Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1997 Dec 1;16(23):6936–6946. doi: 10.1093/emboj/16.23.6936

Solution structure of midkine, a new heparin-binding growth factor.

W Iwasaki 1, K Nagata 1, H Hatanaka 1, T Inui 1, T Kimura 1, T Muramatsu 1, K Yoshida 1, M Tasumi 1, F Inagaki 1
PMCID: PMC1170297  PMID: 9384573

Abstract

Midkine (MK) is a 13 kDa heparin-binding polypeptide which enhances neurite outgrowth, neuronal cell survival and plasminogen activator activity. MK is structurally divided into two domains, and most of the biological activities are located on the C-terminal domain. The solution structures of the two domains were determined by NMR. Both domains consist of three antiparallel beta-strands, but the C-terminal domain has a long flexible hairpin loop where a heparin-binding consensus sequence is located. Basic residues on the beta-sheet of the C-terminal domain form another heparin-binding site. Measurement of NMR signals in the presence of a heparin oligosaccharides verified that multiple amino acids in the two sites participated in heparin binding. The MK dimer has been shown to be the active form, giving signals to endothelial cells and probably to neuronal cells. We present a head-to-head dimer model of MK. The model was supported by the results of cross-linking experiments using transglutaminase. The dimer has a fused heparin-binding site at the dimer interface of the C-terminal domain, and the heparin-binding sites on MK fit the sulfate group clusters on heparin. These features are consistent with the proposed stronger heparin-binding activity and biological activity of the dimer.

Full Text

The Full Text of this article is available as a PDF (972.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adachi Y., Matsubara S., Pedraza C., Ozawa M., Tsutsui J., Takamatsu H., Noguchi H., Akiyama T., Muramatsu T. Midkine as a novel target gene for the Wilms' tumor suppressor gene (WT1). Oncogene. 1996 Nov 21;13(10):2197–2203. [PubMed] [Google Scholar]
  2. Arakawa T., Wen J., Philo J. S. Stoichiometry of heparin binding to basic fibroblast growth factor. Arch Biochem Biophys. 1994 Jan;308(1):267–273. doi: 10.1006/abbi.1994.1037. [DOI] [PubMed] [Google Scholar]
  3. Asai T., Watanabe K., Ichihara-Tanaka K., Kaneda N., Kojima S., Iguchi A., Inagaki F., Muramatsu T. Identification of heparin-binding sites in midkine and their role in neurite-promotion. Biochem Biophys Res Commun. 1997 Jul 9;236(1):66–70. doi: 10.1006/bbrc.1997.6905. [DOI] [PubMed] [Google Scholar]
  4. Cardin A. D., Weintraub H. J. Molecular modeling of protein-glycosaminoglycan interactions. Arteriosclerosis. 1989 Jan-Feb;9(1):21–32. doi: 10.1161/01.atv.9.1.21. [DOI] [PubMed] [Google Scholar]
  5. Chauhan A. K., Li Y. S., Deuel T. F. Pleiotrophin transforms NIH 3T3 cells and induces tumors in nude mice. Proc Natl Acad Sci U S A. 1993 Jan 15;90(2):679–682. doi: 10.1073/pnas.90.2.679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Clore G. M., Brünger A. T., Karplus M., Gronenborn A. M. Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin. J Mol Biol. 1986 Oct 5;191(3):523–551. doi: 10.1016/0022-2836(86)90146-4. [DOI] [PubMed] [Google Scholar]
