1
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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2
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Serrano-Buitrago S, Muñoz-Úbeda M, Almendro-Vedia VG, Sánchez-Camacho J, Maroto BL, Moreno F, Bañuelos J, García-Moreno I, López-Montero I, de la Moya S. Polar ammoniostyryls easily converting a clickable lipophilic BODIPY in an advanced plasma membrane probe. J Mater Chem B 2023; 11:2108-2114. [PMID: 36808432 DOI: 10.1039/d2tb02516g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
A very simple, small and symmetric, but highly bright, photostable and functionalizable molecular probe for plasma membrane (PM) has been developed from an accessible, lipophilic and clickable organic dye based on BODIPY. To this aim, two lateral polar ammoniostyryl groups were easily linked to increase the amphiphilicity of the probe and thus its lipid membrane partitioning. Compared to the BODIPY precursor, the transversal diffusion across lipid bilayers of the ammoniostyryled BODIPY probe was highly reduced, as evidenced by fluorescence confocal microscopy on model membranes built up as giant unilamellar vesicles (GUVs). Moreover, the ammoniostyryl groups endow the new BODIPY probe with the ability to optically work (excitation and emission) in the bioimaging-useful red region, as shown by staining of the plasma membrane of living mouse embryonic fibroblasts (MEFs). Upon incubation, this fluorescent probe rapidly entered the cell through the endosomal pathway. By blocking the endocytic trafficking at 4 °C, the probe was confined within the PM of MEFs. Our experiments show the developed ammoniostyrylated BODIPY as a suitable PM fluorescent probe, and confirm the synthetic approach for advancing PM probes, imaging and science.
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Affiliation(s)
- Sergio Serrano-Buitrago
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | - Mónica Muñoz-Úbeda
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.,Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | - Víctor G Almendro-Vedia
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.,Departamento de Farmacia Galénica y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Juan Sánchez-Camacho
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | - Beatriz L Maroto
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | - Florencio Moreno
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | - Jorge Bañuelos
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Barrio Sarriena s/n, 48080, Bilbao, Spain
| | - Inmaculada García-Moreno
- Departamento de Química-Física de Materiales, Instituto de Química Física Rocasolano, C.S.I.C., 28006, Madrid, Spain
| | - Iván López-Montero
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.,Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain. .,Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo de Juan XXIII 1, 28040, Madrid, Spain
| | - Santiago de la Moya
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
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3
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Balasubramanian H, Sankaran J, Pandey S, Goh CJH, Wohland T. The dependence of EGFR oligomerization on environment and structure: A camera-based N&B study. Biophys J 2022; 121:4452-4466. [PMID: 36335429 PMCID: PMC9748371 DOI: 10.1016/j.bpj.2022.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Number and brightness (N&B) analysis is a fluorescence spectroscopy technique to quantify oligomerization of the mobile fraction of proteins. Accurate results, however, rely on a good knowledge of nonfluorescent states of the fluorescent labels, especially of fluorescent proteins, which are widely used in biology. Fluorescent proteins have been characterized for confocal, but not camera-based, N&B, which allows, in principle, faster measurements over larger areas. Here, we calibrate camera-based N&B implemented on a total internal reflection fluorescence microscope for various fluorescent proteins by determining their propensity to be fluorescent. We then apply camera-based N&B in live CHO-K1 cells to determine the oligomerization state of the epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase that is a crucial regulator of cell proliferation and survival with implications in many cancers. EGFR oligomerization in resting cells and its regulation by the plasma membrane microenvironment are still under debate. Therefore, we investigate the effects of extrinsic factors, including membrane organization, cytoskeletal structure, and ligand stimulation, and intrinsic factors, including mutations in various EGFR domains, on the receptor's oligomerization. Our results demonstrate that EGFR oligomerization increases with removal of cholesterol or sphingolipids or the disruption of GM3-EGFR interactions, indicating raft association. However, oligomerization is not significantly influenced by the cytoskeleton. Mutations in either I706/V948 residues or E685/E687/E690 residues in the kinase and juxtamembrane domains, respectively, lead to a decrease in oligomerization, indicating their necessity for EGFR dimerization. Finally, EGFR phosphorylation is oligomerization dependent, involving the extracellular domain (550-580 residues). Coupled with biochemical investigations, camera-based N&B indicates that EGFR oligomerization and phosphorylation are the outcomes of several molecular interactions involving the lipid content and structure of the cell membrane and multiple residues in the kinase, juxtamembrane, and extracellular domains.
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Affiliation(s)
- Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shambhavi Pandey
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Corinna Jie Hui Goh
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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4
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It Takes More than Two to Tango: Complex, Hierarchal, and Membrane-Modulated Interactions in the Regulation of Receptor Tyrosine Kinases. Cancers (Basel) 2022; 14:cancers14040944. [PMID: 35205690 PMCID: PMC8869822 DOI: 10.3390/cancers14040944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022] Open
Abstract
The search for an understanding of how cell fate and motility are regulated is not a purely scientific undertaking, but it can also lead to rationally designed therapies against cancer. The discovery of tyrosine kinases about half a century ago, the subsequent characterization of certain transmembrane receptors harboring tyrosine kinase activity, and their connection to the development of human cancer ushered in a new age with the hope of finding a treatment for malignant diseases in the foreseeable future. However, painstaking efforts were required to uncover the principles of how these receptors with intrinsic tyrosine kinase activity are regulated. Developments in molecular and structural biology and biophysical approaches paved the way towards better understanding of these pathways. Discoveries in the past twenty years first resulted in the formulation of textbook dogmas, such as dimerization-driven receptor association, which were followed by fine-tuning the model. In this review, the role of molecular interactions taking place during the activation of receptor tyrosine kinases, with special attention to the epidermal growth factor receptor family, will be discussed. The fact that these receptors are anchored in the membrane provides ample opportunities for modulatory lipid-protein interactions that will be considered in detail in the second part of the manuscript. Although qualitative and quantitative alterations in lipids in cancer are not sufficient in their own right to drive the malignant transformation, they both contribute to tumor formation and also provide ways to treat cancer. The review will be concluded with a summary of these medical aspects of lipid-protein interactions.
