1
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Kunová N, Ondrovičová G, Bauer JA, Krajčovičová V, Pinkas M, Stojkovičová B, Havalová H, Lukáčová V, Kohútová L, Košťan J, Martináková L, Baráth P, Nováček J, Zoll S, Kereϊche S, Kutejová E, Pevala V. Polyphosphate and tyrosine phosphorylation in the N-terminal domain of the human mitochondrial Lon protease disrupts its functions. Sci Rep 2024; 14:9923. [PMID: 38688959 PMCID: PMC11061198 DOI: 10.1038/s41598-024-60030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Phosphorylation plays a crucial role in the regulation of many fundamental cellular processes. Phosphorylation levels are increased in many cancer cells where they may promote changes in mitochondrial homeostasis. Proteomic studies on various types of cancer identified 17 phosphorylation sites within the human ATP-dependent protease Lon, which degrades misfolded, unassembled and oxidatively damaged proteins in mitochondria. Most of these sites were found in Lon's N-terminal (NTD) and ATPase domains, though little is known about the effects on their function. By combining the biochemical and cryo-electron microscopy studies, we show the effect of Tyr186 and Tyr394 phosphorylations in Lon's NTD, which greatly reduce all Lon activities without affecting its ability to bind substrates or perturbing its tertiary structure. A substantial reduction in Lon's activities is also observed in the presence of polyphosphate, whose amount significantly increases in cancer cells. Our study thus provides an insight into the possible fine-tuning of Lon activities in human diseases, which highlights Lon's importance in maintaining proteostasis in mitochondria.
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Grants
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- BIOMEDIRES - II. stage, ITMS: 313011W428 European Regional Development Fund
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
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Affiliation(s)
- Nina Kunová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gabriela Ondrovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Veronika Krajčovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Laboratory of Clinical and Molecular Genetics, National Institute of Children's Diseases, Limbová 1, 833 40, Bratislava, Slovakia
| | - Matyáš Pinkas
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Barbora Stojkovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Henrieta Havalová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Július Košťan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna, Biocenter 5, 1030, Vienna, Austria
| | - Lucia Martináková
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Peter Baráth
- Medirex Group Academy, Nitra, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Nováček
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereϊche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic.
| | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
| | - Vladimír Pevala
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
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2
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Homola M, Büttner CR, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Sci Adv 2024; 10:eadk1954. [PMID: 38598627 PMCID: PMC11006232 DOI: 10.1126/sciadv.adk1954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth's climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.
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Affiliation(s)
- Miroslav Homola
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Carina R. Büttner
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Křepelka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Radka Holbová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marten L. Chaillet
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jakub Žák
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Danyil Grybchuk
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Friedrich Förster
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - William H. Wilson
- Marine Biological Association, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | | | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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3
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Koutná E, Lux V, Kouba T, Škerlová J, Nováček J, Srb P, Hexnerová R, Šváchová H, Kukačka Z, Novák P, Fábry M, Poepsel S, Veverka V. Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res 2023; 51:10011-10025. [PMID: 37615563 PMCID: PMC10570030 DOI: 10.1093/nar/gkad674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
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Affiliation(s)
- Eliška Koutná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Vanda Lux
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | | | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Hana Šváchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, Cologne 509 31, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 509 31, Germany
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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4
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Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN. Structural conservation of antibiotic interaction with ribosomes. Nat Struct Mol Biol 2023; 30:1380-1392. [PMID: 37550453 PMCID: PMC10497419 DOI: 10.1038/s41594-023-01047-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
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Affiliation(s)
- Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging at EPFL-UNIL, Batiment Cubotron, Lausanne, Switzerland
| | | | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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5
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Veverka P, Brom T, Janovič T, Stojaspal M, Pinkas M, Nováček J, Hofr C. Electron microscopy reveals toroidal shape of master neuronal cell differentiator REST - RE1-silencing transcription factor. Comput Struct Biotechnol J 2022; 21:731-741. [PMID: 36698979 PMCID: PMC9860152 DOI: 10.1016/j.csbj.2022.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The RE1-Silencing Transcription factor (REST) is essential for neuronal differentiation. Here, we report the first 18.5-angstrom electron microscopy structure of human REST. The refined electron map suggests that REST forms a torus that can accommodate DNA double-helix in the central hole. Additionally, we quantitatively described REST binding to the canonical DNA sequence of the neuron-restrictive silencer element. We developed protocols for the expression and purification of full-length REST and the shortened variant REST-N62 produced by alternative splicing. We tested the mutual interaction of full-length REST and the splicing variant REST-N62. Revealed structure-function relationships of master neuronal repressor REST will allow finding new biological ways of prevention and treatment of neurodegenerative disorders and diseases.