  7. Czubayko F., Schulte A. M., Berchem G. J., Wellstein A. Melanoma angiogenesis and metastasis modulated by ribozyme targeting of the secreted growth factor pleiotrophin. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14753–14758. doi: 10.1073/pnas.93.25.14753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fabri L., Maruta H., Muramatsu H., Muramatsu T., Simpson R. J., Burgess A. W., Nice E. C. Structural characterisation of native and recombinant forms of the neurotrophic cytokine MK. J Chromatogr. 1993 Aug 27;646(1):213–225. doi: 10.1016/s0021-9673(99)87023-x. [DOI] [PubMed] [Google Scholar]
  9. Hatanaka H., Oka M., Kohda D., Tate S., Suda A., Tamiya N., Inagaki F. Tertiary structure of erabutoxin b in aqueous solution as elucidated by two-dimensional nuclear magnetic resonance. J Mol Biol. 1994 Jul 8;240(2):155–166. doi: 10.1006/jmbi.1994.1429. [DOI] [PubMed] [Google Scholar]
  10. Inui T., Bódi J., Kubo S., Nishio H., Kimura T., Kojima S., Maruta H., Muramatsu T., Sakakibara S. Solution synthesis of human midkine, a novel heparin-binding neurotrophic factor consisting of 121 amino acid residues with five disulphide bonds. J Pept Sci. 1996 Jan-Feb;2(1):28–39. doi: 10.1002/psc.45. [DOI] [PubMed] [Google Scholar]
  11. Kadomatsu K., Hagihara M., Akhter S., Fan Q. W., Muramatsu H., Muramatsu T. Midkine induces the transformation of NIH3T3 cells. Br J Cancer. 1997;75(3):354–359. doi: 10.1038/bjc.1997.58. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kadomatsu K., Huang R. P., Suganuma T., Murata F., Muramatsu T. A retinoic acid responsive gene MK found in the teratocarcinoma system is expressed in spatially and temporally controlled manner during mouse embryogenesis. J Cell Biol. 1990 Mar;110(3):607–616. doi: 10.1083/jcb.110.3.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kadomatsu K., Tomomura M., Muramatsu T. cDNA cloning and sequencing of a new gene intensely expressed in early differentiation stages of embryonal carcinoma cells and in mid-gestation period of mouse embryogenesis. Biochem Biophys Res Commun. 1988 Mar 30;151(3):1312–1318. doi: 10.1016/s0006-291x(88)80505-9. [DOI] [PubMed] [Google Scholar]
  14. Kaneda N., Talukder A. H., Ishihara M., Hara S., Yoshida K., Muramatsu T. Structural characteristics of heparin-line domain required for interaction of midkine with embryonic neurons. Biochem Biophys Res Commun. 1996 Mar 7;220(1):108–112. doi: 10.1006/bbrc.1996.0365. [DOI] [PubMed] [Google Scholar]
  15. Kaneda N., Talukder A. H., Nishiyama H., Koizumi S., Muramatsu T. Midkine, a heparin-binding growth/differentiation factor, exhibits nerve cell adhesion and guidance activity for neurite outgrowth in vitro. J Biochem. 1996 Jun;119(6):1150–1156. doi: 10.1093/oxfordjournals.jbchem.a021361. [DOI] [PubMed] [Google Scholar]
  16. Kinnunen T., Raulo E., Nolo R., Maccarana M., Lindahl U., Rauvala H. Neurite outgrowth in brain neurons induced by heparin-binding growth-associated molecule (HB-GAM) depends on the specific interaction of HB-GAM with heparan sulfate at the cell surface. J Biol Chem. 1996 Jan 26;271(4):2243–2248. doi: 10.1074/jbc.271.4.2243. [DOI] [PubMed] [Google Scholar]
  17. Kojima S., Inui T., Kimura T., Sakakibara S., Muramatsu H., Amanuma H., Maruta H., Muramatsu T. Synthetic peptides derived from midkine enhance plasminogen activator activity in bovine aortic endothelial cells. Biochem Biophys Res Commun. 1995 Jan 17;206(2):468–473. doi: 10.1006/bbrc.1995.1066. [DOI] [PubMed] [Google Scholar]
