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Shah AA, Kumar N, Mohinder Singh Bedi P, Akhtar S. Molecular modeling, dynamic simulation, and metabolic reactivity studies of quinazoline derivatives to investigate their anti-angiogenic potential by targeting wild EGFR wt and mutant EGFR T790M receptor tyrosine kinases. J Biomol Struct Dyn 2023:1-23. [PMID: 37921704 DOI: 10.1080/07391102.2023.2274974] [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: 07/25/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Non-small cell lung cancer, head and neck cancer, glioblastoma, and various other cancer types often demonstrate persistent elevation in EGFR tyrosine kinase activity due to acquired mutations in its kinase domain. Any alteration in the EGFR is responsible for triggering the upregulation of tumor angiogenic pathways, such as the PI3k-AKT-mTOR pathway, MAPK-ERK pathway and PLC-Ƴ pathway, which are critically involved in promoting tumor angiogenesis in cancer cells. The emergence of frequently occurring EGFR kinase domain mutations (L858R/T790M/C797S) that confer resistance to approved therapeutic agents has presented a significant challenge for researchers aiming to develop effective and well-tolerated treatments against tumor angiogenesis. In this study, we directed our efforts towards the rational design and development of novel quinazoline derivatives with the potential to act as antagonists against both wild-type and mutant EGFR. Our approach encompasing the application of advanced drug design strategies, including structure-based virtual screening, molecular docking, molecular dynamics, metabolic reactivity and cardiotoxicity prediction studies led to the identification of two prominent lead compounds: QU648, for EGFRwt inhibition and QU351, for EGFRmt antagonism. The computed binding energies of selected leads and their molecular dynamics simulations exhibited enhanced conformational stability of QU648 and QU351 when compared to standard drugs Erlotinib and Afatinib. Notably, the lead compounds also demonstrated promising pharmacokinetic properties, metabolic reactivity, and cardiotoxicity profiles. Collectively, the outcomes of our study provide compelling evidence supporting the potential of QU648 and QU351 as prominent anti-angiogenic agents, effectively inhibiting EGFR activity across various cancer types harboring diverse EGFR mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | | | - Salman Akhtar
- Department of Bioengineering, Integral University, Lucknow, India
- Novel Global Community Educational Foundation, Hebersham, Australia
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2
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Jiang C, Sun J, Li R, Yan S, Chen W, Guo L, Qin G, Wang P, Luo C, Huang W, Zhang Q, Fernie AR, Jackson D, Li X, Yan J. A reactive oxygen species burst causes haploid induction in maize. MOLECULAR PLANT 2022; 15:943-955. [PMID: 35395409 DOI: 10.1016/j.molp.2022.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/27/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Haploid induction (HI) is an important tool in crop breeding. Phospholipase A1 (ZmPLA1)/NOT LIKE DAD (NLD)/MATRILINEAL (MTL) is a key gene controlling HI in maize; however, the underlying molecular mechanism remains unclear. In this study, to dissect why loss of ZmPLA1 function could mediate HI we performed a comprehensive multiple omics analysis of zmpla1 mutant anthers by integrating transcriptome, metabolome, quantitative proteome, and protein modification data. Functional classes of significantly enriched or differentially abundant molecular entities were found to be associated with the oxidative stress response, suggesting that a reactive oxygen species (ROS) burst plays a critical role in HI. In support of this, we further discovered that a simple chemical treatment of pollen with ROS reagents could lead to HI. Moreover, we identified ZmPOD65, which encodes a sperm-specific peroxidase, as a new gene controlling HI. Taken together, our study revealed a likely mechanism of HI, discovered a new gene controlling HI, and created a new method for HI in maize, indicating the importance of ROS balance in maintaining normal reproduction and providing a potential route to accelerate crop breeding.