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5
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Mathur D, Samanta A, Ancona MG, Díaz SA, Kim Y, Melinger JS, Goldman ER, Sadowski JP, Ong LL, Yin P, Medintz IL. Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks. ACS NANO 2021; 15:16452-16468. [PMID: 34609842 PMCID: PMC8823280 DOI: 10.1021/acsnano.1c05871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r4 energy transfer distance (r) dependency versus the 1/r6 dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.
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Affiliation(s)
| | | | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Youngchan Kim
- Center for Materials Physics and Technology Code 6390, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Electronic Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - John Paul Sadowski
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States; American Society for Engineering Education, Washington, D.C. 20001, United States
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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6
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Lucey M, Ashik T, Marzook A, Wang Y, Goulding J, Oishi A, Broichhagen J, Hodson DJ, Minnion J, Elani Y, Jockers R, Briddon SJ, Bloom SR, Tomas A, Jones B. Acylation of the Incretin Peptide Exendin-4 Directly Impacts Glucagon-Like Peptide-1 Receptor Signaling and Trafficking. Mol Pharmacol 2021; 100:319-334. [PMID: 34315812 PMCID: PMC8626645 DOI: 10.1124/molpharm.121.000270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/14/2021] [Indexed: 11/22/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a class B G protein-coupled receptor and mainstay therapeutic target for the treatment of type 2 diabetes and obesity. Recent reports have highlighted how biased agonism at the GLP-1R affects sustained glucose-stimulated insulin secretion through avoidance of desensitization and downregulation. A number of GLP-1R agonists (GLP-1RAs) feature a fatty acid moiety to prolong their pharmacokinetics via increased albumin binding, but the potential for these chemical changes to influence GLP-1R function has rarely been investigated beyond potency assessments for cAMP. Here, we directly compare the prototypical GLP-1RA exendin-4 with its C-terminally acylated analog, exendin-4-C16. We examine relative propensities of each ligand to recruit and activate G proteins and β-arrestins, endocytic and postendocytic trafficking profiles, and interactions with model and cellular membranes in HEK293 and HEK293T cells. Both ligands had similar cAMP potency, but exendin-4-C16 showed ∼2.5-fold bias toward G protein recruitment and a ∼60% reduction in β-arrestin-2 recruitment efficacy compared with exendin-4, as well as reduced GLP-1R endocytosis and preferential targeting toward recycling pathways. These effects were associated with reduced movement of the GLP-1R extracellular domain measured using a conformational biosensor approach and a ∼70% increase in insulin secretion in INS-1 832/3 cells. Interactions with plasma membrane lipids were enhanced by the acyl chain. Exendin-4-C16 showed extensive albumin binding and was highly effective for lowering of blood glucose in mice over at least 72 hours. Our study highlights the importance of a broad approach to the evaluation of GLP-1RA pharmacology. SIGNIFICANCE STATEMENT: Acylation is a common strategy to enhance the pharmacokinetics of peptide-based drugs. This work shows how acylation can also affect various other pharmacological parameters, including biased agonism, receptor trafficking, and interactions with the plasma membrane, which may be therapeutically important.
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Affiliation(s)
- Maria Lucey
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Tanyel Ashik
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Amaara Marzook
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Yifan Wang
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Joëlle Goulding
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Atsuro Oishi
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Johannes Broichhagen
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - David J Hodson
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - James Minnion
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Yuval Elani
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Ralf Jockers
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Stephen J Briddon
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Stephen R Bloom
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Alejandra Tomas
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
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7
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Marzook A, Chen S, Pickford P, Lucey M, Wang Y, Corrêa IR, Broichhagen J, Hodson DJ, Salem V, Rutter GA, Tan TM, Bloom SR, Tomas A, Jones B. Evaluation of efficacy- versus affinity-driven agonism with biased GLP-1R ligands P5 and exendin-F1. Biochem Pharmacol 2021; 190:114656. [PMID: 34129856 PMCID: PMC8346945 DOI: 10.1016/j.bcp.2021.114656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 02/09/2023]
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is an important regulator of glucose homeostasis and has been successfully targeted for the treatment of type 2 diabetes. Recently described biased GLP-1R agonists with selective reductions in β-arrestin versus G protein coupling show improved metabolic actions in vivo. However, two prototypical G protein-favouring GLP-1R agonists, P5 and exendin-F1, are reported to show divergent effects on insulin secretion. In this study we aimed to resolve this discrepancy by performing a side-by-side characterisation of these two ligands across a variety of in vitro and in vivo assays. Exendin-F1 showed reduced acute efficacy versus P5 for several readouts, including recruitment of mini-G proteins, G protein-coupled receptor kinases (GRKs) and β-arrestin-2. Maximal responses were also lower for both GLP-1R internalisation and the presence of active GLP-1R-mini-Gs complexes in early endosomes with exendin-F1 treatment. In contrast, prolonged insulin secretion in vitro and sustained anti-hyperglycaemic efficacy in mice were both greater with exendin-F1 than with P5. We conclude that the particularly low acute efficacy of exendin-F1 and associated reductions in GLP-1R downregulation appear to be more important than preservation of endosomal signalling to allow sustained insulin secretion responses. This has implications for the ongoing development of affinity- versus efficacy-driven biased GLP-1R agonists as treatments for metabolic disease.
