Skip to main content

Structure of Functional Neuropilin-Centred Class 3 Semaphorin and VEGF Receptors

  • Chapter
  • First Online:
The Neuropilins: Role and Function in Health and Disease
  • 463 Accesses

Abstract

Neuropilin functions as a co-receptor for multiple cell surface signalling systems; in particular it regulates VEGF and semaphorin signalling through their respective receptors. The molecular characteristics of neuropilin, the VEGF and semaphorin signalling complexes and their multiple interaction modes have been extensively investigated by structural and biophysical analyses. Much has been learned about the molecular mechanisms by which neuropilin acts as an interaction hub, but the complexities of neuropilin function still pose many questions.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Aci-Sèche S, Sawma P, Hubert P, Sturgis JN, Bagnard D, Jacob L, Genest M, Garnier N (2014) Transmembrane recognition of the semaphorin co-receptors neuropilin 1 and plexin A1: coarse-grained simulations. PLoS ONE 9:e97779

    Article  PubMed  PubMed Central  Google Scholar 

  2. Adams RH, Lohrum M, Klostermann A, Betz H, Püschel AW (1997) The chemorepulsive activity of secreted semaphorins is regulated by furin-dependent proteolytic processing. EMBO J 16:6077–6086

    Google Scholar 

  3. Antipenko A, Himanen JP, van Leyen K, Nardi-Dei V, Lesniak J, Barton WA et al (2003) Structure of the semaphorin-3A receptor binding module. Neuron 39:589–598

    Google Scholar 

  4. Appleton BA, Wu P, Maloney J, Yin J, Liang WC, Stawicki S et al (2007) Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding. EMBO J 26:4902–4912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Aricescu AR, Hon WC, Siebold C, Lu W, van der Merwe PA, Jones EY (2006) Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion. EMBO J 25:701–712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Aricescu AR, Siebold C, Choudhuri K, Chang VT, Lu W, Davis SJ, van der Merwe PA, Jones EY (2007) Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism. Science 317:1217–1220

    Article  CAS  PubMed  Google Scholar 

  7. Barton R, Palacio D, Iovine MK, Berger BW (2015) A cytosolic juxtamembrane interface modulates plexin A3 oligomerization and signal transduction. PLoS One 10:e0116368

    Google Scholar 

  8. Bell CH, Aricescu AR, Jones EY, Siebold C (2011) A dual binding mode for RhoGTPases in plexin signalling. PLoS Biol 9:e1001134

    Google Scholar 

  9. Casazza A, Laoui D, Wenes M, Rizzolio S, Bassani N, Mambretti M, Deschoemaeker S, Van Ginderachter JA, Tamagnone L, Mazzone M (2013) Impeding macrophage entry into hypoxic tumor areas by Sema3A/Nrp1 signaling blockade inhibits angiogenesis and restores antitumor immunity. Cancer Cell 24:695–709

    Article  CAS  PubMed  Google Scholar 

  10. Chen H, He Z, Bagri A, Tessier-Lavigne M (1998) Semaphorin-neuropilin interactions underlying sympathetic axon responses to class III semaphorins. Neuron 21:1283–1290

    Article  CAS  PubMed  Google Scholar 

  11. Chiang MK, Flanagan JG (1995) Interactions between the Flk-1 receptor, vascular endothelial growth factor, and cell surface proteoglycan identified with a soluble receptor reagent. Growth Factors 12:1–10

    Article  CAS  PubMed  Google Scholar 

  12. Cohen T, Gitay-Goren H, Sharon R, Shibuya M, Halaban R, Levi BZ, Neufeld G (1995) VEGF121, a vascular endothelial growth factor (VEGF) isoform lacking heparin binding ability, requires cell-surface heparan sulfates for efficient binding to the VEGF receptors of human melanoma cells. J Biol Chem 270:11322–11326

    Article  CAS  PubMed  Google Scholar 

  13. Dougher AM, Wasserstrom H, Torley L, Shridaran L, Westdock P, Hileman RE, Fromm JR, Anderberg R, Lyman S, Linhardt RJ, Kaplan J, Terman BI (1997) Identification of a heparin binding peptide on the extracellular domain of the KDR VEGF receptor. Growth Factors 14:257–268

