1
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Dutta T, Vlassakis J. Microscale measurements of protein complexes from single cells. Curr Opin Struct Biol 2024; 87:102860. [PMID: 38848654 DOI: 10.1016/j.sbi.2024.102860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Proteins execute numerous cell functions in concert with one another in protein-protein interactions (PPI). While essential in each cell, such interactions are not identical from cell to cell. Instead, PPI heterogeneity contributes to cellular phenotypic heterogeneity in health and diseases such as cancer. Understanding cellular phenotypic heterogeneity thus requires measurements of properties of PPIs such as abundance, stoichiometry, and kinetics at the single-cell level. Here, we review recent, exciting progress in single-cell PPI measurements. Novel technology in this area is enabled by microscale and microfluidic approaches that control analyte concentration in timescales needed to outpace PPI disassembly kinetics. We describe microscale innovations, needed technical capabilities, and methods poised to be adapted for single-cell analysis in the near future.
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Affiliation(s)
- Tanushree Dutta
- Department of Bioengineering, Rice University, Houston, TX 77005, USA. https://twitter.com/duttatanu1717
| | - Julea Vlassakis
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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2
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Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
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Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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3
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Schneider L, Rabe KS, Domínguez CM, Niemeyer CM. Hapten-Decorated DNA Nanostructures Decipher the Antigen-Mediated Spatial Organization of Antibodies Involved in Mast Cell Activation. ACS NANO 2023; 17:6719-6730. [PMID: 36990450 PMCID: PMC10100567 DOI: 10.1021/acsnano.2c12647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The immunological response of mast cells is controlled by the multivalent binding of antigens to immunoglobulin E (IgE) antibodies bound to the high-affinity receptor FcεRI on the cell membrane surface. However, the spatial organization of antigen-antibody-receptor complexes at the nanometer scale and the structural constraints involved in the initial events at the cell surface are not yet fully understood. For example, it is unclear what influence the affinity and nanoscale distance between the binding partners involved have on the activation of mast cells to degranulate inflammatory mediators from storage granules. We report the use of DNA origami nanostructures (DON) functionalized with different arrangements of the haptenic 2,4-dinitrophenyl (DNP) ligand to generate multivalent artificial antigens with full control over valency and nanoscale ligand architecture. To investigate the spatial requirements for mast cell activation, the DNP-DON complexes were initially used in surface plasmon resonance (SPR) analysis to study the binding kinetics of isolated IgE under physiological conditions. The most stable binding was observed in a narrow window of approximately 16 nm spacing between haptens. In contrast, affinity studies with FcεRI-linked IgE antibodies on the surface of rat basophilic leukemia cells (RBL-2H3) indicated virtually no distance-dependent variations in the binding of the differently structured DNP-DON complexes but suggested a supramolecular oligovalent nature of the interaction. Finally, the use of DNP-DON complexes for mast cell activation revealed that antigen-directed tight assembly of antibody-receptor complexes is the critical factor for triggering degranulation, even more critical than ligand valence. Our study emphasizes the significance of DNA nanostructures for the study of fundamental biological processes.
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4
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Philippi M, Richter CP, Kappen M, Watrinet I, Miao Y, Runge M, Jorde L, Korneev S, Holtmannspötter M, Kurre R, Holthuis JCM, Garcia KC, Plückthun A, Steinhart M, Piehler J, You C. Biofunctional Nanodot Arrays in Living Cells Uncover Synergistic Co-Condensation of Wnt Signalodroplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203723. [PMID: 36266931 DOI: 10.1002/smll.202203723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Qualitative and quantitative analysis of transient signaling platforms in the plasma membrane has remained a key experimental challenge. Here, biofunctional nanodot arrays (bNDAs) are developed to spatially control dimerization and clustering of cell surface receptors at the nanoscale. High-contrast bNDAs with spot diameters of ≈300 nm are obtained by capillary nanostamping of bovine serum albumin bioconjugates, which are subsequently biofunctionalized by reaction with tandem anti-green fluorescence protein (GFP) clamp fusions. Spatially controlled assembly of active Wnt signalosomes is achieved at the nanoscale in the plasma membrane of live cells by capturing the co-receptor Lrp6 into bNDAs via an extracellular GFP tag. Strikingly, co-recruitment is observed of co-receptor Frizzled-8 as well as the cytosolic scaffold proteins Axin-1 and Disheveled-2 into Lrp6 nanodots in the absence of ligand. Density variation and the high dynamics of effector proteins uncover highly cooperative liquid-liquid phase separation (LLPS)-driven assembly of Wnt "signalodroplets" at the plasma membrane, pinpointing the synergistic effects of LLPS for Wnt signaling amplification. These insights highlight the potential of bNDAs for systematically interrogating nanoscale signaling platforms and condensation at the plasma membrane of live cells.