  18. Kojima S., Inui T., Muramatsu H., Kimura T., Sakakibara S., Muramatsu T. Midkine is a heat and acid stable polypeptide capable of enhancing plasminogen activator activity and neurite outgrowth extension. Biochem Biophys Res Commun. 1995 Nov 13;216(2):574–581. doi: 10.1006/bbrc.1995.2661. [DOI] [PubMed] [Google Scholar]
  19. Kojima S., Inui T., Muramatsu H., Suzuki Y., Kadomatsu K., Yoshizawa M., Hirose S., Kimura T., Sakakibara S., Muramatsu T. Dimerization of midkine by tissue transglutaminase and its functional implication. J Biol Chem. 1997 Apr 4;272(14):9410–9416. doi: 10.1074/jbc.272.14.9410. [DOI] [PubMed] [Google Scholar]
  20. Kojima S., Muramatsu H., Amanuma H., Muramatsu T. Midkine enhances fibrinolytic activity of bovine endothelial cells. J Biol Chem. 1995 Apr 21;270(16):9590–9596. doi: 10.1074/jbc.270.16.9590. [DOI] [PubMed] [Google Scholar]
  21. Kurtz A., Schulte A. M., Wellstein A. Pleiotrophin and midkine in normal development and tumor biology. Crit Rev Oncog. 1995;6(2):151–177. [PubMed] [Google Scholar]
  22. Li Y. S., Milner P. G., Chauhan A. K., Watson M. A., Hoffman R. M., Kodner C. M., Milbrandt J., Deuel T. F. Cloning and expression of a developmentally regulated protein that induces mitogenic and neurite outgrowth activity. Science. 1990 Dec 21;250(4988):1690–1694. doi: 10.1126/science.2270483. [DOI] [PubMed] [Google Scholar]
  23. Lindahl U., Lidholt K., Spillmann D., Kjellén L. More to "heparin" than anticoagulation. Thromb Res. 1994 Jul 1;75(1):1–32. doi: 10.1016/0049-3848(94)90136-8. [DOI] [PubMed] [Google Scholar]
  24. Maccarana M., Casu B., Lindahl U. Minimal sequence in heparin/heparan sulfate required for binding of basic fibroblast growth factor. J Biol Chem. 1993 Nov 15;268(32):23898–23905. [PubMed] [Google Scholar]
  25. Maeda N., Nishiwaki T., Shintani T., Hamanaka H., Noda M. 6B4 proteoglycan/phosphacan, an extracellular variant of receptor-like protein-tyrosine phosphatase zeta/RPTPbeta, binds pleiotrophin/heparin-binding growth-associated molecule (HB-GAM). J Biol Chem. 1996 Aug 30;271(35):21446–21452. doi: 10.1074/jbc.271.35.21446. [DOI] [PubMed] [Google Scholar]
  26. Mahoney S. A., Perry M., Seddon A., Bohlen P., Haynes L. Transglutaminase forms midkine homodimers in cerebellar neurons and modulates the neurite-outgrowth response. Biochem Biophys Res Commun. 1996 Jul 5;224(1):147–152. doi: 10.1006/bbrc.1996.0998. [DOI] [PubMed] [Google Scholar]
  27. Matsuda Y., Talukder A. H., Ishihara M., Hara S., Yoshida K., Muramatsu T., Kaneda N. Limited proteolysis by chymotrypsin of midkine and inhibition by heparin binding. Biochem Biophys Res Commun. 1996 Nov 1;228(1):176–181. doi: 10.1006/bbrc.1996.1635. [DOI] [PubMed] [Google Scholar]
  28. Matsumoto K., Wanaka A., Takatsuji K., Muramatsu H., Muramatsu T., Tohyama M. A novel family of heparin-binding growth factors, pleiotrophin and midkine, is expressed in the developing rat cerebral cortex. Brain Res Dev Brain Res. 1994 Jun 17;79(2):229–241. doi: 10.1016/0165-3806(94)90127-9. [DOI] [PubMed] [Google Scholar]
  29. Merenmies J., Rauvala H. Molecular cloning of the 18-kDa growth-associated protein of developing brain. J Biol Chem. 1990 Oct 5;265(28):16721–16724. [PubMed] [Google Scholar]
