1
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Leader DP, Milner-White EJ. The conserved crown bridge loop at the catalytic centre of enzymes of the haloacid dehalogenase superfamily. Curr Res Struct Biol 2023; 6:100105. [PMID: 37786806 PMCID: PMC10541634 DOI: 10.1016/j.crstbi.2023.100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/04/2023] Open
Abstract
The crown bridge loop is hexapeptide motif in which the backbone carbonyl group at position 1 is hydrogen bonded to the backbone imino groups of positions 4 and 6. Residues at positions 1 and 4-6 are held in a tight substructure, but different orientations of the plane of the peptide bond between positions 2 and 3 result in two conformers: the 2,3-αRαR crown bridge loop - found in approximately 7% of proteins - and the 2,3-βRαL crown bridge loop, found in approximately 1-2% of proteins. We constructed a relational database in which we identified 60 instances of the 2,3-βRαL conformer, and find that about half occur in enzymes of the haloacid dehalogenase (HAD) superfamily, where they are located next to the catalytic aspartate residue. Analysis of additional enzymes of the HAD superfamily in the extensive SCOPe dataset showed this crown bridge loop to be a conserved feature. Examination of available structures showed that the 2,3-βRαL conformation - but not the 2,3-αRαR conformation - allows the backbone carbonyl group at position 2 to interact with the essential Mg2+ ion. The possibility of interconversion between the 2,3-βRαL and 2,3-αRαR conformations during catalysis is discussed.
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Affiliation(s)
- David P. Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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2
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Galuzzi BG, Mirarchi A, Viganò EL, De Gioia L, Damiani C, Arrigoni F. Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J Chem Inf Model 2022; 62:4748-4759. [PMID: 36126254 PMCID: PMC9554915 DOI: 10.1021/acs.jcim.2c00858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Determining the redox
potentials of protein cofactors
and how they
are influenced by their molecular neighborhoods is essential for basic
research and many biotechnological applications, from biosensors and
biocatalysis to bioremediation and bioelectronics. The laborious determination
of redox potential with current experimental technologies pushes forward
the need for computational approaches that can reliably predict it.
Although current computational approaches based on quantum and molecular
mechanics are accurate, their large computational costs hinder their
usage. In this work, we explored the possibility of using more efficient
QSPR models based on machine learning (ML) for the prediction of protein
redox potential, as an alternative to classical approaches. As a proof
of concept, we focused on flavoproteins, one of the most important
families of enzymes directly involved in redox processes. To train
and test different ML models, we retrieved a dataset of flavoproteins
with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both
short- and long-range effects of the protein matrix on the flavin
cofactor, have been automatically extracted from each protein PDB
file. Our best ML model (XGB) has a performance error below 1 kcal/mol
(∼36 mV), comparing favorably to more sophisticated computational
approaches. We also provided indications on the features that mostly
affect the Em value, and when possible,
we rationalized them on the basis of previous studies.
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Affiliation(s)
- Bruno Giovanni Galuzzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.,SYSBIO Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonio Mirarchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Edoardo Luca Viganò
- Istituto di Ricerche Farmacologiche Mario Negri, Via Mario Negri 2, 20156 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.,SYSBIO Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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3
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Yuly JL, Zhang P, Ru X, Terai K, Singh N, Beratan DN. Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Varner TA, Mohamed-Raseek N, Miller AF. Assignments of 19F NMR resonances and exploration of dynamics in a long-chain flavodoxin. Arch Biochem Biophys 2021; 703:108839. [PMID: 33727041 DOI: 10.1016/j.abb.2021.108839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022]
Abstract
Flavodoxin is a small protein that employs a non-covalently bound flavin to mediate single-electron transfer at low potentials. The long-chain flavodoxins possess a long surface loop that is proposed to interact with partner proteins. We have incorporated 19F-labeled tyrosine in long-chain flavodoxin from Rhodopseudomonas palustris to gain a probe of possible loop dynamics, exploiting the presence of a Tyr in the long loop in addition to Tyr residues near the flavin. We report 19F resonance assignments for all four Tyrs, and demonstration of a pair of resonances in slow exchange, both corresponding to a Tyr adjacent to the flavin. We also provide evidence for dynamics affecting the Tyr in the long loop. Thus, we show that 19F NMR of 19F-Tyr labeled flavodoxin holds promise for monitoring possible changes in conformation upon binding to partner proteins.
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Affiliation(s)
- Taylor A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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5
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Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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6
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Abstract
As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce N2, nitrogenase must also hydrolyze at least 16 equivalents of adenosine triphosphate (MgATP), representing the consumption of a significant quantity of energy available to biological systems. Here, we review natural and engineered electron transfer pathways to nitrogenase, including strategies to redirect or redistribute electron flow in vivo towards NH3 production. Further, we also review strategies to artificially reduce nitrogenase in vitro, where MgATP hydrolysis is necessary for turnover, in addition to strategies that are capable of bypassing the requirement of MgATP hydrolysis to achieve MgATP-independent N2 reduction.
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7
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Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. Int J Mol Sci 2020; 21:ijms21051881. [PMID: 32164177 PMCID: PMC7084853 DOI: 10.3390/ijms21051881] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Flavodoxins are small soluble electron transfer proteins widely present in bacteria and absent in vertebrates. Flavodoxins participate in different metabolic pathways and, in some bacteria, they have been shown to be essential proteins representing promising therapeutic targets to fight bacterial infections. Using purified flavodoxin and chemical libraries, leads can be identified that block flavodoxin function and act as bactericidal molecules, as it has been demonstrated for Helicobacter pylori (Hp), the most prevalent human gastric pathogen. Increasing antimicrobial resistance by this bacterium has led current therapies to lose effectiveness, so alternative treatments are urgently required. Here, we summarize, with a focus on flavodoxin, opportunities for pharmacological intervention offered by the potential protein targets described for this bacterium and provide information on other gastrointestinal pathogens and also on bacteria from the gut microbiota that contain flavodoxin. The process of discovery and development of novel antimicrobials specific for Hp flavodoxin that is being carried out in our group is explained, as it can be extrapolated to the discovery of inhibitors specific for other gastric pathogens. The high specificity for Hp of the antimicrobials developed may be of help to reduce damage to the gut microbiota and to slow down the development of resistant Hp mutants.
