EGFR oligomerization organizes kinase-active dimers into competent signalling platforms

Epidermal growth factor receptor (EGFR) signalling is activated by ligand-induced receptor dimerization. Notably, ligand binding also induces EGFR oligomerization, but the structures and functions of the oligomers are poorly understood. Here, we use fluorophore localization imaging with photobleaching to probe the structure of EGFR oligomers. We find that at physiological epidermal growth factor (EGF) concentrations, EGFR assembles into oligomers, as indicated by pairwise distances of receptor-bound fluorophore-conjugated EGF ligands. The pairwise ligand distances correspond well with the predictions of our structural model of the oligomers constructed from molecular dynamics simulations. The model suggests that oligomerization is mediated extracellularly by unoccupied ligand-binding sites and that oligomerization organizes kinase-active dimers in ways optimal for auto-phosphorylation in trans between neighbouring dimers. We argue that ligand-induced oligomerization is essential to the regulation of EGFR signalling.

[1]  Joseph Schlessinger,et al.  Signal transduction by receptors with tyrosine kinase activity , 1990, Cell.

[2]  S. Skvortsov,et al.  Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network , 2008, Proteomics.

[3]  M. Martin-Fernandez,et al.  Preformed oligomeric epidermal growth factor receptors undergo an ectodomain structure change during signaling. , 2002, Biophysical journal.

[4]  H. Lane,et al.  ERBB Receptors and Cancer: The Complexity of Targeted Inhibitors , 2005, Nature Reviews Cancer.

[5]  Y. Yarden,et al.  Self-phosphorylation of epidermal growth factor receptor: evidence for a model of intermolecular allosteric activation. , 1987, Biochemistry.

[6]  E. Yarmola,et al.  Actin-latrunculin A structure and function. Differential modulation of actin-binding protein function by latrunculin A. , 2000, The Journal of biological chemistry.

[7]  Claus A M Seidel,et al.  A toolkit and benchmark study for FRET-restrained high-precision structural modeling , 2012, Nature Methods.

[8]  Henrik Flyvbjerg,et al.  A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques. , 2006, Biophysical journal.

[9]  W. Press,et al.  Numerical Recipes in C++: The Art of Scientific Computing (2nd edn)1 Numerical Recipes Example Book (C++) (2nd edn)2 Numerical Recipes Multi-Language Code CD ROM with LINUX or UNIX Single-Screen License Revised Version3 , 2003 .

[10]  Jae-Hoon Kim,et al.  Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains , 2002, Cell.

[11]  D. Lambright,et al.  A Novel Pleckstrin Homology Domain-containing Protein Enhances Insulin-stimulated Akt Phosphorylation and GLUT4 Translocation in Adipocytes , 2010, The Journal of Biological Chemistry.

[12]  H. Brismar,et al.  Phage display selection of Affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor. , 2007, Protein engineering, design & selection : PEDS.

[13]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[14]  E. Isacoff,et al.  Molecular basis for multimerization in the activation of the epidermal growth factor receptor , 2016, eLife.

[15]  Edouard C. Nice,et al.  Crystal Structure of a Truncated Epidermal Growth Factor Receptor Extracellular Domain Bound to Transforming Growth Factor α , 2002, Cell.

[16]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[17]  Hongbin Ji,et al.  Regulation of EGFR nanocluster formation by ionic protein-lipid interaction , 2014, Cell Research.

[18]  C. Tacchetti,et al.  Relationships between EGFR signaling-competent and endocytosis-competent membrane microdomains. , 2005, Molecular biology of the cell.

[19]  Yosef Yarden,et al.  Feedback regulation of EGFR signalling: decision making by early and delayed loops , 2011, Nature Reviews Molecular Cell Biology.

[20]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[21]  E. Elson,et al.  Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. , 2007, Biophysical journal.

[22]  Hannes H. Loeffler,et al.  Human Epidermal Growth Factor Receptor (EGFR) Aligned on the Plasma Membrane Adopts Key Features of Drosophila EGFR Asymmetry , 2011, Molecular and Cellular Biology.