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Affiliation(s)
- Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ju Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guochen Qin
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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3
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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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4
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Stanoev A, Nandan AP, Koseska A. Organization at criticality enables processing of time-varying signals by receptor networks. Mol Syst Biol 2020; 16:e8870. [PMID: 32090487 PMCID: PMC7036718 DOI: 10.15252/msb.20198870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023] Open
Abstract
How cells utilize surface receptors for chemoreception is a recurrent question spanning between physics and biology over the past few decades. However, the dynamical mechanism for processing time-varying signals is still unclear. Using dynamical systems formalism to describe criticality in non-equilibrium systems, we propose generic principle for temporal information processing through phase space trajectories using dynamic transient memory. In contrast to short-term memory, dynamic memory generated via "ghost" attractor enables signal integration depending on stimulus history and thereby uniquely promotes integrating and interpreting complex temporal growth factor signals. We argue that this is a generic feature of receptor networks, the first layer of the cell that senses the changing environment. Using the experimentally established epidermal growth factor sensing system, we propose how recycling could provide self-organized maintenance of the critical receptor concentration at the plasma membrane through a simple, fluctuation-sensing mechanism. Processing of non-stationary signals, a feature previously attributed only to neural networks, thus uniquely emerges for receptor networks organized at criticality.
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Affiliation(s)
- Angel Stanoev
- Department of Systemic Cell BiologyMax Planck Institute for Molecular PhysiologyDortmundGermany
| | - Akhilesh P Nandan
- Department of Systemic Cell BiologyMax Planck Institute for Molecular PhysiologyDortmundGermany
| | - Aneta Koseska
- Department of Systemic Cell BiologyMax Planck Institute for Molecular PhysiologyDortmundGermany
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5
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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6
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Stanoev A, Mhamane A, Schuermann KC, Grecco HE, Stallaert W, Baumdick M, Brüggemann Y, Joshi MS, Roda-Navarro P, Fengler S, Stockert R, Roßmannek L, Luig J, Koseska A, Bastiaens PIH. Interdependence between EGFR and Phosphatases Spatially Established by Vesicular Dynamics Generates a Growth Factor Sensing and Responding Network. Cell Syst 2018; 7:295-309.e11. [PMID: 30145116 PMCID: PMC6167251 DOI: 10.1016/j.cels.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/22/2017] [Accepted: 06/07/2018] [Indexed: 12/20/2022]
Abstract
The proto-oncogenic epidermal growth factor receptor (EGFR) is a tyrosine kinase whose sensitivity to growth factors and signal duration determines cellular behavior. We resolve how EGFR's response to epidermal growth factor (EGF) originates from dynamically established recursive interactions with spatially organized protein tyrosine phosphatases (PTPs). Reciprocal genetic PTP perturbations enabled identification of receptor-like PTPRG/J at the plasma membrane and ER-associated PTPN2 as the major EGFR dephosphorylating activities. Imaging spatial-temporal PTP reactivity revealed that vesicular trafficking establishes a spatially distributed negative feedback with PTPN2 that determines signal duration. On the other hand, single-cell dose-response analysis uncovered a reactive oxygen species-mediated toggle switch between autocatalytically activated monomeric EGFR and the tumor suppressor PTPRG that governs EGFR's sensitivity to EGF. Vesicular recycling of monomeric EGFR unifies the interactions with these PTPs on distinct membrane systems, dynamically generating a network architecture that can sense and respond to time-varying growth factor signals.
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Affiliation(s)
- Angel Stanoev
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Amit Mhamane
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Klaus C Schuermann
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Hernán E Grecco
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Wayne Stallaert
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Yannick Brüggemann
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, 44227 Dortmund, Germany
| | - Maitreyi S Joshi
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Pedro Roda-Navarro
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Sven Fengler
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Rabea Stockert
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Lisaweta Roßmannek
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Jutta Luig
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Aneta Koseska
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, 44227 Dortmund, Germany.
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, 44227 Dortmund, Germany.
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7
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Baumdick M, Gelléri M, Uttamapinant C, Beránek V, Chin JW, Bastiaens PIH. A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation. Nat Commun 2018; 9:3847. [PMID: 30242154 PMCID: PMC6155120 DOI: 10.1038/s41467-018-06299-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight into EGFR activation mechanisms in living cells, we develop a Förster resonance energy transfer (FRET)-based conformational EGFR indicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant reveals that Y845 phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C-terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose. Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.