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8
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nat Commun 2019; 10:2074. [PMID: 31061390 PMCID: PMC6502838 DOI: 10.1038/s41467-019-10078-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/12/2019] [Indexed: 02/01/2023] Open
Abstract
Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to –340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°’ = −493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry. The reduction of 2-naphtoyl-CoA to 5,6 dihydro-2-naphtoyl-CoA by 2-naphtoyl-CoA reductase is below the negative redox limit usually encountered in biological hydride transfer. Here, via X-ray crystallography and spectroscopic analysis, the authors elucidated the mechanism behind this.
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10
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Yuly JL, Lubner CE, Zhang P, Beratan DN, Peters JW. Electron bifurcation: progress and grand challenges. Chem Commun (Camb) 2019; 55:11823-11832. [DOI: 10.1039/c9cc05611d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors.
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Affiliation(s)
| | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - David N. Beratan
- Department of Physics
- Duke University
- Durham
- USA
- Department of Chemistry
| | - John W. Peters
- Institute of Biological Chemistry
- Washington State University
- Pullman
- USA
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11
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Houwman JA, Westphal AH, Visser AJWG, Borst JW, van Mierlo CPM. Concurrent presence of on- and off-pathway folding intermediates of apoflavodoxin at physiological ionic strength. Phys Chem Chem Phys 2018; 20:7059-7072. [PMID: 29473921 DOI: 10.1039/c7cp07922b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Flavodoxins have a protein topology that can be traced back to the universal ancestor of the three kingdoms of life. Proteins with this type of architecture tend to temporarily misfold during unassisted folding to their native state and form intermediates. Several of these intermediate species are molten globules (MGs), which are characterized by a substantial amount of secondary structure, yet without the tertiary side-chain packing of natively folded proteins. An off-pathway MG is formed at physiological ionic strength in the case of the F44Y variant of Azotobacter vinelandii apoflavodoxin (i.e., flavodoxin without flavin mononucleotide (FMN)). Here, we show that at this condition actually two folding species of this apoprotein co-exist at equilibrium. These species were detected by using a combination of FMN fluorescence quenching upon cofactor binding to the apoprotein and of polarized time-resolved tryptophan fluorescence spectroscopy. Besides the off-pathway MG, we observe the simultaneous presence of an on-pathway folding intermediate, which is native-like. Presence of concurrent intermediates at physiological ionic strength enables future exploration of how aspects of the cellular environment, like for example involvement of chaperones, affect these species.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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12
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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13
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Segal HM, Spatzal T, Hill MG, Udit AK, Rees DC. Electrochemical and structural characterization of Azotobacter vinelandii flavodoxin II. Protein Sci 2017; 26:1984-1993. [PMID: 28710816 PMCID: PMC5606536 DOI: 10.1002/pro.3236] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/08/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023]
Abstract
Azotobacter vinelandii flavodoxin II serves as a physiological reductant of nitrogenase, the enzyme system mediating biological nitrogen fixation. Wildtype A. vinelandii flavodoxin II was electrochemically and crystallographically characterized to better understand the molecular basis for this functional role. The redox properties were monitored on surfactant-modified basal plane graphite electrodes, with two distinct redox couples measured by cyclic voltammetry corresponding to reduction potentials of -483 ± 1 mV and -187 ± 9 mV (vs. NHE) in 50 mM potassium phosphate, 150 mM NaCl, pH 7.5. These redox potentials were assigned as the semiquinone/hydroquinone couple and the quinone/semiquinone couple, respectively. This study constitutes one of the first applications of surfactant-modified basal plane graphite electrodes to characterize the redox properties of a flavodoxin, thus providing a novel electrochemical method to study this class of protein. The X-ray crystal structure of the flavodoxin purified from A. vinelandii was solved at 1.17 Å resolution. With this structure, the native nitrogenase electron transfer proteins have all been structurally characterized. Docking studies indicate that a common binding site surrounding the Fe-protein [4Fe:4S] cluster mediates complex formation with the redox partners Mo-Fe protein, ferredoxin I, and flavodoxin II. This model supports a mechanistic hypothesis that electron transfer reactions between the Fe-protein and its redox partners are mutually exclusive.
