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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles-encounter complexes-lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)-which exhibits an unexpected, intrinsically highly dynamic behavior-is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á. Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A. Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
- Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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Young D, Pedre B, Ezeriņa D, De Smet B, Lewandowska A, Tossounian MA, Bodra N, Huang J, Astolfi Rosado L, Van Breusegem F, Messens J. Protein Promiscuity in H 2O 2 Signaling. Antioxid Redox Signal 2019; 30:1285-1324. [PMID: 29635930 DOI: 10.1089/ars.2017.7013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Decrypting the cellular response to oxidative stress relies on a comprehensive understanding of the redox signaling pathways stimulated under oxidizing conditions. Redox signaling events can be divided into upstream sensing of oxidants, midstream redox signaling of protein function, and downstream transcriptional redox regulation. Recent Advances: A more and more accepted theory of hydrogen peroxide (H2O2) signaling is that of a thiol peroxidase redox relay, whereby protein thiols with low reactivity toward H2O2 are instead oxidized through an oxidative relay with thiol peroxidases. CRITICAL ISSUES These ultrareactive thiol peroxidases are the upstream redox sensors, which form the first cellular port of call for H2O2. Not all redox-regulated interactions between thiol peroxidases and cellular proteins involve a transfer of oxidative equivalents, and the nature of redox signaling is further complicated through promiscuous functions of redox-regulated "moonlighting" proteins, of which the precise cellular role under oxidative stress can frequently be obscured by "polygamous" interactions. An ultimate goal of redox signaling is to initiate a rapid response, and in contrast to prokaryotic oxidant-responsive transcription factors, mammalian systems have developed redox signaling pathways, which intersect both with kinase-dependent activation of transcription factors, as well as direct oxidative regulation of transcription factors through peroxiredoxin (Prx) redox relays. FUTURE DIRECTIONS We highlight that both transcriptional regulation and cell fate can be modulated either through oxidative regulation of kinase pathways, or through distinct redox-dependent associations involving either Prxs or redox-responsive moonlighting proteins with functional promiscuity. These protein associations form systems of crossregulatory networks with multiple nodes of potential oxidative regulation for H2O2-mediated signaling.
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Affiliation(s)
- David Young
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Brandan Pedre
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezeriņa
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Barbara De Smet
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Aleksandra Lewandowska
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria-Armineh Tossounian
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nandita Bodra
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Leonardo Astolfi Rosado
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank Van Breusegem
- 2 Brussels Center for Redox Biology, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Kurzbach D, Flamm AG, Sára T. Network representation of protein interactions-Experimental results. Protein Sci 2016; 25:1628-36. [PMID: 27272395 PMCID: PMC5338234 DOI: 10.1002/pro.2964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 01/23/2023]
Abstract
A graph theoretical analysis of nuclear magnetic resonance (NMR) data of six different protein interactions has been presented. The representation of the protein interaction data as a graph or network reveals that all of the studied interactions are based on a common functional concept. They all involve a single densely packed hub of functionally correlated residues that mediate the ligand binding events. This is found independent of the kind of protein (folded or unfolded) or ligand (protein, polymer or small molecule). Furthermore, the power of the graph analysis is demonstrated at the examples of the Calmodulin (CaM)/Calcium and the Cold Shock Protein A (CspA)/RNA interaction. The presented approach enables the precise determination of multiple binding sites for the respective ligand molecules.
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Affiliation(s)
- Dennis Kurzbach
- Departement de Chimie, Ecole Normale SuperieurePSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolecules (LBM)24 rue Lhomond75005ParisFrance
| | - Andrea G. Flamm
- Department for Structural and Computational BiologyUniversity of ViennaCampus Vienna BioCenter 5Vienna1030Austria
| | - Tomáš Sára
- Department for Structural and Computational BiologyUniversity of ViennaCampus Vienna BioCenter 5Vienna1030Austria
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Schörghuber J, Sára T, Bisaccia M, Schmid W, Konrat R, Lichtenecker RJ. Novel approaches in selective tryptophan isotope labeling by using Escherichia coli overexpression media. Chembiochem 2015; 16:746-51. [PMID: 25703586 DOI: 10.1002/cbic.201402677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 01/25/2023]
Abstract
NMR-based investigations of large protein complexes require optimized isotopic labeling schemes. We report new methods to introduce stable isotopes into tryptophan residues; these are fine-tuned to the requirements of the particular protein NMR experiment. Selective backbone labeling was performed by using a new α-ketoacid precursor as an additive in cell-based overexpression media. Additionally, we developed synthetic routes to certain isotopologues of indole with (13)C-(1)H spin systems surrounded by (12)C and (2)H. The corresponding proteins, overexpressed in the presence of these precursor compounds, can be effectively analyzed for conformational changes in tryptophan residues in response to external stimuli, such as interaction with other proteins or small molecules.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090 Vienna (Austria)
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Kurzbach D, Kontaxis G, Coudevylle N, Konrat R. NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:149-85. [PMID: 26387102 DOI: 10.1007/978-3-319-20164-1_5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational flexibility and thus not amenable to conventional structural biology techniques. Given their inherent structural flexibility NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This chapter will summarize key advances in NMR methodology. Despite the availability of efficient (multi-dimensional) NMR experiments for signal assignment of IDPs it is discussed that NMR of larger and more complex IDPs demands spectral simplification strategies capitalizing on specific isotope-labeling strategies. Prototypical applications of isotope labeling-strategies are described. Since IDP-ligand association and dissociation processes frequently occur on time scales that are amenable to NMR spectroscopy we describe in detail the application of CPMG relaxation dispersion techniques to studies of IDP protein binding. Finally, we demonstrate that the complementary usage of NMR and EPR data provide a more comprehensive picture about the conformational states of IDPs and can be employed to analyze the conformational ensembles of IDPs.
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Affiliation(s)
- Dennis Kurzbach
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Georg Kontaxis
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Nicolas Coudevylle
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
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