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Affiliation(s)
- Amaara Marzook
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Shiqian Chen
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Phil Pickford
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Maria Lucey
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Yifan Wang
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | | | | | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, United Kingdom
| | - Victoria Salem
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom; Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tricia M Tan
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Stephen R Bloom
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
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8
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Hajdu T, Váradi T, Rebenku I, Kovács T, Szöllösi J, Nagy P. Comprehensive Model for Epidermal Growth Factor Receptor Ligand Binding Involving Conformational States of the Extracellular and the Kinase Domains. Front Cell Dev Biol 2020; 8:776. [PMID: 32850868 PMCID: PMC7431817 DOI: 10.3389/fcell.2020.00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
The epidermal growth factor (EGF) receptor (EGFR) undergoes ligand-dependent dimerization to initiate transmembrane signaling. Although crystallographic structures of the extracellular and kinase domains are available, ligand binding has not been quantitatively analyzed taking the influence of both domains into account. Here, we developed a model explicitly accounting for conformational changes of the kinase and extracellular domains, their dimerizations and ligand binding to monomeric and dimeric receptor species. The model was fitted to ligand binding data of suspended cells expressing receptors with active or inactive kinase conformations. Receptor dimers with inactive, symmetric configuration of the kinase domains exhibit positive cooperativity and very weak binding affinity for the first ligand, whereas dimers with active, asymmetric kinase dimers are characterized by negative cooperativity and subnanomolar binding affinity for the first ligand. The homodimerization propensity of EGFR monomers with active kinase domains is ∼100-times higher than that of dimers with inactive kinase domains. Despite this fact, constitutive, ligand-independent dimers are mainly generated from monomers with inactive kinase domains due to the excess of such monomers in the membrane. The experimental finding of increased positive cooperativity at high expression levels of EGFR was recapitulated by the model. Quantitative prediction of ligand binding to different receptor species revealed that EGF binds to receptor monomers and dimers in an expression-level dependent manner without significant recruitment of monomers to dimers upon EGF stimulation below the phase transition temperature of the membrane. Results of the fitting offer unique insight into the workings of the EGFR.
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Affiliation(s)
- Tímea Hajdu
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tímea Váradi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Rebenku
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Kovács
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllösi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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9
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Szabó Á, Szendi-Szatmári T, Szöllősi J, Nagy P. Quo vadis FRET? Förster's method in the era of superresolution. Methods Appl Fluoresc 2020; 8:032003. [PMID: 32521530 DOI: 10.1088/2050-6120/ab9b72] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although the theoretical foundations of Förster resonance energy transfer (FRET) were laid in the 1940s as part of the quantum physical revolution of the 20th century, it was only in the 1970s that it made its way to biology as a result of the availability of suitable measuring and labeling technologies. Thanks to its ease of application, FRET became widely used for studying molecular associations on the nanometer scale. The development of superresolution techniques at the turn of the millennium promised an unprecedented insight into the structure and function of molecular complexes. Without downplaying the significance of superresolution microscopies this review expresses our view that FRET is still a legitimate tool in the armamentarium of biologists for studying molecular associations since it offers distinct advantages and overcomes certain limitations of superresolution approaches.
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Affiliation(s)
- Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary. MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary
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10
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Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell 2020; 31:695-708. [PMID: 31913761 PMCID: PMC7202077 DOI: 10.1091/mbc.e19-09-0548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein-protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.
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Affiliation(s)
| | | | - Eshan D Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | | | - Keith A Lidke
- Comprehensive Cancer Center, and.,Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - William S Hlavacek
- Comprehensive Cancer Center, and.,Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S Lidke
- Department of Pathology.,Comprehensive Cancer Center, and
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11
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Gocheva G, Ivanova A. A Look at Receptor–Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. Mol Pharm 2019; 16:3293-3321. [DOI: 10.1021/acs.molpharmaceut.9b00250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gergana Gocheva
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
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12
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Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells 2019; 8:E316. [PMID: 30959819 PMCID: PMC6523254 DOI: 10.3390/cells8040316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/25/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is historically the prototypical receptor tyrosine kinase, being the first cloned and the first where the importance of ligand-induced dimer activation was ascertained. However, many years of structure determination has shown that EGFR is not completely understood. One challenge is that the many structure fragments stored at the PDB only provide a partial view because full-length proteins are flexible entities and dynamics play a key role in their functionality. Another challenge is the shortage of high-resolution data on functionally important higher-order complexes. Still, the interest in the structure/function relationships of EGFR remains unabated because of the crucial role played by oncogenic EGFR mutants in driving non-small cell lung cancer (NSCLC). Despite targeted therapies against EGFR setting a milestone in the treatment of this disease, ubiquitous drug resistance inevitably emerges after one year or so of treatment. The magnitude of the challenge has inspired novel strategies. Among these, the combination of multi-disciplinary experiments and molecular dynamic (MD) simulations have been pivotal in revealing the basic nature of EGFR monomers, dimers and multimers, and the structure-function relationships that underpin the mechanisms by which EGFR dysregulation contributes to the onset of NSCLC and resistance to treatment.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
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13
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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14
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MemBright: A Family of Fluorescent Membrane Probes for Advanced Cellular Imaging and Neuroscience. Cell Chem Biol 2019; 26:600-614.e7. [PMID: 30745238 DOI: 10.1016/j.chembiol.2019.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/30/2022]
Abstract
The proper staining of the plasma membrane (PM) is critical in bioimaging as it delimits the cell. Herein, we developed MemBright, a family of six cyanine-based fluorescent turn-on PM probes that emit from orange to near infrared when reaching the PM, and enable homogeneous and selective PM staining with excellent contrast in mono- and two-photon microscopy. These probes are compatible with long-term live-cell imaging and immunostaining. Moreover, MemBright label neurons in a brighter manner than surrounding cells, allowing identification of neurons in acute brain tissue sections and neuromuscular junctions without any use of transfection or transgenic animals. In addition, MemBright probes were used in super-resolution imaging to unravel the neck of dendritic spines. 3D multicolor dSTORM in combination with immunostaining revealed en-passant synapse displaying endogenous glutamate receptors clustered at the axonal-dendritic contact site. MemBright probes thus constitute a universal toolkit for cell biology and neuroscience biomembrane imaging with a variety of microscopy techniques. VIDEO ABSTRACT.