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Affiliation(s)
- Helen M Segal
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, 91125
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, 91125
| | - Michael G Hill
- Division of Chemistry, Occidental College, Los Angeles, California, 90041
| | - Andrew K Udit
- Division of Chemistry, Occidental College, Los Angeles, California, 90041
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, 91125
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14
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Houwman JA, van Mierlo CPM. Folding of proteins with a flavodoxin-like architecture. FEBS J 2017; 284:3145-3167. [PMID: 28380286 DOI: 10.1111/febs.14077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022]
Abstract
The flavodoxin-like fold is a protein architecture that can be traced back to the universal ancestor of the three kingdoms of life. Many proteins share this α-β parallel topology and hence it is highly relevant to illuminate how they fold. Here, we review experiments and simulations concerning the folding of flavodoxins and CheY-like proteins, which share the flavodoxin-like fold. These polypeptides tend to temporarily misfold during unassisted folding to their functionally active forms. This susceptibility to frustration is caused by the more rapid formation of an α-helix compared to a β-sheet, particularly when a parallel β-sheet is involved. As a result, flavodoxin-like proteins form intermediates that are off-pathway to native protein and several of these species are molten globules (MGs). Experiments suggest that the off-pathway species are of helical nature and that flavodoxin-like proteins have a nonconserved transition state that determines the rate of productive folding. Folding of flavodoxin from Azotobacter vinelandii has been investigated extensively, enabling a schematic construction of its folding energy landscape. It is the only flavodoxin-like protein of which cotranslational folding has been probed. New insights that emphasize differences between in vivo and in vitro folding energy landscapes are emerging: the ribosome modulates MG formation in nascent apoflavodoxin and forces this polypeptide toward the native state.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University and Research, The Netherlands
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15
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Houwman JA, André E, Westphal AH, van Berkel WJH, van Mierlo CPM. The Ribosome Restrains Molten Globule Formation in Stalled Nascent Flavodoxin. J Biol Chem 2016; 291:25911-25920. [PMID: 27784783 PMCID: PMC5207065 DOI: 10.1074/jbc.m116.756205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
Folding of proteins usually involves intermediates, of which an important type is the molten globule (MG). MGs are ensembles of interconverting conformers that contain (non-)native secondary structure and lack the tightly packed tertiary structure of natively folded globular proteins. Whereas MGs of various purified proteins have been probed to date, no data are available on their presence and/or effect during protein synthesis. To study whether MGs arise during translation, we use ribosome-nascent chain (RNC) complexes of the electron transfer protein flavodoxin. Full-length isolated flavodoxin, which contains a non-covalently bound flavin mononucleotide (FMN) as cofactor, acquires its native α/β parallel topology via a folding mechanism that contains an off-pathway intermediate with molten globular characteristics. Extensive population of this MG state occurs at physiological ionic strength for apoflavodoxin variant F44Y, in which a phenylalanine at position 44 is changed to a tyrosine. Here, we show for the first time that ascertaining the binding rate of FMN as a function of ionic strength can be used as a tool to determine the presence of the off-pathway MG on the ribosome. Application of this methodology to F44Y apoflavodoxin RNCs shows that at physiological ionic strength the ribosome influences formation of the off-pathway MG and forces the nascent chain toward the native state.
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Affiliation(s)
- Joseline A Houwman
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Estelle André
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Adrie H Westphal
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Carlo P M van Mierlo
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
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16
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Rodríguez-Cárdenas Á, Rojas AL, Conde-Giménez M, Velázquez-Campoy A, Hurtado-Guerrero R, Sancho J. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target. PLoS One 2016; 11:e0161020. [PMID: 27649488 PMCID: PMC5029806 DOI: 10.1371/journal.pone.0161020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022] Open
Abstract
Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91-100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld.
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Affiliation(s)
- Ángela Rodríguez-Cárdenas
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adriana L. Rojas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - María Conde-Giménez
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
- * E-mail: (RHG); (JS)
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- * E-mail: (RHG); (JS)
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17
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van Son M, Lindhoud S, van der Wild M, van Mierlo CPM, Huber M. Double Electron-Electron Spin Resonance Tracks Flavodoxin Folding. J Phys Chem B 2015; 119:13507-14. [PMID: 26101942 DOI: 10.1021/acs.jpcb.5b00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding is one of the important challenges in biochemistry. Understanding the folding process requires mapping of protein structure as it folds. Here we test the potential of distance determination between paramagnetic spin-labels by a pulsed electron paramagnetic resonance method. We use double electron-electron spin resonance (DEER) to study the denaturant-dependent equilibrium folding of flavodoxin. This flavoprotein is spin-labeled with MTSL ((1-oxy-,2,2,5,5-tetramethyl-d-pyrroline-3-methyl)-methanethiosulfonate) at positions 69 and 131. We find that nativelike spin-label separation dominates the distance distributions up to 0.8 M guanidine hydrochloride. At 2.3 M denaturant, the distance distributions show an additional component, which we attribute to a folding intermediate. Upon further increase of denaturant concentration, the protein expands and evidence for a larger number of conformations than in the native state is found. We thus demonstrate that DEER is a versatile technique to expand the arsenal of methods for investigating how proteins fold.
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Affiliation(s)
- Martin van Son
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University , 6700 ET Wageningen, The Netherlands
| | - Matthijs van der Wild
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Carlo P M van Mierlo
- Laboratory of Biochemistry, Wageningen University , 6700 ET Wageningen, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
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18
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Lindhoud S, Pirchi M, Westphal AH, Haran G, van Mierlo CPM. Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level. J Mol Biol 2015; 427:3148-57. [PMID: 26163276 DOI: 10.1016/j.jmb.2015.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/27/2015] [Accepted: 07/01/2015] [Indexed: 10/23/2022]
Abstract
Molten globules (MGs) are compact, partially folded intermediates that are transiently present during folding of many proteins. These intermediates reside on or off the folding pathway to native protein. Conformational evolution during folding of off-pathway MGs is largely unexplored. Here, we characterize the denaturant-dependent structure of apoflavodoxin's off-pathway MG. Using single-molecule fluorescence resonance energy transfer (smFRET), we follow conversion of unfolded species into MG down to denaturant concentrations that favor formation of native protein. Under strongly denaturing conditions, fluorescence resonance energy transfer histograms show a single peak, arising from unfolded protein. The smFRET efficiency distribution shifts to higher value upon decreasing denaturant concentration because the MG folds. Strikingly, upon approaching native conditions, the fluorescence resonance energy transfer efficiency of the MG rises above that of native protein. Thus, smFRET exposes the misfolded nature of apoflavodoxin's off-pathway MG. We show that conversion of unfolded into MG protein is a gradual, second-order-like process that simultaneously involves separate regions within the polypeptide.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Menahem Pirchi
- Chemical Physics Department, Weizmann Institute of Science, Herzl St 234, Rehovot 76100, Israel
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Herzl St 234, Rehovot 76100, Israel.
