SpringerLink
Log in

Glycosylation promotes the cancer regulator EGFR-ErbB2 heterodimer formation — molecular dynamics study

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

ErbB family of receptor tyrosine kinases play significant roles in cellular differentiation and proliferation. Mutation or overexpression of these receptors leads to several cancers in humans. The family has four homologous members including EGFR, ErbB2, ErbB3, and ErbB4. From which all except the ErbB2 bind to growth factors via the extracellular domain to send signals to the cell. However, dimerization of the ErbB receptor occurs in extracellular, transmembrane, and intracellular domains. The ErbB receptors are known to form homodimers and heterodimers in the active form. Heterodimerization increases the variety of identified ligands and signaling pathways that can be activated by these receptors. Furthermore, glycosylation of the ErbB receptors has shown to be critical for their stability, ligand binding, and dimerization. Here, atomistic molecular dynamics simulations on the glycosylated and unglycosylated heterodimer showed that the EGFR-ErbB2 heterodimer is more stable in its dynamical pattern compared to the EGFR-EGFR homodimer. This increased stability is regulated by maintaining the dimeric interface by the attached glycans. It was also shown that the presence of various glycosylation sites within the ErbB2 growth factor binding site leads to occlusion of this site by the glycans that inhibit ligand binding to ErbB2 and participate in further stabilization of the heterodimer construct. Putting together, glycosylation seems to promote the heterodimer formation within the ErbB family members as the dominant molecular mechanism of activation for these receptors.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Data availability

All of the simulation trajectories and the plot data are available.

Code availability

N/A.

References

  1. Appert-Collin, A., Hubert, P., Crémel, G., & Bennasroune, A. (2015). Role of ErbB receptors in cancer cell migration and invasion. Front Pharm, 6(283). https://doi.org/10.3389/fphar.2015.00283

  2. Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, Wemmer DE, Shaw DE (2013) Architecture and membrane interactions of the EGF receptor. Cell 152(3):557–569. https://doi.org/10.1016/j.cell.2012.12.030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Arkhipov A, Shan Y, Kim ET, Dror RO, Shaw DE (2013) Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family. Elife 2:e00708. https://doi.org/10.7554/eLife.00708

    Article  PubMed  PubMed Central  Google Scholar 

  4. Arkhipov A, Shan Y, Kim ET, Shaw DE (2014) Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor. PLoS Comput Biol 10(7):e1003742. https://doi.org/10.1371/journal.pcbi.1003742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Azimzadeh Irani M (2018) Correlation between experimentally indicated and atomistically simulated roles of EGFR N-glycosylation. Mol Simul 44(9):743–748. https://doi.org/10.1080/08927022.2018.1447108

    Article  CAS  Google Scholar 

  6. Azimzadeh Irani M, Ejtehadi MR (2019) GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation. Glycobiology 29(11):803–812. https://doi.org/10.1093/glycob/cwz055

    Article  CAS  PubMed  Google Scholar 

  7. Azimzadeh Irani, M., & Ejtehadi, M. R. (2020). Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response J Biomol Struct Dyn 1–11https://doi.org/10.1080/07391102.2020.1841027

  8. Azimzadeh Irani M, Kannan S, Verma C (2017) Role of N-glycosylation in EGFR ectodomain ligand binding. Proteins 85(8):1529–1549. https://doi.org/10.1002/prot.25314

    Article  CAS  PubMed  Google Scholar 

  9. Beerli RR, Graus-Porta D, Woods-Cook K, Chen X, Yarden Y, Hynes NE (1995) Neu differentiation factor activation of ErbB-3 and ErbB-4 is cell specific and displays a differential requirement for ErbB-2. Mol Cell Biol 15(12):6496–6505

    Article  CAS  Google Scholar 

  10. Berendsen H, van Postma JPM, van Gunsteren W, DiNola AD, Haak JR (1984) Molecular-dynamics with coupling to an external bath. J Chem Phys 81:3684. https://doi.org/10.1063/1.448118