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Affiliation(s)
- Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Márton Gelléri
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany.
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8
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Mitchell RA, Luwor RB, Burgess AW. Epidermal growth factor receptor: Structure-function informing the design of anticancer therapeutics. Exp Cell Res 2018; 371:1-19. [PMID: 30098332 DOI: 10.1016/j.yexcr.2018.08.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 12/19/2022]
Abstract
Research on the epidermal growth factor (EGF) family and the family of receptors (EGFR) has progressed rapidly in recent times. New crystal structures of the ectodomains with different ligands, the activation of the kinase domain through oligomerisation and the use of fluorescence techniques have revealed profound conformational changes on ligand binding. The control of cell signaling from the EGFR-family is complex, with heterodimerisation, ligand affinity and signaling cross-talk influencing cellular outcomes. Analysis of tissue homeostasis indicates that the control of pro-ligand processing is likely to be as important as receptor activation events. Several members of the EGFR-family are overexpressed and/or mutated in cancer cells. The perturbation of EGFR-family signaling drives the malignant phenotype of many cancers and both inhibitors and antagonists of signaling from these receptors have already produced therapeutic benefits for patients. The design of affibodies, antibodies, small molecule inhibitors and even immunotherapeutic drugs targeting the EGFR-family has yielded promising new approaches to improving outcomes for cancer patients. In this review, we describe recent discoveries which have increased our understanding of the structure and dynamics of signaling from the EGFR-family, the roles of ligand processing and receptor cross-talk. We discuss the relevance of these studies to the development of strategies for designing more effective targeted treatments for cancer patients.
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Affiliation(s)
- Ruth A Mitchell
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia; Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Rodney B Luwor
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Antony W Burgess
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia; Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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9
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Abstract
To orchestrate the function and development of multicellular organisms, cells integrate intra- and extracellular information. This information is processed via signal networks in space and time, steering dynamic changes in cellular structure and function. Defects in those signal networks can lead to developmental disorders or cancer. However, experimental analysis of signal networks is challenging as their state changes dynamically and differs between individual cells. Thus, causal relationships between network components are blurred if lysates from large cell populations are analyzed. To directly study causal relationships, perturbations that target specific components have to be combined with measurements of cellular responses within individual cells. However, using standard single-cell techniques, the number of signal activities that can be monitored simultaneously is limited. Furthermore, diffusion of signal network components limits the spatial precision of perturbations, which blurs the analysis of spatiotemporal processing in signal networks. Hybrid strategies based on optogenetics, surface patterning, chemical tools, and protein design can overcome those limitations and thereby sharpen our view into the dynamic spatiotemporal state of signal networks and enable unique insights into the mechanisms that control cellular function in space and time.
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Affiliation(s)
- Dominic Kamps
- Department for Systemic Cell Biology, Max
Planck Institute of Molecular Physiology and Fakultät für
Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology, Max
Planck Institute of Molecular Physiology and Fakultät für
Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
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10
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Lemmon MA, Freed DM, Schlessinger J, Kiyatkin A. The Dark Side of Cell Signaling: Positive Roles for Negative Regulators. Cell 2016; 164:1172-1184. [PMID: 26967284 DOI: 10.1016/j.cell.2016.02.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 12/12/2022]
Abstract
Cell signaling is dominated by analyzing positive responses to stimuli. Signal activation is balanced by negative regulators that are generally considered to terminate signaling. Rather than exerting only negative effects, however, many such regulators play important roles in enhancing cell-signaling control. Considering responses downstream of selected cell-surface receptors, we discuss how receptor internalization affects signaling specificity and how rapid kinase/phosphatase and GTP/GDP cycles increase responsiveness and allow kinetic proofreading in receptor signaling. We highlight the blurring of distinctions between positive and negative signals, recasting signal termination as the response to a switch-like transition into a new cellular state.