| | - Carlo P M van Mierlo
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
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19
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Houwman JA, Westphal AH, van Berkel WJH, van Mierlo CPM. Stalled flavodoxin binds its cofactor while fully exposed outside the ribosome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1317-24. [PMID: 26073784 DOI: 10.1016/j.bbapap.2015.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/26/2015] [Accepted: 06/10/2015] [Indexed: 01/10/2023]
Abstract
Correct folding of proteins is crucial for cellular homeostasis. More than thirty percent of proteins contain one or more cofactors, but the impact of these cofactors on co-translational folding remains largely unknown. Here, we address the binding of flavin mononucleotide (FMN) to nascent flavodoxin, by generating ribosome-arrested nascent chains that expose either the entire protein or C-terminally truncated segments thereof. The native α/β parallel fold of flavodoxin is among the most ancestral and widely distributed folds in nature and exploring its co-translational folding is thus highly relevant. In Escherichia coli (strain BL21(DE3) Δtig::kan) FMN turns out to be limiting for saturation of this flavoprotein on time-scales vastly exceeding those of flavodoxin synthesis. Because the ribosome affects protein folding, apoflavodoxin cannot bind FMN during its translation. As a result, binding of cofactor to released protein is the last step in production of this flavoprotein in the cell. We show that once apoflavodoxin is entirely synthesized and exposed outside the ribosome to which it is stalled by an artificial linker containing the SecM sequence, the protein is natively folded and capable of binding FMN.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Carlo P M van Mierlo
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
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20
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Ye Q, Fu W, Hu Y, Jin C. Long-chain flavodoxin FldB from Escherichia coli. JOURNAL OF BIOMOLECULAR NMR 2014; 60:283-288. [PMID: 25380767 DOI: 10.1007/s10858-014-9874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Qian Ye
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
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21
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Nunthaboot N, Tanaka F, Kokpol S, Visser NV, van Amerongen H, Visser AJWG. Molecular dynamics simulation of energy migration between tryptophan residues in apoflavodoxin. RSC Adv 2014. [DOI: 10.1039/c4ra03779k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
By performing molecular dynamics (MD) simulations of apoflavodoxin over the same timescale as fluorescence anisotropy decay measurements, the anisotropy model of two unidirectional FRET steps from two tryptophan residues to a third one can be reproduced from the tryptophan atomic coordinates in the MD trajectory.
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150, Thailand
| | - Fumio Tanaka
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Sirirat Kokpol
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Nina V. Visser
- Laboratories of Biophysics and Biochemistry
- Microspectroscopy Centre
- Wageningen University
- 6700 ET Wageningen, The Netherlands
| | - Herbert van Amerongen
- Laboratories of Biophysics and Biochemistry
- Microspectroscopy Centre
- Wageningen University
- 6700 ET Wageningen, The Netherlands
| | - Antonie J. W. G. Visser
- Laboratories of Biophysics and Biochemistry
- Microspectroscopy Centre
- Wageningen University
- 6700 ET Wageningen, The Netherlands
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22
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Abstract
Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD(+) and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2.
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23
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Reconstructing a flavodoxin oxidoreductase with early amino acids. Int J Mol Sci 2013; 14:12843-52. [PMID: 23783279 PMCID: PMC3709815 DOI: 10.3390/ijms140612843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/24/2013] [Accepted: 06/13/2013] [Indexed: 11/16/2022] Open
Abstract
Primitive proteins are proposed to have utilized organic cofactors more frequently than transition metals in redox reactions. Thus, an experimental validation on whether a protein constituted solely by early amino acids and an organic cofactor can perform electron transfer activity is an urgent challenge. In this paper, by substituting "late amino acids (C, F, M, T, W, and Y)" with "early amino acids (A, L, and V)" in a flavodoxin, we constructed a flavodoxin mutant and evaluated its characteristic properties. The major results showed that: (1) The flavodoxin mutant has structural characteristics similar to wild-type protein; (2) Although the semiquinone and hydroquinone flavodoxin mutants possess lower stability than the corresponding form of wild-type flavodoxin, the redox potential of double electron reduction Em,7 (fld) reached -360 mV, indicating that the flavodoxin mutant constituted solely by early amino acids can exert effective electron transfer activity.
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24
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Distant residues mediate picomolar binding affinity of a protein cofactor. Nat Commun 2013; 3:1010. [PMID: 22910356 PMCID: PMC3432467 DOI: 10.1038/ncomms2010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/18/2012] [Indexed: 12/11/2022] Open
Abstract
Numerous proteins require cofactors to be active. Computer simulations suggest that cooperative interaction networks achieve optimal cofactor binding. There is a need for the experimental identification of the residues crucial for stabilizing these networks and thus for cofactor binding. Here we investigate the electron transporter flavodoxin, which contains flavin mononucleotide as non-covalently bound cofactor. We show that after binding flavin mononucleotide with nanomolar affinity, the protein relaxes extremely slowly (time constant ~5 days) to an energetically more favourable state with picomolar-binding affinity. Rare small-scale openings of this state are revealed through H/D exchange of N(3)H of flavin. We find that H/D exchange can pinpoint amino acids that cause tight cofactor binding. These hitherto unknown residues are dispersed throughout the structure, and many are located distantly from the flavin and seem irrelevant to flavodoxin's function. Quantification of the thermodynamics of ligand binding is important for understanding, engineering, designing and evolving ligand-binding proteins. Flavodoxin requires tight binding of its FMN cofactor to be active, but the residues involved are unknown. In this biophysical study, FMN binding is shown to change from nanomolar to picomolar affinity on extremely slow protein relaxation and the residues responsible for cofactor binding are identified.