    Article  CAS  Google Scholar 

  11. Black LE, Longo JF, Carroll SL (2019) Mechanisms of receptor tyrosine-protein kinase ErbB-3 (ERBB3) action in human neoplasia. Am J Pathol 189(10):1898–1912. https://doi.org/10.1016/j.ajpath.2019.06.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bragin PE, Mineev KS, Bocharova OV, Volynsky PE, Bocharov EV, Arseniev AS (2016) HER2 transmembrane domain dimerization coupled with self-association of membrane-embedded cytoplasmic juxtamembrane regions. J Mol Biol 428(1):52–61. https://doi.org/10.1016/j.jmb.2015.11.007

    Article  CAS  PubMed  Google Scholar 

  13. Burgess AW, Cho HS, Eigenbrot C, Ferguson KM, Garrett TP, Leahy DJ, Yokoyama S (2003) An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol Cell 12(3):541–552

    Article  CAS  Google Scholar 

  14. Cicenas J (2007) The potential role of the EGFR/ERBB2 heterodimer in breast cancer. Expert Opin Ther Pat 17(6):607–616. https://doi.org/10.1517/13543776.17.6.607

    Article  CAS  Google Scholar 

  15. Ferguson KM, Berger MB, Mendrola JM, Cho H-S, Leahy DJ, Lemmon MA (2003) EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. Mol Cell 11(2):507–517. https://doi.org/10.1016/S1097-2765(03)00047-9

    Article  CAS  PubMed  Google Scholar 

  16. Gassmann M, Casagranda F, Orioli D, Simon H, Lai C, Klein R, Lemke G (1995) Aberrant neural and cardiac development in mice lacking the ErbB4 neuregulin receptor. Nature 378(6555):390–394. https://doi.org/10.1038/378390a0

    Article  CAS  PubMed  Google Scholar 

  17. Geethadevi A, Parashar D, Bishop E, Pradeep S, Chaluvally-Raghavan P (2017) ERBB signaling in CTCs of ovarian cancer and glioblastoma. Genes Cancer 8(11–12):746–751. https://doi.org/10.18632/genesandcancer.162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Graus-Porta D, Beerli RR, Daly JM, Hynes NE (1997) ErbB-2, the preferred heterodimerization partner of all ErbB receptors, is a mediator of lateral signaling. EMBO J 16(7):1647–1655. https://doi.org/10.1093/emboj/16.7.1647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Graus-Porta D, Beerli RR, Hynes NE (1995) Single-chain antibody-mediated intracellular retention of ErbB-2 impairs Neu differentiation factor and epidermal growth factor signaling. Mol Cell Biol 15(3):1182–1191

    Article  CAS  Google Scholar 

  20. Group, W. ((2005-XXXX) ). GLYCAM Web. from University of Georgia, Athens, GA (http://glycam.org)

  21. Heinig M, Frishman D (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32(Web Server issue):W500-502. https://doi.org/10.1093/nar/gkh429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hu S, Sun Y, Meng Y, Wang X, Yang W, Fu W, Guo Y (2015) Molecular architecture of the ErbB2 extracellular domain homodimer. Oncotarget 6(3):1695–1706. https://doi.org/10.18632/oncotarget.2713

    Article  PubMed  PubMed Central  Google Scholar 

  23. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38. https://doi.org/10.1016/0263-7855(96)00018-5

    Article  CAS  PubMed  Google Scholar 

  24. Hynes NE, Lane HA (2005) ERBB receptors and cancer: the complexity of targeted inhibitors. Nat Rev Cancer 5(5):341–354. https://doi.org/10.1038/nrc1609

    Article  CAS  PubMed  Google Scholar 

  25. ** W (2020) ErBb family proteins in cholangiocarcinoma and clinical implications. J Clin Med 9(7):2255. https://doi.org/10.3390/jcm9072255