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15
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Collot M, Boutant E, Lehmann M, Klymchenko AS. BODIPY with Tuned Amphiphilicity as a Fluorogenic Plasma Membrane Probe. Bioconjug Chem 2019; 30:192-199. [PMID: 30562000 DOI: 10.1021/acs.bioconjchem.8b00828] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Staining of the plasma membrane (PM) is essential in bioimaging, as it delimits the cell surface and provides various information regarding the cell morphology and status. Herein, the lipophilicity of a green emitting BODIPY fluorophore was tuned by gradual functionalization with anchors composed of zwitterionic and aliphatic groups, thus yielding three different amphiphilic dyes. We found that BODIPY bearing one or three anchors failed in efficiently staining the PM: the derivative with one anchor showed low affinity to PM and exhibited strong fluorescence in water due to high solubility, whereas BODIPY with three anchors aggregated strongly in media and precipitated before binding to the PM. In sharp contrast, the BODIPY bearing two anchors (B-2AZ, MemBright-488) formed virtually nonfluorescent soluble aggregates in aqueous medium that quickly deaggregated in the presence of PM, leading to a bright soluble molecular form (quantum yield of 0.92). This fluorogenic response allowed for efficient probing of the PM at low concentration (20 nM) with high signal to background ratio images in mono- as well as two-photon excitation microscopy. B-2AZ proved to selectively stain the PM in a more homogeneous manner than the commercially available fluorescently labeled lectin WGA. Finally, it was successfully used in 3D-imaging to reveal fine intercellular tunneling nanotubes in KB cells and to stain the PM in glioblastoma cells in spheroids.
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Affiliation(s)
- Mayeul Collot
- Laboratoire de Biophotonique et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin , 67401 ILLKIRCH Cedex, France
| | - Emmanuel Boutant
- Laboratoire de Biophotonique et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin , 67401 ILLKIRCH Cedex, France
| | - Maxime Lehmann
- Laboratoire de Biophotonique et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin , 67401 ILLKIRCH Cedex, France
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin , 67401 ILLKIRCH Cedex, France
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16
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Baumdick M, Gelléri M, Uttamapinant C, Beránek V, Chin JW, Bastiaens PIH. A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation. Nat Commun 2018; 9:3847. [PMID: 30242154 PMCID: PMC6155120 DOI: 10.1038/s41467-018-06299-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight into EGFR activation mechanisms in living cells, we develop a Förster resonance energy transfer (FRET)-based conformational EGFR indicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant reveals that Y845 phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C-terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose. Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.
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Affiliation(s)
- Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Márton Gelléri
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany.
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17
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Andra KK, Dorsey S, Royer CA, Menon AK. Structural mapping of fluorescently-tagged, functional nhTMEM16 scramblase in a lipid bilayer. J Biol Chem 2018; 293:12248-12258. [PMID: 29903908 DOI: 10.1074/jbc.ra118.003648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/12/2018] [Indexed: 01/25/2023] Open
Abstract
Most members of the TransMEMbrane protein 16 (TMEM16) family are Ca2+-regulated scramblases that facilitate the bidirectional movement of phospholipids across membranes necessary for diverse physiological processes. The nhTMEM16 scramblase (from the fungus Nectria hematococca) is a homodimer with a large cytoplasmic region and a hydrophilic, membrane-exposed groove in each monomer. The groove provides the transbilayer conduit for lipids, but the mechanism by which Ca2+ regulates it is not clear. Because fusion of large protein tags at either the N or C terminus abolishes nhTMEM16 activity, we hypothesized that its cytoplasmic portion containing both termini may regulate lipid translocation via a Ca2+-dependent conformational change. To test this hypothesis, here we used fluorescence methods to map key distances within the nhTMEM16 homodimer and between its termini and the membrane. To this end, we developed functional nhTMEM16 variants bearing an acyl carrier protein (ACP) tag at one or both of the termini. These constructs were fluorescently labeled by ACP synthase-mediated insertion of CoA-conjugated fluorophores and reconstituted into vesicles containing fluorescent lipids to obtain the distance of closest approach between the labeled tag and the membrane via FRET. Fluorescence lifetime measurements with phasor analysis were used to determine the distance between the N and C termini of partnering monomers in the nhTMEM16 homodimer. We now report that the measured distances do not vary significantly between Ca2+-replete and EGTA-treated samples, indicating that whereas the cytoplasmic portion of the protein is important for function, it does not appear to regulate scramblase activity via a detectable conformational change.
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Affiliation(s)
- Kiran K Andra
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065
| | - Savanna Dorsey
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Catherine A Royer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065.