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25
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Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins. Int J Mol Sci 2013; 14:1152-63. [PMID: 23303276 PMCID: PMC3565313 DOI: 10.3390/ijms14011152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/14/2012] [Accepted: 11/20/2012] [Indexed: 11/21/2022] Open
Abstract
Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as “short-chain” with the firmicutes flavodoxins and the “long-chain” with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.
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26
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Lindhoud S, Westphal AH, Visser AJWG, Borst JW, van Mierlo CPM. Fluorescence of Alexa fluor dye tracks protein folding. PLoS One 2012; 7:e46838. [PMID: 23056480 PMCID: PMC3466183 DOI: 10.1371/journal.pone.0046838] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/05/2012] [Indexed: 11/30/2022] Open
Abstract
Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488), which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Antonie J. W. G. Visser
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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27
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Lindhoud S, Westphal AH, Borst JW, van Mierlo CPM. Illuminating the off-pathway nature of the molten globule folding intermediate of an α-β parallel protein. PLoS One 2012; 7:e45746. [PMID: 23029219 PMCID: PMC3448718 DOI: 10.1371/journal.pone.0045746] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
Partially folded protein species transiently form during folding of most proteins. Often, these species are molten globules, which may be on- or off-pathway to the native state. Molten globules are ensembles of interconverting protein conformers that have a substantial amount of secondary structure, but lack virtually all tertiary side-chain packing characteristics of natively folded proteins. Due to solvent-exposed hydrophobic groups, molten globules are prone to aggregation, which can have detrimental effects on organisms. The molten globule observed during folding of the 179-residue apoflavodoxin from Azotobacter vinelandii is off-pathway, as it has to unfold before native protein can form. Here, we study folding of apoflavodoxin and characterize its molten globule using fluorescence spectroscopy and Förster Resonance Energy Transfer (FRET). Apoflavodoxin is site-specifically labeled with fluorescent donor and acceptor dyes, utilizing dye-inaccessibility of Cys69 in cofactor-bound protein. Donor (i.e., Alexa Fluor 488) is covalently attached to Cys69 in all apoflavodoxin variants used. Acceptor (i.e., Alexa Fluor 568) is coupled to Cys1, Cys131 and Cys178, respectively. Our FRET data show that apoflavodoxin's molten globule forms in a non-cooperative manner and that its N-terminal 69 residues fold last. In addition, striking conformational differences between molten globule and native protein are revealed, because the inter-label distances sampled in the 111-residue C-terminal segment of the molten globule are shorter than observed for native apoflavodoxin. Thus, FRET sheds light on the off-pathway nature of the molten globule during folding of an α-β parallel protein.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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28
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Lindhoud S, van den Berg WAM, van den Heuvel RHH, Heck AJR, van Mierlo CPM, van Berkel WJH. Cofactor binding protects flavodoxin against oxidative stress. PLoS One 2012; 7:e41363. [PMID: 22829943 PMCID: PMC3400614 DOI: 10.1371/journal.pone.0041363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 06/20/2012] [Indexed: 11/23/2022] Open
Abstract
In organisms, various protective mechanisms against oxidative damaging of proteins exist. Here, we show that cofactor binding is among these mechanisms, because flavin mononucleotide (FMN) protects Azotobacter vinelandii flavodoxin against hydrogen peroxide-induced oxidation. We identify an oxidation sensitive cysteine residue in a functionally important loop close to the cofactor, i.e., Cys69. Oxidative stress causes dimerization of apoflavodoxin (i.e., flavodoxin without cofactor), and leads to consecutive formation of sulfinate and sulfonate states of Cys69. Use of 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) reveals that Cys69 modification to a sulfenic acid is a transient intermediate during oxidation. Dithiothreitol converts sulfenic acid and disulfide into thiols, whereas the sulfinate and sulfonate forms of Cys69 are irreversible with respect to this reagent. A variable fraction of Cys69 in freshly isolated flavodoxin is in the sulfenic acid state, but neither oxidation to sulfinic and sulfonic acid nor formation of intermolecular disulfides is observed under oxidising conditions. Furthermore, flavodoxin does not react appreciably with NBD-Cl. Besides its primary role as redox-active moiety, binding of flavin leads to considerably improved stability against protein unfolding and to strong protection against irreversible oxidation and other covalent thiol modifications. Thus, cofactors can protect proteins against oxidation and modification.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | | | - Robert H. H. van den Heuvel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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29
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Laptenok SP, Visser NV, Engel R, Westphal AH, van Hoek A, van Mierlo CPM, van Stokkum IHM, van Amerongen H, Visser AJWG. A General Approach for Detecting Folding Intermediates from Steady-State and Time-Resolved Fluorescence of Single-Tryptophan-Containing Proteins. Biochemistry 2011; 50:3441-50. [PMID: 21425856 DOI: 10.1021/bi101965d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergey P. Laptenok
- Department of Physics and Astronomy, Faculty of Exact Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | | | | | | | | | - Ivo H. M. van Stokkum
- Department of Physics and Astronomy, Faculty of Exact Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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30
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Nabuurs SM, van Mierlo CPM. Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of alpha-beta parallel protein flavodoxin. J Biol Chem 2009; 285:4165-4172. [PMID: 19959481 DOI: 10.1074/jbc.m109.087932] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic intermediates that appear early during protein folding often resemble the relatively stable molten globule intermediates formed by several proteins under mildly denaturing conditions. Molten globules have a substantial amount of secondary structure but lack virtually all tertiary side-chain packing characteristics of natively folded proteins. Due to exposed hydrophobic groups, molten globules are prone to aggregation, which can have detrimental effects on organisms. The molten globule that is observed during folding of alpha-beta parallel flavodoxin from Azotobacter vinelandii is a remarkably non-native species. This folding intermediate is helical and contains no beta-sheet and is kinetically off-pathway to the native state. It can be trapped under native-like conditions by substituting residue Phe(44) for Tyr(44). To characterize this species at the residue level, in this study, use is made of interrupted hydrogen/deuterium exchange detected by NMR spectroscopy. In the molten globule of flavodoxin, the helical region comprising residues Leu(110)-Val(125) is shown to be better protected against exchange than the other ordered parts of the folding intermediate. This helical region is better buried than the other helices, causing its context-dependent stabilization against unfolding. Residues Leu(110)-Val(125) thus form the stable core of the helical molten globule of alpha-beta parallel flavodoxin, which is almost entirely structured. Non-native docking of helices in the molten globule of flavodoxin prevents formation of the parallel beta-sheet of native flavodoxin. Hence, to produce native alpha-beta parallel protein molecules, the off-pathway species needs to unfold.