    Article  CAS  PubMed  Google Scholar 

  14. Fairbrother WJ, Champe MA, Christinger HW, Keyt BA, Starovasnik MA (1998) Solution structure of the heparin-binding domain of vascular endothelial growth factor. Structure 6:637–648

    Article  CAS  PubMed  Google Scholar 

  15. Fuh G, Li B, Crowley C, Cunningham B, Wells JA (1998) Requirements for binding and signaling of the kinase domain receptor for vascular endothelial growth factor. J Biol Chem 273:11197–11204

    Article  CAS  PubMed  Google Scholar 

  16. Fuh G, Garcia KC, de Vos AM (2000) The interaction of neuropilin-1 with vascular endothelial growth factor and its receptor flt-1. J Biol Chem 275:26690–26695

    CAS  PubMed  Google Scholar 

  17. Gagnon ML, Bielenberg DR, Gechtman Z, Miao HQ, Takashima S, Soker S, Klagsbrun M (2000) Identification of a natural soluble neuropilin-1 that binds vascular endothelial growth factor: In vivo expression and antitumor activity. Proc Natl Acad Sci U S A 97:2573–2578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gelfand MV, Hagan N, Tata A, Oh WJ, Lacoste B, Kang KT, Kopycinska J, Bischoff J, Wang JH, Gu C (2014) Neuropilin-1 functions as a VEGFR2 co-receptor to guide developmental angiogenesis independent of ligand binding. Elife 3:e03720

    Article  PubMed  PubMed Central  Google Scholar 

  19. Giger RJ, Urquhart ER, Gillespie SK, Levengood DV, Ginty DD, Kolodkin AL (1998) Neuropilin-2 is a receptor for semaphorin IV: insight into the structural basis of receptor function and specificity. Neuron 21:1079–1092

    Article  CAS  PubMed  Google Scholar 

  20. Gitay-Goren H, Soker S, Vlodavsky I, Neufeld G (1992) The binding of vascular endothelial growth factor to its receptors is dependent on cell surface-associated heparin-like molecules. J Biol Chem 267:6093–6098

    CAS  PubMed  Google Scholar 

  21. Gluzman-Poltorak Z, Cohen T, Herzog Y, Neufeld G (2000) Neuropilin-2 is a receptor for the vascular endothelial growth factor (VEGF) forms VEGF-145 and VEGF-165. J Biol Chem 275:18040–18045

    Article  CAS  PubMed  Google Scholar 

  22. Gluzman-Poltorak Z, Cohen T, Shibuya M, Neufeld G (2001) Vascular endothelial growth factor receptor-1 and neuropilin-2 form complexes. J Biol Chem 276:18688–18694

    Article  CAS  PubMed  Google Scholar 

  23. Gu C, Rodriguez ER, Reimert DV, Shu T, Fritzsch B, Richards LJ, Kolodkin AL, Ginty DD (2003) Neuropilin-1 conveys semaphorin and VEGF signaling during neural and cardiovascular development. Dev Cell 5:45–57

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gu C, Yoshida Y, Livet J, Reimert DV, Mann F, Merte J, Henderson CE, Jessell TM, Kolodkin AL, Ginty DD (2005) Semaphorin 3E and plexin-D1 control vascular pattern independently of neuropilins. Science 307:265–268

    Article  CAS  PubMed  Google Scholar 

  25. Guo HF, Vander Kooi CW (2015) Neuropilin functions as an essential cell surface receptor. J Biol Chem 290:29120–29126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Guo HF, Li X, Parker MW, Waltenberger J, Becker PM, Vander Kooi CW (2013) Mechanistic basis for the potent anti-angiogenic activity of semaphorin 3F. Biochemistry 52:7551–7558

    Article  CAS  PubMed  Google Scholar 

  27. Guttmann-Raviv N, Shraga-Heled N, Varshavsky A, Guimaraes-Sternberg C, Kessler O, Neufeld G (2007) Semaphorin-3A and semaphorin-3F work together to repel endothelial cells and to inhibit their survival by induction of apoptosis. J Biol Chem 282:26294–26305

    Article  CAS  PubMed  Google Scholar 

  28. He H, Yang T, Terman JR, Zhang X (2009) Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration. Proc Natl Acad Sci USA 106:15610–15615

