51
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Nanopore-mediated protein delivery enabling three-color single-molecule tracking in living cells. Proc Natl Acad Sci U S A 2021; 118:2012229118. [PMID: 33495347 DOI: 10.1073/pnas.2012229118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Multicolor single-molecule tracking (SMT) provides a powerful tool to mechanistically probe molecular interactions in living cells. However, because of the limitations in the optical and chemical properties of currently available fluorophores and the multiprotein labeling strategies, intracellular multicolor SMT remains challenging for general research studies. Here, we introduce a practical method employing a nanopore-electroporation (NanoEP) technique to deliver multiple organic dye-labeled proteins into living cells for imaging. It can be easily expanded to three channels in commercial microscopes or be combined with other in situ labeling methods. Utilizing NanoEP, we demonstrate three-color SMT for both cytosolic and membrane proteins. Specifically, we simultaneously monitored single-molecule events downstream of EGFR signaling pathways in living cells. The results provide detailed resolution of the spatial localization and dynamics of Grb2 and SOS recruitment to activated EGFR along with the resultant Ras activation.
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52
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Interactions between Ligand-Bound EGFR and VEGFR2. J Mol Biol 2021; 433:167006. [PMID: 33891904 DOI: 10.1016/j.jmb.2021.167006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/21/2022]
Abstract
In this work, we put forward the provocative hypothesis that the active, ligand-bound RTK dimers from unrelated subfamilies can associate into heterooligomers with novel signaling properties. This hypothesis is based on a quantitative FRET study that monitors the interactions between EGFR and VEGFR2 in the plasma membrane of live cells in the absence of ligand, in the presence of either EGF or VEGF, and in the presence of both ligands. We show that direct interactions occur between EGFR and VEGFR2 in the absence of ligand and in the presence of the two cognate ligands. However, there are not significant heterointeractions between EGFR and VEGFR2 when only one of the ligands is present. Since RTK dimers and RTK oligomers are believed to signal differently, this finding suggests a novel mechanism for signal diversification.
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53
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The biophysical basis of receptor tyrosine kinase ligand functional selectivity: Trk-B case study. Biochem J 2021; 477:4515-4526. [PMID: 33094812 DOI: 10.1042/bcj20200671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023]
Abstract
Tropomyosin receptor kinase B (Trk-B) belongs to the second largest family of membrane receptors, Receptor Tyrosine Kinases (RTKs). Trk-B is known to interact with three different neurotrophins: Brain-Derived Neurotrophic Factor (BDNF), Neurotrophin-4 (NT-4), and Neurotrophin-3 (NT-3). All three neurotrophins are involved in survival and proliferation of neuronal cells, but each induces distinct signaling through Trk-B. We hypothesize that the different biological effects correlate with differences in the interactions between the Trk-B receptors, when bound to different ligands, in the plasma membrane. To test this hypothesis, we use quantitative FRET to characterize Trk-B dimerization in response to NT-3 and NT-4 in live cells, and compare it to the previously published data for Trk-B in the absence and presence of BDNF. Our study reveals that the distinct Trk-B signaling outcomes are underpinned by both different configurations and different stabilities of the three ligand-bound Trk-B dimers in the plasma membrane.
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54
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Rosenkranz AA, Slastnikova TA. Epidermal Growth Factor Receptor: Key to Selective Intracellular Delivery. BIOCHEMISTRY (MOSCOW) 2021; 85:967-1092. [PMID: 33050847 DOI: 10.1134/s0006297920090011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epidermal growth factor receptor (EGFR) is an integral surface protein mediating cellular response to a number of growth factors. Its overexpression and increased activation due to mutations is one of the most common traits of many types of cancer. Development and clinical use of the agents, which block EGFR activation, became a prime example of the personalized targeted medicine. However, despite the obvious success in this area, cancer cure remains unattainable in most cases. Because of that, as well as the result of the search for possible ways to overcome the difficulties of treatment, a huge number of new treatment methods relying on the use of EGFR overexpression and its changes to destroy cancer cells. Modern data on the structure, functioning, and intracellular transport of EGFR, its natural ligands, as well as signaling cascades triggered by the EGFR activation, peculiarities of the EGFR expression and activation in oncological disorders, as well as applied therapeutic approaches aimed at blocking EGFR signaling pathway are summarized and analyzed in this review. Approaches to the targeted delivery of various chemotherapeutic agents, radionuclides, immunotoxins, photosensitizers, as well as the prospects for gene therapy aimed at cancer cells with EGFR overexpression are reviewed in detail. It should be noted that increasing attention is being paid nowadays to the development of multifunctional systems, either carrying several different active agents, or possessing several environment-dependent transport functions. Potentials of the systems based on receptor-mediated endocytosis of EGFR and their possible advantages and limitations are discussed.
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Affiliation(s)
- A A Rosenkranz
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - T A Slastnikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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55
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Structure-function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting. Nat Commun 2021; 12:1382. [PMID: 33654076 PMCID: PMC7925532 DOI: 10.1038/s41467-021-21613-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
Mechanistic understanding of oncogenic variants facilitates the development and optimization of treatment strategies. We recently identified in-frame, tandem duplication of EGFR exons 18 - 25, which causes EGFR Kinase Domain Duplication (EGFR-KDD). Here, we characterize the prevalence of ERBB family KDDs across multiple human cancers and evaluate the functional biochemistry of EGFR-KDD as it relates to pathogenesis and potential therapeutic intervention. We provide computational and experimental evidence that EGFR-KDD functions by forming asymmetric EGF-independent intra-molecular and EGF-dependent inter-molecular dimers. Time-resolved fluorescence microscopy and co-immunoprecipitation reveals EGFR-KDD can form ligand-dependent inter-molecular homo- and hetero-dimers/multimers. Furthermore, we show that inhibition of EGFR-KDD activity is maximally achieved by blocking both intra- and inter-molecular dimerization. Collectively, our findings define a previously unrecognized model of EGFR dimerization, providing important insights for the understanding of EGFR activation mechanisms and informing personalized treatment of patients with tumors harboring EGFR-KDD. Finally, we establish ERBB KDDs as recurrent oncogenic events in multiple cancers. An EGFR mutant with kinase domain duplication (EGFR-KDD) was previously identified in an index patient, but the functional and therapeutic implications remain unclear. Here, the authors show that KDD occurs in other ErbB receptors in multiple cancers, and characterize the mechanism and inhibition of EGFR-KDD.
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56
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Kelel M, Yang RB, Tsai TF, Liang PH, Wu FY, Huang YT, Yang MF, Hsiao YP, Wang LF, Tu CF, Liu FT, Lee YL. FUT8 Remodeling of EGFR Regulates Epidermal Keratinocyte Proliferation during Psoriasis Development. J Invest Dermatol 2021; 141:512-522. [PMID: 32888953 DOI: 10.1016/j.jid.2020.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
α-(1,6)-fucosyltransferase 8 (FUT8) is implicated in the pathogenesis of several malignancies, but its role in psoriasis is poorly understood. In this study, we show that FUT8 remodeling of EGFR plays a critical role in the development of psoriasis phenotypes. Notably, elevated FUT8 expression was associated with disease severity in the lesional epidermis of a patient with psoriasis. FUT8 gain of function promoted HaCaT cell proliferation, whereas short hairpin FUT8 reduced cell proliferation and induced a longer S phase with downregulation of cyclin A1 expression. Furthermore, cell proliferation, which is controlled by the activation of EGFR, was shown to be regulated by FUT8 core fucosylation of EGFR. Short hairpin FUT8 significantly reduced EGFR/protein kinase B signaling and slowed EGF‒EGFR complex trafficking to the perinuclear region. Moreover, short hairpin FUT8 reduced ligand-induced EGFR dimerization. Overactivated EGFR was observed in the lesional epidermis of both human patient and psoriasis-like mouse model, whereas conditional knockout of FUT8 in an IL-23 psoriasis-like mouse model ameliorated disease phenotypes and reduced EGFR activation in the epidermis. These findings implied that elevated FUT8 expression in the lesional epidermis is implicated in the development of psoriasis phenotypes, being required for EGFR overactivation and leading to keratinocyte hyperproliferation.