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Affiliation(s)
- Michael Philippi
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Christian P Richter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Marie Kappen
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Isabelle Watrinet
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mercedes Runge
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Lara Jorde
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Sergej Korneev
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Joost C M Holthuis
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, Zurich, 8057, Switzerland
| | - Martin Steinhart
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Changjiang You
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
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5
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Sánchez MF, Dietz MS, Müller U, Weghuber J, Gatterdam K, Wieneke R, Heilemann M, Lanzerstorfer P, Tampé R. Dynamic in Situ Confinement Triggers Ligand-Free Neuropeptide Receptor Signaling. NANO LETTERS 2022; 22:8363-8371. [PMID: 36219818 PMCID: PMC9614963 DOI: 10.1021/acs.nanolett.2c03506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Membrane receptor clustering is fundamental to cell-cell communication; however, the physiological function of receptor clustering in cell signaling remains enigmatic. Here, we developed a dynamic platform to induce cluster formation of neuropeptide Y2 hormone receptors (Y2R) in situ by a chelator nanotool. The multivalent interaction enabled a dynamic exchange of histidine-tagged Y2R within the clusters. Fast Y2R enrichment in clustered areas triggered ligand-independent signaling as determined by an increase in cytosolic calcium and cell migration. Notably, the calcium and motility response to ligand-induced activation was amplified in preclustered cells, suggesting a key role of receptor clustering in sensitizing the dose response to lower ligand concentrations. Ligand-independent versus ligand-induced signaling differed in the binding of arrestin-3 as a downstream effector, which was recruited to the clusters only in the presence of the ligand. This approach allows in situ receptor clustering, raising the possibility to explore different receptor activation modalities.
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Affiliation(s)
- M. Florencia Sánchez
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Marina S. Dietz
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrike Müller
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Julian Weghuber
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
- FFoQSI
- Austrian Competence Centre for Feed and Food Quality, Safety &
Innovation, FFoQSI GmbH, Technopark 1D, 3430 Tulln, Austria
| | - Karl Gatterdam
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Ralph Wieneke
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Peter Lanzerstorfer
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Robert Tampé
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
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6
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Al‐Zaid B, Chacko S, Ezeamuzie CI, Bünemann M, Krasel C, Karimian T, Lanzerstorfer P, Al‐Sabah S. Differential effects of glucose-dependent insulinotropic polypeptide receptor/glucagon-like peptide-1 receptor heteromerization on cell signaling when expressed in HEK-293 cells. Pharmacol Res Perspect 2022; 10:e01013. [PMID: 36177761 PMCID: PMC9523454 DOI: 10.1002/prp2.1013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022] Open
Abstract
The incretin hormones: glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) are important regulators of many aspects of metabolism including insulin secretion. Their receptors (GIPR and GLP-1R) are closely related members of the secretin class of G-protein-coupled receptors. As both receptors are expressed on pancreatic β-cells there is at least the hypothetical possibility that they may form heteromers. In the present study, we investigated GIPR/GLP-1R heteromerization and the impact of GIPR on GLP-1R-mediated signaling and vice versa in HEK-293 cells. Real-time fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) saturation experiments confirm that GLP-1R and GIPR form heteromers. Stimulation with 1 μM GLP-1 caused an increase in both FRET and BRET ratio, whereas stimulation with 1 μM GIP caused a decrease. The only other ligand tested to cause a significant change in BRET signal was the GLP-1 metabolite, GLP-1 (9-36). GIPR expression had no significant effect on mini-Gs recruitment to GLP-1R but significantly inhibited GLP-1 stimulated mini-Gq and arrestin recruitment. In contrast, the presence of GLP-1R improved GIP stimulated mini-Gs and mini-Gq recruitment to GIPR. These data support the hypothesis that GIPR and GLP-1R form heteromers with differential consequences on cell signaling.
