1
|
Scheller J, Ettich J, Wittich C, Pudewell S, Floss DM, Rafii P. Exploring the landscape of synthetic IL-6-type cytokines. FEBS J 2024; 291:2030-2050. [PMID: 37467060 DOI: 10.1111/febs.16909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
Interleukin-6 (IL-6)-type cytokines not only have key immunomodulatory functions that affect the pathogenesis of diseases such as autoimmune diseases, chronic inflammatory conditions, and cancer, but also fulfill important homeostatic tasks. Even though the pro-inflammatory arm has hindered the development of therapeutics based on natural-like IL-6-type cytokines to date, current synthetic trends might pave the way to overcome these limitations and eventually lead to immune-inert designer cytokines to aid type 2 diabetes and brain injuries. Those synthetic biology approaches include mutations, fusion proteins, and inter-cytokine swapping, and resulted in IL-6-type cytokines with altered receptor affinities, extended target cell profiles, and targeting of non-natural cytokine receptor complexes. Here, we survey synthetic cytokine developments within the IL-6-type cytokine family and discuss potential clinical applications.
Collapse
Affiliation(s)
- Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Ettich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Wittich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Silke Pudewell
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Doreen M Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Puyan Rafii
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| |
Collapse
|
2
|
Gardner S, Jin Y, Fyfe PK, Voisin TB, Bellón JS, Pohler E, Piehler J, Moraga I, Bubeck D. Structural insights into IL-11-mediated signalling and human IL6ST variant-associated immunodeficiency. Nat Commun 2024; 15:2071. [PMID: 38453915 PMCID: PMC10920896 DOI: 10.1038/s41467-024-46235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
IL-11 and IL-6 activate signalling via assembly of the cell surface receptor gp130; however, it is unclear how signals are transmitted across the membrane to instruct cellular responses. Here we solve the cryoEM structure of the IL-11 receptor recognition complex to discover how differences in gp130-binding interfaces may drive signalling outcomes. We explore how mutations in the IL6ST gene encoding for gp130, which cause severe immune deficiencies in humans, impair signalling without blocking cytokine binding. We use cryoEM to solve structures of both IL-11 and IL-6 complexes with a mutant form of gp130 associated with human disease. Together with molecular dynamics simulations, we show that the disease-associated variant led to an increase in flexibility including motion within the cytokine-binding core and increased distance between extracellular domains. However, these distances are minimized as the transmembrane helix exits the membrane, suggesting a stringency in geometry for signalling and dimmer switch mode of action.
Collapse
Affiliation(s)
- Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Yibo Jin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Paul K Fyfe
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tomas B Voisin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Junel Sotolongo Bellón
- Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Elizabeth Pohler
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jacob Piehler
- Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
3
|
Fessl T, Majellaro M, Bondar A. Microscopy and spectroscopy approaches to study GPCR structure and function. Br J Pharmacol 2023. [PMID: 38087925 DOI: 10.1111/bph.16297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The GPCR signalling cascade is a key pathway responsible for the signal transduction of a multitude of physical and chemical stimuli, including light, odorants, neurotransmitters and hormones. Understanding the structural and functional properties of the GPCR cascade requires direct observation of signalling processes in high spatial and temporal resolution, with minimal perturbation to endogenous systems. Optical microscopy and spectroscopy techniques are uniquely suited to this purpose because they excel at multiple spatial and temporal scales and can be used in living objects. Here, we review recent developments in microscopy and spectroscopy technologies which enable new insights into GPCR signalling. We focus on advanced techniques with high spatial and temporal resolution, single-molecule methods, labelling strategies and approaches suitable for endogenous systems and large living objects. This review aims to assist researchers in choosing appropriate microscopy and spectroscopy approaches for a variety of applications in the study of cellular signalling.