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Affiliation(s)
- Musin Kelel
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Tsen-Fang Tsai
- Department of Dermatology, National Taiwan University Hospital, Taipei, Taiwan; Department of Dermatology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Fu-Yu Wu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Tien Huang
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Fong Yang
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Ping Hsiao
- Department of Dermatology, Chung Shan Medical University Hospital and Chung Shan Medical University, Taichung, Taiwan
| | - Li-Fang Wang
- Department of Dermatology, National Taiwan University Hospital, Taipei, Taiwan; Department of Dermatology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chen-Fen Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Fu-Tong Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yungling L Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; College of Public Health, China Medical University, Taichung, Taiwan.
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57
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Membrane therapy using DHA suppresses epidermal growth factor receptor signaling by disrupting nanocluster formation. J Lipid Res 2021; 62:100026. [PMID: 33515553 PMCID: PMC7933808 DOI: 10.1016/j.jlr.2021.100026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) signaling drives the formation of many types of cancer, including colon cancer. Docosahexaenoic acid (DHA, 22∶6Δ4,7,10,13,16,19), a chemoprotective long-chain n-3 polyunsaturated fatty acid suppresses EGFR signaling. However, the mechanism underlying this phenotype remains unclear. Therefore, we used super-resolution microscopy techniques to investigate the mechanistic link between EGFR function and DHA-induced alterations to plasma membrane nanodomains. Using isogenic in vitro (YAMC and IMCE mouse colonic cell lines) and in vivo (Drosophila, wild type and Fat-1 mice) models, cellular DHA enrichment via therapeutic nanoparticle delivery, endogenous synthesis, or dietary supplementation reduced EGFR-mediated cell proliferation and downstream Ras/ERK signaling. Phospholipid incorporation of DHA reduced membrane rigidity and the size of EGFR nanoclusters. Similarly, pharmacological reduction of plasma membrane phosphatidic acid (PA), phosphatidylinositol-4,5-bisphosphate (PIP2) or cholesterol was associated with a decrease in EGFR nanocluster size. Furthermore, in DHA-treated cells only the addition of cholesterol, unlike PA or PIP2, restored EGFR nanoscale clustering. These findings reveal that DHA reduces EGFR signaling in part by reshaping EGFR proteolipid nanodomains, supporting the feasibility of using membrane therapy, i.e., dietary/drug-related strategies to target plasma membrane organization, to reduce EGFR signaling and cancer risk.
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58
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Ambrosetti E, Bernardinelli G, Hoffecker I, Hartmanis L, Kiriako G, de Marco A, Sandberg R, Högberg B, Teixeira AI. A DNA-nanoassembly-based approach to map membrane protein nanoenvironments. NATURE NANOTECHNOLOGY 2021; 16:85-95. [PMID: 33139936 DOI: 10.1038/s41565-020-00785-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy-based method for ensemble analysis of membrane protein nanodomains. The method, termed nanoscale deciphering of membrane protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterized the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function.
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Affiliation(s)
- Elena Ambrosetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Giulio Bernardinelli
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ian Hoffecker
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Georges Kiriako
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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59
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Salavessa L, Sauvonnet N. Stoichiometry of Receptors at the Plasma Membrane During Their Endocytosis Using Total Internal Reflection Fluorescent (TIRF) Microscopy Live Imaging and Single-Molecule Tracking. Methods Mol Biol 2021; 2233:3-17. [PMID: 33222124 DOI: 10.1007/978-1-0716-1044-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Determination of protein stoichiometry in living cells is key to understanding basic biological processes. This is particularly important for receptor-mediated endocytosis, a highly regulated mechanism that requires the sequential assembly of numerous factors. Here, we describe a quantitative approach to analyze receptor clustering dynamics at the plasma membrane. Our workflow combines TIRF live imaging of a CRISPR-Cas9-edited cell line expressing a GFP-tagged receptor in a physiological relevant environment, a calibration technique for single-molecule analysis of GFP, and detection and tracking with an open-source software. This method allows to determine the number of receptor molecules at the plasma membrane in real time.
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Affiliation(s)
- Laura Salavessa
- Group intracellular trafficking and tissue homeostasis. Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France.,U1202, INSERM, Paris, France.,Université Paris Sud, Paris-Saclay University, Orsay, France
| | - Nathalie Sauvonnet
- Group intracellular trafficking and tissue homeostasis. Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France. .,U1202, INSERM, Paris, France.
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60
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Casey GR, Zhou X, Lesiak L, Xu B, Fang Y, Becker DF, Stains CI. An Evolutionary Strategy for Identification of Higher Order, Green Fluorescent Host-Guest Pairs Compatible with Living Systems. Chemistry 2020; 26:16721-16726. [PMID: 32725914 DOI: 10.1002/chem.202002423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/26/2020] [Indexed: 11/09/2022]
Abstract
Engineered miniprotein host-small-molecule guest pairs could be utilized to design new processes within cells as well as investigate fundamental aspects of cell signaling mechanisms. However, the development of host-guest pairs capable of functioning in living systems has proven challenging. Moreover, few examples of host-guest pairs with stoichiometries other than 2:1 exist, significantly hindering the ability to study the influence of oligomerization state on signaling fidelity. Herein, we present an approach to identify host-guest systems for relatively small green fluorescent guests by incorporation into cyclic peptides. The optimal host-guest pair produced a 10-fold increase in green fluorescence signal upon binding. Biophysical characterization clearly demonstrated higher order supramolecular assembly, which could be visualized on the surface of living yeast cells using a turn-on fluorescence readout. This work further defines evolutionary design principles to afford host-guest pairs with stoichiometries other than 2:1 and enables the identification of spectrally orthogonal host-guest pairs.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry and Physics, Southeast Missouri State University, Cape Girardeau, MO, 63701, USA
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lauren Lesiak
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bi Xu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Yuan Fang
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Becker
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22904, USA
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61
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Cooperation and Interplay between EGFR Signalling and Extracellular Vesicle Biogenesis in Cancer. Cells 2020; 9:cells9122639. [PMID: 33302515 PMCID: PMC7764760 DOI: 10.3390/cells9122639] [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: 11/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) takes centre stage in carcinogenesis throughout its entire cellular trafficking odyssey. When loaded in extracellular vesicles (EVs), EGFR is one of the key proteins involved in the transfer of information between parental cancer and bystander cells in the tumour microenvironment. To hijack EVs, EGFR needs to play multiple signalling roles in the life cycle of EVs. The receptor is involved in the biogenesis of specific EV subpopulations, it signals as an active cargo, and it can influence the uptake of EVs by recipient cells. EGFR regulates its own inclusion in EVs through feedback loops during disease progression and in response to challenges such as hypoxia, epithelial-to-mesenchymal transition and drugs. Here, we highlight how the spatiotemporal rules that regulate EGFR intracellular function intersect with and influence different EV biogenesis pathways and discuss key regulatory features and interactions of this interplay. We also elaborate on outstanding questions relating to EGFR-driven EV biogenesis and available methods to explore them. This mechanistic understanding will be key to unravelling the functional consequences of direct anti-EGFR targeted and indirect EGFR-impacting cancer therapies on the secretion of pro-tumoural EVs and on their effects on drug resistance and microenvironment subversion.
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62
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Ahmed F, Zapata-Mercado E, Rahman S, Hristova K. The Biased Ligands NGF and NT-3 Differentially Stabilize Trk-A Dimers. Biophys J 2020; 120:55-63. [PMID: 33285113 DOI: 10.1016/j.bpj.2020.11.2262] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022] Open
Abstract
Trk-A is a receptor tyrosine kinase (RTK) that plays an essential role in the development and functioning of the nervous system. Trk-A is expressed in neurons and signals in response to two ligands, NGF and neurotrophin-3 (NT-3), with very different functional consequences. Thus, NGF and NT-3 are "biased" ligands for Trk-A. Because it has been hypothesized that biased RTK ligands induce differential stabilization of RTK dimers, here, we seek to test this hypothesis for NGF and NT-3. In particular, we use Förster resonance energy transfer (FRET) and fluorescence intensity fluctuation spectroscopy to assess the strength of Trk-A interactions and Trk-A oligomer size in the presence of the two ligands. Although the difference in Trk-A behavior in response to the two ligands has been previously attributed to differences in their binding to Trk-A in the endosomes at low pH, here, we further show differences in the stabilities of the NGF- and NT-3-bound Trk-A dimers in the plasma membrane and at neutral pH. We discuss the biological significance of these new findings and their implications for the design of Trk-A ligands with novel functionalities.