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Affiliation(s)
- Bashaier Al‐Zaid
- Department of Pharmacology and Toxicology, Faculty of MedicineKuwait UniversityKuwait CityKuwait
| | - Siby Chacko
- Department of Pharmacology and Toxicology, Faculty of MedicineKuwait UniversityKuwait CityKuwait
| | | | - Moritz Bünemann
- School of Pharmacy, Institute for Pharmacology and ToxicologyThe Philipps University of MarburgMarburgGermany
| | - Cornelius Krasel
- School of Pharmacy, Institute for Pharmacology and ToxicologyThe Philipps University of MarburgMarburgGermany
| | - Tina Karimian
- University of Applied Sciences Upper Austria, School of EngineeringWelsAustria
| | - Peter Lanzerstorfer
- University of Applied Sciences Upper Austria, School of EngineeringWelsAustria
| | - Suleiman Al‐Sabah
- Department of Pharmacology and Toxicology, Faculty of MedicineKuwait UniversityKuwait CityKuwait
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7
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Domínguez CM, García-Chamé M, Müller U, Kraus A, Gordiyenko K, Itani A, Haschke H, Lanzerstorfer P, Rabe KS, Niemeyer CM. Linker Engineering of Ligand-Decorated DNA Origami Nanostructures Affects Biological Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202704. [PMID: 35934828 DOI: 10.1002/smll.202202704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/11/2022] [Indexed: 06/15/2023]
Abstract
News from an old acquaintance: The streptavidin (STV)-biotin binding system is frequently used for the decoration of DNA origami nanostructures (DON) to study biological systems. Here, a surprisingly high dynamic of the STV/DON interaction is reported, which is affected by the structure of the DNA linker system. Analysis of different mono- or bi-dentate linker architectures on DON with a novel high-speed atomic force microscope (HS-AFM) enabling acquisition times as short as 50 ms per frame gave detailed insights into the dynamics of the DON/STV interaction, revealing dwell times in the sub-100 millisecond range. The linker systems are also used to present biotinylated epidermal growth factor on DON to study the activation of the epidermal growth factor receptor signaling cascade in HeLa cells. The studies confirm that cellular activation correlated with the binding properties of linker-specific STV/DON interactions observed by HS-AFM. This work sheds more light on the commonly used STV/DON system and will help to further standardize the use of DNA nanostructures for the study of biological processes.
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Affiliation(s)
- Carmen M Domínguez
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Miguel García-Chamé
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ulrike Müller
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Andreas Kraus
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Klavdiya Gordiyenko
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ahmad Itani
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Heiko Haschke
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Peter Lanzerstorfer
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
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8
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Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders AR, Linden N, Karner A, Preiner J, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Piehler J, Lanzerstorfer P, Springer S. Dissociation of β2m from MHC class I Triggers formation of Noncovalent, transient heavy chain dimers. J Cell Sci 2022; 135:274997. [PMID: 35393611 DOI: 10.1242/jcs.259498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
At the plasma membrane of mammalian cells, major histocompatibility complex class I molecules (MHC-I) present antigenic peptides to cytotoxic T cells. Following the loss of the peptide and the light chain beta-2 microglobulin (β2m), the resulting free heavy chains (FHCs) can associate into homotypic complexes in the plasma membrane. Here, we investigate the stoichiometry and dynamics of MHC-I FHCs assemblies by combining a micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single molecule co-tracking. We identify non-covalent MHC-I FHC dimers mediated by the α3 domain as the prevalent species at the plasma membrane, leading a moderate decrease in the diffusion coefficient. MHC-I FHC dimers show increased tendency to cluster into higher order oligomers as concluded from an increased immobile fraction with higher single molecule co-localization. In vitro studies with isolated proteins in conjunction with molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another FHC in a manner similar to the β2m light chain.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Sara Löchte
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Noemi Linden
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.,Centre for Structural Systems Biology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL, Schenefeld, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | | | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
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9
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Karimian T, Hager R, Karner A, Weghuber J, Lanzerstorfer P. A Simplified and Robust Activation Procedure of Glass Surfaces for Printing Proteins and Subcellular Micropatterning Experiments. BIOSENSORS 2022; 12:bios12030140. [PMID: 35323410 PMCID: PMC8946821 DOI: 10.3390/bios12030140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 05/08/2023]
Abstract