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Affiliation(s)
- Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA.
| | - Daniel M Freed
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Anatoly Kiyatkin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
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11
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Ubiquitination switches EphA2 vesicular traffic from a continuous safeguard to a finite signalling mode. Nat Commun 2015; 6:8047. [PMID: 26292967 PMCID: PMC4560775 DOI: 10.1038/ncomms9047] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/11/2015] [Indexed: 01/15/2023] Open
Abstract
Autocatalytic phosphorylation of receptor tyrosine kinases (RTKs) enables diverse, context-dependent responses to extracellular signals but comes at the price of autonomous, ligand-independent activation. Using a conformational biosensor that reports on the kinase activity of the cell guidance ephrin receptor type-A (EphA2) in living cells, we observe that autonomous EphA2 activation is suppressed by vesicular recycling and dephosphorylation by protein tyrosine phosphatases 1B (PTP1B) near the pericentriolar recycling endosome. This spatial segregation of catalytically superior PTPs from RTKs at the plasma membrane is essential to preserve ligand responsiveness. Ligand-induced clustering, on the other hand, promotes phosphorylation of a c-Cbl docking site and ubiquitination of the receptor, thereby redirecting it to the late endosome/lysosome. We show that this switch from cyclic to unidirectional receptor trafficking converts a continuous suppressive safeguard mechanism into a transient ligand-responsive signalling mode.
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12
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Stegemann L, Schuermann KC, Strassert CA, Grecco HE. Photofunctional surfaces for quantitative fluorescence microscopy: monitoring the effects of photogenerated reactive oxygen species at single cell level with spatiotemporal resolution. ACS APPLIED MATERIALS & INTERFACES 2015; 7:5944-5949. [PMID: 25705918 DOI: 10.1021/acsami.5b00130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we report on the implementation of photofunctional surfaces for the investigation of cellular responses by means of quantitative fluorescence microscopy. The developed substrates are able to produce reactive oxygen species under the fluorescence microscope upon irradiation with visible light, and the behavior of cells grown on these surfaces can be consequently investigated in situ and in real time. Moreover, a suitable methodology is presented to simultaneously monitor phototriggered morphological changes and the associated molecular pathways with spatiotemporal resolution employing time-resolved fluorescence anisotropy at the single cell level. The results showed that morphological changes can be complemented with a quantitative evaluation of the associated molecular signaling cascades for the unambiguous assignment of reactive oxygen species-related photoinduced apoptosis. Indeed, similar phenotypes are associated with different cellular processes. Our methodology facilitates the in vitro design and evaluation of photosensitizers for the treatment of cancer and infectious diseases with the aid of functional fluorescence microscopy.
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Affiliation(s)
- Linda Stegemann
- †Physikalisches Institut and Center for Nanotechnology (CeNTech), Westfälische Wilhelms-Universität Münster, Heisenbergstraße 11, D-48149 Münster, Germany
| | - Klaus C Schuermann
- ‡Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Straße 11, D-44227 Dortmund, Germany
| | - Cristian A Strassert
- †Physikalisches Institut and Center for Nanotechnology (CeNTech), Westfälische Wilhelms-Universität Münster, Heisenbergstraße 11, D-48149 Münster, Germany
| | - Hernán E Grecco
- ‡Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Straße 11, D-44227 Dortmund, Germany
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13
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Guigas G, Weiss M. Membrane protein mobility depends on the length of extra-membrane domains and on the protein concentration. SOFT MATTER 2015; 11:33-37. [PMID: 25407767 DOI: 10.1039/c4sm01846j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diffusion of membrane proteins is not only determined by the membrane anchor friction but also by the overall concentration of proteins and the length of their extra-membrane domains. We have studied the influence of the latter two cues by mesoscopic simulations. As a result, we have found that the total friction of membrane proteins, γ, increases approximately linearly with the length of the extra-membrane domain, L, whereas a slightly nonlinear dependence on the total protein concentration, ϕ was observed. We provide an educated guess for the functional form of γ(L, ϕ) and the associated diffusion coefficient. This expression not only matches our simulation data but it is also in favorable agreement with previously published experimental data. Our findings indicate that diffusion coefficients of membrane proteins are not solely determined by the friction of membrane anchors but also extra-membrane domains and the crowdedness of the membrane need to be considered to obtain a comprehensive view of protein diffusion on cellular membranes.
