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Bozděchová L, Rudolfová A, Hanáková K, Fojtová M, Fajkus J. Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study. Plants (Basel) 2024; 13:850. [PMID: 38592918 PMCID: PMC10975786 DOI: 10.3390/plants13060850] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Anna Rudolfová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Kateřina Hanáková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
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Dave Z, Vondálová Blanářová O, Čada Š, Janovská P, Zezula N, Běhal M, Hanáková K, Ganji SR, Krejci P, Gömöryová K, Peschelová H, Šmída M, Zdráhal Z, Pavlová Š, Kotašková J, Pospíšilová Š, Bryja V. Lyn Phosphorylates and Controls ROR1 Surface Dynamics During Chemotaxis of CLL Cells. Front Cell Dev Biol 2022; 10:838871. [PMID: 35295854 PMCID: PMC8918536 DOI: 10.3389/fcell.2022.838871] [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: 12/18/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are malignancies characterized by the dependence on B-cell receptor (BCR) signaling and by the high expression of ROR1, the cell surface receptor for Wnt-5a. Both, BCR and ROR1 are therapeutic targets in these diseases and the understanding of their mutual cross talk is thus of direct therapeutic relevance. In this study we analyzed the role of Lyn, a kinase from the Src family participating in BCR signaling, as a mediator of the BCR-ROR1 crosstalk. We confirm the functional interaction between Lyn and ROR1 and demonstrate that Lyn kinase efficiently phosphorylates ROR1 in its kinase domain and aids the recruitment of the E3 ligase c-CBL. We show that ROR1 surface dynamics in migrating primary CLL cells as well as chemotactic properties of CLL cells were inhibited by Lyn inhibitor dasatinib. Our data establish Lyn-mediated phosphorylation of ROR1 as a point of crosstalk between BCR and ROR1 signaling pathways.
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Affiliation(s)
- Zankruti Dave
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Olga Vondálová Blanářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavlína Janovská
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Nikodém Zezula
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Běhal
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kateřina Hanáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Sri Ranjani Ganji
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Helena Peschelová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michal Šmída
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine—Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Šárka Pavlová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine—Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotašková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine—Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Šárka Pospíšilová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine—Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Brno, Czech Republic
- *Correspondence: Vítězslav Bryja,
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Hanáková K, Bernatík O, Kravec M, Micka M, Kumar J, Harnoš J, Ovesná P, Paclíková P, Rádsetoulal M, Potěšil D, Tripsianes K, Čajánek L, Zdráhal Z, Bryja V. Comparative phosphorylation map of Dishevelled 3 links phospho-signatures to biological outputs. Cell Commun Signal 2019; 17:170. [PMID: 31870452 PMCID: PMC6927192 DOI: 10.1186/s12964-019-0470-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 09/02/2019] [Accepted: 10/22/2019] [Indexed: 12/28/2022] Open
Abstract
Background Dishevelled (DVL) is an essential component of the Wnt signaling cascades. Function of DVL is controlled by phosphorylation but the molecular details are missing. DVL3 contains 131 serines and threonines whose phosphorylation generates complex barcodes underlying diverse DVL3 functions. In order to dissect the role of DVL phosphorylation we analyzed the phosphorylation of human DVL3 induced by previously reported (CK1ε, NEK2, PLK1, CK2α, RIPK4, PKCδ) and newly identified (TTBK2, Aurora A) DVL kinases. Methods Shotgun proteomics including TiO2 enrichment of phosphorylated peptides followed by liquid chromatography tandem mass spectrometry on immunoprecipitates from HEK293T cells was used to identify and quantify phosphorylation of DVL3 protein induced by 8 kinases. Functional characterization was performed by in-cell analysis of phospho-mimicking/non-phosphorylatable DVL3 mutants and supported by FRET assays and NMR spectroscopy. Results We used quantitative mass spectrometry and calculated site occupancies and quantified phosphorylation of > 80 residues. Functional validation demonstrated the importance of CK1ε-induced phosphorylation of S268 and S311 for Wnt-3a-induced β-catenin activation. S630–643 cluster phosphorylation by CK1, NEK2 or TTBK2 is essential for even subcellular distribution of DVL3 when induced by CK1 and TTBK2 but not by NEK2. Further investigation showed that NEK2 utilizes a different mechanism to promote even localization of DVL3. NEK2 triggered phosphorylation of PDZ domain at S263 and S280 prevents binding of DVL C-terminus to PDZ and promotes an open conformation of DVL3 that is more prone to even subcellular localization. Conclusions We identify unique phosphorylation barcodes associated with DVL function. Our data provide an example of functional synergy between phosphorylation in structured domains and unstructured IDRs that together dictate the biological outcome. Video Abtract.