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Affiliation(s)
- Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Elmer Zapata-Mercado
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Sanim Rahman
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
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63
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Zanetti-Domingues LC, Bonner SE, Martin-Fernandez ML, Huber V. Mechanisms of Action of EGFR Tyrosine Kinase Receptor Incorporated in Extracellular Vesicles. Cells 2020; 9:cells9112505. [PMID: 33228060 PMCID: PMC7699420 DOI: 10.3390/cells9112505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/09/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
EGFR and some of the cognate ligands extensively traffic in extracellular vesicles (EVs) from different biogenesis pathways. EGFR belongs to a family of four homologous tyrosine kinase receptors (TKRs). This family are one of the major drivers of cancer and is involved in several of the most frequent malignancies such as non-small cell lung cancer, breast cancer, colorectal cancer and ovarian cancer. The carrier EVs exert crucial biological effects on recipient cells, impacting immunity, pre-metastatic niche preparation, angiogenesis, cancer cell stemness and horizontal oncogene transfer. While EV-mediated EGFR signalling is important to EGFR-driven cancers, little is known about the precise mechanisms by which TKRs incorporated in EVs play their biological role, their stoichiometry and associations to other proteins relevant to cancer pathology and EV biogenesis, and their means of incorporation in the target cell. In addition, it remains unclear whether different subtypes of EVs incorporate different complexes of TKRs with specific functions. A raft of high spatial and temporal resolution methods is emerging that could solve these and other questions regarding the activity of EGFR and its ligands in EVs. More importantly, methods are emerging to block or mitigate EV activity to suppress cancer progression and drug resistance. By highlighting key findings and areas that remain obscure at the intersection of EGFR signalling and EV action, we hope to cross-fertilise the two fields and speed up the application of novel techniques and paradigms to both.
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Affiliation(s)
- Laura C. Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK;
- Correspondence: (L.C.Z.-D.); (V.H.)
| | - Scott E. Bonner
- The Wood Lab, Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK;
| | - Marisa L. Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK;
| | - Veronica Huber
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
- Correspondence: (L.C.Z.-D.); (V.H.)
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64
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Mechanisms of EGFR Resistance in Glioblastoma. Int J Mol Sci 2020; 21:ijms21228471. [PMID: 33187135 PMCID: PMC7696540 DOI: 10.3390/ijms21228471] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Despite numerous efforts to target epidermal growth factor receptor (EGFR), commonly dysregulated in GBM, approaches directed against EGFR have not achieved the same degree of success as seen in other tumor types, particularly as compared to non-small cell lung cancer (NSCLC). EGFR alterations in glioblastoma lie primarily in the extracellular domain, unlike the kinase domain alterations seen in NSCLC. Small molecule inhibitors are difficult to develop for the extracellular domain. Monoclonal antibodies can be developed to target the extracellular domain but must contend with the blood brain barrier (BBB). We review the role of EGFR in GBM, the history of trialed treatments, and the potential paths forward to target the pathway that may have greater success.
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65
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Martin-Fernandez ML. A brief history of the octopus imaging facility to celebrate its 10th anniversary. J Microsc 2020; 281:3-15. [PMID: 33111321 DOI: 10.1111/jmi.12974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/27/2022]
Abstract
Octopus (Optics Clustered to OutPut Unique Solutions) celebrated in June 2020 its 10th birthday. Based at Harwell, near Oxford, Octopus is an open access, peer reviewed, national imaging facility that offers successful U.K. applicants supported access to single molecule imaging, confocal microscopy, several flavours of superresolution imaging, light sheet microscopy, optical trapping and cryoscanning electron microscopy. Managed by a multidisciplinary team, Octopus has so far assisted >100 groups of U.K. and international researchers. Cross-fertilisation across fields proved to be a strong propeller of success underpinned by combining access to top-end instrumentation with a strong programme of imaging hardware and software developments. How Octopus was born, and highlights of the multidisciplinary output produced during its 10-year journey are reviewed below, with the aim of celebrating a myriad of collaborations with the U.K. scientific community, and reflecting on their scientific and societal impact.
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Affiliation(s)
- M L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, U.K
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66
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Onal S, Turker-Burhan M, Bati-Ayaz G, Yanik H, Pesen-Okvur D. Breast cancer cells and macrophages in a paracrine-juxtacrine loop. Biomaterials 2020; 267:120412. [PMID: 33161320 DOI: 10.1016/j.biomaterials.2020.120412] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023]
Abstract
Breast cancer cells (BCC) and macrophages are known to interact via epidermal growth factor (EGF) produced by macrophages and colony stimulating factor-1 (CSF-1) produced by BCC. Despite contradictory findings, this interaction is perceived as a paracrine loop. Further, the underlying mechanism of interaction remains unclear. Here, we investigated interactions of BCC with macrophages in 2D and 3D. While both BCC and macrophages showed invasion/chemotaxis to fetal bovine serum, only macrophages showed chemotaxis to BCC in custom designed 3D cell-on-a-chip devices. These results were in agreement with gradient simulation results and ELISA results showing that macrophage-derived-EGF was not secreted into macrophage-conditioned-medium. Live cell imaging of BCC in the presence and absence of iressa showed that macrophages but not macrophage-derived-matrix modulated adhesion and motility of BCC in 2D. 3D co-culture experiments in collagen and matrigel showed that BCC changed their multicellular organization in the presence of macrophages. In custom designed 3D co-culture cell-on-a-chip devices, macrophages promoted and reduced migration of BCC in collagen and matrigel, respectively. Furthermore, adherent but not suspended BCC endocytosed EGFR when in contact with macrophages. Collectively, our data revealed that macrophages showed chemotaxis towards BCC whereas BCC required direct contact to interact with macrophage-derived-EGF. Therefore, we propose that the interaction between cancer cells and macrophages is a paracrine-juxtacrine loop of CSF-1 and EGF, respectively.
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Affiliation(s)
- Sevgi Onal
- Graduate Program in Biotechnology and Bioengineering, Turkey
| | - Merve Turker-Burhan
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce Kampusu, Urla, Izmir, 35430, Turkey
| | - Gizem Bati-Ayaz
- Graduate Program in Biotechnology and Bioengineering, Turkey
| | - Hamdullah Yanik
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce Kampusu, Urla, Izmir, 35430, Turkey
| | - Devrim Pesen-Okvur
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce Kampusu, Urla, Izmir, 35430, Turkey.
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Koseska A, Bastiaens PI. Processing Temporal Growth Factor Patterns by an Epidermal Growth Factor Receptor Network Dynamically Established in Space. Annu Rev Cell Dev Biol 2020; 36:359-383. [DOI: 10.1146/annurev-cellbio-013020-103810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The proto-oncogenic epidermal growth factor (EGF) receptor (EGFR) is a tyrosine kinase whose sensitivity and response to growth factor signals that vary over time and space determine cellular behavior within a developing tissue. The molecular reorganization of the receptors on the plasma membrane and the enzyme-kinetic mechanisms of phosphorylation are key determinants that couple growth factor binding to EGFR signaling. To enable signal initiation and termination while simultaneously accounting for suppression of aberrant signaling, a coordinated coupling of EGFR kinase and protein tyrosine phosphatase activity is established through space by vesicular dynamics. The dynamical operation mode of this network enables not only time-varying growth factor sensing but also adaptation of the response depending on cellular context. By connecting spatially coupled enzymatic kinase/phosphatase processes and the corresponding dynamical systems description of the EGFR network, we elaborate on the general principles necessary for processing complex growth factor signals.
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Affiliation(s)
- Aneta Koseska
- Lise Meitner Group Cellular Computations and Learning, Centre of Advanced European Studies and Research (caesar), D-53175 Bonn, Germany
| | - Philippe I.H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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68
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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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69
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Investigations of EGFR configurations on tumor cell surface by high-resolution electron microscopy. Biochem Biophys Res Commun 2020; 532:179-184. [PMID: 32854945 DOI: 10.1016/j.bbrc.2020.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/11/2023]
Abstract
Epidermal growth factor receptor (EGFR) is an important target for tumor therapy in various tumors. The current understanding of EGFR conformations on the cell surface is based on X-ray structural data, molecular dynamic simulations, and fluorescence-localization imaging. Using scanning electron microscope (SEM) and transmission electron microscope (TEM) with the resolution at sub-nanometers, we successfully recognized individual molecules of EGFRs and their assembly details on the surface of triple-negative breast cancer (TNBC) upon one-to-one labeling by Au nanoparticles. Based on our results, we have proposed the possible configurations, structural models, and conformational transitions of EGFR oligomers. Our study shows that the high-resolution electron imaging is an invaluable tool to provide direct evidence of EGFR configuration on tumor cell surfaces, and may play a pivotal role in further understanding of EGFR-associated signaling and tumor therapy.