Depositing biomolecule micropatterns on solid substrates via microcontact printing (µCP) usually requires complex chemical substrate modifications to initially create reactive surface groups. Here, we present a simplified activation procedure for untreated solid substrates based on a commercial polymer metal ion coating (AnteoBindTM Biosensor reagent) that allows for direct µCP and the strong attachment of proteins via avidity binding. In proof-of-concept experiments, we identified the optimum working concentrations of the surface coating, characterized the specificity of protein binding and demonstrated the suitability of this approach by subcellular micropatterning experiments in living cells. Altogether, this method represents a significant enhancement and simplification of existing µCP procedures and further increases the accessibility of protein micropatterning for cell biological research questions.
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Affiliation(s)
- Tina Karimian
- School of Engineering, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Roland Hager
- School of Engineering, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Andreas Karner
- School of Engineering, University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- School of Engineering, University of Applied Sciences Upper Austria, 4600 Wels, Austria
- FFoQSI GmbH, Austrian Competence Center for Feed and Food Quality, Safety & Innovation, 3430 Tulln, Austria
| | - Peter Lanzerstorfer
- School of Engineering, University of Applied Sciences Upper Austria, 4600 Wels, Austria
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10
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Hager R, Müller U, Ollinger N, Weghuber J, Lanzerstorfer P. Subcellular Dynamic Immunopatterning of Cytosolic Protein Complexes on Microstructured Polymer Substrates. ACS Sens 2021; 6:4076-4088. [PMID: 34652152 PMCID: PMC8630788 DOI: 10.1021/acssensors.1c01574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Analysis of protein–protein
interactions in living cells
by protein micropatterning is currently limited to the spatial arrangement
of transmembrane proteins and their corresponding downstream molecules.
Here, we present a robust and straightforward method for dynamic immunopatterning
of cytosolic protein complexes by use of an artificial transmembrane
bait construct in combination with microstructured antibody arrays
on cyclic olefin polymer substrates. As a proof, the method was used
to characterize Grb2-mediated signaling pathways downstream of the
epidermal growth factor receptor (EGFR). Ternary protein complexes
(Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified, and we found
that EGFR downstream signaling is based on constitutively bound (Grb2:SOS1
and Grb2:Gab1) as well as on agonist-dependent protein associations
with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal
analysis further revealed significant differences in stability and
exchange kinetics of protein interactions. Furthermore, we could show
that this approach is well suited to study the efficacy and specificity
of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether,
this method represents a significant enhancement of quantitative subcellular
micropatterning approaches as an alternative to standard biochemical
analyses.
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Affiliation(s)
- Roland Hager
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
| | - Ulrike Müller
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
| | - Nicole Ollinger
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office: FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office: FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Peter Lanzerstorfer
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
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11
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Zhang X, Zhang M, Wu M, Yang L, Liu R, Zhang R, Zhao T, Song C, Liu G, Zhu Q. Photoresponsive Bridged Polysilsesquioxanes for Protein Immobilization/Controlled Release and Micropatterns. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36370-36379. [PMID: 34297533 DOI: 10.1021/acsami.1c10542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein micropatterning on microfabricated surfaces is a promising technology in applications for biochip microarrays, cell attachment, and biosensors. In the present work, a novel photoresponsive polymer based on light-triggered charge shifting bridged polysilsesquioxane (CBPS) is designed and prepared. The organic bridged units containing a photocleavable group of diethylaminocoumarin-4-yl in CBPS could be cleaved rapidly upon irradiation at 410 nm, resulting in the polymer surface switching from a positive charge to a negative charge property. The photoresponsive behavior of CBPS is studied using FTIR, UV-vis, SEM, fluorescence microscopy, and zeta potential analysis. Proteins are easily immobilized on the polymer surface via electrostatic interactions and released after irradiation as required. Combined with photopatterning techniques, accurate protein micropatterns are fabricated by covering a photomask upon irradiation. A gradient protein pattern is also spatially and temporally controlled by regulating irradiation parameters. This smart photoresponsive polymer surface provides a gentle and straightforward strategy to micropattern charged proteins. Moreover, the photoresponsive polymer holds permitting potential in biomedical applications such as conjugating biomolecules, guiding cell arrays, and resisting bacteria.