  30. Michikawa M., Kikuchi S., Muramatsu H., Muramatsu T., Kim S. U. Retinoic acid responsive gene product, midkine, has neurotrophic functions for mouse spinal cord and dorsal root ganglion neurons in culture. J Neurosci Res. 1993 Aug 1;35(5):530–539. doi: 10.1002/jnr.490350509. [DOI] [PubMed] [Google Scholar]
  31. Michikawa M., Xu R. Y., Muramatsu H., Muramatsu T., Kim S. U. Midkine is a mediator of retinoic acid induced neuronal differentiation of embryonal carcinoma cells. Biochem Biophys Res Commun. 1993 May 14;192(3):1312–1318. doi: 10.1006/bbrc.1993.1559. [DOI] [PubMed] [Google Scholar]
  32. Mitsiadis T. A., Muramatsu T., Muramatsu H., Thesleff I. Midkine (MK), a heparin-binding growth/differentiation factor, is regulated by retinoic acid and epithelial-mesenchymal interactions in the developing mouse tooth, and affects cell proliferation and morphogenesis. J Cell Biol. 1995 Apr;129(1):267–281. doi: 10.1083/jcb.129.1.267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Mitsiadis T. A., Salmivirta M., Muramatsu T., Muramatsu H., Rauvala H., Lehtonen E., Jalkanen M., Thesleff I. Expression of the heparin-binding cytokines, midkine (MK) and HB-GAM (pleiotrophin) is associated with epithelial-mesenchymal interactions during fetal development and organogenesis. Development. 1995 Jan;121(1):37–51. doi: 10.1242/dev.121.1.37. [DOI] [PubMed] [Google Scholar]
  34. Mulloy B., Forster M. J., Jones C., Davies D. B. N.m.r. and molecular-modelling studies of the solution conformation of heparin. Biochem J. 1993 Aug 1;293(Pt 3):849–858. doi: 10.1042/bj2930849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Muramatsu H., Inui T., Kimura T., Sakakibara S., Song X. J., Maruta H., Muramatsu T. Localization of heparin-binding, neurite outgrowth and antigenic regions in midkine molecule. Biochem Biophys Res Commun. 1994 Sep 15;203(2):1131–1139. doi: 10.1006/bbrc.1994.2300. [DOI] [PubMed] [Google Scholar]
  36. Muramatsu H., Shirahama H., Yonezawa S., Maruta H., Muramatsu T. Midkine, a retinoic acid-inducible growth/differentiation factor: immunochemical evidence for the function and distribution. Dev Biol. 1993 Oct;159(2):392–402. doi: 10.1006/dbio.1993.1250. [DOI] [PubMed] [Google Scholar]
  37. Nakagawara A., Milbrandt J., Muramatsu T., Deuel T. F., Zhao H., Cnaan A., Brodeur G. M. Differential expression of pleiotrophin and midkine in advanced neuroblastomas. Cancer Res. 1995 Apr 15;55(8):1792–1797. [PubMed] [Google Scholar]
  38. O'Brien T., Cranston D., Fuggle S., Bicknell R., Harris A. L. The angiogenic factor midkine is expressed in bladder cancer, and overexpression correlates with a poor outcome in patients with invasive cancers. Cancer Res. 1996 Jun 1;56(11):2515–2518. [PubMed] [Google Scholar]
  39. Peng H. B., Ali A. A., Dai Z., Daggett D. F., Raulo E., Rauvala H. The role of heparin-binding growth-associated molecule (HB-GAM) in the postsynaptic induction in cultured muscle cells. J Neurosci. 1995 Apr;15(4):3027–3038. doi: 10.1523/JNEUROSCI.15-04-03027.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rance M., Sørensen O. W., Bodenhausen G., Wagner G., Ernst R. R., Wüthrich K. Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering. Biochem Biophys Res Commun. 1983 Dec 16;117(2):479–485. doi: 10.1016/0006-291x(83)91225-1. [DOI] [PubMed] [Google Scholar]