    Google Scholar 

  29. He Z, Tessier-Lavigne M (1997) Neuropilin is a receptor for the axonal chemorepellent. Semaphorin III. Cell 90:739–751

    Article  CAS  PubMed  Google Scholar 

  30. Hernandez-Enriquez B, Wu Z, Martinez E, Olsen O, Kaprielian Z, Maness PF, Yoshida Y, Tessier-Lavigne M, Tran TS (2015) Floor plate-derived neuropilin-2 functions as a secreted semaphorin sink to facilitate commissural axon midline crossing. Genes Dev 29:2617–2632

    PubMed  PubMed Central  Google Scholar 

  31. Jakobsson L, Kreuger J, Holmborn K, Lundin L, Eriksson I, Kjellén L, Claesson-Welsh L (2006) Heparan sulfate in trans potentiates VEGFR-mediated angiogenesis. Dev Cell 10:625–634

    Article  CAS  PubMed  Google Scholar 

  32. Janssen BJ, Robinson RA, Pérez-Brangulí F, Bell CH, Mitchell KJ, Siebold C et al (2010) Structural basis of semaphorin-plexin signalling. Nature 467:1118–1122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Janssen BJC, Malinauskas T, Weir GA, Cader MZ, Siebold C, Jones EY (2012) Neuropilins lock secreted semaphorins onto plexins in a ternary signalling complex. Nat Struct Mol Biol 19:1293–1299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Keyt BA, Berleau LT, Nguyen HV, Chen H, Heinsohn H, Vandlen R, Ferrara N (1996) The carboxyl-terminal domain (111-165) of vascular endothelial growth factor is critical for its mitogenic potency. J Biol Chem 271:7788–7795

    Article  CAS  PubMed  Google Scholar 

  35. Kigel B, Rabinowicz N, Varshavsky A, Kessler O, Neufeld G (2011) Plexin-A4 promotes tumor progression and tumor angiogenesis by enhancement of VEGF and bFGF signaling. Blood 118:4285–4296

    Article  CAS  PubMed  Google Scholar 

  36. Kisko K, Brozzo MS, Missimer J, Schleier T, Menzel A, Leppänen VM, Alitalo K, Walzthoeni T, Aebersold R, Ballmer-Hofer K (2011) Structural analysis of vascular endothelial growth factor receptor-2/ligand complexes by small-angle X-ray solution scattering. FASEB J 25:2980–2986

    Article  CAS  PubMed  Google Scholar 

  37. Klostermann A, Lohrum M, Adams RH, Püschel AW (1998) The chemorepulsive activity of the axonal guidance signal semaphorin D requires dimerization. J Biol Chem 273:7326–7331

    Google Scholar 

  38. Koch S, van Meeteren LA, Morin E, Testini C, Weström S, Björkelund H, Le Jan S, Adler J, Berger P, Claesson-Welsh L (2014) NRP1 presented in trans to the endothelium arrests VEGFR2 endocytosis, preventing angiogenic signaling and tumor initiation. Dev Cell 28:633–646

    Article  CAS  PubMed  Google Scholar 

  39. Kolodkin AL, Levengood DV, Rowe EG, Tai YT, Giger RJ, Ginty DD (1997) Neuropilin is a semaphorin III receptor. Cell 90:753–762

    Article  CAS  PubMed  Google Scholar 

  40. Koppel AM, Raper JA (1998) Collapsin-1 covalently dimerizes, and dimerization is necessary for collapsing activity. J Biol Chem 273:15708–15713

    Google Scholar 

  41. Lemmon MA, Schlessinger J (2010) Cell signaling by receptor tyrosine kinases. Cell 141:1117–1134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Leppänen VM, Prota AE, Jeltsch M, Anisimov A, Kalkkinen N, Strandin T, Lankinen H, Goldman A, Ballmer-Hofer K, Alitalo K (2010) Structural determinants of growth factor binding and specificity by VEGF receptor 2. Proc Natl Acad Sci U S A 107:2425–2430