Collapse
Affiliation(s)
- Tomáš Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Alexey Bondar
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Laboratory of Microscopy and Histology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| |
Collapse
|
4
|
Esch BM, Walter S, Schmidt O, Fröhlich F. Identification of distinct active pools of yeast serine palmitoyltransferase in sub-compartments of the ER. J Cell Sci 2023; 136:jcs261353. [PMID: 37982431 DOI: 10.1242/jcs.261353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Sphingolipids (SPs) are one of the three major lipid classes in eukaryotic cells and serve as structural components of the plasma membrane. The rate-limiting step in SP biosynthesis is catalyzed by the serine palmitoyltransferase (SPT). In budding yeast (Saccharomyces cerevisiae), SPT is negatively regulated by the two proteins, Orm1 and Orm2. Regulating SPT activity enables cells to adapt SP metabolism to changing environmental conditions. Therefore, the Orm proteins are phosphorylated by two signaling pathways originating from either the plasma membrane or the lysosome (or vacuole in yeast). Moreover, uptake of exogenous serine is necessary for the regulation of SP biosynthesis, which suggests the existence of differentially regulated SPT pools based on their intracellular localization. However, measuring lipid metabolic enzyme activity in different cellular sub-compartments has been challenging. Combining a nanobody recruitment approach with SP flux analysis, we show that the nuclear endoplasmic reticulum (ER)-localized SPT and the peripheral ER localized SPT pools are differentially active. Thus, our data add another layer to the complex network of SPT regulation. Moreover, combining lipid metabolic enzyme re-localization with flux analysis serves as versatile tool to measure lipid metabolism with subcellular resolution.
Collapse
Affiliation(s)
- Bianca M Esch
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Florian Fröhlich
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| |
Collapse
|
5
|
Tsutsumi N, Masoumi Z, James SC, Tucker JA, Winkelmann H, Grey W, Picton LK, Moss L, Wilson SC, Caveney NA, Jude KM, Gati C, Piehler J, Hitchcock IS, Garcia KC. Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis. Cell 2023; 186:4189-4203.e22. [PMID: 37633268 PMCID: PMC10528194 DOI: 10.1016/j.cell.2023.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy structure of the extracellular TPO-TPO receptor (TpoR or MPL) signaling complex, revealing the basis for homodimeric MPL activation and providing a structural rationalization for genetic loss-of-function thrombocytopenia mutations. The structure guided the engineering of TPO variants (TPOmod) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPOmod decoupled JAK/STAT from ERK/AKT/CREB activation, driving a bias for megakaryopoiesis and platelet production without causing significant HSC expansion in mice and showing superior maintenance of human HSCs in vitro. These data demonstrate the functional uncoupling of the two primary roles of TPO, highlighting the potential utility of TPOmod in hematology research and clinical HSC transplantation.
Collapse
Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.
| | - Zahra Masoumi
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Sophie C James
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Julie A Tucker
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - William Grey
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Lora K Picton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucie Moss
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Ian S Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
6
|
Prindle JR, de Cuba OIC, Gahlmann A. Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects. J Chem Phys 2023; 159:071002. [PMID: 37589409 PMCID: PMC10908566 DOI: 10.1063/5.0155638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023] Open
Abstract
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
Collapse
Affiliation(s)
- Joshua Robert Prindle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Olivia Isabella Christiane de Cuba
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
| | | |
Collapse
|
7
|
Su Z, Almo SC, Wu Y. Understanding the General Principles of T Cell Engagement by Multiscale Computational Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544116. [PMID: 37333150 PMCID: PMC10274768 DOI: 10.1101/2023.06.07.544116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The use of bispecific antibodies as T cell engagers can bypass the normal TCR-MHC interaction, redirect the cytotoxic activity of T-cells, and lead to highly efficient tumor cell killing. However, this immunotherapy also causes significant on-target off-tumor toxicologic effects, especially when they were used to treat solid tumors. In order to avoid these adverse events, it is necessary to understand the fundamental mechanisms during the physical process of T cell engagement. We developed a multiscale computational framework to reach this goal. The framework combines simulations on the intercellular and multicellular levels. On the intercellular level, we simulated the spatial-temporal dynamics of three-body interactions among bispecific antibodies, CD3 and TAA. The derived number of intercellular bonds formed between CD3 and TAA were further transferred into the multicellular simulations as the input parameter of adhesive density between cells. Through the simulations under various molecular and cellular conditions, we were able to gain new insights of how to adopt the most appropriate strategy to maximize the drug efficacy and avoid the off-target effect. For instance, we discovered that the low antibody binding affinity resulted in the formation of large clusters at the cell-cell interface, which could be important to control the downstream signaling pathways. We also tested different molecular architectures of the bispecific antibody and suggested the existence of an optimal length in regulating the T cell engagement. Overall, the current multiscale simulations serve as a prove-of-concept study to help the future design of new biological therapeutics. SIGNIFICANCE T-cell engagers are a class of anti-cancer drugs that can directly kill tumor cells by bringing T cells next to them. However, current treatments using T-cell engagers can cause serious side-effects. In order to reduce these effects, it is necessary to understand how T cells and tumor cells interact together through the connection of T-cell engagers. Unfortunately, this process is not well studied due to the limitations in current experimental techniques. We developed computational models on two different scales to simulate the physical process of T cell engagement. Our simulation results provide new insights into the general properties of T cell engagers. The new simulation methods can therefore serve as a useful tool to design novel antibodies for cancer immunotherapy.