    Article  CAS  PubMed Central  Google Scholar 

  26. Jura N, Endres NF, Engel K, Deindl S, Das R, Lamers MH, Kuriyan J (2009) Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell 137(7):1293–1307. https://doi.org/10.1016/j.cell.2009.04.025

    Article  PubMed  PubMed Central  Google Scholar 

  27. Karunagaran D, Tzahar E, Beerli RR, Chen X, Graus-Porta D, Ratzkin BJ, Yarden Y (1996) ErbB-2 is a common auxiliary subunit of NDF and EGF receptors: implications for breast cancer. Embo j 15(2):254–264

    Article  CAS  Google Scholar 

  28. Kaszuba K, Grzybek M, Orlowski A, Danne R, Róg T, Simons K, Vattulainen I (2015) N -Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proc Natl Acad Sci 112:4334–4339. https://doi.org/10.1073/pnas.1503262112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kaszuba K, Grzybek M, Orłowski A, Danne R, Róg T, Simons K, Vattulainen I (2015) N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proc Natl Acad Sci U S A 112(14):4334–4339. https://doi.org/10.1073/pnas.1503262112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Kirschner KN, Yongye AB, Tschampel SM, Gonzalez-Outeirino J, Daniels CR, Foley BL, Woods RJ (2008) GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem 29(4):622–655. https://doi.org/10.1002/jcc.20820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lee KF, Simon H, Chen H, Bates B, Hung MC, Hauser C (1995) Requirement for neuregulin receptor erbB2 in neural and cardiac development. Nature 378(6555):394–398. https://doi.org/10.1038/378394a0

    Article  CAS  PubMed  Google Scholar 

  32. Loncharich RJ, Brooks BR, Pastor RW (1992) Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers 32(5):523–535. https://doi.org/10.1002/bip.360320508

    Article  CAS  PubMed  Google Scholar 

  33. Lu C, Mi LZ, Grey MJ, Zhu J, Graef E, Yokoyama S, Springer TA (2010) Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor. Mol Cell Biol 30(22):5432–5443. https://doi.org/10.1128/mcb.00742-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11(8):3696–3713. https://doi.org/10.1021/acs.jctc.5b00255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mehrabi M, Mahdiuni H, Rasouli H, Mansouri K, Shahlaei M, Khodarahmi R (2018) Comparative experimental/theoretical studies on the EGFR dimerization under the effect of EGF/EGF analogues binding: highlighting the importance of EGF/EGFR interactions at site III interface. Int J Biol Macromol 115:401–417. https://doi.org/10.1016/j.ijbiomac.2018.04.066

    Article  CAS  PubMed  Google Scholar 

  36. Mendelsohn J, Baselga J (2006) Epidermal growth factor receptor targeting in cancer. Semin Oncol 33(4):369–385. https://doi.org/10.1053/j.seminoncol.2006.04.003

    Article  CAS  PubMed  Google Scholar 

  37. Olayioye, A., Neve, R., & Hynes, N. (2000). The ErbB signaling network: receptor heterodimerization in development and cancer. EMBO J., 19.

  38. Olayioye MA, Neve RM, Lane HA, Hynes NE (2000) The ErbB signaling network: receptor heterodimerization in development and cancer. EMBO J 19(13):3159–3167. https://doi.org/10.1093/emboj/19.13.3159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Pastor RW, Brooks BR, Szabo A (1988) An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys 65(6):1409–1419. https://doi.org/10.1080/00268978800101881

    Article  Google Scholar 

  40. Patane S (2014) ERBB1/EGFR and ERBB2 (HER2/neu)–targeted therapies in cancer and cardiovascular system with cardiovascular drugs. Int J Cardiol 176(3):1301–1303. https://doi.org/10.1016/j.ijcard.2014.07.161

    Article  PubMed  Google Scholar 

  41. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91(1):1–41. https://doi.org/10.1016/0010-4655(95)00041-D