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Affiliation(s)
- Gernot Guigas
- Experimental Physics I, University of Bayreuth, 95440 Bayreuth, Germany.
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14
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Tsyganov MA, Kolch W, Kholodenko BN. The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. MOLECULAR BIOSYSTEMS 2012; 8:730-43. [DOI: 10.1039/c2mb05375f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Grecco HE, Schmick M, Bastiaens PIH. Signaling from the living plasma membrane. Cell 2011; 144:897-909. [PMID: 21414482 DOI: 10.1016/j.cell.2011.01.029] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 12/10/2010] [Accepted: 01/17/2011] [Indexed: 02/06/2023]
Abstract
Our understanding of the plasma membrane, once viewed simply as a static barrier, has been revolutionized to encompass a complex, dynamic organelle that integrates the cell with its extracellular environment. Here, we discuss how bidirectional signaling across the plasma membrane is achieved by striking a delicate balance between restriction and propagation of information over different scales of time and space and how underlying dynamic mechanisms give rise to rich, context-dependent signaling responses. In this Review, we show how computer simulations can generate counterintuitive predictions about the spatial organization of these complex processes.
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Affiliation(s)
- Hernán E Grecco
- Max Planck Institute for Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski BA. Reaction-diffusion systems in intracellular molecular transport and control. Angew Chem Int Ed Engl 2010; 49:4170-98. [PMID: 20518023 PMCID: PMC3697936 DOI: 10.1002/anie.200905513] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
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Affiliation(s)
- Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Marta Byrska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Kristiana Kandere-Grzybowska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Bartosz A. Grzybowski
- Department of Chemistry, Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, Homepage: http://www.dysa.northwestern.edu
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski B. Reaktions-Diffusions-Systeme für intrazellulären Transport und Kontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905513] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Dehmelt L, Bastiaens PIH. Spatial organization of intracellular communication: insights from imaging. Nat Rev Mol Cell Biol 2010; 11:440-52. [DOI: 10.1038/nrm2903] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Kinkhabwala A, Bastiaens PIH. Spatial aspects of intracellular information processing. Curr Opin Genet Dev 2010; 20:31-40. [PMID: 20096560 DOI: 10.1016/j.gde.2009.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 12/18/2009] [Accepted: 12/29/2009] [Indexed: 12/24/2022]
Abstract
The computational properties of intracellular biochemical networks, for which the cell is assumed to be a 'well-mixed' reactor, have already been widely characterized. What has so far not received systematic treatment is the important role of space in many intracellular computations. Spatial network computations can be divided into two broad categories: those required for essential spatial processes (e.g. polarization, chemotaxis, division, and development) and those for which space is simply used as an extra dimension to expand the computational power of the network. Several pertinent recent examples of each category are discussed that illustrate the often conceptually subtle role of space in the processing of intracellular information.
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Affiliation(s)
- Ali Kinkhabwala
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Verveer PJ, Bastiaens PIH. Quantitative microscopy and systems biology: seeing the whole picture. Histochem Cell Biol 2008; 130:833-43. [DOI: 10.1007/s00418-008-0517-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2008] [Indexed: 12/22/2022]
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Message in a bottle: long-range retrograde signaling in the nervous system. Trends Cell Biol 2007; 17:519-28. [PMID: 18029183 DOI: 10.1016/j.tcb.2007.09.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/07/2007] [Accepted: 09/07/2007] [Indexed: 01/08/2023]
Abstract
In many regions of the nervous system, signals produced by target cells and surrounding glia or in response to in jury are received at axon terminals and then retrogradely propagated to cell bodies where they regulate gene transcription and other cellular processes required for development and adult function. The cellular and molecular mechanisms of axonal retrograde signaling in neurons have traditionally been studied in the context of survival signals provided by target-derived neurotrophic factors, in which signaling endosomes containing endocytosed ligand-receptor complexes and downstream effectors are retrogradely tra nsported by dynein motors. In recent years, this notion has been refined and additional mechanisms for long-range retrograde signaling in axons have been described. This article discusses some outstanding issues in the signaling endosome hypothesis as well as recent findings suggesting the existence of a variety of mechanisms for the retrograde propagation of signals in the nervous system.