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70
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Direct and indirect cholesterol effects on membrane proteins with special focus on potassium channels. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158706. [DOI: 10.1016/j.bbalip.2020.158706] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
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71
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Banik SM, Pedram K, Wisnovsky S, Ahn G, Riley NM, Bertozzi CR. Lysosome-targeting chimaeras for degradation of extracellular proteins. Nature 2020; 584:291-297. [PMID: 32728216 PMCID: PMC7727926 DOI: 10.1038/s41586-020-2545-9] [Citation(s) in RCA: 464] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/22/2020] [Indexed: 01/30/2023]
Abstract
The majority of therapies that target individual proteins rely on specific activity-modulating interactions with the target protein-for example, enzyme inhibition or ligand blocking. However, several major classes of therapeutically relevant proteins have unknown or inaccessible activity profiles and so cannot be targeted by such strategies. Protein-degradation platforms such as proteolysis-targeting chimaeras (PROTACs)1,2 and others (for example, dTAGs3, Trim-Away4, chaperone-mediated autophagy targeting5 and SNIPERs6) have been developed for proteins that are typically difficult to target; however, these methods involve the manipulation of intracellular protein degradation machinery and are therefore fundamentally limited to proteins that contain cytosolic domains to which ligands can bind and recruit the requisite cellular components. Extracellular and membrane-associated proteins-the products of 40% of all protein-encoding genes7-are key agents in cancer, ageing-related diseases and autoimmune disorders8, and so a general strategy to selectively degrade these proteins has the potential to improve human health. Here we establish the targeted degradation of extracellular and membrane-associated proteins using conjugates that bind both a cell-surface lysosome-shuttling receptor and the extracellular domain of a target protein. These initial lysosome-targeting chimaeras, which we term LYTACs, consist of a small molecule or antibody fused to chemically synthesized glycopeptide ligands that are agonists of the cation-independent mannose-6-phosphate receptor (CI-M6PR). We use LYTACs to develop a CRISPR interference screen that reveals the biochemical pathway for CI-M6PR-mediated cargo internalization in cell lines, and uncover the exocyst complex as a previously unidentified-but essential-component of this pathway. We demonstrate the scope of this platform through the degradation of therapeutically relevant proteins, including apolipoprotein E4, epidermal growth factor receptor, CD71 and programmed death-ligand 1. Our results establish a modular strategy for directing secreted and membrane proteins for lysosomal degradation, with broad implications for biochemical research and for therapeutics.
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Affiliation(s)
- Steven M Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Simon Wisnovsky
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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72
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Yu L, Zhang W, Luo W, Dupont RL, Xu Y, Wang Y, Tu B, Xu H, Wang X, Fang Q, Yang Y, Wang C, Wang C. Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T. SCIENCE ADVANCES 2020; 6:eabc1449. [PMID: 32821844 PMCID: PMC7406363 DOI: 10.1126/sciadv.abc1449] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP8-37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 k B T, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 k B T). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.
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Affiliation(s)
- Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
| | - Wendi Luo
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Robert L. Dupont
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yang Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yibing Wang
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Bin Tu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Haiyan Xu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Xiaoguang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Qiaojun Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
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73
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Ras assemblies and signaling at the membrane. Curr Opin Struct Biol 2020; 62:140-148. [DOI: 10.1016/j.sbi.2020.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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74
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Dobner J, Simons IM, Rufinatscha K, Hänsch S, Schwarten M, Weiergräber OH, Abdollahzadeh I, Gensch T, Bode JG, Hoffmann S, Willbold D. Deficiency of GABARAP but not its Paralogs Causes Enhanced EGF-induced EGFR Degradation. Cells 2020; 9:E1296. [PMID: 32456010 PMCID: PMC7291022 DOI: 10.3390/cells9051296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022] Open
Abstract
The γ-aminobutyric acid type A receptor-associated protein (GABARAP) and its close paralogs GABARAPL1 and GABARAPL2 constitute a subfamily of the autophagy-related 8 (Atg8) protein family. Being associated with a variety of dynamic membranous structures of autophagic and non-autophagic origin, Atg8 proteins functionalize membranes by either serving as docking sites for other proteins or by acting as membrane tethers or adhesion factors. In this study, we describe that deficiency for GABARAP alone, but not for its close paralogs, is sufficient for accelerated EGF receptor (EGFR) degradation in response to EGF, which is accompanied by the downregulation of EGFR-mediated MAPK signaling, altered target gene expression, EGF uptake, and EGF vesicle composition over time. We further show that GABARAP and EGFR converge in the same distinct compartments at endogenous GABARAP expression levels in response to EGF stimulation. Furthermore, GABARAP associates with EGFR in living cells and binds to synthetic peptides that are derived from the EGFR cytoplasmic tail in vitro. Thus, our data strongly indicate a unique and novel role for GABARAP during EGFR trafficking.
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Affiliation(s)
- Jochen Dobner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; (J.D.); (I.M.S.)
| | - Indra M. Simons
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; (J.D.); (I.M.S.)
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
| | - Kerstin Rufinatscha
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; (K.R.); (J.G.B.)
| | - Sebastian Hänsch
- Department of Biology, Center for Advanced Imaging (CAi), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany;
| | - Melanie Schwarten
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
- Institute of Biological Information Processing: Molecular and Cell Physiology (IBI-1), Forschungszentrum Jülich, 52425 Jülich, Germany;
| | - Thomas Gensch
- Institute of Biological Information Processing: Molecular and Cell Physiology (IBI-1), Forschungszentrum Jülich, 52425 Jülich, Germany;
| | - Johannes G. Bode
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; (K.R.); (J.G.B.)
| | - Silke Hoffmann
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; (J.D.); (I.M.S.)
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (O.H.W.); (I.A.); (S.H.)
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75
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Kim J, Enciso G. Absolutely robust controllers for chemical reaction networks. J R Soc Interface 2020; 17:20200031. [PMID: 32396809 DOI: 10.1098/rsif.2020.0031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both deterministic and stochastic networks, in the latter case controlling the mean as well as the variance of the target species. We employ a type of network property called absolute concentration robustness (ACR). We provide applications to the control of a multisite phosphorylation model as well as a receptor-ligand signalling system. For this framework, we use the so-called deficiency zero theorem from chemical reaction network theory as well as multiscaling model reduction methods. We show that the target species has approximately Poisson distribution with the desired mean. We further show that ACR controllers can bring robust perfect adaptation to a target species and are complementary to a recently introduced antithetic feedback controller used for stochastic chemical reactions.
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Affiliation(s)
- Jinsu Kim
- Department of Mathematics, University of California Irvine, Irvine, CA 92614, USA
| | - German Enciso
- Department of Mathematics, University of California Irvine, Irvine, CA 92614, USA
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76
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Christie S, Shi X, Smith AW. Resolving Membrane Protein-Protein Interactions in Live Cells with Pulsed Interleaved Excitation Fluorescence Cross-Correlation Spectroscopy. Acc Chem Res 2020; 53:792-799. [PMID: 32227891 DOI: 10.1021/acs.accounts.9b00625] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cell plasma membrane (PM) contains thousands of proteins that sense and respond to the outside environment. These proteins have evolved sensitivity to a wide variety of physical and chemical signals and act as a delivery system across the PM. Membrane proteins are critical for information flow and decision making in the cell and thus are important targets in drug development. A critical aspect of membrane protein function is the way they interact with other proteins, often through the formation of dimers or small oligomers that regulate function at the protein, cell, and organism levels. Resolving membrane protein interactions in a live cell environment is challenging because of the chemical diversity and spatial heterogeneity of the PM. In this Account, we describe a fluorescence technique called pulsed interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) that is ideally suited to quantify membrane associations in live cells. PIE-FCCS is a two-color fluorescence fluctuation method that can simultaneously measure the concentration, mobility, proximity, and oligomerization state of membrane proteins in situ. It has several advantages over two related approaches, single-molecule tracking (SMT) and Förster resonance energy transfer (FRET), including that it measures all of the properties listed above in a single measurement. Another advantage is that PIE-FCCS is most sensitive at the physiological expression levels for many membrane proteins rather than the very low or high levels typical in other techniques. Here, we review the history of FCCS as it has been applied to study membrane protein interactions in cells. We also describe PIE-FCCS and the advantages it has over biochemical approaches like coimmunoprecipitation (co-IP) and proximity ligation assays (PLA). Finally, we review two classes of membrane proteins that have been studied with FCCS and PIE-FCCS: receptor tyrosine kinases (RTKs) and G protein-coupled receptors (GPCRs). For RTKs, ligand induced dimerization directly regulates the catalytic activity of the kinase, but higher order oligomerization and ligand-independent dimerization can complicate this historically simple paradigm. PIE-FCCS data have resolved a low population of EGFR dimers under basal conditions and assembly into multimers when stimulated with ligand. While GPCRs function primarily as monomers, dimerization has been hypothesized to regulate function for some receptors. PIE-FCCS data have established the dimerization potential of rhodopsin at low densities and were critical for the discovery of a novel dimerization interface in human cone opsins. This Account describes the how FCCS and PIE-FCCS can reveal the details of quaternary interactions in each of these receptor systems.