    Article  PubMed  PubMed Central  Google Scholar 

  43. Leppänen VM, Tvorogov D, Kisko K, Prota AE, Jeltsch M, Anisimov A, Markovic-Mueller S, Stuttfeld E, Goldie KN, Ballmer-Hofer K, Alitalo K (2013) Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proc Natl Acad Sci U S A 110:12960–12965

    Article  PubMed  PubMed Central  Google Scholar 

  44. Liu H, Juo ZS, Shim AH, Focia PJ, Chen X, Garcia KC et al (2010) Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1. Cell 142:749–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Love CA, Harlos K, Mavaddat N, Davis SJ, Stuart DI, Jones EY et al (2003) The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D. Nat Struct Biol 10:843–848

    Google Scholar 

  46. Muller YA, Li B, Christinger HW, Wells JA, Cunningham BC, de Vos AM (1997) Vascular endothelial growth factor: crystal structure and functional mapping of the kinase domain receptor binding site. Proc Natl Acad Sci U S A 94:7192–7197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Nakamura F, Tanaka M, Takahashi T, Kalb RG, Strittmatter SM (1998) Neuropilin-1 extracellular domains mediate semaphorin D/III-induced growth cone collapse. Neuron 21:1093–1100

    Article  CAS  PubMed  Google Scholar 

  48. Nogi T, Yasui N, Mihara E, Matsunaga Y, Noda M, Yamashita N et al (2010) Structural basis for semaphorin signalling through the plexin receptor. Nature 467:1123–1127

    Article  CAS  PubMed  Google Scholar 

  49. Park M, Lee ST (1999) The fourth immunoglobulin-like loop in the extracellular domain of FLT-1, a VEGF receptor, includes a major heparin-binding site. Biochem Biophys Res Commun 264:730–734

    Article  CAS  PubMed  Google Scholar 

  50. Parker MW, Hellman LM, Xu P, Fried MG, Vander Kooi CW (2010) Furin processing of semaphorin 3F determines its anti-angiogenic activity by regulating direct binding and competition for neuropilin. Biochemistry 49:4068–4075

    Google Scholar 

  51. Parker MW, Xu P, Li X (2012) Vander Kooi CW (2012) Structural basis for selective vascular endothelial growth factor-A (VEGF-A) binding to neuropilin-1. J Biol Chem 287:11082–11089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Parker MW, Linkugel AD, Vander Kooi CW (2013) Effect of C-terminal sequence on competitive semaphorin binding to neuropilin-1. J Mol Biol 425:4405–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Parker MW, Linkugel AD, Goel HL, Wu T, Mercurio AM, Vander Kooi CW (2015) Structural basis for VEGF-C binding to neuropilin-2 and sequestration by a soluble splice form. Structure 23:677–687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Prahst C, Héroult M, Lanahan AA, Uziel N, Kessler O, Shraga-Heled N, Simons M, Neufeld G, Augustin HG (2008) Neuropilin-1-VEGFR-2 complexing requires the PDZ-binding domain of neuropilin-1. J Biol Chem 283:25110–25114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Rossignol M, Gagnon ML, Klagsbrun M (2000) Genomic organization of human neuropilin-1 and neuropilin-2 genes: identification and distribution of splice variants and soluble isoforms. Genomics 70:211–222

    Article  CAS  PubMed  Google Scholar 

  56. Ruch C, Skiniotis G, Steinmetz MO, Walz T, Ballmer-Hofer K (2007) Structure of a VEGF-VEGF receptor complex determined by electron microscopy. Nat Struct Mol Biol 14:249–250

    Article  CAS  PubMed  Google Scholar 

  57. Sabag AD, Smolkin T, Mumblat Y, Ueffing M, Kessler O, Gloeckner CJ, Neufeld G (2014) The role of the plexin-A2 receptor in Sema3A and Sema3B signal transduction. J Cell Sci 127:5240–5252

    Article  PubMed  Google Scholar 

  58. Sawma P, Roth L, Blanchard C, Bagnard D, Crémel G, Bouveret E, Duneau JP, Sturgis JN, Hubert P (2014) Evidence for new homotypic and heterotypic interactions between transmembrane helices of proteins involved in receptor tyrosine kinase and neuropilin signaling. J Mol Biol 426:4099–4111