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18
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Optical measurement of receptor tyrosine kinase oligomerization on live cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1436-1444. [PMID: 28389201 DOI: 10.1016/j.bbamem.2017.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 12/19/2022]
Abstract
Receptor tyrosine kinases (RTK) are important cell surface receptors that transduce extracellular signals across the plasma membrane. The traditional view of how these receptors function is that ligand binding to the extracellular domains acts as a master-switch that enables receptor monomers to dimerize and subsequently trans-phosphorylate each other on their intracellular domains. However, a growing body of evidence suggests that receptor oligomerization is not merely a consequence of ligand binding, but is instead part of a complex process responsible for regulation of receptor activation. Importantly, the oligomerization dynamics and subsequent activation of these receptors are affected by other cellular components, such as cytoskeletal machineries and cell membrane lipid characteristics. Thus receptor activation is not an isolated molecular event mediated by the ligand-receptor interaction, but instead involves orchestrated interactions between the receptors and other cellular components. Measuring receptor oligomerization dynamics on live cells can yield important insights into the characteristics of these interactions. Therefore, it is imperative to develop techniques that can probe receptor movements on the plasma membrane with optimal temporal and spatial resolutions. Various microscopic techniques have been used for this purpose. Optical techniques including single molecule tracking (SMT) and fluorescence correlation spectroscopy (FCS) measure receptor diffusion on live cells. Receptor-receptor interactions can also be assessed by detecting Förster resonance energy transfer (FRET) between fluorescently-labeled receptors situated in close proximity or by counting the number of receptors within a diffraction limited fluorescence spot (stepwise bleaching). This review will describe recent developments of optical techniques that have been used to study receptor oligomerization on living cells. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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19
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Klymchenko AS. Solvatochromic and Fluorogenic Dyes as Environment-Sensitive Probes: Design and Biological Applications. Acc Chem Res 2017; 50:366-375. [PMID: 28067047 DOI: 10.1021/acs.accounts.6b00517] [Citation(s) in RCA: 636] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes. In this Account, the main examples of environment-sensitive probes are summarized according to their design concepts. Solvatochromic dyes constitute a large class of environment-sensitive probes which change their color in response to polarity. Generally, they are push-pull dyes undergoing intramolecular charge transfer. Emission of their highly polarized excited state shifts to the red in more polar solvents. Excited-state intramolecular proton transfer is the second key concept to design efficient solvatochromic dyes, which respond to the microenvironment by changing relative intensity of the two emissive tautomeric forms. Due to their sensitivity to polarity and hydration, solvatochromic dyes have been successfully applied to biological membranes for studying lipid domains (rafts), apoptosis and endocytosis. As fluorescent labels, solvatochromic dyes can detect practically any type of biomolecular interactions, involving proteins, nucleic acids and biomembranes, because the binding event excludes local water molecules from the interaction site. On the other hand, fluorogenic probes usually exploit intramolecular rotation (conformation change) as a design concept, with molecular rotors being main representatives. These probes were particularly efficient for imaging viscosity and lipid order in biomembranes as well as to light up biomolecular targets, such as antibodies, aptamers and receptors. The emerging concepts to achieve fluorogenic response to the microenvironment include ground-state isomerization, aggregation-caused quenching, and aggregation-induced emission. The ground-state isomerization exploits, for instance, polarity-dependent spiro-lactone formation in silica-rhodamines. The aggregation-caused quenching uses disruption of the self-quenched dimers and nanoassemblies of dyes in less polar environments of lipid membranes and biomolecules. The aggregation-induced emission couples target recognition with formation of highly fluorescent dye aggregates. Overall, solvatochromic and fluorogenic probes enable background-free bioimaging in wash-free conditions as well as quantitative analysis when combined with advanced microscopy, such as fluorescence lifetime (FLIM) and ratiometric imaging. Further development of fluorescent environment-sensitive probes should address some remaining problems: (i) improving their optical properties, especially brightness, photostability, and far-red to near-infrared operating range; (ii) minimizing nonspecific interactions of the probes in biological systems; (iii) their adaptation for advanced microscopies, notably for superresolution and in vivo imaging.
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Affiliation(s)
- Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pharmacologie,
UMR 7213 CNRS, Université de Strasbourg, F-67000 Strasbourg, France
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20
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Valley CC, Lewis AK, Sachs JN. Piecing it together: Unraveling the elusive structure-function relationship in single-pass membrane receptors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1398-1416. [PMID: 28089689 DOI: 10.1016/j.bbamem.2017.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/17/2022]
Abstract
The challenge of crystallizing single-pass plasma membrane receptors has remained an obstacle to understanding the structural mechanisms that connect extracellular ligand binding to cytosolic activation. For example, the complex interplay between receptor oligomerization and conformational dynamics has been, historically, only inferred from static structures of isolated receptor domains. A fundamental challenge in the field of membrane receptor biology, then, has been to integrate experimentally observable dynamics of full-length receptors (e.g. diffusion and conformational flexibility) into static structural models of the disparate domains. In certain receptor families, e.g. the ErbB receptors, structures have led somewhat linearly to a putative model of activation. In other families, e.g. the tumor necrosis factor (TNF) receptors, structures have produced divergent hypothetical mechanisms of activation and transduction. Here, we discuss in detail these and other related receptors, with the goal of illuminating the current challenges and opportunities in building comprehensive models of single-pass receptor activation. The deepening understanding of these receptors has recently been accelerated by new experimental and computational tools that offer orthogonal perspectives on both structure and dynamics. As such, this review aims to contextualize those technological developments as we highlight the elegant and complex conformational communication between receptor domains. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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Affiliation(s)
| | - Andrew K Lewis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
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21
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Kaplan M, Narasimhan S, de Heus C, Mance D, van Doorn S, Houben K, Popov-Čeleketić D, Damman R, Katrukha EA, Jain P, Geerts WJC, Heck AJR, Folkers GE, Kapitein LC, Lemeer S, van Bergen En Henegouwen PMP, Baldus M. EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR. Cell 2016; 167:1241-1251.e11. [PMID: 27839865 DOI: 10.1016/j.cell.2016.10.038] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/08/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.
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Affiliation(s)
- Mohammed Kaplan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Cecilia de Heus
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Dušan Popov-Čeleketić
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Purvi Jain
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Willie J C Geerts
- Biomolecular Imaging, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | | | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
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22
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Collot M, Kreder R, Tatarets AL, Patsenker LD, Mely Y, Klymchenko AS. Bright fluorogenic squaraines with tuned cell entry for selective imaging of plasma membrane vs. endoplasmic reticulum. Chem Commun (Camb) 2016; 51:17136-9. [PMID: 26455447 DOI: 10.1039/c5cc06094j] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rational design of squaraine dyes with lipophilic and zwitterionic groups tunes cell entry, allowing for selective far-red/near-infrared imaging of plasma membrane vs. endoplasmic reticulum. They exhibit up to 110-fold fluorescence enhancement in biomembranes and enable cellular imaging at 1 nM concentration, which make them the brightest membrane probes to date.
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Affiliation(s)
- Mayeul Collot
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401, Illkirch, France.
| | - Rémy Kreder
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401, Illkirch, France.
| | - Anatoliy L Tatarets
- The State Scientific Institution "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, 60, Lenin Ave., Kharkiv, 61001, Ukraine
| | - Leonid D Patsenker
- The State Scientific Institution "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, 60, Lenin Ave., Kharkiv, 61001, Ukraine
| | - Yves Mely
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401, Illkirch, France.
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401, Illkirch, France.