[23]  John Kuriyan,et al.  An Allosteric Mechanism for Activation of the Kinase Domain of Epidermal Growth Factor Receptor , 2006, Cell.

[24]  R. Landgraf,et al.  Functional isolation of activated and unilaterally phosphorylated heterodimers of ERBB2 and ERBB3 as scaffolds in ligand-dependent signaling , 2012, Proceedings of the National Academy of Sciences.

[25]  Y. Yarden,et al.  Epidermal growth factor induces rapid, reversible aggregation of the purified epidermal growth factor receptor. , 1987, Biochemistry.

[26]  Joseph Schlessinger,et al.  Ligand-Induced, Receptor-Mediated Dimerization and Activation of EGF Receptor , 2002, Cell.

[27]  J. Mullins,et al.  Production of large numbers of mitotic mammalian cells by use of the reversible microtubule inhibitor nocodazole. Nocodazole accumulated mitotic cells. , 1980, Experimental cell research.

[28]  R. Roskoski The ErbB/HER family of protein-tyrosine kinases and cancer. , 2014, Pharmacological research.

[29]  A. Verkleij,et al.  A biparatopic anti‐EGFR nanobody efficiently inhibits solid tumour growth , 2011, International journal of cancer.

[30]  Richard J. Wareham,et al.  Measuring EGFR Separations on Cells with ∼10 nm Resolution via Fluorophore Localization Imaging with Photobleaching , 2013, PloS one.

[31]  A. Zachowski Phospholipids in animal eukaryotic membranes: transverse asymmetry and movement. , 1993, The Biochemical journal.

[32]  K. Vuori,et al.  Epidermal Growth Factor Modulates Tyrosine Phosphorylation of p130Cas , 1997, The Journal of Biological Chemistry.

[33]  R. Landgraf,et al.  Oligomers of ERBB3 Have Two Distinct Interfaces That Differ in Their Sensitivity to Disruption by Heregulin* , 2005, Journal of Biological Chemistry.

[34]  T. Yanagida,et al.  EGF signalling amplification induced by dynamic clustering of EGFR. , 2004, Biochemical and biophysical research communications.

[35]  John G. Koland,et al.  Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation , 2014, PLoS Comput. Biol..

[36]  Michael Frankfurter,et al.  Numerical Recipes In C The Art Of Scientific Computing , 2016 .

[37]  J. Schlessinger Cell Signaling by Receptor Tyrosine Kinases , 2000, Cell.

[38]  J. Schlessinger,et al.  Lateral diffusion of epidermal growth factor complexed to its surface receptors does not account for the thermal sensitivity of patch formation and endocytosis. , 1982, Biochemistry.

[39]  G. MacBeath,et al.  High- and Low-Affinity Epidermal Growth Factor Receptor-Ligand Interactions Activate Distinct Signaling Pathways , 2011, PloS one.

[40]  Laura C. Zanetti-Domingues,et al.  Nanometric molecular separation measurements by single molecule photobleaching. , 2015, Methods.

[41]  Xintian Zhang,et al.  A Switch Role of Src in the Biphasic EGF Signaling of ER-Negative Breast Cancer Cells , 2012, PloS one.

[42]  Carl Frieden,et al.  Effect of temperature on the mechanism of actin polymerization. , 1986, Biochemistry.

[43]  Harvey T. McMahon,et al.  Membrane curvature and mechanisms of dynamic cell membrane remodelling , 2005, Nature.

[44]  M. Sliwkowski,et al.  Binding specificities and affinities of egf domains for ErbB receptors , 1999, FEBS letters.

[45]  Laura C. Zanetti-Domingues,et al.  Determining the geometry of oligomers of the human epidermal growth factor family on cells with <10 nm resolution. , 2015, Biochemical Society transactions.

[46]  Hyun-soo Cho,et al.  Structure of the Extracellular Region of HER3 Reveals an Interdomain Tether , 2002, Science.

[47]  Jeffrey K. Hollingsworth Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis , 2017, SC.