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Affiliation(s)
- Sanne M Nabuurs
- From the Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Carlo P M van Mierlo
- From the Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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31
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Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:689-98. [PMID: 19894043 PMCID: PMC2841281 DOI: 10.1007/s00249-009-0556-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/30/2009] [Accepted: 10/09/2009] [Indexed: 11/15/2022]
Abstract
Transient structures in unfolded proteins are important in elucidating the molecular details of initiation of protein folding. Recently, native and non-native secondary structure have been discovered in unfolded A. vinelandii flavodoxin. These structured elements transiently interact and subsequently form the ordered core of an off-pathway folding intermediate, which is extensively formed during folding of this α–β parallel protein. Here, site-directed spin-labelling and paramagnetic relaxation enhancement are used to investigate long-range interactions in unfolded apoflavodoxin. For this purpose, glutamine-48, which resides in a non-native α-helix of unfolded apoflavodoxin, is replaced by cysteine. This replacement enables covalent attachment of nitroxide spin-labels MTSL and CMTSL. Substitution of Gln-48 by Cys-48 destabilises native apoflavodoxin and reduces flexibility of the ordered regions in unfolded apoflavodoxin in 3.4 M GuHCl, because of increased hydrophobic interactions in the unfolded protein. Here, we report that in the study of the conformational and dynamic properties of unfolded proteins interpretation of spin-label data can be complicated. The covalently attached spin-label to Cys-48 (or Cys-69 of wild-type apoflavodoxin) perturbs the unfolded protein, because hydrophobic interactions occur between the label and hydrophobic patches of unfolded apoflavodoxin. Concomitant hydrophobic free energy changes of the unfolded protein (and possibly of the off-pathway intermediate) reduce the stability of native spin-labelled protein against unfolding. In addition, attachment of MTSL or CMTSL to Cys-48 induces the presence of distinct states in unfolded apoflavodoxin. Despite these difficulties, the spin-label data obtained here show that non-native contacts exist between transiently ordered structured elements in unfolded apoflavodoxin.
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32
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Nabuurs SM, Westphal AH, aan den Toorn M, Lindhoud S, van Mierlo CPM. Topological switching between an alpha-beta parallel protein and a remarkably helical molten globule. J Am Chem Soc 2009; 131:8290-5. [PMID: 19456154 DOI: 10.1021/ja9014309] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially folded protein species transiently exist during folding of most proteins. Often these species are molten globules, which may be on- or off-pathway to native protein. Molten globules have a substantial amount of secondary structure but lack virtually all the tertiary side-chain packing characteristic of natively folded proteins. These ensembles of interconverting conformers are prone to aggregation and potentially play a role in numerous devastating pathologies, and thus attract considerable attention. The molten globule that is observed during folding of apoflavodoxin from Azotobacter vinelandii is off-pathway, as it has to unfold before native protein can be formed. Here we report that this species can be trapped under nativelike conditions by substituting amino acid residue F44 by Y44, allowing spectroscopic characterization of its conformation. Whereas native apoflavodoxin contains a parallel beta-sheet surrounded by alpha-helices (i.e., the flavodoxin-like or alpha-beta parallel topology), it is shown that the molten globule has a totally different topology: it is helical and contains no beta-sheet. The presence of this remarkably nonnative species shows that single polypeptide sequences can code for distinct folds that swap upon changing conditions. Topological switching between unrelated protein structures is likely a general phenomenon in the protein structure universe.
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Affiliation(s)
- Sanne M Nabuurs
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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33
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Structural organization of WrbA in apo- and holoprotein crystals. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1288-98. [PMID: 19665595 DOI: 10.1016/j.bbapap.2009.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 11/23/2022]
Abstract
Two previously reported holoprotein crystal forms of the flavodoxin-like E. coli protein WrbA, diffracting to 2.6 and 2.0 A resolution, and new crystals of WrbA apoprotein diffracting to 1.85 A, are refined and analysed comparatively through the lens of flavodoxin structures. The results indicate that differences between apo- and holoWrbA crystal structures are manifested on many levels of protein organization as well as in the FMN-binding sites. Evaluation of the influence of crystal contacts by comparison of lattice packing reveals the protein's global response to FMN binding. Structural changes upon cofactor binding are compared with the monomeric flavodoxins. Topologically non-equivalent residues undergo remarkably similar local structural changes upon FMN binding to WrbA or to flavodoxin, despite differences in multimeric organization and residue types at the binding sites. Analysis of the three crystal structures described here, together with flavodoxin structures, rationalizes functional similarities and differences of the WrbAs relative to flavodoxins, leading to a new understanding of the defining features of WrbAs. The results suggest that WrbAs are not a remote and unusual branch of the flavodoxin family as previously thought but rather a central member with unifying structural features.
