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Pospíšil J, Hrabovský M, Bohačiaková D, Hovádková Z, Jurásek M, Mlčoušková J, Paruch K, Nevolová Š, Damborsky J, Hampl A, Jaros J. Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS Biomater Sci Eng 2022; 8:4789-4806. [PMID: 36202388 PMCID: PMC9667466 DOI: 10.1021/acsbiomaterials.2c00650] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Many dynamic interactions within the cell microenvironment
modulate
cell behavior and cell fate. However, the pathways and mechanisms
behind cell–cell or cell–extracellular matrix interactions
remain understudied, as they occur at a nanoscale level. Recent progress
in nanotechnology allows for mimicking of the microenvironment at
nanoscale in vitro; electron-beam lithography (EBL)
is currently the most promising technique. Although this nanopatterning
technique can generate nanostructures of good quality and resolution,
it has resulted, thus far, in the production of only simple shapes
(e.g., rectangles) over a relatively small area (100 × 100 μm),
leaving its potential in biological applications unfulfilled. Here,
we used EBL for cell-interaction studies by coating cell-culture-relevant
material with electron-conductive indium tin oxide, which formed nanopatterns
of complex nanohexagonal structures over a large area (500 ×
500 μm). We confirmed the potential of EBL for use in cell-interaction
studies by analyzing specific cell responses toward differentially
distributed nanohexagons spaced at 1000, 500, and 250 nm. We found
that our optimized technique of EBL with HaloTags enabled the investigation
of broad changes to a cell-culture-relevant surface and can provide
an understanding of cellular signaling mechanisms at a single-molecule
level.
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Affiliation(s)
- Jakub Pospíšil
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,Core Facility Cellular Imaging, CEITEC, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Miloš Hrabovský
- TESCAN Orsay Holding a.s., Libušina tř. 863, Brno 623 00, Czech Republic
| | - Dáša Bohačiaková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | | | | | - Jarmila Mlčoušková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Kamil Paruch
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Šárka Nevolová
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Jiri Damborsky
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Aleš Hampl
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | - Josef Jaros
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
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Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Sci Rep 2021; 11:1484. [PMID: 33452274 PMCID: PMC7810883 DOI: 10.1038/s41598-020-79398-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/04/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
The PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.
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Affiliation(s)
- Miroslav Jurásek
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jitender Kumar
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Petra Paclíková
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Alka Kumari
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Konstantinos Tripsianes
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Vítězslav Bryja
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic ,grid.418095.10000 0001 1015 3316Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65 Czech Republic
| | - Robert Vácha
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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Jurásek M, Flärdh K, Vácha R. Effect of membrane composition on DivIVA-membrane interaction. Biochim Biophys Acta Biomembr 2019; 1862:183144. [PMID: 31821790 DOI: 10.1016/j.bbamem.2019.183144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022]
Abstract
DivIVA is a crucial membrane-binding protein that helps to localize other proteins to negatively curved membranes at cellular poles and division septa in Gram-positive bacteria. The N-terminal domain of DivIVA is responsible for membrane binding. However, to which lipids the domain binds or how it recognizes the membrane negative curvature remains elusive. Using computer simulations, we demonstrate that the N-terminal domain of Streptomyces coelicolor DivIVA adsorbs to membranes with affinity and orientation dependent on the lipid composition. The domain interacts non-specifically with lipid phosphates via its arginine-rich tip and the strongest interaction is with cardiolipin. Moreover, we observed a specific attraction between a negatively charged side patch of the domain and ethanolamine lipids, which addition caused the change of the domain orientation from perpendicular to parallel alignment to the membrane plane. Similar but less electrostatically dependent behavior was observed for the N-terminal domain of Bacillus subtilis. The domain propensity for lipids which prefer negatively curved membranes could be a mechanism for the cellular localization of DivIVA protein.
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Affiliation(s)
- Miroslav Jurásek
- Faculty of Science, Masaryk University,Kamenice 753/5, Brno 625 00, Czech Republic
| | - Klas Flärdh
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Robert Vácha
- Faculty of Science, Masaryk University,Kamenice 753/5, Brno 625 00, Czech Republic; CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, 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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Tubiana L, Jurásek M, Coluzza I. Implementing efficient concerted rotations using Mathematica and C code ⋆. Eur Phys J E Soft Matter 2018; 41:87. [PMID: 30022359 DOI: 10.1140/epje/i2018-11694-7] [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] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.
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Affiliation(s)
- Luca Tubiana
- Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria.
| | - Miroslav Jurásek
- Faculty of Science, Masaryk University, Kotlářská 2, 602 00, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivan Coluzza
- CIC biomaGUNE Parque Cientfico y Tecnolgico de Gipuzkoa, Paseo Miramn 182, 20014, Donostia / San Sebastin, Gipuzkoa, Spain
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Abstract
The design of complex self-assembled structures remains a challenging task due to the intricate relationship between the properties of the building blocks and the final morphology of the aggregates. Here, we report such a relationship for rod-like particles with one or two attractive patches based on a combination of computer simulations and analytical theory. We investigated the formation of finite aggregates under various conditions and constructed structure diagrams, which can be used to determine and extrapolate the system composition. The size of the clusters is mainly determined by the size of the attractive patches and their geometrical arrangement. We showed that it is challenging to obtain clusters with more than four particles in high yields, and more complex building blocks or additional molecules would need to be used. Moreover, the particles with patch sizes close to the structure boundaries can switch between the aggregate state by a small change in conditions. These findings can be useful for the development of self-assembling building blocks and for the understanding of protein folds of coiled coils under various conditions.
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Affiliation(s)
- Miroslav Jurásek
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic and Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic.
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic and Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic.
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