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Affiliation(s)
- Xin Zhang
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Mengmeng Zhang
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Mingyue Wu
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Linchuan Yang
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Rui Liu
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Rui Zhang
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Tongtong Zhao
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Ci Song
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Gang Liu
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Qingzeng Zhu
- Key Laboratory of Special Functional Aggregated Materials, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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12
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Berger RML, Weck JM, Kempe SM, Hill O, Liedl T, Rädler JO, Monzel C, Heuer-Jungemann A. Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101678. [PMID: 34057291 DOI: 10.1002/smll.202101678] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Indexed: 05/27/2023]
Abstract
Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100× more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses.
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Affiliation(s)
- Ricarda M L Berger
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Johann M Weck
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Simon M Kempe
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Oliver Hill
- Apogenix AG, University of Heidelberg, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
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13
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
| | - Yong Wang
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
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14
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Shi P, Wang Y. Synthetic DNA for Cell-Surface Engineering. Angew Chem Int Ed Engl 2021; 60:11580-11591. [PMID: 33006229 DOI: 10.1002/anie.202010278] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 12/14/2022]
Abstract
The cell membrane is not only a physical barrier, but also a functional organelle that regulates the communication between a cell and its environment. The ability to functionalize the cell membrane with synthetic molecules or nanostructures would advance cellular functions beyond what evolution has provided. The aim of this Minireview is to introduce recent progress in using synthetic DNA and DNA-based nanostructures for cell-surface engineering. We first introduce chemical conjugation and physical binding methods for monovalent and polyvalent surface engineering. We then introduce the application of these methods for either the promotion or inhibition of cell-environment communication in numerous applications, including the promotion of cell-cell recognition, regulation of intracellular pathways, protection of therapeutic cells, and sensing of the intracellular and extracellular microenvironments. Lastly, we summarize current challenges existing in this area and potential solutions to solve these challenges.
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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15
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Martínez-Miguel M, Kyvik AR, M Ernst L, Martínez-Moreno A, Cano-Garrido O, Garcia-Fruitós E, Vazquez E, Ventosa N, Guasch J, Veciana J, Villaverde A, Ratera I. Stable anchoring of bacteria-based protein nanoparticles for surface enhanced cell guidance. J Mater Chem B 2020; 8:5080-5088. [PMID: 32400840 DOI: 10.1039/d0tb00702a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In tissue engineering, biological, physical, and chemical inputs have to be combined to properly mimic cellular environments and successfully build artificial tissues which can be designed to fulfill different biomedical needs such as the shortage of organ donors or the development of in vitro disease models for drug testing. Inclusion body-like protein nanoparticles (pNPs) can simultaneously provide such physical and biochemical stimuli to cells when attached to surfaces. However, this attachment has only been made by physisorption. To provide a stable anchoring, a covalent binding of lactic acid bacteria (LAB) produced pNPs, which lack the innate pyrogenic impurities of Gram-negative bacteria like Escherichia coli, is presented. The reported micropatterns feature a robust nanoscale topography with an unprecedented mechanical stability. In addition, they are denser and more capable of influencing cell morphology and orientation. The increased stability and the absence of pyrogenic impurities represent a step forward towards the translation of this material to a clinical setting.
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Affiliation(s)
- Marc Martínez-Miguel
- Department of Molecular Nanoscience and Organic Materials, Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain.
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