  41. Raulais D., Lagente-Chevallier O., Guettet C., Duprez D., Courtois Y., Vigny M. A new heparin binding protein regulated by retinoic acid from chick embryo. Biochem Biophys Res Commun. 1991 Jan 31;174(2):708–715. doi: 10.1016/0006-291x(91)91475-r. [DOI] [PubMed] [Google Scholar]
  42. Raulo E., Chernousov M. A., Carey D. J., Nolo R., Rauvala H. Isolation of a neuronal cell surface receptor of heparin binding growth-associated molecule (HB-GAM). Identification as N-syndecan (syndecan-3). J Biol Chem. 1994 Apr 29;269(17):12999–13004. [PubMed] [Google Scholar]
  43. Rauvala H. An 18-kd heparin-binding protein of developing brain that is distinct from fibroblast growth factors. EMBO J. 1989 Oct;8(10):2933–2941. doi: 10.1002/j.1460-2075.1989.tb08443.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Ruoslahti E., Yamaguchi Y. Proteoglycans as modulators of growth factor activities. Cell. 1991 Mar 8;64(5):867–869. doi: 10.1016/0092-8674(91)90308-l. [DOI] [PubMed] [Google Scholar]
  45. Schulte A. M., Lai S., Kurtz A., Czubayko F., Riegel A. T., Wellstein A. Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14759–14764. doi: 10.1073/pnas.93.25.14759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Spivak-Kroizman T., Lemmon M. A., Dikic I., Ladbury J. E., Pinchasi D., Huang J., Jaye M., Crumley G., Schlessinger J., Lax I. Heparin-induced oligomerization of FGF molecules is responsible for FGF receptor dimerization, activation, and cell proliferation. Cell. 1994 Dec 16;79(6):1015–1024. doi: 10.1016/0092-8674(94)90032-9. [DOI] [PubMed] [Google Scholar]
  47. Tomomura M., Kadomatsu K., Matsubara S., Muramatsu T. A retinoic acid-responsive gene, MK, found in the teratocarcinoma system. Heterogeneity of the transcript and the nature of the translation product. J Biol Chem. 1990 Jun 25;265(18):10765–10770. [PubMed] [Google Scholar]
  48. Tsutsui J., Kadomatsu K., Matsubara S., Nakagawara A., Hamanoue M., Takao S., Shimazu H., Ohi Y., Muramatsu T. A new family of heparin-binding growth/differentiation factors: increased midkine expression in Wilms' tumor and other human carcinomas. Cancer Res. 1993 Mar 15;53(6):1281–1285. [PubMed] [Google Scholar]
  49. Unoki K., Ohba N., Arimura H., Muramatsu H., Muramatsu T. Rescue of photoreceptors from the damaging effects of constant light by midkine, a retinoic acid-responsive gene product. Invest Ophthalmol Vis Sci. 1994 Nov;35(12):4063–4068. [PubMed] [Google Scholar]
  50. Wagner G., Braun W., Havel T. F., Schaumann T., Go N., Wüthrich K. Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol. 1987 Aug 5;196(3):611–639. doi: 10.1016/0022-2836(87)90037-4. [DOI] [PubMed] [Google Scholar]
  51. Yayon A., Klagsbrun M., Esko J. D., Leder P., Ornitz D. M. Cell surface, heparin-like molecules are required for binding of basic fibroblast growth factor to its high affinity receptor. Cell. 1991 Feb 22;64(4):841–848. doi: 10.1016/0092-8674(91)90512-w. [DOI] [PubMed] [Google Scholar]
  52. Yoshida Y., Goto M., Tsutsui J., Ozawa M., Sato E., Osame M., Muramatsu T. Midkine is present in the early stage of cerebral infarct. Brain Res Dev Brain Res. 1995 Mar 16;85(1):25–30. doi: 10.1016/0165-3806(94)00183-z. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES