Lans I, Navarro JA, Hervás M, Edmondson DE, De la Rosa MA, Gómez-Moreno C, Mayhew SG, Medina M. Dual role of FMN in flavodoxin function: electron transfer cofactor and modulation of the protein-protein interaction surface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:262-71. [PMID: 19900400 DOI: 10.1016/j.bbabio.2009.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/29/2009] [Accepted: 10/30/2009] [Indexed: 10/20/2022]
Abstract
Flavodoxin (Fld) replaces Ferredoxin (Fd) as electron carrier from Photosystem I (PSI) to Ferredoxin-NADP(+) reductase (FNR). A number of Anabaena Fld (AnFld) variants with replacements at the interaction surface with FNR and PSI indicated that neither polar nor hydrophobic residues resulted critical for the interactions, particularly with FNR. This suggests that the solvent exposed benzenoid surface of the Fld FMN cofactor might contribute to it. FMN has been replaced with analogues in which its 7- and/or 8-methyl groups have been replaced by chlorine and/or hydrogen. The oxidised Fld variants accept electrons from reduced FNR more efficiently than Fld, as expected from their less negative midpoint potential. However, processes with PSI (including reduction of Fld semiquinone by PSI, described here for the first time) are impeded at the steps that involve complex re-arrangement and electron transfer (ET). The groups introduced, particularly chlorine, have an electron withdrawal effect on the pyrazine and pyrimidine rings of FMN. These changes are reflected in the magnitude and orientation of the molecular dipole moment of the variants, both factors appearing critical for the re-arrangement of the finely tuned PSI:Fld complex. Processes with FNR are also slightly modulated. Despite the displacements observed, the negative end of the dipole moment points towards the surface that contains the FMN, still allowing formation of complexes competent for efficient ET. This agrees with several alternative binding modes in the FNR:Fld interaction. In conclusion, the FMN in Fld not only contributes to the redox process, but also to attain the competent interaction of Fld with FNR and PSI.
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Affiliation(s)
- Susana Frago
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems (BIFI). Universidad de Zaragoza, 50009 Zaragoza, Spain
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40
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Medina M. Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+. FEBS J 2009; 276:3942-58. [PMID: 19583765 DOI: 10.1111/j.1742-4658.2009.07122.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This minireview covers the research carried out in recent years into different aspects of the function of the flavoproteins involved in cyanobacterial photosynthetic electron transfer from photosystem I to NADP(+), flavodoxin and ferredoxin-NADP(+) reductase. Interactions that stabilize protein-flavin complexes and tailor the midpoint potentials in these proteins, as well as many details of the binding and electron transfer to protein and ligand partners, have been revealed. In addition to their role in photosynthesis, flavodoxin and ferredoxin-NADP(+) reductase are ubiquitous flavoenzymes that deliver NAD(P)H or low midpoint potential one-electron donors to redox-based metabolisms in plastids, mitochondria and bacteria. They are also the basic prototypes for a large family of diflavin electron transferases with common functional and structural properties. Understanding their mechanisms should enable greater comprehension of the many physiological roles played by flavodoxin and ferredoxin-NADP(+) reductase, either free or as modules in multidomain proteins. Many aspects of their biochemistry have been extensively characterized using a combination of site-directed mutagenesis, steady-state and transient kinetics, spectroscopy and X-ray crystallography. Despite these considerable advances, various key features of the structural-function relationship are yet to be explained in molecular terms. Better knowledge of these systems and their particular properties may allow us to envisage several interesting applications of these proteins beyond their physiological functions.
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Affiliation(s)
- Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular and BFIF, Universidad de Zaragoza, Spain.
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41
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Xu X, Keizers PHJ, Reinle W, Hannemann F, Bernhardt R, Ubbink M. Intermolecular dynamics studied by paramagnetic tagging. JOURNAL OF BIOMOLECULAR NMR 2009; 43:247-54. [PMID: 19274444 DOI: 10.1007/s10858-009-9308-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 02/23/2009] [Indexed: 05/15/2023]
Abstract
Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media.
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Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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42
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The courtship of proteins: Understanding the encounter complex. FEBS Lett 2009; 583:1060-6. [DOI: 10.1016/j.febslet.2009.02.046] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 02/25/2009] [Accepted: 02/27/2009] [Indexed: 11/15/2022]
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Goñi G, Herguedas B, Hervás M, Peregrina JR, De la Rosa MA, Gómez-Moreno C, Navarro JA, Hermoso JA, Martínez-Júlvez M, Medina M. Flavodoxin: a compromise between efficiency and versatility in the electron transfer from Photosystem I to Ferredoxin-NADP(+) reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1787:144-54. [PMID: 19150326 DOI: 10.1016/j.bbabio.2008.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 12/01/2008] [Accepted: 12/09/2008] [Indexed: 11/18/2022]
Abstract
Under iron-deficient conditions Flavodoxin (Fld) replaces Ferredoxin in Anabaena as electron carrier from Photosystem I (PSI) to Ferredoxin-NADP(+) reductase (FNR). Several residues modulate the Fld interaction with FNR and PSI, but no one appears as specifically critical for efficient electron transfer (ET). Fld shows a strong dipole moment, with its negative end directed towards the flavin ring. The role of this dipole moment in the processes of interaction and ET with positively charged surfaces exhibited by PSI and FNR has been analysed by introducing single and multiple charge reversal mutations on the Fld surface. Our data confirm that in this system interactions do not rely on a precise complementary surface of the reacting molecules. In fact, they indicate that the initial orientation driven by the alignment of dipole moment of the Fld molecule with that of the partner contributes to the formation of a bunch of alternative binding modes competent for the efficient ET reaction. Additionally, the fact that Fld uses different interaction surfaces to dock to PSI and to FNR is confirmed.
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Affiliation(s)
- Guillermina Goñi
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009-Zaragoza, Spain
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Petoukhov MV, Vicente JB, Crowley PB, Carrondo MA, Teixeira M, Svergun DI. Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering. Structure 2008; 16:1428-36. [PMID: 18786405 DOI: 10.1016/j.str.2008.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 06/01/2008] [Accepted: 06/03/2008] [Indexed: 10/21/2022]
Abstract
Flavodiiron proteins (FDP) are modular enzymes which function as NO and/or O(2) reductases. Although the majority is composed of two structural domains, the homolog found in Escherichia coli, flavorubredoxin, possesses an extra C-terminal module consisting of a linker and a rubredoxin (Rd) domain necessary for interprotein redox processes. In order to investigate the location of the Rd domain with respect to the flavodiiron structural core, small-angle X-ray scattering was used to construct low-resolution structural models of flavorubredoxin. Scattering patterns from the Rd domain, the FDP core, and full-length flavorubredoxin were collected. The latter two species were found to be tetrameric in solution. Ab initio shape reconstruction and rigid-body modeling indicate a peripheral location for the Rd domains, which appear to have weak contacts with the FDP core. This finding suggests that Rd behaves as an independent domain and is freely available to participate in redox reactions with protein partners.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
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45
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Volkov AN, Bashir Q, Worrall JAR, Ubbink M. Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome C and cytochrome C peroxidase. J Mol Biol 2008; 385:1003-13. [PMID: 19026661 DOI: 10.1016/j.jmb.2008.10.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/16/2008] [Accepted: 10/30/2008] [Indexed: 10/21/2022]
Abstract
Transient protein interactions mediate many vital cellular processes such as signal transduction or intermolecular electron transfer. However, due to difficulties associated with their structural characterization, little is known about the principles governing recognition and binding in weak transient protein complexes. In particular, it has not been well established whether binding hot spots, which are frequently found in strong static complexes, also govern transient protein interactions. To address this issue, we have investigated an electron transfer complex of physiological partners from yeast: yeast iso-1-cytochrome c (Cc) and yeast cytochrome c peroxidase (CcP). Using isothermal titration calorimetry and NMR spectroscopy, we show that Cc R13 is a hot-spot residue, as R13A mutation has a strong destabilizing effect on binding. Furthermore, we employ a double-mutant cycle to illustrate that Cc R13 interacts with CcP Y39. The present results, in combination with those of earlier mutational studies, have enabled us to outline the extent of the energetically important Cc-CcP binding region. Based on our analysis, we propose that binding energy hot spots, which are prevalent in static protein complexes, could also govern transient protein interactions.
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Affiliation(s)
- Alexander N Volkov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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Shan J, Zheng JJ. Optimizing Dvl PDZ domain inhibitor by exploring chemical space. J Comput Aided Mol Des 2008; 23:37-47. [PMID: 18780146 DOI: 10.1007/s10822-008-9236-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 08/08/2008] [Indexed: 10/21/2022]
Abstract
Because of advances in the high-throughput screening technology, identification of a hit that can bind to a target protein has become a relatively easy task; however, in the process of drug discovery, the following hit-to-lead and lead optimization still remain challenging. In a typical hit-to-lead and lead optimization process, the analogues of the most promising hits are synthesized for the development of structure-activity relationship (SAR) analysis, and in turn, in the effort of optimization of lead compounds, such analysis provides guidance for the further synthesis. The synthesis processes are usually long and labor-intensive. In silico searching has becoming an alternative approach to explore SAR especially with millions of compounds ready to be screened and most of them can be easily obtained. Here, we report our discovery of 15 new Dishevelled PDZ domain inhibitors by using such an approach. In our studies, we first developed a pharmacophore model based on NSC668036, an inhibitor previously identified in our laboratory; based on the model, we then screened the ChemDiv database by using an algorithm that combines similarity search and docking procedures; finally, we selected potent inhibitors based on docking analysis and examined them by using NMR spectroscopy. NMR experiments showed that all the 15 compounds we chose bound to the PDZ domain tighter than NSC668036.
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Affiliation(s)
- Jufang Shan
- Department of Structural Biology, St. Jude Children's Research Hospital, 322 N. Lauderdale St., MS #311, Memphis, TN 38105, USA
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Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins 2008; 72:848-62. [PMID: 18260112 DOI: 10.1002/prot.21979] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ferredoxin (Fd) interacts with ferredoxin-NADP(+) reductase (FNR) to transfer two electrons to the latter, one by one, which will finally be used to reduce NADP(+) to NADPH. The formation of a transient complex between Fd and FNR is required for the electron transfer (ET), and extensive mutational and crystallographic studies have been reported to characterize such protein-protein interaction. However, some aspects of the association mechanism still remain unclear. Moreover, in spite of their structural differences, flavodoxin (Fld) can replace Fd in its function and interact with FNR to transfer electrons with only slightly lower efficiency. Although crystallographic structures for the FNR:Fd association have been reported, experimental structural data for the FNR:Fld interaction are highly elusive. We have modeled here the interactions between FNR and both of its protein partners, Fd and Fld, using surface energy analysis, computational rigid-body docking simulations, and interface side-chain refinement. The results, consistent with previous experimental data, suggest the existence of alternative binding modes in these ET proteins.
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Affiliation(s)
- Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
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48
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Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cavalieri C, Biermann N, Vlasie MD, Einsle O, Merli A, Ferrari D, Rossi GL, Ubbink M. Structural Comparison of Crystal and Solution States of the 138 kDa Complex of Methylamine Dehydrogenase and Amicyanin from Paracoccus versutus. Biochemistry 2008; 47:6560-70. [DOI: 10.1021/bi7023749] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chiara Cavalieri
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Nikolai Biermann
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Monica D. Vlasie
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Oliver Einsle
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Angelo Merli
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Davide Ferrari
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gian Luigi Rossi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany, and Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Crowley PB, Ganji P, Ibrahim H. Protein Surface Recognition: Structural Characterisation of Cytochrome c–Porphyrin Complexes. Chembiochem 2008; 9:1029-33. [DOI: 10.1002/cbic.200700736] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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