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23
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Bocharov EV, Lesovoy DM, Pavlov KV, Pustovalova YE, Bocharova OV, Arseniev AS. Alternative packing of EGFR transmembrane domain suggests that protein-lipid interactions underlie signal conduction across membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1254-61. [PMID: 26903218 DOI: 10.1016/j.bbamem.2016.02.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
The human epidermal growth factor receptor (EGFR) of HER/ErbB receptor tyrosine kinase family mediates a broad spectrum of cellular responses transducing biochemical signals via lateral dimerization in plasma membrane, while inactive receptors can exist in both monomeric and dimeric forms. Recently, the dimeric conformation of the helical single-span transmembrane domains of HER/ErbB employing the relatively polar N-terminal motifs in a fashion permitting proper kinase activation was experimentally determined. Here we describe the EGFR transmembrane domain dimerization via an alternative weakly polar C-terminal motif A(661)xxxG(665) presumably corresponding to the inactive receptor state. During association, the EGFR transmembrane helices undergo a structural adjustment with adaptation of inter-molecular polar and hydrophobic interactions depending upon the surrounding membrane properties that directly affect the transmembrane helix packing. This might imply that signal transduction through membrane and allosteric regulation are inclusively mediated by coupled protein-protein and protein-lipid interactions, elucidating paradoxically loose linkage between ligand binding and kinase activation.
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Affiliation(s)
- Eduard V Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation.
| | - Dmitry M Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Yulia E Pustovalova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Olga V Bocharova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Alexander S Arseniev
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
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24
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McCabe Pryor M, Steinkamp MP, Halasz AM, Chen Y, Yang S, Smith MS, Zahoransky-Kohalmi G, Swift M, Xu XP, Hanein D, Volkmann N, Lidke DS, Edwards JS, Wilson BS. Orchestration of ErbB3 signaling through heterointeractions and homointeractions. Mol Biol Cell 2015; 26:4109-23. [PMID: 26378253 PMCID: PMC4710241 DOI: 10.1091/mbc.e14-06-1114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
Members of the ErbB family of receptor tyrosine kinases are capable of both homointeractions and heterointeractions. Because each receptor has a unique set of binding sites for downstream signaling partners and differential catalytic activity, subtle shifts in their combinatorial interplay may have a large effect on signaling outcomes. The overexpression and mutation of ErbB family members are common in numerous human cancers and shift the balance of activation within the signaling network. Here we report the development of a spatial stochastic model that addresses the dynamics of ErbB3 homodimerization and heterodimerization with ErbB2. The model is based on experimental measures for diffusion, dimer off-rates, kinase activity, and dephosphorylation. We also report computational analysis of ErbB3 mutations, generating the prediction that activating mutations in the intracellular and extracellular domains may be subdivided into classes with distinct underlying mechanisms. We show experimental evidence for an ErbB3 gain-of-function point mutation located in the C-lobe asymmetric dimerization interface, which shows enhanced phosphorylation at low ligand dose associated with increased kinase activity.
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Affiliation(s)
- Meghan McCabe Pryor
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Mara P Steinkamp
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Adam M Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Ye Chen
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Shujie Yang
- Department of OB/GYN, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | | | | | - Mark Swift
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Xiao-Ping Xu
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Dorit Hanein
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Niels Volkmann
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Jeremy S Edwards
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131 Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
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25
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Valley CC, Arndt-Jovin DJ, Karedla N, Steinkamp MP, Chizhik AI, Hlavacek WS, Wilson BS, Lidke KA, Lidke DS. Enhanced dimerization drives ligand-independent activity of mutant epidermal growth factor receptor in lung cancer. Mol Biol Cell 2015; 26:4087-99. [PMID: 26337388 PMCID: PMC4710239 DOI: 10.1091/mbc.e15-05-0269] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022] Open
Abstract
Epidermal growth factor receptor kinase mutations drive oncogenesis, but the molecular mechanism of pathological signal initiation is poorly understood. Using high-resolution microscopy methods, the authors reveal that these kinase mutations induce structural changes in the receptor ectodomain that lead to enhanced, ligand-independent dimerization. Mutations within the epidermal growth factor receptor (EGFR/erbB1/Her1) are often associated with tumorigenesis. In particular, a number of EGFR mutants that demonstrate ligand-independent signaling are common in non–small cell lung cancer (NSCLC), including kinase domain mutations L858R (also called L834R) and exon 19 deletions (e.g., ΔL747-P753insS), which collectively make up nearly 90% of mutations in NSCLC. The molecular mechanisms by which these mutations confer constitutive activity remain unresolved. Using multiple subdiffraction-limit imaging modalities, we reveal the altered receptor structure and interaction kinetics of NSCLC-associated EGFR mutants. We applied two-color single quantum dot tracking to quantify receptor dimerization kinetics on living cells and show that, in contrast to wild-type EGFR, mutants are capable of forming stable, ligand-independent dimers. Two-color superresolution localization microscopy confirmed ligand-independent aggregation of EGFR mutants. Live-cell Förster resonance energy transfer measurements revealed that the L858R kinase mutation alters ectodomain structure such that unliganded mutant EGFR adopts an extended, dimerization-competent conformation. Finally, mutation of the putative dimerization arm confirmed a critical role for ectodomain engagement in ligand-independent signaling. These data support a model in which dysregulated activity of NSCLC-associated kinase mutants is driven by coordinated interactions involving both the kinase and extracellular domains that lead to enhanced dimerization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Donna J Arndt-Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Narain Karedla
- III. Institute of Physics, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Mara P Steinkamp
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Alexey I Chizhik
- III. Institute of Physics, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - William S Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Bridget S Wilson
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
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26
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS One 2015; 10:e0121513. [PMID: 25837709 PMCID: PMC4383379 DOI: 10.1371/journal.pone.0121513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/03/2015] [Indexed: 01/01/2023] Open
Abstract
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.