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Affiliation(s)
- Shaun Christie
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
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77
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Manuel AM, Dai Y, Freeman LA, Jia P, Zhao Z. Dense module searching for gene networks associated with multiple sclerosis. BMC Med Genomics 2020; 13:48. [PMID: 32241259 PMCID: PMC7118851 DOI: 10.1186/s12920-020-0674-5] [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] [Indexed: 02/07/2023] Open
Abstract
Background Multiple sclerosis (MS) is a complex disease in which the immune system attacks the central nervous system. The molecular mechanisms contributing to the etiology of MS remain poorly understood. Genome-wide association studies (GWAS) of MS have identified a small number of genetic loci significant at the genome level, but they are mainly non-coding variants. Network-assisted analysis may help better interpret the functional roles of the variants with association signals and potential translational medicine application. The Dense Module Searching of GWAS tool (dmGWAS version 2.4) developed in our team is applied to 2 MS GWAS datasets (GeneMSA and IMSGC GWAS) using the human protein interactome as the reference network. A dual evaluation strategy is used to generate results with reproducibility. Results Approximately 7500 significant network modules were identified for each independent GWAS dataset, and 20 significant modules were identified from the dual evaluation. The top modules included GRB2, HDAC1, JAK2, MAPK1, and STAT3 as central genes. Top module genes were enriched with functional terms such as “regulation of glial cell differentiation” (adjusted p-value = 2.58 × 10− 3), “T-cell costimulation” (adjusted p-value = 2.11 × 10− 6) and “virus receptor activity” (adjusted p-value = 1.67 × 10− 3). Interestingly, top gene networks included several MS FDA approved drug target genes HDAC1, IL2RA, KEAP1, and RELA, Conclusions Our dmGWAS network analyses highlighted several genes (GRB2, HDAC1, IL2RA, JAK2, KEAP1, MAPK1, RELA and STAT3) in top modules that are promising to interpret GWAS signals and link to MS drug targets. The genes enriched with glial cell differentiation are important for understanding neurodegenerative processes in MS and for remyelination therapy investigation. Importantly, our identified genetic signals enriched in T cell costimulation and viral receptor activity supported the viral infection onset hypothesis for MS.
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Affiliation(s)
- Astrid M Manuel
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA
| | - Leorah A Freeman
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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78
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Trenker R, Jura N. Receptor tyrosine kinase activation: From the ligand perspective. Curr Opin Cell Biol 2020; 63:174-185. [PMID: 32114309 PMCID: PMC7813211 DOI: 10.1016/j.ceb.2020.01.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Receptor tyrosine kinases (RTKs) are single-span transmembrane receptors in which relatively conserved intracellular kinase domains are coupled to divergent extracellular modules. The extracellular domains initiate receptor signaling upon binding to either soluble or membrane-embedded ligands. The diversity of extracellular domain structures allows for coupling of many unique signaling inputs to intracellular tyrosine phosphorylation. The combinatorial power of this receptor system is further increased by the fact that multiple ligands can typically interact with the same receptor. Such ligands often act as biased agonists and initiate distinct signaling responses via activation of the same receptor. Mechanisms behind such biased agonism are largely unknown for RTKs, especially at the level of receptor-ligand complex structure. Using recent progress in understanding the structures of active RTK signaling units, we discuss selected mechanisms by which ligands couple receptor activation to distinct signaling outputs.
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Affiliation(s)
- Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
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79
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Mesquita FS, van der Goot FG, Sergeeva OA. Mammalian membrane trafficking as seen through the lens of bacterial toxins. Cell Microbiol 2020; 22:e13167. [PMID: 32185902 PMCID: PMC7154709 DOI: 10.1111/cmi.13167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
A fundamental question of eukaryotic cell biology is how membrane organelles are organised and interact with each other. Cell biologists address these questions by characterising the structural features of membrane compartments and the mechanisms that coordinate their exchange. To do so, they must rely on variety of cargo molecules and treatments that enable targeted perturbation, localisation, and labelling of specific compartments. In this context, bacterial toxins emerged in cell biology as paradigm shifting molecules that enabled scientists to not only study them from the side of bacterial infection but also from the side of the mammalian host. Their selectivity, potency, and versatility made them exquisite tools for uncovering much of our current understanding of membrane trafficking mechanisms. Here, we will follow the steps that lead toxins until their intracellular targets, highlighting how specific events helped us comprehend membrane trafficking and establish the fundamentals of various cellular organelles and processes. Bacterial toxins will continue to guide us in answering crucial questions in cellular biology while also acting as probes for new technologies and applications.
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Affiliation(s)
| | | | - Oksana A Sergeeva
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
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80
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Hey T, Butler K, Jackson S, Thiyagalingam J. Machine learning and big scientific data. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190054. [PMID: 31955675 PMCID: PMC7015290 DOI: 10.1098/rsta.2019.0054] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
This paper reviews some of the challenges posed by the huge growth of experimental data generated by the new generation of large-scale experiments at UK national facilities at the Rutherford Appleton Laboratory (RAL) site at Harwell near Oxford. Such 'Big Scientific Data' comes from the Diamond Light Source and Electron Microscopy Facilities, the ISIS Neutron and Muon Facility and the UK's Central Laser Facility. Increasingly, scientists are now required to use advanced machine learning and other AI technologies both to automate parts of the data pipeline and to help find new scientific discoveries in the analysis of their data. For commercially important applications, such as object recognition, natural language processing and automatic translation, deep learning has made dramatic breakthroughs. Google's DeepMind has now used the deep learning technology to develop their AlphaFold tool to make predictions for protein folding. Remarkably, it has been able to achieve some spectacular results for this specific scientific problem. Can deep learning be similarly transformative for other scientific problems? After a brief review of some initial applications of machine learning at the RAL, we focus on challenges and opportunities for AI in advancing materials science. Finally, we discuss the importance of developing some realistic machine learning benchmarks using Big Scientific Data coming from several different scientific domains. We conclude with some initial examples of our 'scientific machine learning' benchmark suite and of the research challenges these benchmarks will enable. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.
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Affiliation(s)
- Tony Hey
- Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot OX11 0QX, UK
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81
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Mansouri-Fard S, Ghaedi M, Shokri MR, Bahadori T, Khoshnoodi J, Golsaz-Shirazi F, Jeddi-Tehrani M, Amiri MM, Shokri F. Inhibitory Effect of Polyclonal Antibodies Against HER3 Extracellular Subdomains on Breast Cancer Cell Lines. Asian Pac J Cancer Prev 2020; 21:439-447. [PMID: 32102522 PMCID: PMC7332115 DOI: 10.31557/apjcp.2020.21.2.439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Indexed: 11/25/2022] Open
Abstract
Objective: Human epidermal growth factor receptor 3 (HER3) is a unique member of the tyrosine kinase receptors with an inactive kinase domain and is the preferable dimerization partner for HER2 which lead to potent tumorigenic signaling. Methods: In this study, the expression plasmids coding for the human HER3 subdomains were transfected into CHO-K1 cells. Produced proteins were characterized by ELISA and SDS-PAGE. Rabbits were immunized and produced polyclonal antibodies (pAbs) that were characterized by ELISA, Immunoblotting and flowcytometry and their inhibitory effects were assessed by XTT on BT-474 and JIMT-1 breast cancer cell lines. Result: The recombinant subdomains were highly immunogenic in rabbits. The pAbs reacted with the recombinant subdomains as well as commercial HER3 and the native receptor on tumor cell membranes and could significantly inhibit growth of Trastuzumab sensitive (BT-474) and resistant (JIMT-1) breast cancer cell lines in vitro. Conclusion: It seems that HER3 extra cellular domains (ECD) induce a strong anti-tumor antibody response and may prove to be potentially useful for immunotherapeutic applications.