Collapse
|
8
|
Stoneman MR, Raicu V. Fluorescence-Based Detection of Proteins and Their Interactions in Live Cells. J Phys Chem B 2023. [PMID: 37205844 DOI: 10.1021/acs.jpcb.3c01419] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent advances in fluorescence-based microscopy techniques, such as single molecule fluorescence, Förster resonance energy transfer (FRET), fluorescence intensity fluctuations analysis, and super-resolution microscopy have expanded our ability to study proteins in greater detail within their native cellular environment and to investigate the roles that protein interactions play in biological functions, such as inter- and intracellular signaling and cargo transport. In this Perspective, we provide an up-to-date overview of the current state of the art in fluorescence-based detection of proteins and their interactions in living cells with an emphasis on recent developments that have facilitated the characterization of the spatial and temporal organization of proteins into oligomeric complexes in the presence and absence of natural and artificial ligands. Further advancements in this field will only deepen our understanding of the underlying mechanisms of biological processes and help develop new therapeutic targets.
Collapse
Affiliation(s)
- Michael R Stoneman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Valerică Raicu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| |
Collapse
|
9
|
Tsirigotaki A, Dansercoer A, Verschueren KHG, Marković I, Pollmann C, Hafer M, Felix J, Birck C, Van Putte W, Catteeuw D, Tavernier J, Fernando Bazan J, Piehler J, Savvides SN, Verstraete K. Mechanism of receptor assembly via the pleiotropic adipokine Leptin. Nat Struct Mol Biol 2023; 30:551-563. [PMID: 36959263 DOI: 10.1038/s41594-023-00941-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/06/2023] [Indexed: 03/25/2023]
Abstract
The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling.
Collapse
Affiliation(s)
- Alexandra Tsirigotaki
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ann Dansercoer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Koen H G Verschueren
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Iva Marković
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Christoph Pollmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Maximillian Hafer
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Catherine Birck
- Integrated Structural Biology Platform, Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | | | - Dominiek Catteeuw
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Orionis Biosciences, Ghent, Belgium
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- ħ Bioconsulting llc, Stillwater, MN, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Kenneth Verstraete
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| |
Collapse
|
10
|
Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
Collapse
|
11
|
Niederauer C, Seynen M, Zomerdijk J, Kamp M, Ganzinger KA. The K2: Open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging. HARDWAREX 2023; 13:e00404. [PMID: 36923558 PMCID: PMC10009532 DOI: 10.1016/j.ohx.2023.e00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Imaging the dynamics and interactions of biomolecules at the single-molecule level in live cells and reconstituted systems has generated unprecedented knowledge about the biomolecular processes underlying many cellular functions. To achieve the speed and sensitivity needed to detect and follow individual molecules, these experiments typically require custom-built microscopes or custom modifications of commercial systems. The costs of such single-molecule microscopes, their technical complexity and the lack of open-source documentation on how to build custom setups therefore limit the accessibility of single-molecule imaging techniques. To advance the adaptation of dynamic single-molecule imaging by a wider community, we present the "K2": an open-source, simultaneous triple-color total internal reflection fluorescence (TIRF) microscope specifically designed for live-cell and single-molecule imaging. We explain our design considerations and provide step-by-step building instructions, parts list and full CAD models. The modular design of this TIRF microscope allows users to customize it to their scientific and financial needs, or to re-use parts of our design to improve the capabilities of their existing setups without necessarily having to build a full copy of the K2 microscope.