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Abstract
The specificity of cellular responses to receptor stimulation is encoded by the spatial and temporal dynamics of downstream signalling networks. Temporal dynamics are coupled to spatial gradients of signalling activities, which guide pivotal intracellular processes and tightly regulate signal propagation across a cell. Computational models provide insights into the complex relationships between the stimuli and the cellular responses, and reveal the mechanisms that are responsible for signal amplification, noise reduction and generation of discontinuous bistable dynamics or oscillations.
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Affiliation(s)
- Boris N Kholodenko
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.
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Iiyama M, Kakihana K, Kurosu T, Miura O. Reactive oxygen species generated by hematopoietic cytokines play roles in activation of receptor-mediated signaling and in cell cycle progression. Cell Signal 2006; 18:174-82. [PMID: 15982852 DOI: 10.1016/j.cellsig.2005.04.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Accepted: 04/05/2005] [Indexed: 11/25/2022]
Abstract
Hematopoietic cytokines, including interleukin (IL)-3 and erythropoietin (Epo), regulate hematopoiesis by stimulating their receptors coupled with the Jak2 tyrosine kinase to induce receptor tyrosine phosphorylation and activate mainly the STAT5, PI3K/Akt, and Ras/MEK/ERK signaling pathways. Here we demonstrate that IL-3 or Epo induces a rapid and transient (peaking at 30 min) as well as late progressive increase in reactive oxygen species (ROS) in a hematopoietic progenitor model cell line, 32Dcl3, and its subclone expressing the Epo receptor (EpoR), 32D/EpoR-Wt. The cytokine-induced ROS generation was not affected in 32Dcl3 cells depleted of mitochondrial DNA. The antioxidant N-acetyl-L-cysteine (NAC) inhibited IL-3-induced tyrosine phosphorylation of Jak2, IL-3 receptor betac subunit (IL-3Rbetac), and STAT5 as well as activation-specific phosphorylation of Akt, MEK, and ERK, while treatment of cells with H2O2 activated these signaling events. NAC also inhibited the EpoR-induced transphosphorylation of IL-3Rbetac. Moreover, NAC treatment reduced the expression levels of c-Myc, Cyclin D2, and Cyclin E, and induced expression of p27, thus inhibiting the G1 to S phase transition of cells cultured with IL-3. Further studies have shown that the degradation of c-Myc was facilitated or inhibited by treatment of cells with NAC or H2O2, respectively. These data indicate that the rapid generation of ROS by cytokine stimulation, which is at least partly independent of mitochondria, may play a role in activation of Jak2 and the STAT5, PI3K/Akt, and Ras/MEK/ERK signaling pathways as well as in transactivation of cytokine receptors. The cytokine-induced ROS generation was also implicated in G1 to S progression, possibly through stabilization of c-Myc and induction of G1 phase Cyclin expression leading to suppression of p27.
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Affiliation(s)
- Mitsuko Iiyama
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
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Wimmer-Kleikamp SH, Lackmann M. Eph-modulated cell morphology, adhesion and motility in carcinogenesis. IUBMB Life 2005; 57:421-31. [PMID: 16012051 DOI: 10.1080/15216540500138337] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Eph receptor tyrosine kinases (Ephs) and their membrane anchored ephrin ligands (ephrins) form an essential cell-cell communication system that directs the positioning, adhesion and migration of cells and cell layers during development. While less prominent in normal adult tissues, there is evidence that up-regulated expression and de-regulated function of Ephs and ephrins in a large variety of human cancers may promote a more aggressive and metastatic tumour phenotype. However, in contrast to other RTKs, Ephs do not act as classical proto-oncogenes and do not effect cell proliferation or differentiation. Mounting evidence suggests that Eph receptors, through de-regulated re-emergence of their mode of action in the embryo may direct cell movements and positioning during metastasis, invasion and tumour angiogenesis. This review discusses these and other emerging roles of Eph receptors during oncogenesis.
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Affiliation(s)
- Sabine H Wimmer-Kleikamp
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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