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Affiliation(s)
- Samaneh Mansouri-Fard
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojgan Ghaedi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Shokri
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Tannaz Bahadori
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalal Khoshnoodi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Forough Golsaz-Shirazi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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82
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Lo CH, Huber EC, Sachs JN. Conformational states of TNFR1 as a molecular switch for receptor function. Protein Sci 2020; 29:1401-1415. [PMID: 31960514 DOI: 10.1002/pro.3829] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
Tumor necrosis factor receptor 1 (TNFR1) is a transmembrane receptor that plays a key role in the regulation of the inflammatory pathway. While inhibition of TNFR1 has been the focus of many studies for the treatment of autoimmune diseases such as rheumatoid arthritis, activation of the receptor is important for the treatment of immunodeficiency diseases such as HIV and neurodegenerative diseases such as Alzheimer's disease where a boost in immune signaling is required. In addition, activation of other TNF receptors such as death receptor 5 or FAS receptor is important for cancer therapy. Here, we used a previously established TNFR1 fluorescence resonance energy transfer (FRET) biosensor together with a fluorescence lifetime technology as a high-throughput screening platform to identify a novel small molecule that activates TNFR1 by increasing inter-monomeric spacing in a ligand-independent manner. This shows that the conformational rearrangement of pre-ligand assembled receptor dimers can determine the activity of the receptor. By probing the interaction between the receptor and its downstream signaling molecule (TRADD) our findings support a new model of TNFR1 activation in which varying conformational states of the receptor act as a molecular switch in determining receptor function.
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Affiliation(s)
- Chih Hung Lo
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Evan C Huber
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
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83
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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84
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DDR1 autophosphorylation is a result of aggregation into dense clusters. Sci Rep 2019; 9:17104. [PMID: 31745115 PMCID: PMC6863838 DOI: 10.1038/s41598-019-53176-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/25/2019] [Indexed: 12/11/2022] Open
Abstract
The collagen receptor DDR1 is a receptor tyrosine kinase that promotes progression of a wide range of human disorders. Little is known about how ligand binding triggers DDR1 kinase activity. We previously reported that collagen induces DDR1 activation through lateral dimer association and phosphorylation between dimers, a process that requires specific transmembrane association. Here we demonstrate ligand-induced DDR1 clustering by widefield and super-resolution imaging and provide evidence for a mechanism whereby DDR1 kinase activity is determined by its molecular density. Ligand binding resulted in initial DDR1 reorganisation into morphologically distinct clusters with unphosphorylated DDR1. Further compaction over time led to clusters with highly aggregated and phosphorylated DDR1. Ligand-induced DDR1 clustering was abolished by transmembrane mutations but did not require kinase activity. Our results significantly advance our understanding of the molecular events underpinning ligand-induced DDR1 kinase activity and provide an explanation for the unusually slow DDR1 activation kinetics.
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85
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Kozer N, Clayton AHA. In-cell structural dynamics of an EGF receptor during ligand-induced dimer-oligomer transition. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 49:21-37. [PMID: 31740999 DOI: 10.1007/s00249-019-01410-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a membrane protein that regulates cell proliferation, differentiation and survival, and is a drug target for cancer therapy. Ligand-induced activation of the EGFR kinase is generally regarded to require ligand-bound-dimers, while phosphorylation and down-stream signalling is modulated by oligomers. Recent work has unveiled changes in EGFR dynamics from ligand-induced dimerization in membranes extracted from cells, however, less is known about the changes in EGFR dynamics that accompany the ligand-induced oligomerization in a live cell environment. Here, we determine the dynamics of a c-terminal GFP tag attached to EGFR in the unliganded dimer and in the liganded oligomers. By means of the single-frequency polarized phasor ellipse approach we extracted two correlation times on the sub-nanosecond and super-nanosecond timescales, respectively. EGF binding to the EGFR-GFP dimer lengthened the sub-nanosecond correlation time (from 0.1 to 1.3 ns) and shortened the super-nanosecond correlation time (from 210 to 56 ns) of the c-terminal GFP probe. The sub-nanosecond depolarization processes were assigned to electronic energy migration between proximal GFPs in the EGFR dimer or oligomer, while the super-nanosecond correlation times were assigned to nanosecond fluctuations of the GFP probe in the EGFR complex. Accordingly, these results show that ligand binding increased the average separation between the c-terminal tags and increased their rotational mobility. We propose that the dynamics are linked to an inhibitory function of the c-terminal tail in the un-liganded dimer and to the requirement of facile stochastic switching between kinase activation and cytoplasmic adaptor/effector binding in the active oligomers.
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Affiliation(s)
- Noga Kozer
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, School of Science, Swinburne University of Technology, Melbourne, Australia
| | - Andrew H A Clayton
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, School of Science, Swinburne University of Technology, Melbourne, Australia.
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86
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Paul MD, Hristova K. The transition model of RTK activation: A quantitative framework for understanding RTK signaling and RTK modulator activity. Cytokine Growth Factor Rev 2019; 49:23-31. [PMID: 31711797 DOI: 10.1016/j.cytogfr.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/10/2019] [Indexed: 01/15/2023]
Abstract
Here, we discuss the transition model of receptor tyrosine kinase (RTK) activation, which is derived from biophysical investigations of RTK interactions and signaling. The model postulates that (1) RTKs can interact laterally to form dimers even in the absence of ligand, (2) different unliganded RTK dimers have different stabilities, (3) ligand binding stabilizes the RTK dimers, and (4) ligand binding causes structural changes in the RTK dimer. The model is grounded in the principles of physical chemistry and provides a framework to understand RTK activity and to make predictions in quantitative terms. It can guide basic research aimed at uncovering the mechanism of RTK activation and, in the long run, can empower the search for modulators of RTK function.
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Affiliation(s)
- Michael D Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States.
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87
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Váradi T, Schneider M, Sevcsik E, Kiesenhofer D, Baumgart F, Batta G, Kovács T, Platzer R, Huppa JB, Szöllősi J, Schütz GJ, Brameshuber M, Nagy P. Homo- and Heteroassociations Drive Activation of ErbB3. Biophys J 2019; 117:1935-1947. [PMID: 31653451 PMCID: PMC7018998 DOI: 10.1016/j.bpj.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/19/2023] Open
Abstract
Dimerization or the formation of higher-order oligomers is required for the activation of ErbB receptor tyrosine kinases. The heregulin (HRG) receptor, ErbB3, must heterodimerize with other members of the family, preferentially ErbB2, to form a functional signal transducing complex. Here, we applied single molecule imaging capable of detecting long-lived and mobile associations to measure their stoichiometry and mobility and analyzed data from experiments globally, taking the different lateral mobility of monomeric and dimeric molecular species into account. Although ErbB3 was largely monomeric in the absence of stimulation and ErbB2 co-expression, a small fraction was present as constitutive homodimers exhibiting a ∼40% lower mobility than monomers. HRG stimulation increased the homodimeric fraction of ErbB3 significantly and reduced the mobility of homodimers fourfold compared to constitutive homodimers. Expression of ErbB2 elevated the homodimeric fraction of ErbB3 even in unstimulated cells and induced a ∼2-fold reduction in the lateral mobility of ErbB3 homodimers. The mobility of ErbB2 was significantly lower than that of ErbB3, and HRG induced a less pronounced decrease in the diffusion coefficient of all ErbB2 molecules and ErbB3/ErbB2 heterodimers than in the mobility of ErbB3. The slower diffusion of ErbB2 compared to ErbB3 was abolished by depolymerizing actin filaments, whereas ErbB2 expression induced a substantial rearrangement of microfilaments, implying a bidirectional interaction between ErbB2 and actin. HRG stimulation of cells co-expressing ErbB3 and ErbB2 led to the formation of ErbB3 homodimers and ErbB3/ErbB2 heterodimers in a competitive fashion. Although pertuzumab, an antibody binding to the dimerization arm of ErbB2, completely abolished the formation of constitutive and HRG-induced ErbB3/ErbB2 heterodimers, it only slightly blocked ErbB3 homodimerization. The results imply that a dynamic equilibrium exists between constitutive and ligand-induced homo- and heterodimers capable of shaping transmembrane signaling.