    Article  CAS  PubMed  Google Scholar 

  59. Shraga-Heled N, Kessler O, Prahst C, Kroll J, Augustin H, Neufeld G (2007) Neuropilin-1 and neuropilin-2 enhance VEGF121 stimulated signal transduction by the VEGFR-2 receptor. FASEB J 21:915–926

    Article  CAS  PubMed  Google Scholar 

  60. Siebold C, Jones EY (2013) Structural insights into semaphorins and their receptors. Semin Cell Dev Biol 24:139–145

    Article  CAS  PubMed  Google Scholar 

  61. Soker S, Takashima S, Miao HQ, Neufeld G, Klagsbrun M (1998) Neuropilin-1 is expressed by endothelial and tumor cells as an isoform-specific receptor for vascular endothelial growth factor. Cell 92:735–745

    Article  CAS  PubMed  Google Scholar 

  62. Soker S, Miao HQ, Nomi M, Takashima S, Klagsbrun M (2002) VEGF165 mediates formation of complexes containing VEGFR-2 and neuropilin-1 that enhance VEGF165-receptor binding. J Cell Biochem 85:357–368

    Article  CAS  PubMed  Google Scholar 

  63. Takahashi T, Fournier A, Nakamura F, Wang LH, Murakami Y, Kalb RG et al (1999) Plexin–neuropilin-1 complexes form functional semaphorin-3A receptors. Cell 99:59–69

    Article  CAS  PubMed  Google Scholar 

  64. Tamagnone L, Artigiani S, Chen H, He Z, Ming GI, Song H et al (1999) Plexins are a large family of receptors for transmembrane, secreted, and GPI-anchored semaphorins in vertebrates. Cell 99:71–80

    Article  CAS  PubMed  Google Scholar 

  65. Teran M, Nugent MA (2015) Synergistic binding of vascular endothelial growth factor-A and its receptors to heparin selectively modulates complex affinity. J Biol Chem 290:16451–16462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Tong Y, Hota PK, Penachioni JY, Hamaneh MB, Kim S, Alviani RS et al (2009) Structure and function of the intracellular region of the plexin-b1 transmembrane receptor. J Biol Chem 284:35962–35972

    Google Scholar 

  67. Vander Kooi CW, Jusino MA, Perman B, Neau DB, Bellamy HD, Leahy DJ (2007) Structural basis for ligand and heparin binding to neuropilin B domains. Proc Natl Acad Sci U S A 104:6152–6157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Wang Y, He H, Srivastava N, Vikarunnessa S, Chen YB, Jiang J et al (2012) Plexins are GTPase-activating proteins for Rap and are activated by induced dimerization. Sci Signal 5:ra6

    Google Scholar 

  69. Wang Y, Pascoe HG, Brautigam CA, He H, Zhang X (2013) Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin. Elife 2:e01279

    Google Scholar 

  70. Wiesmann C, Fuh G, Christinger HW, Eigenbrot C, Wells JA, de Vos AM (1997) Crystal structure at 1.7 A resolution of VEGF in complex with domain 2 of the Flt-1 receptor. Cell 91:695–704

    Article  CAS  PubMed  Google Scholar 

  71. Xu D, Fuster MM, Lawrence R, Esko JD (2011) Heparan sulfate regulates VEGF165- and VEGF121-mediated vascular hyperpermeability. J Biol Chem 286:737–745

    Article  CAS  PubMed  Google Scholar 

  72. Yang Y, Xie P, Opatowsky Y, Schlessinger J (2010) Direct contacts between extracellular membrane-proximal domains are required for VEGF receptor activation and cell signaling. Proc Natl Acad Sci U S A 107:1906–1911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Zhang L, Polyansky A, Buck M (2015) Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS One 10:e0121513

    Google Scholar 

Download references

Acknowledgement

EYJ is funded by Cancer Research UK (A10976), the UK Medical Research Council (G9900061) and the Wellcome Trust (grant 090532/Z/09/Z supporting the Wellcome Trust Centre for Human Genetics).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to E. Yvonne Jones .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Jones, E.Y. (2017). Structure of Functional Neuropilin-Centred Class 3 Semaphorin and VEGF Receptors. In: Neufeld, G., Kessler, O. (eds) The Neuropilins: Role and Function in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-48824-0_2

Download citation

Publish with us

Policies and ethics