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N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proc Natl Acad Sci U S A 2015; 112:4334-9. [PMID: 25805821 DOI: 10.1073/pnas.1503262112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) regulates several critical cellular processes and is an important target for cancer therapy. In lieu of a crystallographic structure of the complete receptor, atomistic molecular dynamics (MD) simulations have recently shown that they can excel in studies of the full-length receptor. Here we present atomistic MD simulations of the monomeric N-glycosylated human EGFR in biomimetic lipid bilayers that are, in parallel, also used for the reconstitution of full-length receptors. This combination enabled us to experimentally validate our simulations, using ligand binding assays and antibodies to monitor the conformational properties of the receptor reconstituted into membranes. We find that N-glycosylation is a critical determinant of EGFR conformation, and specifically the orientation of the EGFR ectodomain relative to the membrane. In the absence of a structure for full-length, posttranslationally modified membrane receptors, our approach offers new means to structurally define and experimentally validate functional properties of cell surface receptors in biomimetic membrane environments.
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29
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Abstract
Optical imaging assays, especially fluorescence molecular assays, are minimally invasive if not completely noninvasive, and thus an ideal technique to be applied to live specimens. These fluorescence imaging assays are a powerful tool in biomedical sciences as they allow the study of a wide range of molecular and physiological events occurring in biological systems. Furthermore, optical imaging assays bridge the gap between the in vitro cell-based analysis of subcellular processes and in vivo study of disease mechanisms in small animal models. In particular, the application of Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM), well-known techniques widely used in microscopy, to the optical imaging assay toolbox, will have a significant impact in the molecular study of protein-protein interactions during cancer progression. This review article describes the application of FLIM-FRET to the field of optical imaging and addresses their various applications, both current and potential, to anti-cancer drug delivery and cancer research.
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Affiliation(s)
- Shilpi Rajoria
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
| | - Lingling Zhao
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Xavier Intes
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Margarida Barroso
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
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30
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Atta D, Okasha A. Single molecule laser spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:1173-1179. [PMID: 25156641 DOI: 10.1016/j.saa.2014.07.085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 07/10/2014] [Accepted: 07/29/2014] [Indexed: 06/03/2023]
Abstract
In this article, we discussed some single molecule spectroscopy techniques and methods. We have chosen the simplicity in this survey based on our laboratory experience in this field. We concentrated on the imaging by both techniques the wide field and the scanning microscopes. Other imaging enhancements on the technique like extended resolution wide field, the total internal reflection imaging, and its derivatives are also reviewed. In addition to the imaging techniques, some diffusion techniques also are discussed like fluorescence correlation spectroscopy. The related methods like Forester resonance transfer, photo-induced electron transfer and anisotropy (steady state and time decay) are also discussed. In addition, we elucidated some simple details about the theory behind the FCS and its resulting curve fitting. This review is preceded by general introduction and ended with the conclusion.
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Affiliation(s)
- Diaa Atta
- Spectroscopy Department, Physics Division, National Research Center, 12311 Dokki, Cairo, Egypt.
| | - Ali Okasha
- Spectroscopy Department, Physics Division, National Research Center, 12311 Dokki, Cairo, Egypt
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31
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Turriani E, Höbartner C, Jovin TM. Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence. Nucleic Acids Res 2014; 43:40-50. [PMID: 25505142 PMCID: PMC4288166 DOI: 10.1093/nar/gku1268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Among the deoxyribozymes catalyzing the ligation of two RNA substrates, 7S11 generates a branched RNA containing a 2',5'-linkage. We have attached the small fluorogenic probe Bimane to the triphosphate terminated RNA substrate and utilized emission intensity and anisotropy to follow structural rearrangements leading to a catalytically active complex upon addition of Mg(2+). Bimane coupled to synthetic oligonucleotides is quenched by nearby guanines via photoinduced electron transfer. The degree of quenching is sensitive to changes in the base pairing of the residues involved and in their distances to the probe. These phenomena permit the characterization of various sequential processes in the assembly and function of 7S11: binding of Mg(2+) to the triphosphate moiety, release of quenching of the probe by the 5'-terminal G residues of R-RNA as they engage in secondary base-pair interactions, local rearrangement into a distinct active conformation, and continuous release of the Bimane-labeled pyrophosphate during the course of reaction at 37°C. It was possible to assign equilibrium and rate constants and structural interpretations to the sequence of conformational transitions and catalysis, information useful for optimizing the design of next generation deoxyribozymes. The fluorescent signatures, thermodynamic equilibria and catalytic function of numerous mutated (base/substituted) molecules were examined.
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Affiliation(s)
- Elisa Turriani
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Höbartner
- Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany and Institute for Organic and Biomolecular Chemistry, Georg August University Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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32
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Cao R, Naivar MA, Wilder M, Houston JP. Expanding the potential of standard flow cytometry by extracting fluorescence lifetimes from cytometric pulse shifts. Cytometry A 2014; 85:999-1010. [PMID: 25274073 PMCID: PMC4257068 DOI: 10.1002/cyto.a.22574] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 12/29/2022]
Abstract
Fluorescence lifetime measurements provide information about the fluorescence relaxation, or intensity decay, of organic fluorophores, fluorescent proteins, and other inorganic molecules that fluoresce. The fluorescence lifetime is emerging in flow cytometry and is helpful in a variety of multiparametric, single cell measurements because it is not impacted by nonlinearity that can occur with fluorescence intensity measurements. Yet time-resolved cytometry systems rely on major hardware modifications making the methodology difficult to reproduce. The motivation of this work is, by taking advantage of the dynamic nature of flow cytometry sample detection and applying digital signal processing methods, to measure fluorescence lifetimes using an unmodified flow cytometer. We collect a new lifetime-dependent parameter, referred to herein as the fluorescence-pulse-delay (FPD), and prove it is a valid representation of the average fluorescence lifetime. To verify we generated cytometric pulses in simulation, with light emitting diode (LED) pulsation, and with true fluorescence measurements of cells and microspheres. Each pulse is digitized and used in algorithms to extract an average fluorescence lifetime inherent in the signal. A range of fluorescence lifetimes is measurable with this approach including standard organic fluorophore lifetimes (∼1 to 22 ns) as well as small, simulated shifts (0.1 ns) under standard conditions (reported herein). This contribution demonstrates how digital data acquisition and signal processing can reveal time-dependent information foreshadowing the exploitation of full waveform analysis for quantification of similar photo-physical events within single cells.