Graphical abstract ![]()
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Affiliation(s)
- Kateřina Hanáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondřej Bernatík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Kravec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Miroslav Micka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jitender Kumar
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jakub Harnoš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petra Ovesná
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Matěj Rádsetoulal
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - David Potěšil
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Konstantinos Tripsianes
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukáš Čajánek
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. .,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic. .,Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Harnoš J, Cañizal MCA, Jurásek M, Kumar J, Holler C, Schambony A, Hanáková K, Bernatík O, Zdráhal Z, Gömöryová K, Gybeľ T, Radaszkiewicz TW, Kravec M, Trantírek L, Ryneš J, Dave Z, Fernández-Llamazares AI, Vácha R, Tripsianes K, Hoffmann C, Bryja V. Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nat Commun 2019; 10:1804. [PMID: 31000703 PMCID: PMC6472409 DOI: 10.1038/s41467-019-09651-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 02/16/2018] [Accepted: 03/20/2019] [Indexed: 01/17/2023] Open
Abstract
Dishevelled (DVL) is the key component of the Wnt signaling pathway. Currently, DVL conformational dynamics under native conditions is unknown. To overcome this limitation, we develop the Fluorescein Arsenical Hairpin Binder- (FlAsH-) based FRET in vivo approach to study DVL conformation in living cells. Using this single-cell FRET approach, we demonstrate that (i) Wnt ligands induce open DVL conformation, (ii) DVL variants that are predominantly open, show more even subcellular localization and more efficient membrane recruitment by Frizzled (FZD) and (iii) Casein kinase 1 ɛ (CK1ɛ) has a key regulatory function in DVL conformational dynamics. In silico modeling and in vitro biophysical methods explain how CK1ɛ-specific phosphorylation events control DVL conformations via modulation of the PDZ domain and its interaction with DVL C-terminus. In summary, our study describes an experimental tool for DVL conformational sampling in living cells and elucidates the essential regulatory role of CK1ɛ in DVL conformational dynamics.
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Affiliation(s)
- Jakub Harnoš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic.,Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Maria Consuelo Alonso Cañizal
- Department of Pharmacology and Toxicology, University of Würzburg, Würzburg, 97078, Germany.,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, 97078, Germany.,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Miroslav Jurásek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Jitender Kumar
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Cornelia Holler
- Max Planck Institute for the Science of Light, Erlangen, 91058, Germany.,Biology Department, Developmental Biology, Friedrich-Alexander University Erlangen-Nüremberg, Erlangen, 91058, Germany
| | - Alexandra Schambony
- Max Planck Institute for the Science of Light, Erlangen, 91058, Germany.,Biology Department, Developmental Biology, Friedrich-Alexander University Erlangen-Nüremberg, Erlangen, 91058, Germany
| | - Kateřina Hanáková
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Ondřej Bernatík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | | | - Marek Kravec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Lukáš Trantírek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65, Czech Republic
| | - Jan Ryneš
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Zankruti Dave
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | | | - Robert Vácha
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Konstantinos Tripsianes
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Carsten Hoffmann
- Department of Pharmacology and Toxicology, University of Würzburg, Würzburg, 97078, Germany.,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, 97078, Germany.,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic. .,Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65, Czech Republic.
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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. [PMID: 28623194 DOI: 10.1074/jbc.a116.771097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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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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