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Key Words
- CD, circular dichroism
- CoIP, coimmunoprecipitation
- DLS, dynamic light scattering
- Differentiation
- EM
- EM, electron microscopy
- Electron microscopy
- IDRs, intrinsically disordered regions
- NRSE, neuron-restrictive silencer element
- NRSF
- NRSF, neuron-restrictive silencer factor
- Neuron-restrictive silencer factor
- Neuronal
- PCNA, proliferating cell nuclear antigen
- RD1/2, repressor domain 1/2
- RE1, repressor element-1
- RE1-silencing transcription factor
- REST
- REST, RE1-silencing transcription factor
- REST-FL, full-length REST
- REST-N62
- REST-N62, splicing isoform of REST, also known as REST4 or REST4-S3
- REST4
- ZF, zinc finger
- aa, amino acid(s)
- bp, base pair(s)
- kDa, kilodaltons
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Affiliation(s)
- Pavel Veverka
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Tomáš Brom
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Tomáš Janovič
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Martin Stojaspal
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | | | - Jiří Nováček
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Ctirad Hofr
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Corresponding author.
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6
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Asai S, Moravcová J, Žáková L, Selicharová I, Hadravová R, Brzozowski AM, Nováček J, Jiráček J. Characterization of insulin crystalline form in isolated β-cell secretory granules. Open Biol 2022; 12:220322. [PMID: 36541100 PMCID: PMC9768635 DOI: 10.1098/rsob.220322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Insulin is stored in vivo inside the pancreatic β-cell insulin secretory granules. In vitro studies have led to an assumption that high insulin and Zn2+ concentrations inside the pancreatic β-cell insulin secretory granules should promote insulin crystalline state in the form of Zn2+-stabilized hexamers. Electron microscopic images of thin sections of the pancreatic β-cells often show a dense, regular pattern core, suggesting the presence of insulin crystals. However, the structural features of the storage forms of insulin in native preparations of secretory granules are unknown, because of their small size, fragile character and difficult handling. We isolated and investigated the secretory granules from MIN6 cells under near-native conditions, using cryo-electron microscopic (Cryo-EM) techniques. The analysis of these data from multiple intra-granular crystals revealed two different rhomboidal crystal lattices. The minor lattice has unit cell parameters (a ≃ b ≃ 84.0 Å, c ≃ 35.2 Å), similar to in vitro crystallized human 4Zn2+-insulin hexamer, whereas the largely prevalent unit cell has more than double c-axis (a ≃ b ≃ c ≃ 96.5 Å) that probably corresponds to two or three insulin hexamers in the asymmetric unit. Our experimental data show that insulin can be present in pancreatic MIN6 cell granules in a microcrystalline form, probably consisting of 4Zn2+-hexamers of this hormone.
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Affiliation(s)
- Seiya Asai
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 11610 Prague 6, Czech Republic,Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague 2, Czech Republic
| | - Jana Moravcová
- CEITEC, Cryo-Electron Microscopy and Tomography Core Facility, Masaryk University, Kamenice 5, 62500 Bohunice, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 11610 Prague 6, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 11610 Prague 6, Czech Republic
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 11610 Prague 6, Czech Republic
| | - Andrzej Marek Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Jiří Nováček
- CEITEC, Cryo-Electron Microscopy and Tomography Core Facility, Masaryk University, Kamenice 5, 62500 Bohunice, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 11610 Prague 6, Czech Republic
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7
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Hrebík D, Gondová M, Valentová L, Füzik T, Přidal A, Nováček J, Plevka P. Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules. Acta Crystallogr D Struct Biol 2022; 78:1337-1346. [DOI: 10.1107/s2059798322009299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air–water interface. Here, it is shown that coating cryo-EM grids with a negatively charged polyelectrolyte, such as single-stranded DNA, before applying the sample reduces the aggregation of macromolecules and improves their distribution. The single-stranded DNA-coated grids enabled the determination of high-resolution structures from samples that aggregated on conventional grids. The polyelectrolyte coating reduces the diffusion of macromolecules and thus may limit the negative effects of the contact of macromolecules with the grid support and blotting paper, as well as of the shear forces on macromolecules during grid blotting. Coating grids with polyelectrolytes can readily be employed in any laboratory dealing with cryo-EM sample preparation, since it is fast, simple, inexpensive and does not require specialized equipment.