    Article  CAS  Google Scholar 

  42. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Sali A (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34(Database issue):D291–D295. https://doi.org/10.1093/nar/gkj059

    Article  CAS  PubMed  Google Scholar 

  43. Plowman GD, Culouscou JM, Whitney GS, Green JM, Carlton GW, Foy L, Shoyab M (1993) Ligand-specific activation of HER4/p180erbB4, a fourth member of the epidermal growth factor receptor family. Proc Natl Acad Sci U S A 90(5):1746–1750. https://doi.org/10.1073/pnas.90.5.1746

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Plowman GD, Whitney GS, Neubauer MG, Green JM, McDonald VL, Todaro GJ, Shoyab M (1990) Molecular cloning and expression of an additional epidermal growth factor receptor-related gene. Proc Natl Acad Sci U S A 87(13):4905–4909

    Article  CAS  Google Scholar 

  45. Poger D, Mark AE (2014) Activation of the epidermal growth factor receptor: a series of twists and turns. Biochemistry 53(16):2710–2721. https://doi.org/10.1021/bi401632z

    Article  CAS  PubMed  Google Scholar 

  46. Rahnama S, Azimzadeh Irani M, Amininasab M, Ejtehadi MR (2021) S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study. Sci Rep 11(1):15162. https://doi.org/10.1038/s41598-021-94602-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Rose M, Maurer A, Wirtz J, Bleilevens A, Waldmann T, Wenz M, Gaisa NT (2020) EGFR activity addiction facilitates anti-ERBB based combination treatment of squamous bladder cancer. Oncogene 39(44):6856–6870. https://doi.org/10.1038/s41388-020-01465-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Roskoski R (2004) The ErbB/HER receptor protein-tyrosine kinases and cancer. Biochem Biophys Res Commun 319(1):1–11. https://doi.org/10.1016/j.bbrc.2004.04.150

    Article  CAS  PubMed  Google Scholar 

  49. Ross JS, Fletcher JA (1998) The HER-2/neu oncogene in breast cancer: prognostic factor, predictive factor, and target for therapy. Stem Cells 16(6):413–428. https://doi.org/10.1002/stem.160413

    Article  CAS  PubMed  Google Scholar 

  50. Sanders JM, Wampole ME, Thakur ML, Wickstrom E (2013) Molecular determinants of epidermal growth factor binding: a molecular dynamics study. PLoS One 8(1):e54136. https://doi.org/10.1371/journal.pone.0054136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Seshacharyulu P, Ponnusamy MP, Haridas D, Jain M, Ganti AK, Batra SK (2012) Targeting the EGFR signaling pathway in cancer therapy. Expert Opin Ther Targets 16(1):15–31. https://doi.org/10.1517/14728222.2011.648617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Sibilia M, Wagner EF (1995) Strain-dependent epithelial defects in mice lacking the EGF receptor. Science 269(5221):234–238. https://doi.org/10.1126/science.7618085

    Article  CAS  PubMed  Google Scholar 

  53. Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL (1987) Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235(4785):177–182. https://doi.org/10.1126/science.3798106

    Article  CAS  PubMed  Google Scholar 

  54. Stroop CJM, Weber W, Gerwig GJ, Nimtz M, Kamerling JP, Vliegenthart JFG (2000) Characterization of the carbohydrate chains of the secreted form of the human epidermal growth factor receptor. Glycobiology 10(9):901–917. https://doi.org/10.1093/glycob/10.9.901

    Article  CAS  PubMed  Google Scholar 

  55. Taylor, E., Pol-Fachin, L., Lins, R., & Lower, S. (2016). Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation, dimerization and EGF hormone binding: EGF binding provides major stability to EGFR. Proteins: Structure, Function, and Bioinformatics, 85. https://doi.org/10.1002/prot.25220

  56. Threadgill DW, Dlugosz AA, Hansen LA, Tennenbaum T, Lichti U, Yee D et al (1995) Targeted disruption of mouse EGF receptor: effect of genetic background on mutant phenotype. Science 269(5221):230–234. https://doi.org/10.1126/science.7618084