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Affiliation(s)
- Ruofan Cao
- Department of Chemical Engineering, New Mexico State UniversityLas Cruces, New Mexico, 88003-001
| | | | | | - Jessica P Houston
- Department of Chemical Engineering, New Mexico State UniversityLas Cruces, New Mexico, 88003-001
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33
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Bessman NJ, Freed DM, Lemmon MA. Putting together structures of epidermal growth factor receptors. Curr Opin Struct Biol 2014; 29:95-101. [PMID: 25460273 DOI: 10.1016/j.sbi.2014.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 09/23/2014] [Accepted: 10/01/2014] [Indexed: 01/15/2023]
Abstract
Numerous crystal structures have been reported for the isolated extracellular region and tyrosine kinase domain of the epidermal growth factor receptor (EGFR) and its relatives, in different states of activation and bound to a variety of inhibitors used in cancer therapy. The next challenge is to put these structures together accurately in functional models of the intact receptor in its membrane environment. The intact EGFR has been studied using electron microscopy, chemical biology methods, biochemically, and computationally. The distinct approaches yield different impressions about the structural modes of communication between extracellular and intracellular regions. They highlight possible differences between ligands, and also underline the need to understand how the receptor interacts with the membrane itself.
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Affiliation(s)
- Nicholas J Bessman
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, United States; Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, United States
| | - Daniel M Freed
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, United States
| | - Mark A Lemmon
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, United States; Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, United States.
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Arndt-Jovin DJ, Botelho MG, Jovin TM. Structure-function relationships of ErbB RTKs in the plasma membrane of living cells. Cold Spring Harb Perspect Biol 2014; 6:a008961. [PMID: 24691959 DOI: 10.1101/cshperspect.a008961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We review the states of the ErbB family of receptor tyrosine kinases (RTKs), primarily the EGF receptor (EGFR, ErbB1, HER1) and the orphan receptor ErbB2 as they exist in living mammalian cells, focusing on four main aspects: (1) aggregation state and distribution in the plasma membrane; (2) conformational features of the receptors situated in the plasma membrane, compared to the crystallographic structures of the isolated extracellular domains; (3) coupling of receptor disposition on filopodia with the transduction of signaling ligand gradients; and (4) ligand-independent receptor activation by application of a magnetic field.
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Affiliation(s)
- Donna J Arndt-Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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35
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Burgess AW, Henis YI, Hynes NE, Jovin T, Levitzki A, Pinkas-Kramarski R, Yarden Y. EGF receptor family: twisting targets for improved cancer therapies. Growth Factors 2014; 32:74-81. [PMID: 24641597 DOI: 10.3109/08977194.2014.896355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epidermal growth factor receptor (EGFR) undergoes a conformational change in response to ligand binding. The ligand-induced changes in cell surface aggregation and mobility have a profound effect on the function of all the family members. Ligand also activates the EGFR intracellular kinase, stimulating proliferation and cell survival. The EGFR family are often activated, overexpressed or mutated in cancer cells and therapeutic drugs (including antibodies) can slow the progress of some cancers. This article provides a brief, annotated summary of the presentations and discussion which occurred at the Epidermal Growth Factor Receptor - Future Directions Conference held in Jerusalem in November 2013.
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Affiliation(s)
- Antony W Burgess
- The Walter & Eliza Hall Institute of Medical Research, Burgess Lab Structural Biology , Parkville , Australia
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36
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Bharde AA, Palankar R, Fritsch C, Klaver A, Kanger JS, Jovin TM, Arndt-Jovin DJ. Magnetic nanoparticles as mediators of ligand-free activation of EGFR signaling. PLoS One 2013; 8:e68879. [PMID: 23894364 PMCID: PMC3720882 DOI: 10.1371/journal.pone.0068879] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 06/03/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Magnetic nanoparticles (NPs) are of particular interest in biomedical research, and have been exploited for molecular separation, gene/drug delivery, magnetic resonance imaging, and hyperthermic cancer therapy. In the case of cultured cells, magnetic manipulation of NPs provides the means for studying processes induced by mechanotransduction or by local clustering of targeted macromolecules, e.g. cell surface receptors. The latter are normally activated by binding of their natural ligands mediating key signaling pathways such as those associated with the epidermal growth factor (EGFR). However, it has been reported that EGFR may be dimerized and activated even in the absence of ligands. The present study assessed whether receptor clustering induced by physical means alone suffices for activating EGFR in quiescent cells. METHODOLOGY/PRINCIPAL FINDINGS The EGFR on A431 cells was specifically targeted by superparamagnetic iron oxide NPs (SPIONs) carrying either a ligand-blocking monoclonal anti-EGFR antibody or a streptavidin molecule for targeting a chimeric EGFR incorporating a biotinylated amino-terminal acyl carrier peptide moiety. Application of a magnetic field led to SPION magnetization and clustering, resulting in activation of the EGFR, a process manifested by auto and transphosphorylation and downstream signaling. The magnetically-induced early signaling events were similar to those inherent to the ligand dependent EGFR pathways. Magnetization studies indicated that the NPs exerted magnetic dipolar forces in the sub-piconewton range with clustering dependent on Brownian motion of the receptor-SPION complex and magnetic field strength. CONCLUSIONS/SIGNIFICANCE We demonstrate that EGFR on the cell surface that have their ligand binding-pocket blocked by an antibody are still capable of transphosphorylation and initiation of signaling cascades if they are clustered by SPIONs either attached locally or targeted to another site of the receptor ectodomain. The results suggest that activation of growth factor receptors may be triggered by ligand-independent molecular crowding resulting from overexpression and/or sequestration in membrane microdomains.
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Affiliation(s)
- Atul A. Bharde
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Raghavendra Palankar
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cornelia Fritsch
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Arjen Klaver
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Johannes S. Kanger
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Thomas M. Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donna J. Arndt-Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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