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8
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Domanski M, Dedic E, Pérez ME, Cléry A, Campagne S, Uldry AC, Braga S, Heller M, Rabl J, Afanasyev P, Boehringer D, Nováček J, Allain FT, Mühlemann O. 40S hnRNP particles are a novel class of nuclear biomolecular condensates. Nucleic Acids Res 2022; 50:6300-6312. [PMID: 35687109 PMCID: PMC9226511 DOI: 10.1093/nar/gkac457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. Here, we report the biochemical purification of native 40S hnRNP particles and the determination of their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents. Isolated 40S hnRNP particles dissociate upon RNA digestion and can be reconstituted in vitro on defined RNAs in the presence of the individual protein components, demonstrating a scaffolding role for RNA in nucleating particle formation. Finally, we revealed their nanometer scale, condensate-like nature, promoted by intrinsically disordered regions of A-group hnRNPs. Collectively, we identify nuclear 40S hnRNP particles as novel dynamic biomolecular condensates.
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Affiliation(s)
- Michal Domanski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Maria Escura Pérez
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Sébastien Campagne
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Sophie Braga
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Manfred Heller
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Daniel Boehringer
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Nováček
- Cryo-Electron Microscopy and Tomography Core Facility, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Frédéric T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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9
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Moravcová J, Pinkas M, Holbová R, Nováček J. Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography. J Vis Exp 2021. [PMID: 34866622 DOI: 10.3791/62351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in situ. Owing to the strong interaction of an electron with the matter, high-resolution cryo-ET studies are limited to specimens with a thickness of less than 200 nm, which restricts the applicability of cryo-ET only to the peripheral regions of a cell. A complex workflow that comprises the preparation of thin cellular cross-sections by cryo-focused ion beam micromachining (cryo-FIBM) was introduced during the last decade to enable the acquisition of cryo-ET data from the interior of larger cells. We present a protocol for the preparation of cellular lamellae from a sample vitrified by plunge freezing utilizing Saccharomyces cerevisiae as a prototypical example of a eukaryotic cell with wide utilization in cellular and molecular biology research. We describe protocols for vitrification of S. cerevisiae into isolated patches of a few cells or a continuous monolayer of the cells on a TEM grid and provide a protocol for lamella preparation by cryo-FIB for these two samples.
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Affiliation(s)
- Jana Moravcová
- Central European Institute of Technology, Masaryk University
| | - Matyáš Pinkas
- Central European Institute of Technology, Masaryk University
| | - Radka Holbová
- Central European Institute of Technology, Masaryk University
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University;
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10
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Koval' T, Kouba T, Sudzinová P, Pospíšil J, Brezovská B, Hnilicová J, Šanderová H, Janoušková M, Šiková M, Halada P, Sýkora M, Barvík I, Nováček J, Trundová M, Dušková J, Skálová T, Chon UR, Murakami KS, Krásný L, Dohnálek J. Deciphering the role of unique bacterial transcription-associated factor HelD. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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11
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Kasari V, Pochopien AA, Margus T, Murina V, Turnbull K, Zhou Y, Nissan T, Graf M, Nováček J, Atkinson GC, Johansson MJO, Wilson DN, Hauryliuk V. A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. Nucleic Acids Res 2019; 47:8807-8820. [PMID: 31299085 PMCID: PMC7145556 DOI: 10.1093/nar/gkz600] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/14/2019] [Accepted: 07/11/2019] [Indexed: 11/12/2022] Open
Abstract
Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3′-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.