Collapse
|
12
|
Bai X, Sun P, Wang X, Long C, Liao S, Dang S, Zhuang S, Du Y, Zhang X, Li N, He K, Zhang Z. Structure and dynamics of the EGFR/HER2 heterodimer. Cell Discov 2023; 9:18. [PMID: 36781849 PMCID: PMC9925823 DOI: 10.1038/s41421-023-00523-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/15/2023] [Indexed: 02/15/2023] Open
Abstract
HER2 belongs to the human epidermal growth factor receptor tyrosine kinase family. Its overexpression or hyperactivation is a leading cause for multiple types of cancers. HER2 functions mainly through dimerization with other family members, such as EGFR. However, the molecular details for heterodimer assembly have not been completely understood. Here, we report cryo-EM structures of the EGF- and epiregulin-bound EGFR/HER2 ectodomain complexes at resolutions of 3.3 Å and 4.5 Å, respectively. Together with the functional analyses, we demonstrate that only the dimerization arm of HER2, but not that of EGFR, is essential for their heterodimer formation and signal transduction. Moreover, we analyze the differential membrane dynamics and transient interactions of endogenous EGFR and HER2 molecules in genome-edited cells using single-molecule live-cell imaging. Furthermore, we show that the interaction with HER2 could allow EGFR to resist endocytosis. Together, this work deepens our understanding of the unique structural properties and dynamics of the EGFR/HER2 complex.
Collapse
Affiliation(s)
- Xue Bai
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Pengyu Sun
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinghao Wang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Changkun Long
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Shuyun Liao
- grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Song Dang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shangshang Zhuang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Du
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinyi Zhang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Nan Li
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kangmin He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China. .,Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
13
|
Banger A, Pasch P, Blawitzki L, Weber S, Otten M, Monzel C, Schmidt S, Voskuhl J, Hartmann L. Detection of Lectin Clustering in Self‐Assembled, Glycan‐Functionalized Amphiphiles by Aggregation‐Induced Emission Luminophores. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Alexander Banger
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Peter Pasch
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Luca‐Cesare Blawitzki
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Simon Weber
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Marius Otten
- Department for Physical Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Cornelia Monzel
- Department for Experimental Medical Physics Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Stephan Schmidt
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Jens Voskuhl
- Institute of Organic Chemistry University of Duisburg‐Essen Universitätsstrasse 2 45141 Essen Germany
| | - Laura Hartmann
- Department for Organic Chemistry and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| |
Collapse
|
14
|
Wilson SC, Caveney NA, Yen M, Pollmann C, Xiang X, Jude KM, Hafer M, Tsutsumi N, Piehler J, Garcia KC. Organizing structural principles of the IL-17 ligand-receptor axis. Nature 2022; 609:622-629. [PMID: 35863378 PMCID: PMC9477748 DOI: 10.1038/s41586-022-05116-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022]
Abstract
The IL-17 family of cytokines and receptors have central roles in host defence against infection and development of inflammatory diseases1. The compositions and structures of functional IL-17 family ligand-receptor signalling assemblies remain unclear. IL-17E (also known as IL-25) is a key regulator of type 2 immune responses and driver of inflammatory diseases, such as allergic asthma, and requires both IL-17 receptor A (IL-17RA) and IL-17RB to elicit functional responses2. Here we studied IL-25-IL-17RB binary and IL-25-IL-17RB-IL-17RA ternary complexes using a combination of cryo-electron microscopy, single-molecule imaging and cell-based signalling approaches. The IL-25-IL-17RB-IL-17RA ternary signalling assembly is a C2-symmetric complex in which the IL-25-IL-17RB homodimer is flanked by two 'wing-like' IL-17RA co-receptors through a 'tip-to-tip' geometry that is the key receptor-receptor interaction required for initiation of signal transduction. IL-25 interacts solely with IL-17RB to allosterically promote the formation of the IL-17RB-IL-17RA tip-to-tip interface. The resulting large separation between the receptors at the membrane-proximal level may reflect proximity constraints imposed by the intracellular domains for signalling. Cryo-electron microscopy structures of IL-17A-IL-17RA and IL-17A-IL-17RA-IL-17RC complexes reveal that this tip-to-tip architecture is a key organizing principle of the IL-17 receptor family. Furthermore, these studies reveal dual actions for IL-17RA sharing among IL-17 cytokine complexes, by either directly engaging IL-17 cytokines or alternatively functioning as a co-receptor.
Collapse
Affiliation(s)
- Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Yen
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christoph Pollmann
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Xinyu Xiang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximillian Hafer
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Piehler
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
15
|
Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). eLife 2022; 11:e76870. [PMID: 35976226 PMCID: PMC9531946 DOI: 10.7554/elife.76870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
Collapse
Affiliation(s)
- Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Joseph Ferrie
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| |
Collapse
|