    Article  CAS  PubMed  Google Scholar 

  57. Ullrich A, Coussens L, Hayflick JS, Dull TJ, Gray A, Tam AW, Seeburg PH (1984) Human epidermal growth factor receptor cDNA sequence and aberrant expression of the amplified gene in A431 epidermoid carcinoma cells. Nature 309:418. https://doi.org/10.1038/309418a0

    Article  CAS  PubMed  Google Scholar 

  58. van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Bonvin AMJJ (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428(4):720–725. https://doi.org/10.1016/j.jmb.2015.09.014

    Article  CAS  PubMed  Google Scholar 

  59. Ward MD, Leahy DJ (2015) Kinase activator-receiver preference in ErbB heterodimers is determined by intracellular regions and is not coupled to extracellular asymmetry*. J Biol Chem 290(3):1570–1579. https://doi.org/10.1074/jbc.M114.612085

    Article  CAS  PubMed  Google Scholar 

  60. Wee P, Wang Z (2017) Epidermal growth factor receptor cell proliferation signaling pathways. Cancers 9(5):52. https://doi.org/10.3390/cancers9050052

    Article  CAS  PubMed Central  Google Scholar 

  61. WL, D. (2002). The PyMOL molecular graphics system.

  62. Yamamoto T, Ikawa S, Akiyama T, Semba K, Nomura N, Miyajima N, Toyoshima K (1986) Similarity of protein encoded by the human c-erb-B-2 gene to epidermal growth factor receptor. Nature 319(6050):230–234. https://doi.org/10.1038/319230a0

    Article  CAS  PubMed  Google Scholar 

  63. Yarden Y (2001) The EGFR family and its ligands in human cancer: signalling mechanisms and therapeutic opportunities. Eur J Cancer 37:3–8. https://doi.org/10.1016/S0959-8049(01)00230-1

    Article  Google Scholar 

  64. Yarden Y, Sliwkowski MX (2001) Untangling the ErbB signalling network. Nat Rev Mol Cell Biol 2(2):127–137. https://doi.org/10.1038/35052073

    Article  CAS  PubMed  Google Scholar 

  65. Zhang J, Saba NF, Chen GZ, Shin DM (2015) Targeting HER (ERBB) signaling in head and neck cancer: an essential update. Mol Aspects Med 45:74–86. https://doi.org/10.1016/j.mam.2015.07.001

    Article  PubMed  PubMed Central  Google Scholar 

  66. Zhen Y, Caprioli RM, Staros JV (2003) Characterization of glycosylation sites of the epidermal growth factor receptor. Biochemistry 42(18):5478–5492. https://doi.org/10.1021/bi027101p

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The support and resources from the high performance computing center of Shahid Beheshti University (SARMAD) are gratefully acknowledged.

Author information

Authors and Affiliations

  1. Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Post Code: 1983969411, Tehran, Iran

    Zahra Motamedi, Hassan Rajabi-Maham & Maryam Azimzadeh Irani

Authors
  1. Zahra Motamedi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hassan Rajabi-Maham
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maryam Azimzadeh Irani
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Z.M set up all the models for simulations, and M.A.I carried out the simulations. Data were analyzed by Z.M and M.A.I and they both contributed equally in providing the figures and plots and writing of the manuscript. H.R.M contributed to the interpretation of the results. All authors read the manuscript thoroughly.

Corresponding author

Correspondence to Maryam Azimzadeh Irani.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 16009 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Motamedi, Z., Rajabi-Maham, H. & Azimzadeh Irani, M. Glycosylation promotes the cancer regulator EGFR-ErbB2 heterodimer formation — molecular dynamics study. J Mol Model 27, 361 (2021). https://doi.org/10.1007/s00894-021-04986-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-021-04986-9

Keywords

Search

Navigation