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34
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5-fluorotryptophan as dual probe for ground-state heterogeneity and excited-state dynamics in apoflavodoxin. FEBS Lett 2009; 583:2785-8. [PMID: 19619543 DOI: 10.1016/j.febslet.2009.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 07/13/2009] [Accepted: 07/13/2009] [Indexed: 11/21/2022]
Abstract
The apoflavodoxin protein from Azotobacter vinelandii harboring three tryptophan (Trp) residues, was biosynthetically labeled with 5-fluorotryptophan (5-FTrp). 5-FTrp has the advantage that chemical differences in its microenvironment can be sensitively visualized via (19)F NMR. Moreover, it shows simpler fluorescence decay kinetics. The occurrence of FRET was earlier observed via the fluorescence anisotropy decay of WT apoflavodoxin and the anisotropy decay parameters are in excellent agreement with distances between and relative orientations of all Trp residues. The anisotropy decay in 5-FTrp apoflavodoxin demonstrates that the distances and orientations are identical for this protein. This work demonstrates the added value of replacing Trp by 5-FTrp to study structural features of proteins via (19)F NMR and fluorescence spectroscopy.
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35
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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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36
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Guelker M, Stagg L, Wittung-Stafshede P, Shamoo Y. Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:523-34. [PMID: 19465766 PMCID: PMC2685730 DOI: 10.1107/s0907444909010075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 03/18/2009] [Indexed: 11/10/2022]
Abstract
The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.
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Affiliation(s)
- Megan Guelker
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Loren Stagg
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Pernilla Wittung-Stafshede
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
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37
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Martínez-Junza V, Rizzi AC, Alagaratnam S, Bell TDM, Canters GW, Braslavsky SE. Flavodoxin Relaxes in Microseconds Upon Excitation of the Flavin Chromophore: Detection of a UV-Visible Silent Intermediate by Laser Photocalorimetry. Photochem Photobiol 2009; 85:107-10. [DOI: 10.1111/j.1751-1097.2008.00402.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Fantuzzi A, Artali R, Bombieri G, Marchini N, Meneghetti F, Gilardi G, Sadeghi SJ, Cavazzini D, Rossi GL. Redox properties and crystal structures of a Desulfovibrio vulgaris flavodoxin mutant in the monomeric and homodimeric forms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:496-505. [PMID: 19118653 DOI: 10.1016/j.bbapap.2008.11.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 11/21/2008] [Accepted: 11/26/2008] [Indexed: 11/24/2022]
Abstract
The mutant S64C of the short-chain flavodoxin from Desulfovibrio vulgaris has been designed to introduce an accessible and reactive group on the protein surface. Crystals have been obtained of both the monomeric and homodimeric forms of the protein, with the cofactor FMN in either the oxidized or the one electron-reduced (semiquinone) state, and the structures have been determined to high resolution. The redox properties of the different species have been investigated and the variations observed with respect to wild type have been related to the structural changes induced by the mutation and S-S bridge formation.
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Affiliation(s)
- Andrea Fantuzzi
- Imperial College London, Division of Molecular Biosciences, South Kensington, SW72AZ, London, United Kingdom
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39
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Engel R, Westphal AH, Huberts DH, Nabuurs SM, Lindhoud S, Visser AJ, van Mierlo CP. Macromolecular Crowding Compacts Unfolded Apoflavodoxin and Causes Severe Aggregation of the Off-pathway Intermediate during Apoflavodoxin Folding. J Biol Chem 2008; 283:27383-27394. [DOI: 10.1074/jbc.m802393200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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40
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Abstract
Submolecular details of Azotobacter vinelandii apoflavodoxin (apoFD) (un)folding are revealed by time-resolved fluorescence anisotropy using wild-type protein and variants lacking one or two of apoFD's three tryptophans. ApoFD equilibrium (un)folding by guanidine hydrochloride follows a three-state model: native <--> unfolded <--> intermediate. In native protein, W128 is a sink for Förster resonance energy transfer (FRET). Consequently, unidirectional FRET with a 50-ps transfer correlation time occurs from W167 to W128. FRET from W74 to W167 is much slower (6.9 ns). In the intermediate, W128 and W167 have native-like geometry because the 50-ps transfer time is observed. However, non-native structure exists between W74 and W167 because instead of 6.9 ns the transfer correlation time is 2.0 ns. In unfolded apoFD this 2.0-ns transfer correlation time is also detected. This decrease in transfer correlation time is a result of W74 and W167 becoming solvent accessible and randomly oriented toward one another. Apparently W74 and W167 are near-natively separated in the folding intermediate and in unfolded apoFD. Both tryptophans may actually be slightly closer in space than in the native state, even though apoFD's radius increases substantially upon unfolding. In unfolded apoFD the 50-ps transfer time observed for native and intermediate folding states becomes 200 ps as W128 and W167 are marginally further separated than in the native state. Apparently, apoFD's unfolded state is not a featureless statistical coil but contains well-defined substructures. The approach presented is a powerful tool to study protein folding.