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Affiliation(s)
- Tímea Váradi
- Institute of Applied Physics, TU Wien, Vienna, Austria; Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | | | | | - Gyula Batta
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Department of Genetics and Applied Microbiology, Faculty of Science of Technology, University of Debrecen, Debrecen, Hungary
| | - Tamás Kovács
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | - René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - János Szöllősi
- 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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88
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Garg AA, Jones TH, Moss SM, Mishra S, Kaul K, Ahirwar DK, Ferree J, Kumar P, Subramaniam D, Ganju RK, Subramaniam VV, Song JW. Electromagnetic fields alter the motility of metastatic breast cancer cells. Commun Biol 2019; 2:303. [PMID: 31428691 PMCID: PMC6687738 DOI: 10.1038/s42003-019-0550-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions between cells and their environment influence key physiologic processes such as their propensity to migrate. However, directed migration controlled by extrinsically applied electrical signals is poorly understood. Using a novel microfluidic platform, we found that metastatic breast cancer cells sense and respond to the net direction of weak (∼100 µV cm-1), asymmetric, non-contact induced Electric Fields (iEFs). iEFs inhibited EGFR (Epidermal Growth Factor Receptor) activation, prevented formation of actin-rich filopodia, and hindered the motility of EGF-treated breast cancer cells. The directional effects of iEFs were nullified by inhibition of Akt phosphorylation. Moreover, iEFs in combination with Akt inhibitor reduced EGF-promoted motility below the level of untreated controls. These results represent a step towards isolating the coupling mechanism between cell motility and iEFs, provide valuable insights into how iEFs target multiple diverging cancer cell signaling mechanisms, and demonstrate that electrical signals are a fundamental regulator of cancer cell migration.
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Affiliation(s)
- Ayush Arpit Garg
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Travis H. Jones
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Sarah M. Moss
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Sanjay Mishra
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Kirti Kaul
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Dinesh K. Ahirwar
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Jessica Ferree
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Prabhat Kumar
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Deepa Subramaniam
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Ramesh K. Ganju
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Vish V. Subramaniam
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Jonathan W. Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210 USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
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89
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Singh DR, King C, Salotto M, Hristova K. Revisiting a controversy: The effect of EGF on EGFR dimer stability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183015. [PMID: 31295474 DOI: 10.1016/j.bbamem.2019.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/23/2019] [Accepted: 07/02/2019] [Indexed: 12/26/2022]
Abstract
EGFR is a receptor tyrosine kinase that plays a critical role in cell proliferation, differentiation, survival and migration. Its activating ligand, EGF, has long been believed to stabilize the EGFR dimer. Two research studies aimed at quantitative measurements of EGFR dimerization, however, have led to contradicting conclusions and have questioned this view. Given the controversy, here we sought to measure the dimerization of EGFR in the absence and in the presence of saturating EGF concentrations, and to tease out the effect of ligand on dimer stability, using a FRET-based quantitative method. Our measurements show that the dissociation constant is decreased ~150 times due to ligand binding, indicative of significant dimer stabilization. In addition, our measurements demonstrate that EGF binding induces a conformational change in the EGFR dimer.
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Affiliation(s)
- Deo R Singh
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Christopher King
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Matt Salotto
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Kalina Hristova
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America.
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90
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Agarwal G, Smith AW, Jones B. Discoidin domain receptors: Micro insights into macro assemblies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118496. [PMID: 31229648 DOI: 10.1016/j.bbamcr.2019.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022]
Abstract
Assembly of cell-surface receptors into specific oligomeric states and/or clusters before and after ligand binding is an important feature governing their biological function. Receptor oligomerization can be mediated by specific domains of the receptor, ligand binding, configurational changes or other interacting molecules. In this review we summarize our understanding of the oligomeric state of discoidin domain receptors (DDR1 and DDR2), which belong to the receptor tyrosine kinase family (RTK). DDRs form an interesting system from an oligomerization perspective as their ligand collagen(s) can also undergo supramolecular assembly to form fibrils. Even though DDR1 and DDR2 differ in the domains responsible to form ligand-free dimers they share similarities in binding to soluble, monomeric collagen. However, only DDR1b forms globular clusters in response to monomeric collagen and not DDR2. Interestingly, both DDR1 and DDR2 are assembled into linear clusters by the collagen fibril. Formation of these clusters is important for receptor phosphorylation and is mediated in part by other membrane components. We summarize how the oligomeric status of DDRs shares similarities with other members of the RTK family and with collagen receptors. Unraveling the multiple macro-molecular configurations adopted by this receptor-ligand pair can provide novel insights into the intricacies of cell-matrix interactions.
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Affiliation(s)
- Gunjan Agarwal
- Biomedical Engineering Department, The Ohio State University, Columbus, OH 43210, USA.
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Blain Jones
- Biomedical Engineering Department, The Ohio State University, Columbus, OH 43210, USA
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91
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A general method to quantify ligand-driven oligomerization from fluorescence-based images. Nat Methods 2019; 16:493-496. [PMID: 31110281 DOI: 10.1038/s41592-019-0408-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 01/30/2023]
Abstract
Here, we introduce fluorescence intensity fluctuation spectrometry for determining the identity, abundance and stability of protein oligomers. This approach was tested on monomers and oligomers of known sizes and was used to uncover the oligomeric states of the epidermal growth factor receptor and the secretin receptor in the presence and absence of their agonist ligands. This method is fast and is scalable for high-throughput screening of drugs targeting protein-protein interactions.
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92
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Abstract
It is challenging to predict the docked conformations of two proteins. Current methods are susceptible to errors from treating proteins as rigid bodies and from an inability to compute relative Boltzmann populations of different docked conformations. Here, we show that by using the ClusPro server as a front end to generate possible protein-protein contacts, and using Modeling Employing Limited Data (MELD) accelerated molecular dynamics (MELD × MD) as a back end for atomistic simulations, we can find 16/20 native dimer structures of small proteins as those having the lowest free energy, starting from good-bound-backbone structures. We show that atomistic MD free energies can be used to identify native protein dimer structures.
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Affiliation(s)
- Emiliano Brini
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, United States
| | - Dima Kozakov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794-3600, United States
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, New York 11794-5250, United States
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, United States
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790-3400, United States
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93
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Abstract
Receptor tyrosine kinases (RTKs) play important roles in cell growth, motility, differentiation, and survival. These single-pass membrane proteins are grouped into subfamilies based on the similarity of their extracellular domains. They are generally thought to be activated by ligand binding, which promotes homodimerization and then autophosphorylation in trans. However, RTK interactions are more complicated, as RTKs can interact in the absence of ligand and heterodimerize within and across subfamilies. Here, we review the known cross-subfamily RTK heterointeractions and their possible biological implications, as well as the methodologies which have been used to study them. Moreover, we demonstrate how thermodynamic models can be used to study RTKs and to explain many of the complicated biological effects which have been described in the literature. Finally, we discuss the concept of the RTK interactome: a putative, extensive network of interactions between the RTKs. This RTK interactome can produce unique signaling outputs; can amplify, inhibit, and modify signaling; and can allow for signaling backups. The existence of the RTK interactome could provide an explanation for the irreproducibility of experimental data from different studies and for the failure of some RTK inhibitors to produce the desired therapeutic effects. We argue that a deeper knowledge of RTK interactome thermodynamics can lead to a better understanding of fundamental RTK signaling processes in health and disease. We further argue that there is a need for quantitative, thermodynamic studies that probe the strengths of the interactions between RTKs and their ligands and between different RTKs.
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Affiliation(s)
- Michael D. Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
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94
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Diwanji D, Thaker T, Jura N. More than the sum of the parts: Toward full-length receptor tyrosine kinase structures. IUBMB Life 2019; 71:706-720. [PMID: 31046201 DOI: 10.1002/iub.2060] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/20/2019] [Indexed: 01/01/2023]
Abstract
Intercellular communication governs complex physiological processes ranging from growth and development to the maintenance of cellular and organ homeostasis. In nearly all metazoans, receptor tyrosine kinases (RTKs) are central players in these diverse and fundamental signaling processes. Aberrant RTK signaling is at the root of many developmental diseases and cancers and it remains a key focus of targeted therapies, several of which have achieved considerable success in patients. These therapeutic advances in targeting RTKs have been propelled by numerous genetic, biochemical, and structural studies detailing the functions and molecular mechanisms of regulation and activation of RTKs. The latter in particular have proven to be instrumental for the development of new drugs, selective targeting of mutant forms of RTKs found in disease, and counteracting ensuing drug resistance. However, to this day, such studies have not yet yielded high-resolution structures of intact RTKs that encompass the extracellular and intracellular domains and the connecting membrane-spanning transmembrane domain. Technically challenging to obtain, these structures are instrumental to complete our understanding of the mechanisms by which RTKs are activated by extracellular ligands and of the effect of pathological mutations that do not directly reside in the catalytic sites of tyrosine kinase domains. In this review, we focus on the recent progress toward obtaining such structures and the insights already gained by structural studies of the subdomains of the receptors that belong to the epidermal growth factor receptor, insulin receptor, and platelet-derived growth factor receptor RTK families. © 2019 IUBMB Life, 71(6):706-720, 2019.