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Affiliation(s)
- Villu Kasari
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Agnieszka A Pochopien
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Tõnu Margus
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Kathryn Turnbull
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Yang Zhou
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Tracy Nissan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, 10691, Sweden.,School of Life Science, University of Sussex, Brighton, BN19RH, UK
| | - Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Gemma C Atkinson
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Marcus J O Johansson
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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12
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Sicorello A, Kelly G, Oregioni A, Nováček J, Sklenář V, Pastore A. The Structural Properties in Solution of the Intrinsically Mixed Folded Protein Ataxin-3. Biophys J 2019; 115:59-71. [PMID: 29972812 DOI: 10.1016/j.bpj.2018.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 10/28/2022] Open
Abstract
It has increasingly become clear over the last two decades that proteins can contain both globular domains and intrinsically unfolded regions that can both contribute to function. Although equally interesting, the disordered regions are difficult to study, because they usually do not crystallize unless bound to partners and are not easily amenable to cryo-electron microscopy studies. NMR spectroscopy remains the best technique to capture the structural features of intrinsically mixed folded proteins and describe their dynamics. These studies rely on the successful assignment of the spectrum, a task not easy per se given the limited spread of the resonances of the disordered residues. Here, we describe the structural properties of ataxin-3, the protein responsible for the neurodegenerative Machado-Joseph disease. Ataxin-3 is a 42-kDa protein containing a globular N-terminal Josephin domain and a C-terminal tail that comprises 13 polyglutamine repeats within a low complexity region. We developed a strategy that allowed us to achieve 87% assignment of the NMR spectrum using a mixed protocol based on high-dimensionality, high-resolution experiments and different labeling schemes. Thanks to the almost complete spectral assignment, we proved that the C-terminal tail is flexible, with extended helical regions, and interacts only marginally with the rest of the protein. We could also, for the first time to our knowledge, observe the structural propensity of the polyglutamine repeats within the context of the full-length protein and show that its structure is stabilized by the preceding region.
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Affiliation(s)
- Alessandro Sicorello
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Geoff Kelly
- Medical Research Council Biomolecular NMR Centre, The Francis Crick Institute, London, United Kingdom
| | - Alain Oregioni
- Medical Research Council Biomolecular NMR Centre, The Francis Crick Institute, London, United Kingdom
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Annalisa Pastore
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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13
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Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M. Structural basis for the multitasking nature of the potato virus Y coat protein. Sci Adv 2019; 5:eaaw3808. [PMID: 31328164 PMCID: PMC6636993 DOI: 10.1126/sciadv.aaw3808] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/10/2019] [Indexed: 05/02/2023]
Abstract
Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
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Affiliation(s)
- Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Martin Polák
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- University of Nova Gorica, Vipavska cesta, 5000 Nova Gorica, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Corresponding author.
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14
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Melková K, Zapletal V, Jansen S, Nomilner E, Zachrdla M, Hritz J, Nováček J, Zweckstetter M, Jensen MR, Blackledge M, Žídek L. Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics. J Biol Chem 2018; 293:13297-13309. [PMID: 29925592 DOI: 10.1074/jbc.ra118.001769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and α-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior.
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Affiliation(s)
- Kateřina Melková
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Zapletal
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Séverine Jansen
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Erik Nomilner
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Zachrdla
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Nováček
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Markus Zweckstetter
- the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,the German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany, and
| | | | | | - Lukáš Žídek
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic, .,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
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15
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Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell 2017; 68:515-527.e6. [PMID: 29100052 DOI: 10.1016/j.molcel.2017.10.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Abstract
Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
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Affiliation(s)
- Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Jan Ole Frister
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andre Heuer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lauri Peil
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Agata L Starosta
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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16
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Srb P, Nováček J, Kadeřávek P, Rabatinová A, Krásný L, Žídková J, Bobálová J, Sklenář V, Žídek L. Triple resonance ¹⁵Ν NMR relaxation experiments for studies of intrinsically disordered proteins. J Biomol NMR 2017; 69:133-146. [PMID: 29071460 DOI: 10.1007/s10858-017-0138-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-labeled proteins. We show that the third spectral dimension combined with non-uniform sampling provides relaxation rates for almost all residues of a protein with extremely poor chemical shift dispersion, the C terminal domain of [Formula: see text]-subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by [Formula: see text] only showed that the presence of [Formula: see text] has a negligible effect on [Formula: see text], [Formula: see text], and on the cross-relaxation rate (calculated from NOE and [Formula: see text]), and that these relaxation rates can be used to calculate accurate spectral density values. Partially [Formula: see text]-labeled sample was used to test if the observed increase of [Formula: see text] [Formula: see text] in the presence of [Formula: see text] corresponds to the [Formula: see text] dipole-dipole interactions in the [Formula: see text],[Formula: see text]-labeled sample.