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41
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Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008; 6:579-91. [PMID: 18587410 DOI: 10.1038/nrmicro1931] [Citation(s) in RCA: 1083] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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42
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Frago S, Goñi G, Herguedas B, Peregrina JR, Serrano A, Perez-Dorado I, Molina R, Gómez-Moreno C, Hermoso JA, Martínez-Júlvez M, Mayhew SG, Medina M. Tuning of the FMN binding and oxido-reduction properties by neighboring side chains in Anabaena flavodoxin. Arch Biochem Biophys 2007; 467:206-17. [PMID: 17904516 DOI: 10.1016/j.abb.2007.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 08/13/2007] [Accepted: 08/13/2007] [Indexed: 11/23/2022]
Abstract
Contribution of three regions (phosphate-binding, 50's and 90's loops) of Anabaena apoflavodoxin to FMN binding and reduction potential was studied. Thr12 and Glu16 did not influence FMN redox properties, but Thr12 played a role in FMN binding. Replacement of Trp57 with Glu, Lys or Arg moderately shifted E(ox/sq) and E(sq/hq) and altered the energetic of the FMN redox states binding profile. Our data indicate that the side chain of position 57 does not modulate E(ox/sq) by aromatic stacking or solvent exclusion, but rather by influencing the relative strength of the H-bond between the N(5) of the flavin and the Asn58-Ile59 bond. A correlation was observed between the isoalloxazine increase in solvent accessibility and less negative E(sq/hq). Moreover, E(sq/hq) became less negative as positively charged residues were added near to the isoalloxazine. Ile59 and Ile92 were simultaneously mutated to Ala or Glu. These mutations impaired FMN binding, while shifting E(sq/hq) to less negative values and E(ox/sq) to more negative. These effects are discussed on the bases of the X-ray structures of some of the Fld mutants, suggesting that in Anabaena Fld the structural control of both electron transfer steps is much more subtle than in other Flds.
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Affiliation(s)
- Susana Frago
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009-Zaragoza, Spain
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43
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Hu Y, Li Y, Zhang X, Guo X, Xia B, Jin C. Solution structures and backbone dynamics of a flavodoxin MioC from Escherichia coli in both Apo- and Holo-forms: implications for cofactor binding and electron transfer. J Biol Chem 2006; 281:35454-66. [PMID: 16963438 DOI: 10.1074/jbc.m607336200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Flavodoxins play central roles in the electron transfer involving various biological processes in microorganisms. The mioC gene of Escherichia coli encodes a 16-kDa flavodoxin and locates next to the chromosomal replication initiation origin (oriC). Extensive researches have been carried out to investigate the relationship between mioC transcription and replication initiation. Recently, the MioC protein was proposed to be essential for the biotin synthase activity in vitro. Nevertheless, the exact role of MioC in biotin synthesis and its physiological function in vivo remain elusive. In order to understand the molecular basis of the biological functions of MioC and the cofactor-binding mechanisms of flavodoxins, we have determined the solution structures of both the apo- and holo-forms of E. coli MioC protein at high resolution by nuclear magnetic resonance spectroscopy. The overall structures of both forms consist of an alpha/beta sandwich, which highly resembles the classical flavodoxin fold. However, significant diversities are observed between the two forms, especially the stabilization of the FMN-binding loops and the notable extension of secondary structures upon FMN binding. Structural comparison reveals fewer negative charged and aromatic residues near the FMN-binding site of MioC, as compared with that of flavodoxin 1 from E. coli, which may affect both the redox potentials and the redox partner interactions. Furthermore, the backbone dynamics studies reveal the conformational flexibility at different time scales for both apo- and holo-forms of MioC, which may play important roles for cofactor binding and electron transfer.
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Affiliation(s)
- Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, Peking University, Beijing 100871, China
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44
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Bollen YJM, Kamphuis MB, van Mierlo CPM. The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates. Proc Natl Acad Sci U S A 2006; 103:4095-100. [PMID: 16537490 PMCID: PMC1449652 DOI: 10.1073/pnas.0509133103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many native proteins occasionally form partially unfolded forms (PUFs), which can be detected by hydrogen/deuterium exchange and NMR spectroscopy. Knowledge about these metastable states is required to better understand the onset of folding-related diseases. So far, not much is known about where PUFs reside within the energy landscape for protein folding. Here, four PUFs of the relatively large apoflavodoxin (179 aa) are identified. Remarkably, at least three of them are partially misfolded conformations. The misfolding involves side-chain contacts as well as the protein backbone. The rates at which the PUFs interconvert with native protein have been determined. Comparison of these rates with stopped-flow data positions the PUFs in apoflavodoxin's complex folding energy landscape. PUF1 and PUF2 are unfolding excursions that start from native apoflavodoxin but do not continue to the unfolded state. PUF3 and PUF4 could be similar excursions, but their rates of formation suggest that they are on a dead-end folding route that starts from unfolded apoflavodoxin and does not continue all of the way to native protein. All PUFs detected thus are off the protein's productive folding route.
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Affiliation(s)
- Yves J. M. Bollen
- *Department of Structural Biology, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands; and
| | - Monique B. Kamphuis
- Laboratory of Biochemistry, Wageningen University, 6703 HA, Wageningen, The Netherlands
| | - Carlo P. M. van Mierlo
- Laboratory of Biochemistry, Wageningen University, 6703 HA, Wageningen, The Netherlands
- To whom correspondence should be addressed. E-mail:
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45
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Kuznetsova S, Zauner G, Schmauder R, Mayboroda OA, Deelder AM, Aartsma TJ, Canters GW. A Förster-resonance-energy transfer-based method for fluorescence detection of the protein redox state. Anal Biochem 2005; 350:52-60. [PMID: 16430854 DOI: 10.1016/j.ab.2005.11.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 11/23/2005] [Accepted: 11/25/2005] [Indexed: 11/21/2022]
Abstract
A method for fluorescence detection of a protein's redox state based on resonance energy transfer from an attached fluorescence label to the prosthetic group of the redox protein is described and tested for proteins containing three types of prosthetic groups: a type-1 copper site (azurin, amicyanin, plastocyanin, and pseudoazurin), a heme group (cytochrome c550), and a flavin mononucleotide (flavodoxin). This method permits one to reliably distinguish between reduced and oxidized proteins and to perform potentiometric titrations at submicromolar concentrations.
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Affiliation(s)
- Sofya Kuznetsova
- Leiden Institute of Chemistry-Gorlaeus Laboratories, Leiden University, The Netherlands
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