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Affiliation(s)
- Devan Diwanji
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tarjani Thaker
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
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95
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Abstract
Bruton’s tyrosine kinase (Btk) activation on the cell membrane is critical for B cell proliferation and development, and Btk inhibition is a promising treatment for several hematologic cancers and autoimmune diseases. Here, we examine Btk activation using the results of long-timescale molecular dynamics simulations. In our simulations, Btk lipid-binding modules dimerized on the membrane in a single predominant conformation. We observed that the phospholipid PIP3—in addition to its expected role of recruiting Btk to the membrane—allosterically mediated dimer formation and stability by binding at two novel sites. Our results provide strong evidence that PIP3-mediated dimerization of Btk at the cell membrane is a critical step in Btk activation and suggest a potential approach to allosteric Btk inhibitor development. Bruton’s tyrosine kinase (Btk) is critical for B cell proliferation and activation, and the development of Btk inhibitors is a vigorously pursued strategy for the treatment of various B cell malignancies. A detailed mechanistic understanding of Btk activation has, however, been lacking. Here, inspired by a previous suggestion that Btk activation might depend on dimerization of its lipid-binding PH–TH module on the cell membrane, we performed long-timescale molecular dynamics simulations of membrane-bound PH–TH modules and observed that they dimerized into a single predominant conformation. We found that the phospholipid PIP3 stabilized the dimer allosterically by binding at multiple sites, and that the effects of PH–TH mutations on dimer stability were consistent with their known effects on Btk activity. Taken together, our simulation results strongly suggest that PIP3-mediated dimerization of Btk at the cell membrane is a critical step in Btk activation.
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96
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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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97
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Clarke DT, Martin-Fernandez ML. A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor. Methods Protoc 2019; 2:mps2010012. [PMID: 31164594 PMCID: PMC6481046 DOI: 10.3390/mps2010012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
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Affiliation(s)
- David T Clarke
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
| | - Marisa L Martin-Fernandez
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
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98
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Quinn SD, Srinivasan S, Gordon JB, He W, Carraway KL, Coleman MA, Schlau-Cohen GS. Single-Molecule Fluorescence Detection of the Epidermal Growth Factor Receptor in Membrane Discs. Biochemistry 2019; 58:286-294. [PMID: 29553754 PMCID: PMC6173994 DOI: 10.1021/acs.biochem.8b00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The epidermal growth factor receptor (EGFR) is critical to normal cellular signaling pathways. Moreover, it has been implicated in a range of pathologies, including cancer. As a result, it is the primary target of many anticancer drugs. One limitation to the design and development of these drugs has been the lack of molecular-level information about the interactions and conformational dynamics of EGFR. To overcome this limitation, this work reports the construction and characterization of functional, fluorescently labeled, and full-length EGFR in model membrane nanolipoprotein particles (NLPs) for in vitro fluorescence studies. To demonstrate the utility of the system, we investigate ATP-EGFR interactions. We observe that ATP binds at the catalytic site providing a means to measure a range of distances between the catalytic site and the C-terminus via Förster resonance energy transfer (FRET). These ATP-based experiments suggest a range of conformations of the C-terminus that may be a function of the phosphorylation state for EGFR. This work is a proof-of-principle demonstration of single-molecule studies as a noncrystallographic assay for EGFR interactions in real-time and under near-physiological conditions. The diverse nature of EGFR interactions means that new tools at the molecular level have the potential to significantly enhance our understanding of receptor pathology and are of utmost importance for cancer-related drug discovery.
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Affiliation(s)
- Steven D. Quinn
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
| | - Shwetha Srinivasan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
| | - Jesse B. Gordon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Kermit L. Carraway
- University of California Davis School of Medicine, Biochemistry and Molecular Medicine, Sacramento, California, USA
| | - Matthew A. Coleman
- Lawrence Livermore National Laboratory, Livermore, California, USA
- University of California Davis School of Medicine, Radiation Oncology, Sacramento, California, USA
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
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99
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Kim DH, Park S, Kim DK, Jeong MG, Noh J, Kwon Y, Zhou K, Lee NK, Ryu SH. Direct visualization of single-molecule membrane protein interactions in living cells. PLoS Biol 2018; 16:e2006660. [PMID: 30543635 PMCID: PMC6307816 DOI: 10.1371/journal.pbio.2006660] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Interactions between membrane proteins are poorly understood despite their importance in cell signaling and drug development. Here, we present a co-immunoimmobilization assay (Co-II) enabling the direct observation of membrane protein interactions in single living cells that overcomes the limitations of currently prevalent proximity-based indirect methods. Using Co-II, we investigated the transient homodimerizations of epidermal growth factor receptor (EGFR) and beta-2 adrenergic receptor (β2-AR) in living cells, revealing the differential regulation of these receptors’ dimerizations by molecular conformations and microenvironment in a plasma membrane. Co-II should provide a simple, rapid, and robust platform for visualizing both weak and strong protein interactions in the plasma membrane of living cells. Protein–protein interactions govern cellular processes. The majority of these physical interactions previously identified are strong/permanent interactions, which typically remain unbroken even after purification. The weak/transient interactions between proteins have been implicated in the control of dynamic cellular process that maintain cellular homeostasis and trigger signaling cascades upon environmental changes. However, these interactions are poorly investigated, mainly due to the methodological limitations. Here, we have developed a co-immunoimmobilization assay called Co-II that enables the direct visualization of protein–protein interactions in the membrane of living cells at the single-molecule level. Co-II is based on the intuitive concept that if the protein of interest is immobilized, the interacting protein must be co-immobilized. The use of intrinsic protein diffusivity fundamentally overcomes the limitations of proximity-based methods. Using Co-II, we study the transient homodimerizations of EGFR and β2-AR in living cells, which have been implicated in several types of cancers and heart diseases. We show that the dimerization of these receptors is differently regulated by molecular conformations and the microenvironment in the plasma membrane.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Soyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dong-Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Min Gyu Jeong
- Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jungeun Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yonghoon Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kai Zhou
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nam Ki Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- * E-mail: (SHR); (NKL)
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- * E-mail: (SHR); (NKL)
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100
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De Keersmaecker H, Camacho R, Rantasa DM, Fron E, Uji-I H, Mizuno H, Rocha S. Mapping Transient Protein Interactions at the Nanoscale in Living Mammalian Cells. ACS NANO 2018; 12:9842-9854. [PMID: 30192513 DOI: 10.1021/acsnano.8b01227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein-protein interactions (PPIs) form the basis of cellular processes, regulating cell behavior and fate. PPIs can be extremely transient in nature, which hinders their detection. In addition, traditional biochemical methods provided limited information on the spatial distribution and temporal dynamics of PPIs that is crucial for their regulation in the crowded cellular environment. Given the pivotal role of membrane micro- and nanodomains in the regulation of PPIs at the plasma membrane, the development of methods to visualize PPIs with a high spatial resolution is imperative. Here, we present a super-resolution fluorescence microscopy technique that can detect and map short-lived transient protein-protein interactions on a nanometer scale in the cellular environment. This imaging method is based on single-molecule fluorescence microscopy and exploits the effect of the difference in the mobility between cytosolic and membrane-bound proteins in the recorded fluorescence signals. After the development of the proof of concept using a model system based on membrane-bound modular protein domains and fluorescently labeled peptides, we applied this imaging approach to investigate the interactions of cytosolic proteins involved in the epidermal growth factor signaling pathway (namely, Grb2, c-Raf, and PLCγ1). The detected clusters of Grb2 and c-Raf were correlated with the distribution of the receptor at the plasma membrane. Additionally, the interactions of wild type PLCγ1 were compared with those detected with truncated mutants, which provided important information regarding the role played by specific domains in the interaction with the membrane. The results presented here demonstrate the potential of this technique to unravel the role of membrane heterogeneity in the spatiotemporal regulation of cell signaling.
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Affiliation(s)
| | | | | | | | - Hiroshi Uji-I
- Research Institute for Electronic Science , Hokkaido University , N20W10 Kita Ward, Sapporo 001-0020 , Japan
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