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Affiliation(s)
- Pavel Srb
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí, 542/2, 166 10, Praha 6, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Alžbeta Rabatinová
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Videňská 1083, 142 20, Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Videňská 1083, 142 20, Prague, Czech Republic
| | - Jitka Žídková
- Institute of Analytical Chemistry of the Czech Academy of Sciences v.v.i., Veveří 97, 602 00, Brno, Czech Republic
| | - Janette Bobálová
- Institute of Analytical Chemistry of the Czech Academy of Sciences v.v.i., Veveří 97, 602 00, Brno, Czech Republic
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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17
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Jansen S, Melková K, Trošanová Z, Hanáková K, Zachrdla M, Nováček J, Župa E, Zdráhal Z, Hritz J, Žídek L. Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau. J Biol Chem 2017; 292:6715-6727. [PMID: 28258221 DOI: 10.1074/jbc.m116.771097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is involved in neuronal development and is less characterized than its homolog Tau, which has various roles in neurodegeneration. Using NMR methods providing single-residue resolution and quantitative comparison, we investigated molecular interactions important for the regulatory roles of MAP2c in microtubule dynamics. We found that MAP2c and Tau significantly differ in the position and kinetics of sites that are phosphorylated by cAMP-dependent protein kinase (PKA), even in highly homologous regions. We determined the binding sites of unphosphorylated and phosphorylated MAP2c responsible for interactions with the regulatory protein 14-3-3ζ. Differences in phosphorylation and in charge distribution between MAP2c and Tau suggested that both MAP2c and Tau respond to the same signal (phosphorylation by PKA) but have different downstream effects, indicating a signaling branch point for controlling microtubule stability. Although the interactions of phosphorylated Tau with 14-3-3ζ are supposed to be a major factor in microtubule destabilization, the binding of 14-3-3ζ to MAP2c enhanced by PKA-mediated phosphorylation is likely to influence microtubule-MAP2c binding much less, in agreement with the results of our tubulin co-sedimentation measurements. The specific location of the major MAP2c phosphorylation site in a region homologous to the muscarinic receptor-binding site of Tau suggests that MAP2c also may regulate processes other than microtubule dynamics.
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Affiliation(s)
- Séverine Jansen
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Melková
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zuzana Trošanová
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Hanáková
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Milan Zachrdla
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Nováček
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Erik Župa
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jozef Hritz
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Lukáš Žídek
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
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Louša P, Nedozrálová H, Župa E, Nováček J, Hritz J. Phosphorylation of the regulatory domain of human tyrosine hydroxylase 1 monitored using non-uniformly sampled NMR. Biophys Chem 2017; 223:25-29. [PMID: 28282625 DOI: 10.1016/j.bpc.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Human tyrosine hydroxylase 1 (hTH1) activity is regulated by phosphorylation of its regulatory domain (RD-hTH1) and by an interaction with the 14-3-3 protein. The RD-hTH1 is composed of a structured region (66-169) preceded by an intrinsically disordered protein region (IDP, hTH1_65) containing two phosphorylation sites (S19 and S40) which are highly relevant for its increase in activity. The NMR signals of the IDP region in the non-phosphorylated, singly phosphorylated (pS40) and doubly phosphorylated states (pS19_pS40) were assigned by non-uniformly sampled spectra with increased dimensionality (5D). The structural changes induced by phosphorylation were analyzed by means of secondary structure propensities. The phosphorylation kinetics of the S40 and S19 by kinases PKA and PRAK respectively were monitored by non-uniformly sampled time-resolved NMR spectroscopy followed by their quantitative analysis.
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Affiliation(s)
- Petr Louša
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Hana Nedozrálová
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Erik Župa
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jiří Nováček
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.
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19
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Kubáň V, Nováček J, Bumba L, Žídek L. NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. Biomol NMR Assign 2015; 9:435-440. [PMID: 26138689 DOI: 10.1007/s12104-015-9625-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
The self-processing module (SPM) is an internal segment of the FrpC protein (P415-F591) secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis during meningococcal infection of human upper respiratory tract. SPM mediates 'protein trans-splicing', a unique natural mechanism for editing of proteins, which involves a calcium-dependent autocatalytic cleavage of the peptide bond between D414 and P415 and covalent linkage of the cleaved fragment through its carboxy-terminal group of D414 to [Formula: see text]-amino group of lysine residue within a neighboring polypeptide chain. We present an NMR resonance assignment of the calcium-free SPM, which displays characteristic features of intrinsically disordered proteins. Non-uniformly sampled 5D HN(CA)CONH, 4D HCBCACON, and HCBCANCO spectra were recorded to resolve poorly dispersed resonance frequencies of the disordered protein and 91 % of SPM residues were unambiguously assigned. Analysis of the chemical shifts revealed that two regions of the intrinsically disordered SPM (A95-S101 and R120-I127) have a tendency to form a helical structure, whereas the residues P1-D7 and G36-A40 have the propensity to adopt a [Formula: see text]-structure.
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Affiliation(s)
- Vojtěch Kubáň
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jiří Nováček
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the ASCR, v. v. i, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Žídek
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
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20
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MacRaild CA, Zachrdla M, Andrew D, Krishnarjuna B, Nováček J, Žídek L, Sklenář V, Richards JS, Beeson JG, Anders RF, Norton RS. Conformational dynamics and antigenicity in the disordered malaria antigen merozoite surface protein 2. PLoS One 2015; 10:e0119899. [PMID: 25742002 PMCID: PMC4351039 DOI: 10.1371/journal.pone.0119899] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/16/2015] [Indexed: 12/14/2022] Open
Abstract
Merozoite surface protein 2 (MSP2) of Plasmodium falciparum is an abundant, intrinsically disordered protein that is GPI-anchored to the surface of the invasive blood stage of the malaria parasite. Recombinant MSP2 has been trialled as a component of a malaria vaccine, and is one of several disordered proteins that are candidates for inclusion in vaccines for malaria and other diseases. Nonetheless, little is known about the implications of protein disorder for the development of an effective antibody response. We have therefore undertaken a detailed analysis of the conformational dynamics of the two allelic forms of MSP2 (3D7 and FC27) using NMR spectroscopy. Chemical shifts and NMR relaxation data indicate that conformational and dynamic properties of the N- and C-terminal conserved regions in the two forms of MSP2 are essentially identical, but significant variation exists between and within the central variable regions. We observe a strong relationship between the conformational dynamics and the antigenicity of MSP2, as assessed with antisera to recombinant MSP2. Regions of increased conformational order in MSP2, including those in the conserved regions, are more strongly antigenic, while the most flexible regions are minimally antigenic. This suggests that modifications that increase conformational order may offer a means to tune the antigenicity of MSP2 and other disordered antigens, with implications for vaccine design.
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Affiliation(s)
- Christopher A. MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Australia
- * E-mail:
| | - Milan Zachrdla
- NCBR, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Dean Andrew
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia
| | - Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Australia
| | - Jiří Nováček
- NCBR, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Lukáš Žídek
- NCBR, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Vladimír Sklenář
- NCBR, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jack S. Richards
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia
| | - James G. Beeson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia
| | - Robin F. Anders
- Department of Biochemistry, La Trobe University, Victoria, 3086, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Australia
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21
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Nováček J, Žídek L, Sklenář V. Toward optimal-resolution NMR of intrinsically disordered proteins. J Magn Reson 2014; 241:41-52. [PMID: 24656079 DOI: 10.1016/j.jmr.2013.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their important roles in fundamental cellular processes, there is an urgent need to characterize the conformational behavior of IDPs at the highest possible level. The unique feature of NMR spectroscopy in the context of IDPs is its ability to supply details of their structural and temporal alterations at atomic-level resolution. Here, we briefly review recently proposed NMR-based strategies to characterize transient states populated by IDPs and summarize the latest achievements and future prospects in methodological development. Because low chemical shift dispersion represents the major obstacle encountered when studying IDPs by nuclear magnetic resonance, particular attention is paid to techniques allowing one to approach the physical limits of attainable resolution.