[48]  Alexander D. MacKerell,et al.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. , 2005, The journal of physical chemistry. B.

[49]  S. Simon,et al.  Endocytic trafficking of activated EGFR is AP-2 dependent and occurs through preformed clathrin spots , 2009, Journal of Cell Science.

[50]  J. Schlessinger,et al.  Signaling by Receptor Tyrosine Kinases , 1993 .

[51]  A. Sorkin,et al.  Live-cell fluorescence imaging reveals high stoichiometry of Grb2 binding to the EGF receptor sustained during endocytosis , 2014, Journal of Cell Science.

[52]  George A. Khoury,et al.  Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. , 2013, Journal of chemical theory and computation.

[53]  L. Pike,et al.  Different Epidermal Growth Factor (EGF) Receptor Ligands Show Distinct Kinetics and Biased or Partial Agonism for Homodimer and Heterodimer Formation* , 2014, The Journal of Biological Chemistry.

[54]  D. Shaw,et al.  Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor , 2013, Cell.

[55]  Kenneth M. Mackenzie,et al.  Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure. , 2013, The Journal of chemical physics.

[56]  I. Madshus,et al.  Cholesterol is important in control of EGF receptor kinase activity but EGF receptors are not concentrated in caveolae. , 2002, Journal of cell science.

[57]  R. Dror,et al.  Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. , 2005, The Journal of chemical physics.

[58]  Linda J Pike,et al.  Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system , 2008, Proceedings of the National Academy of Sciences.

[59]  M. Lemmon,et al.  Complex relationship between ligand binding and dimerization in the epidermal growth factor receptor. , 2014, Cell reports.

[60]  P. Lei,et al.  Epidermal growth factor (EGF) induces apoptosis in a transfected cell line expressing EGF receptor on its membrane , 2006, Cell biology international.

[61]  L. Pike,et al.  Palmitoylation of the EGF receptor impairs signal transduction and abolishes high-affinity ligand binding. , 2009, Biochemistry.

[62]  M. Klein,et al.  Constant pressure molecular dynamics algorithms , 1994 .

[63]  Derek Toomre,et al.  Spatial control of EGF receptor activation by reversible dimerization on living cells , 2010, Nature.

[64]  R. Rand,et al.  The influence of cholesterol on phospholipid membrane curvature and bending elasticity. , 1997, Biophysical journal.

[65]  J. Sethna,et al.  Minimal model of plasma membrane heterogeneity requires coupling cortical actin to criticality. , 2010, Biophysical journal.

[66]  W. S. Hlavacek,et al.  Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach. , 2013, Molecular bioSystems.

[67]  Hjalmar Brismar,et al.  Cellular studies of binding, internalization and retention of a radiolabeled EGFR-binding affibody molecule. , 2007, Nuclear medicine and biology.

[68]  K. Carraway,et al.  Fluorescent-labeled growth factor molecules serve as probes for receptor binding and endocytosis. , 1993, Biochemistry.

[69]  Anton Arkhipov,et al.  Architecture and Membrane Interactions of the EGF Receptor , 2013, Cell.

[70]  A. Demchenko,et al.  Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers , 2013, TheScientificWorldJournal.

[71]  Patricia Grob,et al.  Analysis of the Role of the C-Terminal Tail in the Regulation of the Epidermal Growth Factor Receptor , 2015, Molecular and Cellular Biology.

[72]  J. Settleman,et al.  Temporal resolution of autophosphorylation for normal and oncogenic forms of EGFR and differential effects of gefitinib. , 2012, Biochemistry.

[73]  Hyun-soo Cho,et al.  EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. , 2003, Molecular cell.

[74]  Edouard C. Nice,et al.  Ligand-induced Dimer-Tetramer Transition during the Activation of the Cell Surface Epidermal Growth Factor Receptor-A Multidimensional Microscopy Analysis* , 2005, Journal of Biological Chemistry.

[75]  A Kusumi,et al.  Compartmentalized structure of the plasma membrane for receptor movements as revealed by a nanometer-level motion analysis , 1994, The Journal of cell biology.