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Affiliation(s)
- Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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22
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Papoušková V, Kadeřávek P, Otrusinová O, Rabatinová A, Šanderová H, Nováček J, Krásný L, Sklenář V, Žídek L. Corrigendum: Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis. Chembiochem 2013. [DOI: 10.1002/cbic.201300497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Nováček J, Janda L, Dopitová R, Žídek L, Sklenář V. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. J Biomol NMR 2013; 56:291-301. [PMID: 23877929 DOI: 10.1007/s10858-013-9761-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/07/2013] [Indexed: 05/21/2023]
Abstract
Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional (13)C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Nováček et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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24
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Papoušková V, Kadeřávek P, Otrusinová O, Rabatinová A, ŠSanderová H, Nováček J, Krásný L, Sklenář V, Žídek L. Structural study of the partially disordered full-length δ subunit of RNA polymerase from Bacillus subtilis. Chembiochem 2013; 14:1772-9. [PMID: 23868186 DOI: 10.1002/cbic.201300226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/14/2013] [Indexed: 11/08/2022]
Abstract
The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well-folded N-terminal domain was determined based on inter-proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C-terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C-terminal domain. Various (15) N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C-terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C-terminal tail with the N-terminal domain and with itself were identified. A propensity of the C-terminal domain to form β-type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well-balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C-terminal domain. The results showed that the δ subunit consists of a well-ordered N-terminal domain and a flexible C-terminal domain that exhibits a complex hierarchy of partial ordering.
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Affiliation(s)
- Veronika Papoušková
- Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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25
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Nyarko A, Song Y, Nováček J, Žídek L, Barbar E. Multiple recognition motifs in nucleoporin Nup159 provide a stable and rigid Nup159-Dyn2 assembly. J Biol Chem 2012; 288:2614-22. [PMID: 23223634 DOI: 10.1074/jbc.m112.432831] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dyn2 is the yeast ortholog of the molecular hub LC8, which binds disordered proteins and promotes their self-association and higher order assembly. Dyn2 is proposed to dimerize and stabilize the Nup82-Nsp1-Nup159 complex of the nuclear pore assembly through its interaction with nucleoporin Nup159. Nup159 has six LC8 recognition motifs separated by short linkers. NMR experiments reported here show that the Dyn2 binding domain of Nup159 is intrinsically disordered and that binding of one equivalent of Dyn2 dimer aligns two Nup159 chains along the full Dyn2 binding domain to form a bivalent scaffold that promotes binding of other Dyn2 dimers. Isothermal titration calorimetry of Dyn2 binding to Nup constructs of increasing lengths determine that the third LC8 recognition motifs does not bind Dyn2. A new approach to identifying active LC8 recognition motifs based on NMR-detected β-sheet propensities is presented. Isothermal titration calorimetry experiments also show that, due to unfavorable entropy changes, a Nup-Dyn2 complex with three Dyn2 dimers is more stable than the wild-type complex with five Dyn2 dimers. The calorimetric results argue that, from a thermodynamics perspective, only three Dyn2 dimers are needed for optimal stability and suggest that the evolutionary adaptation of multiple tandem LC8 recognition motifs imparts to the complex other properties such as rigidity and a kink in the rod-like structure. These findings extend the repertoire of functions of intrinsically disordered protein to fine-tuning and versatile assembly of higher order macromolecular complexes.
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Affiliation(s)
- Afua Nyarko
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
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26
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Nováček J, Haba NY, Chill JH, Zídek L, Sklenář V. 4D non-uniformly sampled HCBCACON and ¹J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins. J Biomol NMR 2012; 53:139-48. [PMID: 22580891 DOI: 10.1007/s10858-012-9631-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/11/2012] [Indexed: 05/23/2023]
Abstract
A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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27
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Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Zídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V. 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomol NMR 2011; 50:1-11. [PMID: 21424579 DOI: 10.1007/s10858-011-9496-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 02/28/2011] [Indexed: 05/21/2023]
Abstract
Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of (13)C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Brno, Czech Republic
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28
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Motáčková V, Nováček J, Zawadzka-Kazimierczuk A, Kazimierczuk K, Žídek L, Šanderová H, Krásný L, Koźmiński W, Sklenář V. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR 2010; 48:169-77. [PMID: 20890634 PMCID: PMC2966349 DOI: 10.1007/s10858-010-9447-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/01/2010] [Indexed: 05/11/2023]
Abstract
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.
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Affiliation(s)
- Veronika Motáčková
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jiří Nováček
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | | | - Lukáš Žídek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Šanderová
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
| | - Vladimír Sklenář
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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